Podcasts about renee rao

Bruce Ames Sr Scientist at CHORI, and Prof Emeritus of Biochem and Molecular Bio, at UC Berkeley. Rhonda Patrick Ph.D. biomedical science, postdoc at CHORI in Dr. Ames lab. The effects of micronutrients on metabolism, inflammation, DNA damage, and aging.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. [inaudible] [inaudible]. Speaker 1: Welcome to spectrum the science and technology show [00:00:30] on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi there. My name is Renee Rao and I'll be hosting today's show this week on spectrum. We present part two of our two interviews with Bruce Ames and Rhonda Patrick. Dr Ames is a senior scientist at Children's Hospital, Oakland Research Institute, director of their [00:01:00] nutrition and metabolism center and a professor emeritus of biochemistry and molecular biology at the University of California Berkeley. Rhonda Patrick has a phd in biomedical science. Dr. Patrick is currently a postdoctoral fellow at Children's Hospital, Oakland Research Institute and Dr Ames lab. She currently conducts clinical trials looking at the effects of nutrients on metabolism, inflammation, DNA damage and aging. In February of 2014 she published [00:01:30] a paper in the Federation of American Societies for Experimental Biology Journal on how vitamin D regulates serotonin synthesis and how this relates to autism. In part one Bruce and Rondo described his triage theory for micronutrients in humans and their importance in health and aging. In part two they discussed public health risk factors, research funding models, and the future work they wish to do. Here is part two of Brad Swift's interview with Dr Ames [00:02:00] and Patrick. Speaker 4: Is there a discussion going on in public health community about this sort of important that Rhonda, that one, Speaker 5: I think that people are becoming more aware of the importance of micronutrient deficiencies in the u s population. We've got now these national health and examination surveys that people are doing, examining the levels of these essential vitamins and minerals. 70% of the populations not getting enough vitamin D, 45% [00:02:30] population is not getting enough magnesium, 60% not getting enough vitamin K, 25% is not getting enough vitamin CS, 60% not getting enough vitamin E and on and on, 90% not getting enough calcium testing. It's very difficult to get. So I think that with these surveys that are really coming out with these striking numbers on these micronutrient deficiencies in the population, I'm in the really widespread and with triage, the numbers that tell you may be wrong because the thinking short term instead of long term, really what you want to know Speaker 6: [00:03:00] is what level [inaudible] indeed to keep a maximum lifespan. And our paper discussed all at and uh, but I must say the nutrition community hasn't embraced it yet, but they will because we're showing it's true and we may need even more of certain things. But again, you don't want to overdo it. Okay. Speaker 4: So talk a little bit about risk factors in general. In health, a lot of people, as you were saying, are very obsessed with chemicals or so maybe their risk assessment is [00:03:30] misdirected. What do you think are the big health issues, the big health risks? Speaker 6: I think obesity is like smoking. Smoking is eight or 10 years off your life. Each cigarette takes 10 minutes off your life. I mean, it's a disaster and smoking levels are going down and down because people understand. Finally, there's still a lot of people smoke, but obesity is just as bad years of expensive diabetes and the costs can be used. [00:04:00] Whatever you look at out timers of brain dysfunction of all sites is higher in the obese and there's been several studies of the Diet of the obese and it's horrible. I mean it's sugar, it's comfort food and they're not eating fruits and vegetables and the not eating berries and nuts and not eating fish. And so it's doing the main and the country is painful. Speaker 5: I think that the biggest risk in becoming unhealthy and increasing your [00:04:30] risk of age related diseases, inflammatory diseases comes down to micronutrient intake and people are not getting enough of that. And we know that we quantified it, we know they're not getting enough. And so I think that people like to focus on a lot of what not eat, don't eat sugar and that's right. You shouldn't eat a lot of sugar. I mean there's a lot of bad effects on, you know, constantly having insulin signaling activated. You can become insulin resistant in type two diabetic and these things are important. But I think you also need to realize you need to focus on what you're not getting as opposed to only focusing on what you should not [00:05:00] be getting. Yeah, Speaker 6: a colleague, lowest scold, and I wrote over a hundred papers trying to put risk in perspective. That part to been in pesticide is really uninteresting. Organic food and regular food doesn't matter. It's makes you feel good, but you're really not either improving the environment or helping your health. Now that you're not allowed to say that, things like that in Berkeley. But anyway, it's your diet. You should be worried about getting a good balanced time. So if you put out a thousand [00:05:30] hypothetical risks, you're lost space. Nobody knows what's important anymore and that's where we're getting. Don't smoke and eat a good diet. You're way ahead of the game and exercise and exercise. Right.Speaker 4: And in talking about the current situation with funding, when you think back Bruce, in the early days of your career and the opportunities that were there for getting funding vastly Speaker 6: different. [00:06:00] Well, there was much less money in the system, but I always was able to get funded my whole career and I've always done reasonably well. But now it's a little discouraging when I think I have big ideas that are gonna really cut health care costs and we have big ideas on obesity and I just can't get any of this funded [inaudible] but now if you're an all original, it's hopeless putting it at grant, [00:06:30] I just have given up on it. Speaker 5: Well the ANA, the NIH doesn't like to fund. Speaker 6: Yeah. If you're thinking differently than everybody else you do and they're only funding eight or 9% of grants, you just can't get funded. I didn't want to work on a 1% so I'm funding it out of my own pocket with, I made some money from a biotech company of one my students and that's what's supporting my lamb and few rich people who saw potential gave me some money. But it's really tough [00:07:00] now getting enough money to do this. That's an interesting model. Self funding. Well, Rhonda is trying to do that with a, she has a blog and people supporting her in, Speaker 5: I'm trying to do some crowdfunding where instead of going to the government and then all these national institute of cancer, aging, whatever, which essentially uses taxpayer dollar anyways to fund research. I'm just going to the people, that's what I'm trying to do. My ultimate goal is to go to the people, tell them about this research I'm doing and [00:07:30] my ideas how we're going to do it and have them fund it. People are willing to give money to make advances in science. They just need to know about it. What did you tell him what your app is? So, so I have an app called found my fitness, which is the name of my platform where I basically break down science and nutrition and fitness to people and I explained to them mechanisms. I explained to them context, you know, because it's really hard to keep up with all these press releases and you're bombarded with and some of them are accurate and some aren't and most of the time you just have no idea what is going on. Speaker 5: It's very [00:08:00] difficult to sort of navigate through all that mess. So I have developed a platform called found my fitness where I'm trying to basically educate people by explaining and breaking down the science behind a lot of these different types of website. And it's an app, it's a website that's also an app can download on your iPhone called found my fitness. And I have short videos, youtube videos that I do where I talk about particular science topics or health nutrition topics. I also have a podcast where I talk about them. I'm interviewing other scientists in the field and things like that. And also I've got a news community site [00:08:30] where people can interact posts, new news, science stories or nutrition stories, whatever it is and people comment. So we're kind of building in community where people can interact and ask questions and Speaker 6: Rhonda makes a video every once in a while and puts it up on her website and she has people supporting at least some of this and she hopes to finally get enough money coming in. We'll support her research. Speaker 5: No, I think we're heading that way. I think that scientists are going to have to findSpeaker 6: new creative ways to fund their research. Uh, particularly if they have creative ideas [00:09:00] is, Bruce mentioned it because it's so competitive to get that less than 10% funding. The NIH doesn't really fun, really creative and risky, but it's, you need somebody who gets it. If when you put out a new idea, right, and if it's against conventional wisdom, which I'd like to do with the occasion arises, then it's almost impossible anyway. Speaker 4: Even with your reputation. Speaker 6: Yeah, it's hard. I've just given [00:09:30] up writing grants now. It's a huge amount of work and when they keep on getting turned down, even though I think these are wonderful ideas, luckily I can keep a basal level supporting the lab. I found a rich fellow who had an autistic grandkid guy named Jorgensen and he supported Rhonda and he supported her for a year and she was able to do all these things. Yeah, my age, I want to have [00:10:00] a lot of big ideas and I just like to get them out there anyway. We shouldn't complain. We're doing okay. Right. It's a very fulfilling job. There's nothing more fulfilling than doing science in my opinion. Yes. Speaker 7: You're listening to spectrum and k a Alex Berkley. Today's guests are Dr. Bruce Ames and Dr Rhonda Patrick of Children's Hospital Oakland Research Institute. [00:10:30] Oh, Speaker 4: the ames test. When you came up with that, was that, what was the process involved with?Speaker 6: Well, how do you devise that? Well, I was always half a geneticist and half a bio chemist and I thought you Taishan is really important. And nobody was testing new substances out there to see if there were mutagens. And so I thought it'd be nice to develop a simple, easy test in bacteria for doing that. That [00:11:00] was cheap and quick. And then I became interested in the relation of carcinogens to mutagens and so I was trying to convince people at the active forms of carcinogens were muted. There were other people in that area too, but I was an early enthusiastic for that idea and anyway, it's just came from my knowledge of two different fields, but that's a long time ago. I'm more excited about the brain now. The current stuff Speaker 4: doing obviously is it's more [00:11:30] exciting. Yeah. Do you both spend time paying attention to other areas of science? Speaker 6: I read an enormous amount and every 10 or 15 years I seem to change my feel of and follow off something that seems a little hotter than the other things and I've been reasonably successful at that, so that's what I liked to do. I am constantly Speaker 5: about all the latest research coming out. I mean, that's like pretty much all I do is I'm very excited about the new [00:12:00] field of epigenetics, where we're connecting what we eat, our lifestyle, how much stress we are under, how much exercise we do, how much sleep we get, how this is actually changing, methylation patterns, acetylation patterns. In our DNA and how that can change gene expression, turn on genes, turn off genes. I mean how this all relates to the way we age, how it relates to behavior, how it relates to us passing on behaviors to our children, grandchildren, you know, this is a field that's to me really exciting and something that I've spend quite a bit of time reading about. So for both of [00:12:30] you, what have been in the course of your career, the technologies, Speaker 6: the discoveries that have impacted your work the most? Well obviously understanding DNA and all the things it does was a huge advance for biology. And I was always half a geneticist, so I was hopping up and down when that Watson Crick paper came out and I gave it in the Journal club to all these distinguished biochemists and they said very speculative. [00:13:00] I said I was young script. I said, you guys be quiet. This is the paper of the century. And it made a huge difference. And there's been one advance after another. A lot of technical advances, little companies spring up, making your life easier and all of that. So it's been fun going through this. Speaker 5: I think, you know, in terms of my own research, which got me to where I'm at now, a lot of the, the technological advances in making transgenic mouse models, [00:13:30] knocking out certain genes, being able to manipulate, doing, inserting viral vectors with a specific gene and with a certain promoter on it and targeting it to a certain tissue so you can, you know, look specifically at what it's doing in that tissue or knock it out and what it's doing and that tissue. That for me is a, been a very useful technology that's helped me learn a lot. In addition, I like to do a lot of imaging. So these fluorescent proteins that we can, you know, you use to tag on, look at other proteins where they're located both tissue wise and also intracellularly inside the cell. Doing [00:14:00] that in real time. So there's now live cell imaging we can do and see things dynamically. Like for example, looking at Mitochondria and how they move and what they're doing in real time. Like that for me is also been really a useful technology and helping me understand Mitochondria. And how they function, dysfunction can occur. So I think a, those, those have been really important technologies for me. Speaker 6: And then computers change biology. Google made a huge difference. You can put two odd facts into Google and outcome Molly's paper. You'd spend years in a library [00:14:30] trying to figure all this stuff out. So Google really made theoretical biology possible. And I think this whole paper that Rhonda did, she couldn't have done it without Google. That's was the technology that opened it all up. This is so much literature and nobody can read all this and remember it all that we need the search. And so is this kind of a boom in theoretical biology? Well, [00:15:00] I wouldn't say there's a boom yet, but there's so much information out there that people haven't put together. Speaker 5: Yeah, people have been generating data over the years. There's tons of data out there and there's a lot of well done research that people haven't put together, connected the dots and made big picture understanding of complex things. So I think that there is an opening for that. And I do think that people will start to do that more and they are starting to do it more and more. Speaker 6: So in the past there really wasn't a theoretical biology that was certainly Darwin was [00:15:30] theoretical you could say and lots of people had big ideas in the unified fields, but it was rare. Speaker 5: I think we have more of an advantage in that we can provide mechanisms a little easier because we can read all this data. You know people like Darwin, they were doing theoretical work but they were also making observations. So what we're doing now is we're looking at observations other people have made and putting those together. Speaker 8: [00:16:00] [inaudible] and [inaudible] is a public affairs show on k a l x Berkeley. This is part two of a two part interview with Bruce Ames and Rhonda Patrick. Speaker 6: Are there, are other scientists active in the longevity field whose work you admire that you would love to collaborate with? [00:16:30] Well or associated with? Always collaborates. So science is both very collegial and very competitive. You think somebody might get their first. But one of the tricks I like in my lab is we have half a dozen really good people with different expertise and we sit around a table and discuss things and it's no one person can know all medicine. And so [00:17:00] anyways, that helps. Yeah. And it might be collaborating with this guy now because both of you contribute something that the other person doesn't have a technique or whatever. And in three years we might be competing with them, but that's why it's good to keep good relations with everybody. But business is the same way companies compete and collaborate. Yeah. Speaker 5: I, I personally am in terms of the field of longevity. Uh, I admire the work of Elizabeth Blackburn [00:17:30] who discovered, uh, won the Nobel prize for be playing a role in discovering the enzyme telomerase Speaker 6: that was done at Berkeley, by the way. Speaker 5: Yeah. And she's now a professor at UCLA. So I would be really excited to set up a collaboration with her. Speaker 6: Well, what are the lab's research plans going forward now? Uh, well, other than Ryan Reinders next two papers. Yeah. Rhonda has these papers to get out. And I'd like to get the whole business [00:18:00] of tuning up our metabolism on firmer ground, convince nutrition people who are expert in one particular environment or most people studied B six for their whole lives or study Niacin for their whole lives or magnesium. And I buy it at the experts in a particular field to think about triage and what protein do we measure that tells you you're short a not getting enough, the vulnerable ones and get that idea [00:18:30] out and do a few examples and convince people that RDA should be based on long term effects rather than short term. And then Rhonda and I were talking the other day and we both got excited about drugs. This money to be made. Speaker 6: So pharmaceutical companies compete on getting new and better drugs and they can be billion dollar drugs but nutrition, nobody can make money out of it. And so there, [00:19:00] do you want to do a clinical trial on Vitamin d the way you do with the drug? Food and drug wants a double blind randomized controlled clinical trial. That's the gold standard for drugs. But it's not for nutrition is nutrition. You have to measure if 20% of the population is low on vitamin D, you don't want to do a study where you don't measure who's low and who's high because otherwise it's designed to fail. So you have to measure [00:19:30] things. Now, vitamin D actually many more deficient, but a lot of vitamins, 10% of lower 20% is low and you can't just lump them in with all the people have enough and do a randomized on one clinical trial and think it's going to mean something without measuring something. Speaker 6: Rhonda has one of her videos on our website to [inaudible] all these doctors who saved the vitamins are useless. They're all based on clinical trials that are designed for drugs [00:20:00] and they don't measure anything. So you have to know who should deficient and then taking that amount of value and makes you sufficient. I think, uh, some interesting re ongoing research in our lab is also the cornea bar. Yeah. So yeah, Joyce mechanical amp is directing a project on the Corey bar. We were deciding how do you get vitamins and minerals into the poor and we made a little bar, which is kind of all the components of a Mediterranean diet that people [00:20:30] aren't getting enough vitamins and all the vitamins and minerals and fish oil and vitamin D and soluble fiber and insoluble fiber and plant polyphenols and we can raise everybody's HDL in a couple of weeks and this is the mass of people aren't eating, they think they're eating good tide aren't and obese people or have their metabolism all fouled up and you were even learning how to make progress there. So Speaker 5: cool thing about it is that you can take a population [00:21:00] of people that eats very unhealthy and they are obese, meaning they have a BMI of 30 or above and you can give them this nutritional bar that has a variety of micronutrients. It has essential fatty acids and some polyphenols fiber and give it to them twice a day on top of their crappy diet. You don't tell them to change your diet at all. It's like keep doing what you're doing, but here, eat those twice a day on top of what you're doing and you can see that, you know after a few weeks that these changes start to occur where their HDLs raise or LDS lower. I mean there's, there's a lot of positive effects, you know, lower c reactive protein. So [00:21:30] I think this is really groundbreaking research because it's, it says, look, you can take someone who's eating a terrible diet completely, probably micronutrient division in many essential vitamins and minerals and such are eating a bunch of sugar and crap and processed foods and on and on and on and yet you can give them this nutritional bar that has a combination of micronutrients in it and you can quantify changes that are positive. Speaker 5: I think that's a really exciting ongoing project in our lab, Speaker 6: Bruce Ames and Rhonda Patrick, thanks very much [00:22:00] for being on spectrum. It's a pleasure. Absolutely a pleasure. Thanks for having us. Speaker 7: Aw. [inaudible] to learn more about the work aims and Patrick's are doing. Visit their websites. Bruce seems.org and found my fitness.com spectrum shows are archived on iTunes yet we've created this simple link for you. The link is tiny url.com/k a Alex spectrum Speaker 3: [00:22:30] and now a calendar of the science and technology events happening locally over the next two weeks. Rick Kreisky joins me to present the calendar on Sunday July 13th the bay area meetup, random acts of science will host an event to do science with paper papers, one of the most commonly available materials with a variety of science applications. Everything from the dynamics of classic paper airplanes launching paper rockets and building structures in [00:23:00] Origami will be discussed. The group will also learn about fibers and paper and how to create their own homemade paper. Raw materials will be provided, but attendees are also welcome to bring their own. The event will be held July 13th from two to 3:00 PM outside the genetics and plant biology building on the UC Berkeley campus. It is free and open to anyone interested in coming basics. The Bay area art science, interdisciplinary collaborative sessions. [00:23:30] We'll have their fifth event on Monday the 14th from six 30 to 10:00 PM at the ODC theater, three one five three 17th street in San Francisco. Speaker 3: The theme is monsters. Professor John Haffer. Nick, we'll introduce the audience to a peracetic fly that turns European honey bees into zombies, author and translator, Eric Butler. We'll explain how literature and film have made the Vampire [00:24:00] a native of Eastern Europe into a naturalized American with a preference for the Golden State Marine biologist David McGuire. Well, disentangle the media fueled myth of the shark from its true nature and Kyle Taylor, senior scientist for the gluing plant project will show off plants that glow in the dark. Admission will be on a sliding scale from absolutely nothing. Up to 20 bucks. Visit basics.com for more info. [00:24:30] That's B double a s I c s.com. On Saturday, July 19th you see Berkeley molecular and cell biology Professor Kathleen Collins will host the latest iteration of the monthly lecture series. Signs that cow Professor Collins will discuss the connections between the seemingly incontrovertible fact of human aging. A fascinating enzyme known as telomerase and malignant cancers. Speaker 3: While cancer cells can grow indefinitely [00:25:00] all normally functioning human tissues will eventually die out. This is because with each success of cell division, the protective cap or a telomere at the end of each chromosome is gradually degraded while the enzyme to limb arrays or pairs this damage in embryos. It is not fully active in adult human tissues. Perhaps to prevent the uncontrollable growth of cancer cells. Professor Collins will discuss telomeres and telomerase function and how they affect the balance of human aging [00:25:30] and immortality. The free public talk will be held July 19th in room one 59 of Mulford Hall on the UC Berkeley campus. The lecture will begin at 11:00 AM sharp science need is a monthly science happy hour for adults 21 and over the pairs. Lightning talks with interactive stations on the back patio of the El Rio bar at three one five eight mission street in San Francisco. Speaker 3: [00:26:00] The theme for July Science Neat is backyard science and we'll feature the science of things right here in the bay area from plants to plankton and beetles. Two bikes. Admission is $4 and the event will be on Tuesday, July 22nd from six 30 to 8:30 PM and now a few of our favorite science stories. Rick's back to present the news. The rocky planets that are closest to our son generally have an iron core [00:26:30] that makes up about a third of their mass that is surrounded by rock that makes up the other two thirds. Mercury is an exception and is the other way around. With a massive iron core that takes up about percent of the planet's mass. This has been difficult to explain. If mercury had been built up by collisions the way that Venus and earth and Mars where we'd expect it to have a similar composition in a letter published in nature geoscience on July six Eric s [00:27:00] fog and Andreas Roofer of Arizona State University report their simulations that suggests that collisions may have stripped away Mercury's mantle, some moon and planet sized rocks would bounce off of each other, sometimes knocking one body out of its orbit while the impactor and the leftover debris coalesced into a planet. Speaker 3: This model is consistent with Mercury's high abundance of [inaudible] elements that have been observed recently by NASA's messenger spacecraft [00:27:30] in their so called hit and run model. Mercury is missing metal would end up coalescing onto Venus or in your report compiled by UC Berkeley. Scientist has definitively linkedin gene that has helped Tibetan populations thrive in high altitude environments to hit or too little known human ancestor. The Denisovans, the Denisovans along with any thoughts when extinct around 40 to 50,000 years ago about the time that modern human began to ascend [00:28:00] and Aaliyah is a version of a gene in this case and unusually of the gene e p a s one which regulates hemoglobin production has been common among Tibetans since their move several thousand years ago. John Habit areas at around 15,000 feet of elevation. Well, most people have Leos that caused them to develop thick blood at these high elevations, which can later lead to cardiovascular problems. The tobacco wheel raises hemoglobin levels only slightly allowing possessors [00:28:30] to avoid negative side effects. So the report, which will later republished in the journal Nature details the unique presence of the advantageous aliyah. Among Tibetans and conclusively matches it with the genome of the Denisovans. This is significant because as principle author, Rasmus Nielsen, UC Berkeley professor of integrative biology writes, it shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species. Nielsen added that there are many other [00:29:00] potential species to explore as sources of human DNA Speaker 8: [inaudible].Speaker 4: This show marks the end of our production of spectrum. I want to thank Rick Karnofsky, Renee, Rau, and Alex Simon for their help in producing spectrum. I want to extend a blanket thank you to all the guests who took the time to appear on spectrum over the three years we have been on Calex to Sandra Lenna, [00:29:30] Erin and Lorraine. Thanks for your guidance and help to Joe, Peter and Greg. Thanks for your technical assistance and encouragement to listeners. Thanks for tuning in and Speaker 7: stay tuned to Calico [inaudible]. See acast.com/privacy for privacy and opt-out information.

Cathryn Carson is an Assoc Prof of History, and the Ops Lead of the Social Sciences D- Lab at UC Berkeley. Fernando Perez is a research scientist at the Henry H. Wheeler Jr. Brain Imaging Center at U.C. Berkeley. Berkeley Institute for Data Science.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Mm MM. Speaker 3: Uh Huh [inaudible]. Speaker 4: [00:00:30] We'll come to spectrum the science and technology show on Katie l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events. Speaker 3: [inaudible].Speaker 1: Hello and good afternoon. My name is Renee Rao and I'll be hosting today's show this week [00:01:00] on spectrum present part two of our two part series on big data at cal. The Berkeley Institute for data science bids is only four months old. Two people involved with shaping the institute are Catherine Carson and Fernando Perez. They are today's guest Catherine Carson is an associate professor of history and associate dean of social sciences and the operational lead of the social sciences data lab at UC Berkeley for Nana Perez is a research scientist at the Henry H. Wheeler [00:01:30] Jr Brain imaging center at UC Berkeley. He created the iPod iPhone project while he was a graduate student in 2001 and continues to lead the project today. In part two they talk about teaching data science. Brad Swift conducts the interview Speaker 5: on the teaching side of things. Does data science just fold into the domains in the fields and some faculty embrace it, others don't. How does the teaching of data science move [00:02:00] forward at an undergraduate level? Yeah, there there've been some really interesting institutional experiments in the last year or two here at Berkeley. Thinking about last semester, fall of 2013 stat one 57 which was reproducible collaborative data science pitched at statistics majors simply because you have to start with the size that can fit in a classroom [00:02:30] and training students in the practices of scientific collaboration around open source production of software tools or to look at what was Josh Bloom's course, so that's astro four 50 it's listed as special topics in astrophysics just because Josh happens to be a professor in the astronomy department and so you have to list it somewhere. The course is actually called Python for science Speaker 6: [00:03:00] and it's a course that Josh has run for the last, I think this is, this was its fourth iteration and that course is a completely interdisciplinary course that it's open to students in any field. The examples really do not privilege and the homework sets do not privilege astronomy in any way and we see students. I liked her a fair bit in that course as a guest lecture and we see students from all departments participating. This last semester it was packed to the gills. We actually had problems because we couldn't find a room large enough to accommodate. So word of mouth is working. In terms of students finding these [00:03:30] courses, Speaker 5: it's happening. I wouldn't say it's working in part because it's very difficult to get visibility across this campus landscape. I am sure there are innovations going on that even the pis and bids aren't aware of and one of the things we want to do is stimulate more innovation in places like the the professional schools. We'll be training students who need to be able to use these tools as well. What do they have in mind or there [00:04:00] are other formats of instruction beyond traditional semester courses. What would intensive training stretched out over a much shorter time look like? What gaps are there in the undergraduate or graduate curriculum that can effectively be filled in that way? The Python bootcamp is another example of this that's been going on for Speaker 6: for about four years. Josh and I teach a a bootcamp on also python for data science that is immediately before the beginning of the fall semester. Literally the weekend before [00:04:30] and it's kind of, it's a prerequisite for the semester long course, but it's three days of intensive hands-on scientific bite on basically programming and data analysis and computing for three days. We typically try to get a large auditorium and we got 150 to 200 people. A combination of undergrads, Grad Students, postdocs, folks from LVL campus faculty and also a few folks from industry. We always leave, leave a few slots available for people from outside the university to come and that one a has been very popular at [00:05:00] tends to, it's intense to have very good attendance be, it serves as an on ramp for the course because we advertise the in the semester course during the bootcamp and that one has been fairly successful so far and I think it has worked well. Speaker 6: We see issues with it too. That would be that we would like to address three days is probably not enough. Um, it means because it's a single environment, it means that we have to have examples that are a little bit above that can accommodate everyone, but it means they're not particularly interesting for any one group. It would be, I think it would be great to have [00:05:30] things of this nature that might be a little bit better focused at the life sciences and the social sciences that the physical sciences, so that the examples are more relevant for a given community that may be better targeted at the undergraduate and the graduate level so that you can kind of select a little bit in tune the requirements or the methodological base a little bit better to the audience. But so far we've had to kind of bootstrapping with what we have. Speaker 6: There's another interesting course on campus offered by the ice school by Raymond Lecture at the high school called working with open data [00:06:00] that is very much aimed at folks who are the constituency of the high school that have an intersection of technical background with a broader interdisciplinary kind of skills that are the hallmark of the high school and they work with openly available data sets that are existing on the Internet to create basically interesting analysis projects out of them and that's of course that that I've seen come up with some very, very successful and compelling projects at the end of the semester Speaker 7: about the teaching and preparation in universities. In [00:06:30] the course of doing interviews on spectrum, a number of people have said that really the only way to tackle sciences interdisciplinary, the big issues of science is with an interdisciplinary approach, but that that's not being taught in universities as the way to do science. Sarah way to break that down using data science as a vehicle. Speaker 5: I can speak about that as a science and technology studies scholar. The practice of interdisciplinarity, what makes it actually work is one of the [00:07:00] the most challenging social questions that can be asked of contemporary science and adding into that the fact that scientists get trained inside this existing institution that we've inherited from let's roughly say the Middle Ages with a set of disciplines that have been in their current form since roughly the late 19th century. That is the interface where I expect in the next oh two to five decades major transformations in research universities. [00:07:30] We don't yet know what an institution or research institution will look like that does not take disciplines as it sort of zero order ground level approximation to the way to encapsulate truth. But we do see, and I think bids is like data science in general and an example of this. We do see continual pressure to open up the existing disciplines and figure out how to do connections across them. It's [00:08:00] not been particularly easy for Berkeley to do that in part because of the structure of academic planning at our institution and in part because we have such disciplinary strengths here, but I think the invitation for the future that that word keeps coming back invitation. The invitation for the future for us is to understand what we mean by practicing interdisciplinarity and then figure out how to hack the institution so that it learns how to do it better. [inaudible] Speaker 8: [inaudible] [00:08:30] you're listening to structure fun. K A, l ex Berkeley Fasten Kirsten and Fernando Perez are our guests. They're part of the Berkeley Institute for Data Science for Bids [inaudible] Oh, Speaker 6: it seems that data science has an almost unlimited [00:09:00] application. Are there, are you feeling limits? I don't know about limits specifically because I think in principle almost any discipline can have some of its information and whatever the concepts and constructs of that discipline can probably be represented in a way that is amicable to quantitative analysis of some sort. In that regard, probably almost any discipline can have a data science aspect to it. I think it's important not to sort of [00:09:30] over fetishize it so that we don't lose sight of the fact that there's other aspects of intellectual work in all disciplines that are still important. That theory still has a role. That model building still has a role that, uh, knowing what questions to ask, it's still important that hypotheses still matter. I'm not so sure that it's so much an issue of drawing arbitrary limits around it, but rather of being knowledgeable and critical users of the tools and the approaches that are offered. Speaker 6: Because in terms of domain [00:10:00] applications, I actually recently saw at the strata conference, which is one of these more industry oriented big data conferences that took place a few weeks ago in Silicon Valley. It's in Santa Clara. One of the best talks that I saw at the conference was an analysis half the poem, if I told him that Gertrude Stein wrote about Picasso After Picasso painted this very famous portrait of her. And that poem has a very, very repetitive rhythmic structure. It has very few words and it's a long poem with a very peculiar linguistic structure. And [00:10:30] this hardest, I, I'm blanking on his name right now, but he's an artist who works kind of at the intersection of digital arts in, in linguistics wrote basically a custom one off visual analysis and visualization tool to work on the structure of this poem to visualize it, to turn it into music. Speaker 6: And it was a beautiful talk. It was a beautiful and very interesting talk and this was kind of the exact opposite of this was tiny data. This was one poem and in fact during the Q and a they asked him and he said, well I've tried to use the tool [00:11:00] on a few other things and there's a few songs in hip hop that it works well with, but it's almost, it's almost custom made for this one poem, right? So this was sort of tiny data, completely non generalizable and yet I thought it was fascinating and beautiful talk. So that's kind of an example that I would have never have thought of as as data science. Any examples of misapplication? Speaker 5: I think we can admit that data science is a buzzword that is [00:11:30] exactly through, it's almost indefinable nature creates space for people to do methodologically problematic and in many cases also uninteresting work. Just throwing data into an analysis without asking is this the right analysis will get you stupid or misleading answers. It's the garbage in out principle. So yeah, like any intellectual tool in the toolkit, [00:12:00] there are misleading conclusions that can be drawn and one of the powers that Berkeley brings to this effort in data science is a focus on the methodology, the intelligent development of methodology along with just building things that look like tools on their own. I think that's going to be the place with the sweet spot for universities because of the emphasis on rigor and stringency and reasoning [00:12:30] along with just getting out results that look good and are attractive Speaker 7: with data science. Are there infrastructure challenges that are worth talking about either in industry or at an academic institution? Because I know that computing power now through Amazon, Google organizations like that are enormous and so industry is sort of giving up the idea of having their own [00:13:00] computational capacity and they're using cloud virtual universities I would think are following suit. Speaker 6: Yes, there is work being done already on campus in that regard. We've had some intersection with those teams. The university right now, uh, we've had since last year a new CIO on campus, Larry Conrad, who's been spearheading an effort to sort of reimagine what the research computing infrastructure for campus should look like. [00:13:30] Considering these questions precisely of what is happening in industry, what are the models that are successfully being used at other institutions to provide larger scales off competitional resources across all disciplines and beyond the disciplines that have been traditionally the ones that have super computers. Well, there's a long history of departments, again, like physics, like competition, fluid dynamics, teams like quantum chemistry teams that have had either their own clusters or that have large budgets who have access to the supercomputing centers at [00:14:00] the doe labs and things of that nature. But as we've been saying today, all of a sudden those needs are exploding across all disciplines and the usage patterns are changing and that often what is the bottleneck is maybe not the amount of raw compute power, but the ability to operate over a very large data sets, so maybe storage is the issue or maybe throughput biologists often end up buying computers that look really weird. Speaker 6: Too many supercomputing centers because they, the actual things that they need are skewed in a different way and so there are certainly [00:14:30] challenges in that regard when we do know that Berkeley is right now at least in the midst of making a very concerted and serious attempt at at least taking a step forward on this problem. Speaker 7: A lot of data is derived from personal information. Are there privacy concerns that you have [inaudible] Speaker 5: they're all quite definitely in so many different ways that the input of experts who have thought about questions of consent, of privacy, [00:15:00] of the challenges around keeping de identified data d identified when it is possible through analytics to understand what patterns are emerging from them that is going to be so key. Especially to working with social data. And so one of the still open questions for all of us working with data that is about people is how to develop the practices that will do the protections necessary [00:15:30] in order to avoid the kinds of catastrophic misuses and violations of privacy that many of us do. Fear will be coming our way as so much data becomes available so fast with so many invitations to just make use of it and worry about the consequences later. That's not the responsible way forward. And I would like to see bids and Berkeley take on that challenge as part of its very deliberate agenda. Speaker 8: [00:16:00] Okay. Spectrum is a public affairs show on k a l ex Berkeley. Our guests are Cathryn Carson and Fernando Perez. In the next segment they talk about institutional reactions to bids. Oh, Speaker 7: are there any impediments that you've run into within the bids process [00:16:30] of getting up and running? Cause it's been going since, uh, Speaker 5: it's not been going on that long as it, it's only December of 2013. Pretty recent, but I'm sure there's gotta be some institutional pushback or no, it's, it's been incredible actually how much support the institution has given. What bids is though, is a laboratory for the kind of collaboration that we're trying to instantiate. And so you have 13 brilliant Co-pi eyes each with their own vision and figuring out where [00:17:00] the intersection is and how to get the different sets of expertise and investments where they, where those intersections lie and how to get them aligned. I mean, that's, that's one of the fascinating challenges in front of beds as a laboratory in the small, for the process at large that we're trying to do Speaker 7: on the tools and programming side. How would you break up what languages are providing, what kind of capability, [00:17:30] and are there new languages that are ascendent and other languages that are languages that are losing their grip? I'm sort of curious. It's a, it's another trivia questions that I think might have some interest for people. No, I think there's, there's clearly an ascendance. I think naturally the expansion of the surface of people interested in these problems Speaker 6: is naturally driving the growth and importance of high level languages that are immediately usable by domain scientists. We're not full time programmers [00:18:00] and professional programmers. Traditionally a lot of the high end computing had been done in languages like c, c plus plus for trend and some Java that are languages that tend to be more the purview of, of people who do lots of software development. And a lot of that did happen in departments like physics and chemistry and computer science, but not so much in other disciplines. And so we're seeing the rise of open source languages like Python and r that are immediately applicable and easy to use for data analysis where a few commands [00:18:30] can load a file, compute some statistics on it, produce a few visualizations, and you can do that in five lines of code, not having to write a hundred or 500 lines of c plus plus. Speaker 6: Right. And so the languages like that are, they're not new. Both I think are came out in the late eighties early nineties python came out in 1991 but they're seeing a huge amount of growth in recent years for this reason. There's also a growth of either new tools to extend these languages [00:19:00] or new languages as well. Tools for example, that connect these languages to databases or extensions to these languages to couple them to databases in better ways so that people don't have to only write raw sequel, which SQL is not the classic language for interacting with databases, so extensions to couple existing languages to database back ends. A lot of work is being done in that direction and there are some novel languages. For example, there's a team at MIT that about two years ago started [00:19:30] a project for a new language called Julia that is aimed at numerical computing, but it's sort of re-imagining. Speaker 6: What would you do if you wanted to create a language like python with the strengths of language like python or Ruby or r, but if you were doing that today with the lessons of the last 20 years, that would be good for numerical computing, but it would be easy to use for domain scientists. That would be high level, that would be interactive, that would feel like a scripting tool, but that would also give you very high performance. [00:20:00] If you had the the last 20 years of lessons and the advances in some of the underlying technology and improved compiler machinery that we have today, how would you go about that problem? And I think the Giulia team at MIT is making rapid progress and it has caught the intention of people in the statistics community of people in the numerical analysis and algorithms community. Some prominent people have become very interested in how to become active participants in its development. Speaker 6: So we're seeing both mature tools like python and are growing in their strength and and their importance. At the latest Strada Conference, [00:20:30] for example, there was a an analysis of kind of the the abstracts submitted that had r and python in their names versus things like excel or sequel or Java and Python and are clearly dominating that space, but also these, these kinds of more novels, sort of research level languages that whose futures still not clear because they're very, very young, but at least they're exploring sort of the frontier of what will we do in the next five or 10 years. And is this an area that's ripe for a commercial software creators who develop [00:21:00] a tool that would be specific to data science and sort of the same way that Mat lab is kind of specific now it's kind of a generic tool for mathematics. Obviously my answer here is extremely biased, but I'm, I sort of think that the space for a, the window to create a proprietary data science language is closed already. Speaker 6: I think the community simply would not adopt a new one. There are some existing successful ones such as mat lab, IDL, which is smaller than Madlib. It is widely used in the astronomy and astrophysics. [00:21:30] And Physics Communities Mathematica, which is a project that came out of the mathematics and physics world and that is very, very sophisticated and interesting. Maple, which is also a mathematics language. Those are successful existing proprietary languages. I think the mood has changed to these are products that came out in the eighties and the nineties. I think the, the window for that, uh, as a purely proprietary offer has closed. I think what we're going to see is the continued growth and the rise potential. You have new entrants that are fundamentally [00:22:00] open source, but yet that maintain, as I said earlier, a healthy dialogue with industry because it doesn't mean, for example, in the art world there are companies that build very successful commercial products around are there is a product called r studio that is a development environment for analysis in our, and that's a company, there's a company called I think revolution analytics. Speaker 6: I think they built some sort of sort of large scale backend high-performance version of our, I don't know the details, I don't use it, but I've seen their website. I think they're a large company that builds kind of our for the enterprise. So I think [00:22:30] that's what we're going to see moving forward at the base. People want the base technology, the base language to be open source. And I think for us as universities and for me as a scientist, I think that's a Tenet I'm not willing to compromise on because I do not want a result that I obtain or result that I published or a tool that I educate my students with to have a black box that I'm legally prevented from opening and to tell my student, well, this is a result about nature, but you can't understand how it was achieved because you are legally prevented from opening the box. [00:23:00] I think that is fundamentally unacceptable. But what is, I think a perfectly sensible way forward, is to have these base layers that are open on top of which domain specific tools can be created by industry that add value for specific problems, for specific domains that may be add performance, whatever. Catherine Carson and Fernando Perez. Thanks very much for coming on spectrum. Thanks for having us here. Thanks much. Speaker 8: [inaudible]Speaker 9: [00:23:30] all spectrums. Past shows are archived on iTunes university. We've created a simple link for you. The link is tiny url.com/k Speaker 1: a l x Speaker 8: spectrum Speaker 1: Rick Curtis Skin. I will present a few of the science and technology events [00:24:00] happening locally over the next two weeks. Speaker 10: Counter culture, labs and pseudo room present gravitational waves, results and implications with Bicep to collaborator Jamie Tolan at the pseudo room, hackerspace to one 41 Broadway in Oakland on Sunday, April 27th at 7:00 PM recently, scientists from the Bicep to experiment recorded their data findings demonstrating [00:24:30] evidence of gravitational waves that may imply cosmic inflation. The bicep to experiment is an international collaboration of research and technology from many institutions including a team at Stanford University work. Jamie Tolan works. Jamie will discuss the results of the bicep two experiment and its scientific contribution to current theories that attempt to explain the why, what and how of our universe. The event will be free. Speaker 1: On April 30th UCLA professor [00:25:00] of geography, Jared diamond will give this year's Horace m Albright Lecture in conversation. Diamond is best known for his Pulitzer Prize winning book, guns, germs and steel and this lecture he will discuss his newest book, the world until yesterday, what we can learn from traditional societies. The book is about how traditional peoples differ from members of modern industrial societies and their reactions to danger. He will then produce B in a question answer session with the audience doors open at 6:00 PM [00:25:30] the event is free and open to the public on a first come first served basis will be held Wednesday, April 30th from seven to 8:30 PM in the International House Auditorium at two two nine nine Piedmont Avenue Berkeley. Speaker 10: The theme of Mays science at the theater is science remix. Joined Berkeley lab scientists at the East Bay Center for the Performing Arts in Richmond, California on May 1st at 7:00 PM they'll discuss how discovery [00:26:00] happens. Help you show what science means to you and reveal why science can be as personal as you want it to be. Light refreshments will be served, but bring your imagination and participate at this free event. Speaker 1: A feature spectrum is to present new stories about science that we find particularly interesting. Rick Carnesi joins me in presenting the news. Speaker 10: Nature News reported on April 13th that a team of scientists from [00:26:30] Caltech have estimated that Mars's atmosphere was probably never thick enough to keep temperatures on the planet surface above freezing for very long. Edwin kite now at Princeton used from the Mars reconnaissance orbiter to catalog more than 300 craters and an 84,000 square kilometer area near the planets equator. The sizes of the creators were compared to computer models with varying atmospheres. Dance [00:27:00] or atmospheres would have broken up small objects as they do on earth, but the high frequency of smaller craters on Mars suggest the upper limit of atmospheric pressure on Mars was only one or two bar. This most likely means a temperatures on Mars have typically been below freezing. Did the team notes that their findings do allow the possibility of scenarios of Mars having a slightly thicker atmosphere at times. Do you perhaps to volcanic activity or gas is released by the large impact events and these could have [00:27:30] made Mars warmer for decades or centuries at a time, allowing water to flow. Then Speaker 1: science daily reports one of the first social science experiments to rest on. Big Data has been published in plus one. A chair of investigators from Simon Fraser University analyzed when humans start to experience and age-related decline in cognitive motor skills. The researchers analyze the digital performances of over 3000 starcraft two players, age 16 to 44 starcraft two is a ruthless intergalactic computer [00:28:00] game that players often undertake to win serious money. Their performance records, which can be easily accessed, represent thousands of hours worth of strategic real time. Cognitive based moves performed at various skill levels using complex statistical modeling. Researchers distilled meaning from this colossal compilation of information about how players responded to their opponents and more importantly, how long they took to react after around 24 years of age, players show slowing and a measure of cognitive speed that is known to be important for performance. [00:28:30] Explains Joe Thompson lead author of the study. This cognitive performance decline is present even at higher levels of skill, but there's a silver lining in this earlier than expected slippery slope into old age. Thompson says older players, those slower seem to compensate by employing simpler strategies and using the games interface more efficiently. The younger players enabling them to retain their skill despite cognitive motor speed losses. These findings says Thompson suggests that our cognitive motor capabilities are not stable across our adulthood, but are constantly [00:29:00] in flux and that our day to day performance is a result of the constant interplay between change and adaptation. Speaker 2: [inaudible]Speaker 11: and music heard during this show was written and produced by Alex Simon. Today's interview was edited by Rene Rau. Thank you for listening to spectrum. If you have comments about the show, please send them to us via email or email [00:29:30] address is spectrum dot kalx@yahoo.com join us in two weeks at this same tone. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Steve Blank, lecturer Haas School of Business UCB. He has been a entrepreneur in Silicon Valley since the 1970s. He has been teaching and developing curriculum for entrepreneurship training. Built a method for high tech startups, the Lean LaunchPad.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Okay. Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, a [00:00:30] biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hello and good afternoon. My name is Renee Rao and I'll be hosting today's show. Today we present part two of two interviews with Steve Blank. I lecture at the High School of business at UC Berkeley. Steve has been a serial entrepreneur in silicon valley since the late 1970s in the early two thousands he retired from the day to day involvement [00:01:00] of running a company. He has been teaching entrepreneurship training ever since. By 2011 he was said to have devised a scientific method for launching high tech startups, dubbed the lean launchpad. The National Science Foundation caught wind of this and asked Steve to build a variation for teaching scientists and engineers how to launch startups. In 2013 Steve partnered with UCLA and the NSF to offer the lean launch pad class for life science and healthcare. In part two, Steve Talks about getting [00:01:30] the NSF lean launch pad classes going, the evolution of startup companies and innovation, and now Brad swift continued his interview with Steve Blank. Speaker 4: Okay. Speaker 5: In your experience with these scientists and teaching them, are these people self selected? They're the ones who are anxious and eager and there are other scientists maybe back in the lab are reluctant afraid of the process. Speaker 4: So just the personality of it. Yeah, so this goes back to the comment I made earlier about entrepreneurs being artists. It was the implicit comment [00:02:00] I just kind of both through in the beginning, but as important is that you can't assign entrepreneurship as a job, right? If you really think about them, you can't split up a room and say, those of you on the left, you're going to be musicians. And those are you on the right, you're working on the assembly line like, Oh yeah, WTI. I mean, it doesn't work. It doesn't work like that. All right. Entrepreneurship is a calling. Just like art, just like music, just like writing is something you have to passionately want to do, but much like art, we've learned something [00:02:30] a couple hundred years ago that very early on in people's lives in elementary school and junior high school in high school, we want to have our depreciation. Speaker 4: They're not intensive classes, but their exposure to art that people might not know their artists. They might not know they have a passion to paint or to sculpt or to write or to entertain. I will contend because entrepreneurship is an art. We actually need those type of classes early on because scientists didn't understand [00:03:00] that not was their passion to invent and create. They might actually have an equal passion to wait a minute, I actually want to take this thing all the way through when I want to see what happens. If hundreds of thousands of people were being affected by this medicine, not just, here's my paper in the latest publication. It doesn't mean everybody could do that, but it means we've not yet gotten the culture to where we could say, well is this something that kind of excites you? And I think we're getting better to understand what it takes to do that. Speaker 4: Would you have any [00:03:30] idea what that would look like? The kind of exposure that you would be talking about in grammar school or Middle School? Sure. It turns out one of the unintended consequences of teaching the scientists that National Science Foundation is, remember their professors, almost all of them tenured running labs and universities across the country. And so here they take this class from the national science foundation and about half or two thirds of them now go back to their own universities, pissed cause they go, how come we're not teaching this? And so what happens is the National Science Foundation asked [00:04:00] me and Jerry Angle, who was the head of entrepreneurship at Haas, why don't you guys put on a course through a nonprofit called NCIA to teach educators in the United States who want to learn how to teach this class. And so we teach the lean launchpad for educators. We teach now 300 educators a year. Speaker 4: One of the outgrowths of that class was entrepreneur educators from middle school and high school started showing up and I went, you're not really teaching this to kids. They went, [00:04:30] oh Steve, you should see our class. And I went, oh my gosh, this is better than I'm doing. So they'd taken the same theory and they modified the language. So it was age appropriate. And so the two schools that had some great programs were Hawkin school outside of Cleveland and Dunn's school here in California. And in fact they're going to hold their own version of the educator class in June of 2014 for middle school and high school educators who were interested in teaching this type of entrepreneurial education. So I think it's starting to be transformative. I think we [00:05:00] have found the process to engage people early and not treated like we're teaching accounting to do, treating it like we're teaching art. Speaker 4: And again, we're still experiment thing. I wish I could tell you we got it now. I don't think so. I think we're learning, but the speed at which we're learning through it makes me smile. That's great. It is great. The Passion of the educators really is exciting. And Are you able to teach us remotely so that scientists from around the country don't have to come to you and sort of stop what they're doing? I was teaching the class [00:05:30] remotely. It's now taught in person in multiple regions. So that's how we solved that problem. But my lectures were recorded and not only were they recorded, they were recorded with really interesting animation. So instead of just watching me was a talking head. These are broken up into two minute clips and it's basically how to start a company and it's on you udacity.com so if you want to see the lean launch pad class in the lectures, it's on your udacity.com it's called the p two 45 but by accident we made these lectures public to not only the [00:06:00] national science foundation scientists, but we opened it up to everybody. Speaker 4: And surprisingly there is now over a quarter million people have taken the class. I've had people stop me at conferences and have told me that the Arabic translation, which I didn't even know existed, it's the standard in the Middle East. I had people from Dubai and Saudi Arabia in Lebanon literally within 10 feet go, oh well we recognize you. And I went, who are you turning over, Mr Blank, you worthy? I went, what's going on? I laugh not because it's me, but because [00:06:30] this is the power of the democratization of entrepreneurship. I have to tell you a funny story is that I grew up with the entrepreneur cluster was silicon valley and something in the last five years that I've gotten to travel with both Berkeley and Stanford and National Science Foundation to different countries to talk and teach about entrepreneurship. And my wife and I happened to be on vacation in Prague and when I really knew the world had changed as my wife had said, you know Steve, we're kind of tired of eating hotel food. Speaker 4: I wonder if there were ending entrepreneurs and Proc, I didn't want to, I [00:07:00] don't know. You know, let me go tweet and any entrepreneurs and Prague, you know, looking for a good check. Brie hall and hour and a half later we're having dinner with 55 entrepreneurs and Prague television is there and they said, Steve, you don't understand. Here's why. Here's an entrepreneur community everywhere. The only thing we still have unique in the bay area is that entrepreneurship and innovation. We've become a company town. That is our product. Much like Hollywood used to be movies in Detroit used to be cars in Pittsburgh steel. [00:07:30] While obviously there are people who do other stuff, teach in restaurants, put the business. The business to the bay area really is entrepreneurship and innovation. While we tell stories about the entrepreneurs, the unheralded part of that ecosystem is that we have equally insane financial people. Speaker 4: Why Silicon Valley happened was that the venture capitalist in the 1970s in Boston when it wasn't clear whether it was going to be Boston or Silicon Valley to be the center of entrepreneurship, the venture capitalist in Boston continued to act [00:08:00] like bankers, venture capitalists in Silicon Valley. They decided to act like pirates and the pirates want and so what really differentiates the observational make with an entrepreneurship is everywhere in the world. Entrepreneurial clusters only happen when all these things, these components, primarily entrepreneurs, but a heavy dose of risk capital capable of writing not only small checks but large checks and doubling and tripling down on startups. That's why you have the Facebooks and the googles and the twitters [00:08:30] around here. You also have a culture let's people know and understand. In the 1950s and sixties people came to San Francisco and Berkeley to live an alternate personal lifestyle, but they were hitting 30 miles south to have an alternate business lifestyle around Stanford and it was this kind of magic combination of great weather, the ability to do things in both business and your personal life that you couldn't anywhere else. These cultural phenomenons actually were and under appreciated until a very smart professor at Berkeley [inaudible] [00:09:00] wrote a book called regional advantage that actually described a lot of these things and open my eyes about why this region actually won. Speaker 1: You're listening to spectrum on k a Alex Berkeley. Steve Blank is our guest. He's a former entrepreneur and current lecturer at the High School of business. And the next segment he talks about how startups has changed since he first began in Silicon Valley in the 1970s Speaker 4: is entrepreneurship then changed as a result [00:09:30] of that. What really happened was the harmonic conversion of a really interesting set of events. One is, is that if you think back on how startups worked in the, in the golden age of Silicon Valley in the seventies and eighties to build a startup required millions if not tens of millions of dollars, not to run it, but just to start it, you needed to buy computers, either mainframes or mini computers and then workstations. You needed to license millions of dollars of expensive software. The only venture people were either in [00:10:00] Boston or silicon valley and they lived on sand hill road and nowhere else, and therefore it was kind of a formal process and the cost of entry was literally millions or tens of millions of dollars. There was no other way to get computing. There was no other way to get money. The second is, we had no theory about startups. Speaker 4: That is, there were no management tools at all. But what happened starting out of the rubble actually of the last Internet bubble, things change in technology in a way. I don't think people outside the technology business appreciate it off. Probably the biggest [00:10:30] one was actually generated by Amazon. It turns out Amazon created something called Amazon web services. And if you're a consumer, all you know is Amazon maybe for kindle and for sure for their books or their website. But if you're a programmer, Amazon has become the computing utility. You no longer have to buy computers from your laptop. You literally log in to hundreds of millions of dollars of computers and you have access to the world's largest computing resource ever assembled [00:11:00] for pennies, for pennies, and you don't need any storage. You're storing it all and online and all the computing. So number one, Amazon web services truly turned computing hardware and software into a pennies per gigabyte and MIPS, et Cetera, in a way that was unbelievable 10 years earlier. Speaker 4: Two is that changed the cost of entry of an early stage venture. You no longer needed millions of dollars. In fact, if you were smart entrepreneur, you could start on your credit card and if you didn't have your credit card, maybe some friends and family, [00:11:30] and that started a very different wave because it changed venture capital. It used to be there were either doctors or dentists or other reform of venture capital firms like Kleiner Perkins and Mayfield and sequoia. But the fact is that now after a ton of entrepreneurs could start on their credit cards, they still didn't need $20 million. Maybe eventually they did, but they could just take $100,000 or half a million dollars and get pretty far. And that created a new class of super angels or angel investors [00:12:00] that just never existed before. Kind of this intermediate level. And so venture capital changed. And also with that change, it changed where they could be located. Speaker 4: You no longer had to be located to be a investor in New York, Boston, or San Diego. Th that amount of capital could be available in the London or Helsinki or Estonia or Jordan, Beijing. Third is, and I will take credit for some of this, the invention of a new way to look and how to build these startups. It used to be that if you were building [00:12:30] a physical product, you would do something called the functional Spec or you'd get requirements from a customer. You build a specification and then you'd make an early version of the product called Alpha test, maybe a less buggy version called Beta test, which foist on some poor unsuspecting customers and then you'd have a party at something called first customer ship and that process was called waterfall development and from beginning to end typically took years and insight in the software business and Toyota had it even [00:13:00] earlier is that we could build products differently, we could build products incrementally and iteratively and that's called agile engineering and for startups, how you want to build your products is agily and iteratively because almost always what you believe on day one are all the customer features that they need. Speaker 4: It's a pretty safe bet. You're not a visionary, you're actually hallucinating and that most of the features you would historically have built in go unused on needed and unwanted. But if [00:13:30] in fact you could actually test intermediate versions of the product iteratively and rapidly on those customers with a formal process which I invented called customer development, those two hand in hand change the speed and trajectory of how startups get built. And so now you see these startups coming out of nowhere and getting acquired in three years, but they have tens of millions of customer. Where did that come from? Well, in the old days we'd still be writing the software, building the hardware. Speaker 6: Aw, it's [00:14:00] a public affairs show, k, a l X. Berkeley. Our guest is Steve Link a lecture at UC Berkeley's Haas School of business. The next segment, Steve Talks about his current work, trying to understand how innovation drives some companies and fails in others. Speaker 4: If I can, the unintended consequence of all this stuff. Remember this whole lean startup stuff has become a movement by itself. Harvard business review contacts me and says, Steve, [00:14:30] every large corporation is now desperately struggling how to deal with continuous disruption in the 21st century. That is all the rules that worked in the 20th century, you know, be number one in market share, you know, like be number one and two, I mean all the Jack Welsh rules, you follow those who be out of business in seven years. Why, you know, globalization in China Inc Internet has made consumers flighty very little brand loyalty. Pricing is almost transparent. Cost of starting a new business is infinitely lower. All of the things [00:15:00] that made you strong in the 20th century as a corporation are no longer true. Some of them are obviously, but not really. And so every large corporation are trying to relearn a set of rules and guess where they're looking for, they're looking at startups of how do we be as innovative as apple as that. Speaker 4: That is, the models are now silicon valley and other technology companies. And so my article, the lean startup changes everything became the cover of the Harvard Business Review and May, 2013 what was interesting is that I started [00:15:30] getting calls from executives whose titles I had never heard of before. It turns out almost every large company is now appointing a VP of corporate innovation. I had never heard of it. You know what's that? And when you go talk to them, and I've talked to a bunch of them, now you find out that they're all struggling to solve this continuous disruption problem by trying to build innovation inside the DNA of large corporations in the u s and overseas and the first sign of companies [00:16:00] trying to do that is appointing somebody typically as a corporate staff person to have some kind of internal incubator. I could politely say, that's a nice first step put it really doesn't solve the problem. Speaker 4: It actually just points out what the problem is and can I digress for another 10 seconds? It turns out that the problem that corporations are having is not a tactical organizational problem. The things I described, the globalization, the effect of the [00:16:30] Internet, et Cetera, are just strategic problems that every corporation is facing. The last time companies faced something, this major was in the 1920s, uh, u s corporations grew from small mom and pop businesses from the 1870s to 1920s and they kind of came up with a form of organization called functional organizations, meaning you had a head of sales, a head of marketing, a head of manufacturing, but by function that was the only way companies were organized. But by 1920, some [00:17:00] u s corporations spans from New York to San Francisco. And so there was a geography problem here. You had a head of sales tryna run multiple geography. Speaker 4: It wasn't even the same time zone. And some companies like dupont had a different problem while they also had geography problems. Dupont made everything from explosives to paint. But you only had one marketing group and one manufacture. How do, how do you manage that? And for about five or six years for corporations, dupont, General Motors, Sears and standard oil, understood. They had a strategy [00:17:30] problem and attacked it by playing with the structure of the company, meaning how the company was organized and they all finally decided that they were going to organize in a radically different form called divisions. Instead of just having functions, they would actually break up like for example, General Motors into the Buick Division and ultimate build division or whatever, or for dupont explosives divisions and the paint division and on top of a thin layer of corporate staff, but now have a company organized by divisions first changed in [00:18:00] 50 years and how companies were organized. Speaker 4: Fast forward 40 years later, the third form of corporate organization to emerged called Matrix organizations where you start with a functional organization, but now all of a sudden we would have specific projects pop up, gee, I want to work on the new fad six fighter. Well, I have an engineering group, but let me put together a team that could pull out of engineering and pull out a product management and put together for our temporary amount of time and then they'll go back into their functions and then be pulled out again. But that's it. Those are the only three forms [00:18:30] of corporate organization. I'll contend that we're facing a common strategy problem that is not solvable by just pasting on vps of innovation. I believe it's solvable by rethinking on the highest possible level is do we need a fourth form of corporate organization? And I gotta tell you I got the answer, but I'm not going to tell you now. Okay.Speaker 5: Is this sort of then turning all the operations research that's been done over the past? You know, since World War II, [00:19:00] that was when it seemed to be salient. Is it on its ear now? Is this, Speaker 4: so if you really think about what we built for the last 150 years is corporations were the epitome of operational efficiency through operations research, the output of business schools. I mean all our stuff has had to be continuous execution, driving to the lowest cost provider and outsourcing and all that stuff. That's great. But you're going out of business and in fact, companies that do that, [00:19:30] I will contend have a much shorter lifespan that companies that now do continuous innovation. That is, if you think about the difference between Amazon and Netflix and apple, when jobs was alive versus standard US companies, the distinction was they were continuously innovating, ruined Leslie, innovating, and it was not some department that was innovating. It's a big idea. It was the entire company was innovating, yet they were making obscene profits. So clearly there are some models of some companies who [00:20:00] have figured out and in fact HP in the 70s and eighties had figured out how to do and then they lost the formula. I think we now actually have a theory, a strategy of how to do that and some really specific tactics. How, I know we could do this in detail for u s corporations and corporations worldwide, but I want to start at the u s and we're going to be talking and writing about that in the next year. Speaker 5: Great. So that's what you're actively working. Speaker 4: Oh, actively working. And I'm Hank Chesboro who have inventor of open innovation here at Haas business school and with Alexander Osterwalder [00:20:30] and venture of the business model canvas. All have been part of some of these discussions. You know, I just get smarter by hanging out with much smarter people. And I'm not the only one who's thinking about that. There are lots of very smart people trying to crack the code and at the same time, companies are raising their hand and the symptom of raising their hand is they're appointing vps of innovation and her likes saying, yeah, you know, here's what we are. Oops, it doesn't quite work. And finance has different rules and but wait a minute, I'm trying to be innovative, but the HR manual doesn't allow me to hire people. No, [00:21:00] no. Legal says I can't use our brand here. So what you're really finding is that it's not an org problem. Speaker 4: It's not anybody's trying to be mean. Is that what we're missing is the CEO and board conversation is, oh my gosh, maybe we need to get innovation in every part of the company, not by exception. That's the idea I'll telegraph for now. And how do you do that without affecting current profits? And it's quite possible because again, there are these experiments of companies that are insanely from a profitable, who've done this. [00:21:30] Now can we just make a teachable and doable by other corporations? And the answer is yes, we're going to go do that. Do you see that pace of technology accelerating? Absolutely. I think we're in the golden age of both technology and entrepreneurship. You ain't seen anything yet. I'm still constantly amazed sitting here smiling. When you say that is why I still love to teach is that, you know, I get to see my students come up with things. Speaker 4: You hear the 400th hotel automation package or the whatever, but you know, and then you see something, again, drones are three d printing [00:22:00] or you could do white with your phone, you're gonna make a turn on or you're a password through. It's just things that are unimaginable. And then you watch the next generation of Steve Jobs that said, you know, the current version silicon valley is you go on much. Who single handedly is val to obsolete the automobile industry? And at the same time just wrecking havoc in this space launch industry, single individual who had, by the way, zero qualifications to do any of those. Congratulations. Welcome to entrepreneurship. He had the will to be disruptive [00:22:30] and he understood that the technology was about at the edge of being able to do what he did. That's how we got the iPod and the iPhone or else in a perfect world and Nokia would still have 89% market share. If I was General Motors and Ford, I'd be really concerned. Steve Blank, thanks very much for coming on spectrum. Great. Thanks for having me. Speaker 6: You'd like more insight into Steve Blank's ideas. Go to his website, Steve blank.com [00:23:00] as Steve mentioned, the Lean launch pad course is available. I knew udacity.com to learn more about the NSF mean launchpad curriculum, search for NSF [inaudible] your local to the bay area. Go to [inaudible] dot com if you're interested in startup appreciation materials for educators, go to n c I n aa.org/l l p. Stretching shows [00:23:30] are archived on iTunes yet it gives created a simple link for you. The link is tiny url.com/calex spectrum and now a few some technology events happening locally over the next two weeks. Brad Swift joins me for the calendar. Speaker 3: California's coastal waters are home to one of the four richest temperate marine biota is in the world. The California Academy of Sciences will be holding [00:24:00] a series of lectures and events to explore this incredible diversity of life. They look, explain what makes this region so productive and why it needs to be protected on Saturday, March 22nd from nine to 11:00 AM a variety of Speakers will consider the impacts of human activity on the local marine ecosystems and the establishment and efficacy of marine protected areas. They will also discuss how diversity is monitored in California's oceans and which areas will need to be most closely scrutinized for future impact. For more information on the [00:24:30] March 22nd event. Please visit cal academy.org Speaker 5: on Monday, March 31st University of Maryland professor of human development, Nathan Fox will give a lecture on his recent studies on whether experiences shaped the brain and neural circuitry for emerging cognitive and social behaviors over the first years of life. Something that many developmental scientists take for granted. Foxes study the Bucharest early intervention project [00:25:00] is the first randomized trial of a family intervention for children who experienced significant psychosocial neglect early in their lives. A group of infants living in institutions in Romania were recruited and randomized to be taken out of the institution and placed into family foster care homes or to remain in the institution. He then followed up with the children several times over the next eight years and examine the lasting [00:25:30] effects of the deprivation and which, if any interventions were successful in assuaging the harmful effects, the free public talk will be held on March 31st from 12 to 1:30 PM on the UC Berkeley campus in room 31 50 of Tolman hall Speaker 3: on Wednesday per second. You see Berkeley's department of Environmental Science Policy and management will present a speech by Chris Mooney, a journalist who's written several books on the resistance that many [00:26:00] Americans have to accepting scientific conclusions. His lecture will be titled The Science of why we don't believe in science and we'll examine the reasons behind Americans disinterest in scientific solutions to the world's problems. The free public lecture will be held on Wednesday, April 2nd at 7:00 PM in the International House Auditorium of UC Berkeley. Here at spectrum, we like to present new stories we find particularly interesting. Brad Swift joins me in presenting the news. Speaker 5: UC Berkeley Professor, Dr. Richard Kramer [00:26:30] and his research team have been able to temporarily restore light sensitivity to mice, missing a majority of their rods and cones in healthy mammals. The eyes detect light with specialized photo receptor cells or rods and cones and then transmit a signal to their optic nerve cells which eventually communicate with the brain. Dr. Kramer and his team explored the effects of a similarly light-sensitive molecule known as d n a Q in healthy mice and mice [00:27:00] with a degenerative disease that caused them to lose nearly all their rods and cones. After dosing, the mice with d n a Q, the mice were exposed to lights and their optic nerve activity was measured via electrode arrays. The diseased mice showed strong light sensitivity. The team next examined a small number of animals in light and dark conditions to test whether the sensitivity conferred any perception of the light. In the diseased mice, [00:27:30] the injected mice were better able to form an association between a light stimuli and electric shock than those in the control group. While millions of humans suffer from similar degenerative retinal conditions, definitive conclusions on the broader therapeutic and deleterious effects of the molecule. D n a Q are still years away. Speaker 3: In a recent study published in the journal bio materials, UC Berkeley researchers were able to eliminate the transmission rep [00:28:00] of a common infection. Staphylococcus Aureus is a bacterium that commonly infects patients who've had surgeries involving prosthetic joints and artificial heart, bowels, staff, or aces. Ability to adhere to medical advices is key to experience as once introduced to the body. It can cause severe illness. UC Berkeley Bio and mechanical engineering, Professor Mohammad [inaudible] fraud and others in his lab examined how the clusters of staff warriors were able to adhere so well to certain Yana surfaces as well as the type of surfaces [00:28:30] that increased or decreased the bacteria's ability to clean. They quickly found that while staff [inaudible] can adhere to a variety of flattened curves services, it does seem to have a preference for certain structures including a tubular pillar where the bacteria was able to partially embed itself within holes in the structure. Professor, my fraud expressed hope that the improved understanding of these preferences could allow the design of medical devices built to attenuate bacterial adhesion while escaping the need to chemically damaged the bacteria to prevent transmission Speaker 7: [00:29:00] [inaudible]. Speaker 5: The music heard during the show was written and produced by Alex Simon. Speaker 1: Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Our email address is spectrum to a k a l ex@yahoo.com Trina's in two weeks at the same time. [inaudible] Speaker 8: [00:29:30] [inaudible]. See acast.com/privacy for privacy and opt-out information.

Dr. Josephine Yuen is the Ex Dir of E3S Center a collaboration of UCB, MIT, Stanford and UTEP. She is a Physical Chemist, Ph.D. from Cornell. She explains the e3s Center goals, Community College program, and focus on getting the research right.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible] [inaudible]. [inaudible]. Speaker 1: Welcome to spectrum [00:00:30] the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi and good afternoon. My name is Brad Swift. I'm the host of today's show. Our guest is Dr Josephine u n. She is the executive director of the [inaudible] center, a collaboration of UC Berkeley, MIT, Stanford, [00:01:00] and the University of Texas at El Paso. Dr [inaudible] is a physical chemist by training with a phd from Cornell University and she was also a postdoctoral fellow at the Argonne National Laboratory. She became a member of technical staff in bell laboratories and eventually held director level positions in product development, product management, manufacturing and supply line management. More recently, she was the CEO of try form x INC which develops and manufactures precision polymer [00:01:30] optics for the communications consumer products and medical industries. After spending 30 years in industry, she was a program director at the National Science Foundation. Today she talks with me about the [inaudible] center here at Berkeley, Josephine Ewen. Welcome to spectrum. Speaker 1: Thank you.Speaker 3: What is the origin story of e three s? How did it all get started? Speaker 1: Well, let's first understand what e three s stands for. It's [00:02:00] an acronym and this acronym for a center does headquarted in UC Berkeley and it's the center for energy efficient electronics science. Our story really began at the National Science Foundation. The National Science Foundation has several programs that fund centers intended to bring researchers from many institutions together to solve difficult problems [00:02:30] and one of those programs is the science and Technology Center program. Way Back and I believe most probably was 2008 there was a solicitation asking technical community and that is universities. Did you submit proposals for a new science and technology center? This type of solicitation comes out once every three years or so and so in two and nine professor [00:03:00] [inaudible] off the east department submitted a proposal that brings together researchers from various institutions, namely UC Berkeley, MIT, and Stanford to propose a new center, a new center that will do research necessary to come up with an alternative to the current day trend system. Speaker 1: No, you may want to ask, why do we need that? After all, transistors are everywhere and [00:03:30] it's in every aspects of our life. The reason we need an alternative is that we need an nutrient system or any kind of electronic components that would draw significantly less energy. Pol consumption in electronic devices have been dropping by virtue of the fact that through miniature isolation, the electronic industry has made great gains, not only in power consumption but in the cost of the device, [00:04:00] but unfortunately, miniaturization has hit a brick wall. It no longer is delivering the benefits it has delivered 10 plus years ago and you can see it by the very fact that the operating voltage of those devices in the past 10 plus years ago when the line was shrinks, you can see a big drop in the operating voltage, but in the last 10 years it's more or less flattened out and [00:04:30] even though the line was has shrunk further, we see that the operating voltage is around a vote, maybe slightly less than a vote now in the state of the art devices, but really we want to get to a device that can operate in the millivolt range and that is what the centers set out to do and we're doing the research necessary to get there. [inaudible] Speaker 3: I wanted to have [00:05:00] you talk about the themes of research at e three s and what made choosing themes and appealing method for your organization? Speaker 1: The center is researching different scientific concepts to achieve different device approaches. No one knows what is the best approach at this point. The current c Moss transistor is ubiquitous. There's no reason to believe is replacing will be [00:05:30] equally ubiquitous. The replacement may be a different solution for different application. That's why our research portfolio includes four themes. Not all four themes address the transistor. If you think of a integrated circuit, it's really a network of switches and the wires that connect us, which is three of the themes, address a different [00:06:00] type of switch while one theme address, how do you have more efficient wires or lower power consumption wires? Today's wars are copper wires, metal to wires, but we are doing research to have the communication between switches being done optically Speaker 3: and just for the record, what are the four themes? Speaker 1: The first theme is Nano Electronics. [00:06:30] The second theme is Nano mechanics. The third theme is nanophotonics and the fourth theme is Nano magnetics and you can see the first, second and fourth addresses. How do you get a different type of switch? While the third theme addresses the interconnection, namely the use of light for the interconnection amongst the switches [00:07:00] that we also call optical interconnect. Speaker 3: How interdisciplinary is the center? Do you have a sense of that in terms of the investigators and the researchers? Speaker 1: The center is highly into disciplinary disciplines involved. Our electrical engineering, chemistry material science and Physics Speaker 4: [inaudible]Speaker 3: [00:07:30] you are listening to spectrum of public affairs show on k a l x Berkeley public. Our guest is Josephine n. She is the executive director of the three s center. In the next segment she details the e three s community college outreach group. [inaudible]. An [00:08:00] interesting part of the e three s center is the program you've developed with community colleges. Do you want to explain how that program began and what its goals are? Speaker 1: A science and technology center is expected to educate besides do research and the education is not only have graduate students, so in I'll propose which NSF we decided to focus [00:08:30] on community college students. The reason we decided to do that is because in California we have the largest community college system in the country and many women and underrepresented minority start their post high school education. In community colleges. Our needs to increase its output of workers in this fuse [00:09:00] state utilizes science and technology disciplines and in order to do that we have to be able to encourage and groom participants from populations that are typically underrepresented in the technical world and this really based on that consideration that we say less focus on encouraging students, helping students from community colleges [00:09:30] develop a career in science and engineering. Speaker 3: What can you tell me about how the program is working and how people participate in it? From the community college side, Speaker 1: we have a program on campus called the transfer to excellence and this program while started by the East Rehab Center has now expanded to include other centers. This has been made possible because in addition to [00:10:00] the east area centers grind, the National Science Foundation also gave us an additional three years grant to expand the community college program and that has allowed the program to place students not only in the [inaudible] center but also to other centers on campus. Namely coins, the deals with Nana mechanics and also [inaudible] that deals with [00:10:30] synthetic bio fuse. The students from community college come on campus in the summer for nine weeks to do research, the first weakest bootcamp with the learn some of the basics to prepare them to go into the labs and then for the other eight weeks they work in the lab on individual projects and at the end, in the last week of the internship, they have to [00:11:00] present their work both in terms of giving talks and also in the form of posters in a poster session and that typically takes place at the beginning of August. And how large is that program? Last summer we hosted approximately 15 students. Speaker 3: Does that sort of what your target is for each summer? Speaker 1: Yes. Between 12 to 15 is off target [inaudible]. Speaker 3: And how do people [00:11:30] in community colleges get involved in it? How do they get selected or how do they apply? Speaker 1: In the fall we go through what we consider our recruitment face. We Post the information about the program on the website of our center. The staff of the center also goes out on campus to recruit. We host workshops to share information about a program and also to provide pointers to potential [00:12:00] applicants, how best to prepare the application. We also have webinars with, again, the purpose of encouraging and guiding potential applicants and how to apply and we also work with various community college or Nay stations to promote the program. For example, we ran a workshop in a Mesa conference. Is it statewide? [00:12:30] Yes. We're very proud to say that we have brought students from Mount Shasta down to south of San Diego from the bay area to the central valley Speaker 3: and I suppose the hope is that the students will then go to four year colleges get degrees. Are you tracking at all their progress in that effort? Speaker 1: Yes. Clearly the number one goal of this program [00:13:00] is to use research to deepen the interests of these students in science and engineering and you can ensure that they will get a good career in science engineering. Minimally a four year degree is necessary, so helping the students to transfer to a four year institution is number one goal. In addition, we want to excite them enough that they would even set this sites to go to graduate [00:13:30] school. The program provides one on one advising on the transfer process, particularly to UC Berkeley but also to four year institution in general and this advising is done by tap advices, which is the transfer alliance projects. There's part of UC Berkeley's campus, 87% of our 2012 class has transferred [00:14:00] to to what you see last fall. Most of them came to UC Berkeley, but others went to other ucs as well and I believe one of them actually transferred to Columbia Speaker 3: and for students that are in community colleges it might be listening. The best way to find out about it is to go on your website. Speaker 1: Yes. That's the best way to find out about the program and is also through our website which is www.ethrees-center.org [00:14:30] this website not only provides information but it just through this website you do your online application, Speaker 3: the community college students that are coming, what are their science requirements? Speaker 1: The program takes students the summer before they apply to transfer to a four year institution. By then we expect the students [00:15:00] to have completed two calculus courses and three signs or engineering courses including one laboratory course. Speaker 2: Okay. Speaker 5: From is a science and technology show on KALX Berkeley. We are talking with Josephine. You went [00:15:30] in the next segment she talks about the hope of research migrating from the lab to Congress. Speaker 2: [inaudible]Speaker 3: the center's focus now is on research. Is there at some point if you're successful with your research, a capability to implement and build something that would be a prototype of sorts. Speaker 1: [00:16:00] We are very much in the science face of our center. As a matter of fact, we are very much encouraged by our funder to really focus on understanding the science as opposed to just using empirical methods to achieve device demonstration. Part of the center's strategic plan costs for at the end of our sentence life, which we expect to be 10 years. We will be [00:16:30] able to have one technology, namely our science will be mature enough that we have a technology that can be commercialized. On the other hand, we are expected along the way to be able to really understand how realistic our approaches so we will be expected to have certain types of prototype demonstration in the second five years [00:17:00] of our center. Also each theme we expect that I'll research may have some near term applications and actually as a example in theme three which is the Nanophotonics we expect that I'll work in photo detectors can have near term applications. Speaker 3: So in a sense kind of spinning off some of the early successes within the center or do you have to move it out of the center to other [00:17:30] players? Speaker 1: They have different ways of transferring the knowledge that we gained through our research. The center has industry partners. This industry partners are leaders in the electronics industry. They have recognized the neat off the center and we should clearly we see them s one of the avenues to transfer technology that Nia term along the term [00:18:00] technologies that may come after center, but as you know, they also many other venues including potentially some of our students taking technologies and creating companies [inaudible] Speaker 3: so the industry partners also are able to feed back to you, give you some reflection on your research. Speaker 1: The feedback will enable the center to conduct this research to be practical and useful Speaker 3: [00:18:30] with the publications. Are there any restrictions on who you can publish with? Are you seeking out open source journals? Speaker 1: The Sentis research results are publish through peer review journals. Many of these journals, one could argue is not open source because you need a subscription to get to them. However, the journals allow the authors to post the papers on [00:19:00] their own website. I'll send to identifies on our website, our list of publications and through the authors own website, the public can gain access to those papers. Speaker 3: Are there other centers or other research groups that are doing very similar work that you pay close attention to? Speaker 1: Yes, there is a center in Notre Dame that [00:19:30] is partially funded by DARPA and another government agency. That center involves not only Notre Dame, Bifido is headquartered there, but it also has members from many of the academic institutions. The name of the center is leased. The center has similar goals as us. We are not the only people that recognized the problem the semiconductor industry is facing, [00:20:00] so there are many efforts and many researchers around the world working on different approaches to solving the problem. We are one of several centers. We believe we differentiate ourselves in part because we have really put a strong emphasis on establishing the science and understanding what has prevented an easy solution. Speaker 3: In your personal [00:20:30] story, you've spent some time on both sides of the granting process being with the NSF. What does it like seeing both sides of the process?Speaker 1: I was the SPI, our program officer at the National Science Foundation before coming to UC Berkeley at the Star Center. A programs officer's job is to figure out what area to fund. And in conjunction with review panels, recommend [00:21:00] which particular proposals you fund. And then after the award, the program office is job is to advise, guide, oversee the delivery of results and ensure that the grantee is in compliance with the program requirements. But when you are grantee, your job is to deliver on what you promise. So a lot of the focus is on results delivery [00:21:30] while a programs office job is to facilitate guide help, but not directly involved with the results delivery [inaudible] which do you prefer? My background prior to going to national science foundation was in private industry. So I have a very strong operating background. So to a certain extent, one can argue that given the number of years I've spent [00:22:00] operating or delivering results, that comes to me more naturally. Speaker 6: Josephine n, thank you very much for coming on spectrum. Speaker 1: Thank you for having me. Speaker 2: [inaudible]Speaker 5: for more details [00:22:30] on the [inaudible] center and their educational program, which covers pre college undergraduate, graduate and postdoc opportunities. Go to the e three s website, which is e three s-center.org spectrum shows are archived on iTunes university and we have created a simple link to help you get there. The link is tiny url.com/kalx [00:23:00] spectrum Speaker 2: [inaudible].Speaker 5: We hope you can get out to a few of the science and technology events happening locally over the next two years. Two weeks. Speaker 6: Renee Rao and chase Jacabowski present the calendar this Monday, February 24th come check out the next edition of nerd night. East Bay featuring lectures such as explosions, [00:23:30] back drafts and sprinklers, how Hollywood gets fire science wrong by Joel Sipe. Then listen to Brian Dote from sweet Mary's coffee and he'll show us how a cherry becomes black gold in his lecture home coffee roasting on the with tools you probably already have and last Vincent tank way will teach us about hyper velocity launchers in his lecture. Hyper velocity launchers, how to launch a projectile at 10 meters per second. That's right. 10 meters per second. Once again, nerd night takes [00:24:00] place. February 24th at the new parkway cinema in Oakland. Doors Open at 7:00 PM on Monday, March 3rd Dr. Edward Stone of Caltech will be giving a talk about the voyager spacecraft missions into interstellar space launched in 1977 to explore Jupiter, Saturn, Uranus, and Neptune. The two voyager spacecrafts continue their journeys as they search for the Helio pause. Speaker 6: The heliopause is a boundary between the solar wind and the local interstellar medium. [00:24:30] Recently in August, 2012 voyager one seem to be finally entering into the heliopause. The spacecraft reported finding depleted low energy particles originating from inside the heliosphere as well as low energy cosmic rays from nearby regions of the Milky Way. These in subsequent observations of the heliopause are revealing new aspects of the complex interaction of our son with a local interstellar medium to hear a complete history and learn where the voyager is. Now. Join Dr. Stone on [00:25:00] March 3rd at 4:15 PM in [inaudible] room number one on my name, March 3rd at 7:30 PM hello fellow Dr Jacqueline. Ferritin will speak in the planetarium of the California Academy of Sciences. At the close of 2013 the Italian stars with planets orbiting them toppled more than 1000 the majority of these so-called exoplanets have not actually been seen, but rather inferred from their effect on their host stars through pain seeking technical methods and tremendous telescope [00:25:30] 10 handful of indirectly image and these giant planets have shown fascinating diversity in their sizes, temperatures, weather, and relationships to their parents. Speaker 6: Sends over the past several years, an entirely new and mysterious breed of planets has emerged. As genres have discovered a collection of orphans. Planets that are moving through the galaxy, seemingly unattached to a star in this talk fairly will highlight how we discovered these seemingly impossible objects and review how these strange, exotic planets may be key [00:26:00] players in our understanding of planet formation and evolution. Her talk will be held seven 30 on Monday night, March 3rd go to cal academy.org to reserve tickets. A feature of spectrum is to present new stories we find interesting. Tracy Jakubowski and Renee Rao present our news, the deal. Cal reports a new project from UC Berkeley. Researchers may soon allow the power of ocean waves to join solar and wind power as a commercialized source of energy. [00:26:30] The project is led by Marcus Lehman, a visiting graduate student in the Mechanical Engineering Department and supervised by razor alum and assistant professor of mechanical engineering and principal investigator of the research. Speaker 6: The project focuses on building a prototype of a sea floor carpet that can generate electricity by mimicking the properties of the muddy sea floor. Therefore, the group is designing a c floor carpet waive dampening system that will harness the energy of waves passing over it. Theoretically, the [00:27:00] energy generated by 10 meters of sea floor carpet will be roughly equivalent to the energy conducted by a stadium sized soccer field completely covered by solar panels. As more and more people move to live near coastlines, the researchers expect wave power to be a top contender as the next big renewable resource, especially because waves have very high energy density. The cost of building devices to harness wave power is high. LM said, the ocean is a difficult place to work and our devices have to be sturdy enough to combat [00:27:30] the oceans, corrosive and harsh environments, but there's an increasing need for clean and as socially acceptable forms of generating power. Speaker 6: We're working hard with scientists and engineers to make this happen and it's only a matter of time. A recent study published in the Open Access Journal microbiome examine the GI tract of premature infants in the neonatal intensive care unit or NICU. The lead author of the study, Brandon Brooks, a graduate student in the plant and microbial biology department at UC Berkeley, collaborated [00:28:00] with researchers university of Pittsburgh to swab the most touched surfaces at the NICU, as well as collect samples from two premature babies. In a small pilot study, they discovered the microbial environment of the baby's GI tracks was strikingly similar to that of the NICU, which was particularly interesting given that the premature babies were treated with antibiotics and should have had a very limited diversity of micro organisms within their GI tract. Well, most of the micro organisms were opportunistic. A few contain genes that conferred resistance [00:28:30] to antibiotics and disinfectant that was used within the NICU. The study provided an important insight into how the pathogenic, as well as nonpathogenic organisms are able to move from even the most sterile of environments to our bodies. Speaker 4: [inaudible] [inaudible] Speaker 7: the music heard during the show was written and produced by [00:29:00] Alex Simon Speaker 8: [inaudible].Speaker 7: Thank you for listening to spectrum. If you have comments about the show, please send them to us via email or email address, spectrum dev, QA, and lex@yahoo.com genus in two weeks time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Michel Maharbiz & Daniel Cohen. Michel is an Assoc Prof with EECS-UCB. His research is building micro/nano interfaces to cells and organisms: bio-derived fabrication methods. Daniel received his PhD from UCB and UCSF Dept of Bioengineering in 2013.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute [00:00:30] program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi and good afternoon. My name is Brad Swift. I'm the host of today's show. Today we are presenting part one of two interviews with Michelle and Harb is and Daniel Cohen. Michelle is an associate professor with the Department of Electrical Engineering and computer science at UC Berkeley and the Co director of the Berkeley Sensor and actuator center. [00:01:00] His current research interests include building micro and nano interfaces to cells and organisms and exploring bio derived fabrication methods. Daniel Cohen received his phd from the Joint UC Berkeley and UCLA Department of bioengineering program in 2013 his phd advisor was Michelle Ma harvests. Together they have been working on the fronts project and NSF f Free Grant [00:01:30] F re stands for emerging frontiers and research and innovation fronts is the acronym for flexible, resorbable, organic and nanomaterial therapeutic systems. In part one of our interview, we discuss how they came to the challenge of measuring and understanding the so-called wound field. Here's part one, Michelle [inaudible] and Daniel cone. Welcome to spectrum. Thank you. Thanks. How was it that [00:02:00] electrical fields generated by wounds was discovered? So I think Daniel should take this one cause he's the, he's the group historian on this topic. In fact, he gave us a little dissertation during this thesis talk Speaker 4: in the day when electricity was sort of still a parlor trick. There was a lot of work being done to try to figure out where it was coming from. There was a lot of mysticism associated with it. And this is in the mid to late 17 hundreds and so Galvani is a name most people have heard. Galvanism was a term [00:02:30] coined for his work and what he found was all the work with frog legs. So he used to dissect frogs and could show that if you had dissimilar metals in contact with different parts of the muscle and the nerves, the legs with twitch and amputate the frog leg. So his conclusion was that electricity had something to do with life and their living things were made alive by having this spark of life. And this was a really super controversial idea because for a long time there had been a philosophical debate raging about vitalism versus mechanism, which is the idea that all living things are special because of some intrinsic vital force versus the idea [00:03:00] that physical principles explain life. Speaker 4: So the vitalist really liked this idea that electricity is the spark that makes living things special. There's a lot of dispute about this, but eventually Volta who is right after him and who the vault is named after showed that it was really just the movement of ions and things in salt solutions, but it was a little too late and the mystical aspect of this had come along. So the problem then was that this idea prevailed into the early 18 hundreds and so Galvani his nephew Aldini started doing [00:03:30] these experiments in England where he was given permission to take executed criminals and basically play with the corpses and he was able to create a corpus that would go like this. And raise an arm or wink an eye at an audience. And this was the idea of the reanimated corpse. So people were having a lot of fun with this, but it wasn't clear that it wasn't mystical. Speaker 4: And so this is the long answer to the question, but that's the backdrop where the science starts to come in. So the first thing is Frankenstein gets published out of this, and everybody's getting into the whole vitalism idea [00:04:00] at this point. And Frankenstein was written as a part of a horror story competition. It was almost a joke. But the funny thing is Frankenstein. Well, how would you say Frankenstein? The monster came to life to lightning? Like that's a line. It wasn't a Hollywood fabrication and everyone assumed that. But Mary Shelley never wrote anything about lightning or electricity. She in fact, wrote the technology was too dangerous to describe in texts for the average person. But in her preface, she explains that the whole origin of this idea, and this is where the answer to the question comes from, was that [00:04:30] she had writer's block when she was writing the story and she overheard her husband Percy Shelley and Lord Byron having an argument about work done by Erasmus, Darwin and Erasmus. Speaker 4: Darwin was a big natural philosopher or scientist at the time who was a big vitalist. So he's really into the idea of the spark of life and also this idea of spontaneous generation that where does life come from when you have a compost heap, fruit flies appear. There was an idea that be composing garbage produced life, and that was part of spontaneous generation. And he did a lot of experiments where he'd seal things like wet flour into a bell jar [00:05:00] and to show that organisms came out in a sealed environment and they just didn't know about microorganisms and things like that. So he did a famous experiment where he dehydrated some species called Vermicelli all. Sorry, I made the mistake. I'm about to talk about 40 cello, which is a little organism. And when he added water again, they came back to life. Now, Lord Byron and Percy Shelley didn't understand any of this, and the conversation that Mary Shelley eavesdropped on was one where they said that Erasmus Darwin had taken Vermicelli Pasta, put it inside the Bell Jar, sealed [00:05:30] it, and through some magic of his own allowed it to twitch. Speaker 4: So he had essentially given life to pasta. Now Mary Shelley wrote that she didn't believe any of this was actually really what happened. But this idea of animating the inanimate gave her the idea for Frankenstein. Then she writes the one line that links it to electricity, which is, and if any technology would have done this, it would probably have been galvanism, which is this idea of applying electricity to something. And so that's where this whole idea of life and electricity came from. By that point, the scientists had finally [00:06:00] caught up with all the mysticism and started to do more serious experiments, and that's when Carlo met Tucci in 18 and 30 something found that when you cut yourself, there's some sort of electrical signal at the injury source. And that was his main contribution that was called the wound current or the wound field and then after him was the guy who really formalized the whole thing, which was do Bob Raymond, who was a German electrophysiologist who found that if you have any sort of injury, he could actually measure a current flowing at the side of the injury. Speaker 4: He could show that that changed over time. He cut his own thumb and [00:06:30] measured the current flow and they didn't have an explanation for why it happened, but they knew that it had something to do with the electric chemistry there. This was the birth of electrophysiology and then he went off and did all these things with action potentials in neurons, which is why almost no one's heard about this injury side and the fact that electricity's everywhere in the body normally and it's not mystical, it's electrochemical. We're much more familiar with the neural stuff and this other stuff on the wound side sort of languished until maybe the late 19 hundreds because it was rare. It was weird. It wasn't clearly important [00:07:00] and a lot of the players involved were so caught up in all sorts of other things that we tend to forget about this. So that was the whole long winded history of where the wound field came from. But it's a good story. It is a good story. Yeah. Speaker 5: [inaudible] you are listening to spectrum KALX Berkeley. Our guests are Michael ml harvest and and Daniel Colon. They're both bioengineers in the next segment they talk about the genesis of the fronts [00:07:30] project. Speaker 6: Michelle, when you approached the NSF yeah. For a grant for this idea, how long had you been thinking about it? The smart bandage idea, how far down stream were you with the idea? We had been toying with the idea for quite some time and there's a bit of background to this as well. So my group amongst other things builds flexible electrode systems. [00:08:00] You can call them for neuroscience in your engineering, and most of those systems are intended to record electrical signals across many different points across many electrodes usually honor in the brain. And so we had this basic technology lying around. This is sort of a competence that the group has had for quite awhile. The other thing that was beginning to intrigue us, and I have to credit Daniel for sort of beginning of the discussions and kind of pushing this along in the early years, so Daniel and I have like a tube man club of sitting around thinking of crazy things and [00:08:30] one of the things that Daniel had been interested in was the idea of resorbing or having so some of the materials disappear as they do their job in the body and this is a notion that's become very popular recently actually over the last couple of years in into community in the engineering community in general. Speaker 6: Which brings us to another question I had, which is the difference between resorptionSpeaker 4: and absorption. Absorption might imply that you're taking the components up and they're becoming part of the body. Resorption is really just a very strange [00:09:00] semantic term. That means something like the body's breaking it down or it's breaking down in some form and it's not really the same as that material winding up elsewhere in your tissues. It may just get excreted or it may go somewhere else. So really we use it when we don't really know what's going on. Yeah, we had been looking at this general area and then I think the last piece of the puzzle, I think in our minds looking at the extant literature, the idea that we could take meaningful electrical data from a wound began to really interest us. And so the [00:09:30] two parts of this really are one, can you use portable, resorbable systems? Something like a bandage, you know, something that that isn't going to require you to walk around with a handcart. Speaker 4: Can you use systems like this to measure electrical signals that are relevant to wounds? And then the other question is if you can do that, and if you have, you know, you learn about this, and by the way, we're not the first people to try to do this. There are a number of people that have been measuring electrical signals in the wounds as Daniel set for quite some time. If you can do this, is there a value to [00:10:00] trying to control or modulate that electrical information or those fields or those currents in the wound? Is there a therapeutic value? Perhaps there are scientific value. Is there something you can learn about the way the body works or tissue works? Both of those are open questions and you know we can delve into each of those, but those are really kind of how we think about them separately a little bit. Speaker 4: The flip side is that when we do a lot of this kind of design for medical things, you will want to know what's already happening and how the body handles its own injuries. And this field doesn't just arise passively. So they had no way of knowing [00:10:30] this when it was first discovered. But when you get this electric field, there is a navigational effect for incoming cells to the injury. So it actually helps guide things in like a lighthouse to the wound site. And so a lot of my phd work was showing how you can steer ourselves with a controlled electric field so you can really hurt them like sheep based on how the electric field goes. And that means that that was a source of this bio inspired part of it, which is we're not adding something that's not already there. We're taking something that's already there and we're modulating it to maybe improve. Speaker 4: [00:11:00] So evolutionary tools or things that the body has, it just happened to work well enough for us to survive as a species. It doesn't mean it's optimized and this field tends to go away very quickly. Nobody really knows whether extending the duration of the field would improve the healing or if we could shape it. Maybe you can control how scar tissue forms and things like that. So there's this idea of looking at how the body already heals itself and then figuring out where you might start to control it. And electricity is one of the areas that's really been under utilized in medical technology for the sort of thing. Yeah. I think for those of your audience [00:11:30] that are sort of tech junkies, if you will, the resurgence of this type of thing. Occurrent Lee I think arises because we've gotten very good at building very low power, very small electronics, and there's been a whole slew of new polymers and sort of new flexible substrates that are also conductive or can hold conductors. And so those two things together rekindled interest and trying to build gadgets that sit Speaker 6: on the skin. Or in the NSF case, we're not only doing the skin, but we're trying to develop a tool longterm [00:12:00] for surgeons to do something inside the body. So it'd be nice to be able to leave something that will help you heal, but then it'll be resorts so you don't have to reopen. Right. Speaker 5: Spectrum is a public affairs show on k a l x Berkeley. Our guests are Michelle. My heart is in Daniel Cohen of UC Berkeley. They want to build a smart bandage for wounds. In the next segment, they talk about the focus of their research. Speaker 6: [00:12:30] So in your approach to the NSF, was there some sort of focus, there's a technological focus and an application focus? The technological focus for the NSF was to point out that there was a lot of fundamental engineering science that had to be done to produce the type of systems that could do this. You know, we're looking at resorbable batteries are real parts wise, how you would build these systems, what polymers you'd use, what the rates of resorption. There's a lot of just fundamental stuff going on. If you posit that there'll be value to [00:13:00] these kinds of things. That's one focus as the other focus. I would say application wise we're looking at two things. The most ambitious is that you could develop systems that a surgeon could use for internal wounds. So the dream is a surgeon is, for example, let's say you have to resect the part of your intestine. Speaker 6: You then have to fuse the two parts that are left behind. There are methods for doing this and there's still research going on into what we know. The clinical methodology for this. It would be very useful if you could leave behind something that [00:13:30] could tell you, if nothing else, the state of how that is healing but would then go away because you're certainly not going to go back and open somebody's abdomen to take out a little piece of sensor that was doing something to intestine. Right? That'd be a not a good idea, and so that idea, that dream that you could leave behind, very small, very thin things that could take data if nothing else. Take data is really what was one of the applications. The other one is surface wounds. There are lots of surface wounds caused by illness. For example, advanced diabetes produces a [00:14:00] lot of problems in the extremities and wounds that are chronic that don't heal very well. Speaker 6: There's just a lot of ongoing interest in surface wounds and not just the technologies for understanding how they may be healing, but in things that maybe could help heal those surface wounds. Those are our full side view welders. I think of them as there are specific things we want to show we can do with our partners at UCLA, but there's also an entire wealth of engineering science that has to be done to build the fundamental. So the NSF was okay with that broad [00:14:30] a portfolio of research. Well, so that's sort of what their mandate is to go broad like that. Cause that seems like you're, you're doing stuff. Speaker 4: I think their main concern here is that they specifically discourage healthcare applications as NIH can fund those. But the difference is that what engineers have found for a long time now is that we don't actually know how to engineer biology. So any technology brings quantification Speaker 6: and an engineering mindset to solving this, like tissue engineering, growing organs. We don't have a lot of engineering for that. But if we start [00:15:00] to monitor everything we can, that chemical signals mechanical, electrical, we build up a set of stimulus and response type rules. We understand how to perturb these systems. So in the same way that you might build a bridge according to a manual of how you build a bridge and how you look at the loads in it and the ways of building a bridge, we might someday build organs. So if that's the pitch, that's much more fundamental science and that's really where it has a medical application. But we can't do it without science and engineering principles that just don't exist right now. There's two points I should mention. First of all, the key is this work [00:15:30] is really looking at the fundamentals of the engineering and the science. Speaker 6: We certainly have our foot into clinical side because I think it informs some of this, right? So that what you're doing is relevant so that someday you could go down that path so you're not in isolation because if you're not assuming that you're headed in this great direction. Exactly. And then you find clinical guys saying less clinically. Right. So the other were very good. And the second thing is that, um, we're funded under a slightly broader grant mechanism than usual. So we have a, what's called an NSF. Every, I think this is emerging frontiers and research and innovation I think [00:16:00] is what it is and these are sort of headline or marquee type thing. So we're very lucky that we were awarded one of these and so I think the NSF has really looking for this broad, far reaching hard-hitting effort. I think there's a good point to mention that this project is really a big collaboration between a number of us and I'd like to mention who they are because some of the material work has done by very talented people in the department on a rds and the Vec Subramanian are two professors in the ECS department and they're very well known for flexible printed systems and [00:16:30] the materials that go into them and we work also with Shovel Roy at UCF and Mike Harrison and Mike is a sort of brilliant pediatric surgeon and shovel. Speaker 6: Roy's well known for the technologies he builds at the interface with clinical need. It's really the fact that all these people come together that we're building all of these tools. Speaker 7: [inaudible]Speaker 3: spectrum is a science and technology show on KALX Berkeley. We are talking with Michelle Mull Harvest Daniel Cohen. [00:17:00] They are researching the electrical field that is generated by wounds in mammals. Their hope is to collect meaningful data from sensors embedded in bandages placed on wounds. Speaker 6: If you approached interpreting and analyzing the electrical field data that you're getting out of the wounds in an animal right now we're being very cautious. We started a first few experiments with rodents over the last six months. What we've [00:17:30] built is a, is a series of systems. You can think of them as insulators with lots of little electrodes all over them. An array of of little electrodes. They're on order of a centimeter or less in terms of you can think of a postage stamp, maybe a bit smaller. We have different varieties of them. Some are stiff, some are very flexible. You can think of it as contact lenses or transparency paper, that kind of thing. And these arrays are connected to electrical sensing equipment. There's a miniaturize a little board that runs everything [00:18:00] and sends data to a block and all this data is collected and what we're currently looking at as a variety of different signals on both open wounds. Speaker 6: So if I, for example, cut the skin and on pressure wounds, pressure wounds or something that people that don't see clinics very often or hospitals aren't familiar with but in fact are huge, huge problem in hospitals right now. Then we lay these arrays over the tissue and we measure a variety of different things. One thing we measure what's known as electrical impedance between different [00:18:30] points on the array and you can think of electrical impedance as how much resistance to an electric current that tissue might produce. It's not a steady current, it's a time bearing current, so we sort of wiggle the current on and off, on and off negative, positive, negative, a sinusoidal and how quickly that current responds and how much of it there is. That allows us to calculate the impedance and there's a lot you can tell from that. You can tell whether things are very wet and conductive. Speaker 6: You can tell whether the tissue is tight knit, so that doesn't let things through a oily. You can tell whether there [00:19:00] might be changes in from one tissue to another. You can infer things about what tissues are might be underneath. The other thing we measure is actually electric potential when the wounds are immediately after they're made. We try to look at what kind of potentials arise and how they're changing. So right now that's in terms of measurement. That's really what we're looking at it. And another thing I should point out as we do these measurements as a function of frequency across a wide range of frequency spectrum up to hundreds of kilohertz. And that's sort of the rapidity with which we wiggle the signal because different components in the tissue [00:19:30] will respond differently at different legal frequencies. Once we have that complete plot, we can look at the difference between them and by to see whether we can build models that tell us, oh well we've, you see this type of distribution. Speaker 6: There's a in tech skin for example. So the dream, in this case, you put your bandaid on and your doctor checks his eye, his or her iPhone every 12 to 24 hours and just gets a different little map of how it's working without ever having to remove the dressing. How are you doing in understanding what those signals mean in terms of healing? [00:20:00] But we just had a meeting, they're doing great. They've basically collected a great deal of data on the latest set of wounds they did and now they're in fact proposing models and seeing how the data fits. They're fitting their models to the data to try to use those fits as ways of discriminating different types of tissues. So we're in the middle of it right now. I couldn't tell you much. We're still putting all that story together for publication. So, and are you able to leverage the work that other people are doing? Oh, absolutely. Sure. Well, I mean you always do that. Like I said, nothing is in a vacuum, right? So absolutely. We follow [00:20:30] the literature and, and we build off of what other people have found and try to add our own contributions. That's, that's how it works. Maybe these ideas came from discoveries from the 18 hundreds and then later on in the 1980s onwards, a bunch of really good developmental biologists have really pioneered a lot of this and gone down as, as showing that Speaker 4: even in an embryo you can detect changes in electrical potential at the surface of the embryo where limbs will form and things like that. So there's a huge amount of stuff out there that gave us the idea for the original thing, but we're barely scratching the surface. [00:21:00] We were technologist, right? We're engineers. So part of one thing and figure it out. Yeah. So the idea of trying to analyze the wound field data, do you have to solve that problem first before you can take on anything else? Like trying to instigate the healing? Yeah. Yeah, I would say so. You would never put this in the body without knowing, knowing that a real lot works. But on the surface it's a different healing mechanism than say a fracture, but it's still the idea that we don't necessarily know what the cause and [00:21:30] effect is yet. So we have to show that getting a field out relates to some state that we can say the wound is in and that we can intelligently put a field back in that actually helps. So we need some metric of success. And without that metric, that number that says the wound is doing better or worse, we're not confident saying that our stimulation is helping. So that's why getting this data first is really important. Speaker 6: The parameter space is fairly large, right? To number of things you could possibly change. Some of the effects are very subtle. And so just willy nilly going [00:22:00] in there and saying, oh, I applied some fields, you know, likely not gonna be very useful. And then there's another subtlety, which is that there are probably clinical contexts in which this is of limited utility, even if it works. And so that is, uh, something we spend a lot of time thinking about. So let me give you an example. Let's say I told you I can make that little cut on your knees heal 5% faster with a $15 bandaid. I'm pretty sure you're not going to buy a $15 [inaudible] except maybe once for the novelty of it. You know it tickles. But [00:22:30] there are contexts where, and Daniel alluded to this earlier, for example, scar formation is a big deal, right? Speaker 6: How a scar forms and the trajectory of the wound healing for certain load-bearing wounds of really big deal, right? Think of your abdomen if you had to go in there and hurt those muscles or hernia. And there are many things like this and so if, and I want to be very careful to say if if it was founded, electrical interventions can affect that type of healing in a way that produces a useful outcome, right? Much better scar developments so that your load bearing properties are [00:23:00] maybe not as good as the original, but a lot better than just letting it sit around with a dressing. That'll be a very big deal. But that's a very big space, right? Speaker 4: And that's why we split it into this in Vivo work on monitoring the surface and wound properties and in vitro work where we have cells and tissues and culture where we can directly stimulate them in culture in a very controlled environment and watch exactly how they respond to different shapes of fields and types of fields and come up with a way of describing how they behave. That doesn't require the Nvivo work. So we have two parallel tracks [00:23:30] right now and hopefully we can put them together. Speaker 5: [inaudible] be sure to catch part two of this interview with Michelle Maha Urbis and Daniel Cohen on the next spectrum in two weeks. In that interview, Michelle and Daniel talk about the limitations of sensors on or in humans, the ethics of sensing and inputs into living systems and moving research discoveries Speaker 8: into startup companies. Spectrum shows are [00:24:00] archived on iTunes university. We've created a simple link to get you there. The link is tiny url.com/k a l ex spectrum. We hope you can get out to a few of the science and technology events happening locally over the next two weeks. Renee Rao and Rick Karnofsky present the calendar Speaker 9: nerd night east space first show of 2014 will be happening January 27th the show features three great Speakers. [00:24:30] First nerd night, San Francisco alum, Bradley boy tech. We'll guide you through how scientists organize and present some of the vast amounts of data available today. Then the Chabot space centers, Benjamin [inaudible] will discuss the most likely places to find life off of planet earth. Of course, finally KQ Eighties Lisa Allah Ferris will tell you what you need to know about Obamacare. The show will be held this Monday, the 27th at the new Parkway Theater in Oakland. Doors open at seven to get tickets for the HR event. [00:25:00] Go to East Bay nerd night, spelled n I t e.com this February 2nd the California Academy of Sciences will host a lecture on the Ice Age Fonda of the bay area. There's a good chance that wherever you happen to be sitting or standing is a spot where Colombian mamis giants laws direwolves, saber tooth cats and other megafauna. Also Rome during the ice age. Learn about the real giants of San Francisco and how you can embark upon [00:25:30] a local journey to see evidence of these extraordinary extinct animals. The lecture will be held@theacademyonfebruarysecondfromninefortyfiveamtotwelvepmticketsareavailableonlineatcalacademy.orgSpeaker 8: February's East Bay Science cafe. We'll be on Wednesday the fifth from seven to 9:00 PM at Cafe Val Paris, CEO 1403 Solano in Albany, Dr. Harry Green. We'll discuss his book [00:26:00] tracks and shadows field biology as art green, a herpetologist at Cornell blends personal memoir with natural history. He'll discuss the nuts and bolts of field research and teaching how he sees science aiding and in conservation and appreciation of nature, as well as give many tales about his favorite subject. Snakes. For more information about this free event, visit the cafes page on the website of the Berkeley Natural History Museum at BN [00:26:30] h m. Dot berkeley.edu/about/science cafe dot PHP. A feature of spectrum is to present news stories we find interesting. Rick Karnofsky and Rene Rao present our news in a letter published in January 15th nature. James us or would a locomotor biomechanist at the Royal Veterinary College at the University of London and colleagues explain why Birds Migrate In v-shaped [00:27:00] formations. The team fitted several northern bald ibis is with gps trackers and accelerometers to measure wing movement. They found that the birds positioned themselves in optimum positions that agree with their aerodynamic models. Further the birds flap in phase with one another when in such permissions instead of the antifreeze flapping, they performed when following immediately behind each other. This in phase flapping maximizes lifted the plot [00:27:30] and is surprising as a team noted. The aerodynamic accomplishments were previously not thought possible for birds because of the complex flight dynamics and sensory feedback that would be required to perform such a feat. Speaker 9: The tenuous place in the human family tree of artifice guest room, it is a 4.4 million year old African primate has recently been solidified. Fossil remains Ardipithecus Ramidus or rd as a species is known first discovered by UC Berkeley [00:28:00] Professor Tim White and his team in Ethiopia in the 1990s and have proven a consternation to classify ever sense rd displays an unusual mixture of human and ape traits. Fossils reveals small human like teeth and upper pelvis adapted to bipedal motion, but a disproportionately small brain and grasping large toes, best suited for climbing trees. Scientists split over whether rd was our distant relative, essentially an ape that retained a few human features from along a common ancestor [00:28:30] or our close cousin, possibly even an ancestor. Recently Tim white among many others coauthored a paper with Arizona State Universities, William Kimball in which they successfully linked the rd to Australopithecus and thereby to humans. The team examine the basis of rd skulls and found surprising similarities to human and Australopithecines skulls indicating that those had already been may have been small. It was far more similar to a hominids than an apes Speaker 7: in in Speaker 9: [00:29:00] the music heard during the show was written and produced by Alex Simon. Speaker 1: Thank you for listening to spectrum. We are happy to hear from listeners. If you have comments about the show, please send them to us via email. Our email address is spectrum dot k a l ex hate yahoo.com. [00:29:30] Join us in two weeks at this same Speaker 10: hi [inaudible]. See acast.com/privacy for privacy and opt-out information.

Richard Norgaard Prof Emeritus of Energy and Resources at UC Berkeley. Among the founders of ecological economics, his research addresses how environmental problems challenge scientific understanding and the policy process. Part two of two.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly [00:00:30] 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi there and good afternoon. My name is Renee Rao and I'll be hosting today's show today. We present part two of our interview with Richard Norgaard, professor emeritus of the energy resources group at UC Berkeley. He's among the founders of the field of ecological economics. His recent research addresses how environmental problems challenged scientific understanding [00:01:00] and the policy process, how ecologists and economists understand systems differently and how globalization affects environmental governance. In part two of the interview Norgaard talks about interdisciplinary problem solving. He also shares his thoughts on sustainability co-evolution and confronting a change in climate. Speaker 4: You've been very interested in them multi-disciplinary collaborative research model. Yeah, this is true. I've had very interesting experiences working in groups with people who think very differently [00:01:30] and I don't know when it starts. I guess probably the first project was a Ford Foundation funded project where eight or nine of us from different disciplines were set up as an Alaska pipeline team in 1970 the summer of 70 and we spent the summer talking to pipeline engineers to state officials, federal officials, scientists in the area, wildlife management people, native Americans, the Eskimo [00:02:00] about what's going on and as a team we tried to assess what's really the potential of [inaudible] Bay oil field for the state of Alaska and what are the myths, how do we break those myths and try to come up with a better understanding. Shortly after I came to Berkeley, Robert Vandenbosch from biological control entomology came into my office and said, we need an economist to work on pesticide use, and I didn't know anything about pesticide use other than what I'd read in silence swing by Rachel Carson and I [00:02:30] had an incredible experience working with Vandenbosch, Carl Huffaker, many, many anthropologists, but rather quickly. Speaker 4: Also just because there weren't other economists doing it. Found myself on a presidential advisory committee working with the council on environmental quality on pesticide policy, a working on on 19 University National Science Foundation Integrated Pest Management Project. And you get out in the field, you talked to farmers, [00:03:00] end up talking to the pesticide industry people and you learn a lot and you try to assemble it and try to change how things are working. So early in my career I got very involved with these interdisciplinary activities, but the, the strongest experience was just joining the knowledges, being on national academy committees with the former president of Stanford University whose names Donald Kennedy, a tremendous scientist that was able to work across [00:03:30] scientific fields with other people. But I was seen scientists involved in collective understanding or using their judgment together to try to say, this is what science can say and this is what society probably should do given what we know. Speaker 4: But it was a judgment process. It wasn't that there was a great big computer model that put all of our understanding together. And have you seen that process improving over time? I think there's more people participating in processes [00:04:00] like that. And the intergovernmental panel on climate change is certainly a massive experiment along those lines. And the Millennium Ecosystem assessment was one of these, we're doing it more. What we're not doing is actually teaching undergraduate students and graduate students that this is how science works when it really comes to understanding complex systems. It's a matter of getting in a room together and talking a lot and bringing your knowledges together. [00:04:30] And then that raises new questions that we can go back and study and do deeper research in small teams of maybe interdisciplinary or maybe it's strictly disciplinary, but it's that does my knowledge fit together with this other person's knowledge? Speaker 4: And if not, what does it mean? And if it does, great, you know, science does not come together. And if it did, who would know, who would be smart enough to know and how would we know that person knew? And so there's a great problem, you got to do it together [00:05:00] and we're not teaching that yet. I think the energy and resources group does, but it's not quite as explicit or as open as it should be. And is that what makes that program so distinctive? Well, I tried to leave that mark on it and had the advantage of serving on the admissions committee. And certainly one of my criteria was to bring people to the program who had enough experience to have a sense of identity [00:05:30] and a sense of voice, experiential knowledge that they could bring to the group, but also to not just take the most brilliant students we could find on the list that best matched the interest of the professors, but to actually try to select 15 to 22 students who could learn together, who had different understanding, who had different disciplinary backgrounds or experiential knowledge. Speaker 4: And so I literally tried to set it up as a shared learning to the extent I could. There's many people involved [00:06:00] in the, in the decision process, and of course the applicants this themselves have to say, yes, your best intentions are never carried out. But that was certainly an influence I tried to have. And to some extent did. And the book that you're working on now or I've just completed? Well, I just try authored a book, David Schlossberg and John Drysek. I have to say that they basically did most of the writing. We had try edited a handbook in Oxford Handbook on climate change in society [00:06:30] and so we decided we ought to build a write up a shorter book, a 200 page book that would be for lay people are educated obviously, but uh, a broader audience, a much broader audience. And the title of that is climate challenge society, right. And I [inaudible] wordpress. Yes. So I, I can say I contributed to the title climate challenge society and climate challenge in both ways that were having difficulty coming to grips with the concept of climate change. But we're also challenged [00:07:00] by the consequences of climate change and that books currently out. That book came out a couple of months ago. I have no idea how it's selling yet. I'm, I'm hopeful. Speaker 2: [inaudible] spectrums. Brad Swift is interviewing Richard Norgaard and ecological economists. Next segment. He talks about the book that he's currently writing. Speaker 4: [00:07:30] The book I'm writing now as the unusual title economism and the economy scene. And so elaborate on the first term economism. Uh, there's several ways to get into this, but you probably understand the difference between environmentalism and environmental science and that environmentalism is the movement. It draws on environmental science, but not as rigorously as it probably should. It doesn't mind using old [00:08:00] environmental science if that suits its purposes better. But environmentalism also feeds back on environmental science that environmental scientists needed speak to environmental ism environmentalist's and so they will choose words to speak to their public. We don't use the word economism. And the quickest way to say this, the difference between environmentalism and economism is that we don't use the word economism because there isn't any difference between economics and economists. [00:08:30] And they're kind of so tightly bound that we don't see the difference that, but economism is the beliefs we hold as a people. Speaker 4: And those beliefs help keep the economy going there. The ideas that are invoked in political discourse. You can think of it as just like we think of environmentalism as only kind of a religious movement or a movement that brings people their social identity. Economism is similar in that way that our economic beliefs help rationalize where we are in the economy [00:09:00] or economic beliefs. Help rationalize allowing our corporations to use cheap labor abroad or economic beliefs. Sort of explain how the system we're in exists and why it's there. Almost everything in our lives on a daily basis and to understand that we have economism that intertwines with economic sciences. Economists themselves are engaged in this belief system in partly perpetrating it and [00:09:30] partly changing it. So that's the nature of the next book, the second term as econo scene and he wrote a familiar, many of them audience would be familiar with the idea of the Anthropocene, the idea that we're now in a new geological era, an era in which people are the primary drivers of environmental change, and that's controversial among the scientific community, but it's begun to be used quite a bit. Speaker 4: And anthropocene to me is very vague. It doesn't [00:10:00] identify what it is. It's doing the driving. If you use the word econo scene, you should say, Nah, it's the economic system that we're in that's doing the driving and it's the economic system that we need to change. I mean we're not going to transform people. We're going to transform our social organization to solve this problem. And so econo scene to my mind is at least since post World War II is the appropriate term. As you look at the current economic system [00:10:30] you and mentioned earlier that the growth paradigm isn't really sustainable. Sustainability is a buzz word of the moment in so many areas. How can we define that and how do we pursue sustainability? I think we're so far from sustainability that it's very difficult to find and we're in this very difficult to understand very complex big system that has all these different feedbacks. Speaker 4: You know, the idea that we can comprehend sustainability is [00:11:00] like, can we comprehend the full environmental system? I don't think so. I think we have a strong sense that we're in a danger zone and we need to move out of it. And we know what directions we need to go. And that means slowing down the rates of material flows, slowing down the rates of energy use, slowing down the amount of toxic materials we're putting into the environment or pulling out of with the environment and transforming and releasing back into the environment. And [00:11:30] we have certain equity concepts that sort of says that those who are doing more of it should cut back more than those who are doing less of it. And I think as we move in those directions, we will see the system responding and we'll eventually get a better sense of sustainability, but we'll never really understand sustainability. Speaker 4: It's a really important word, but the idea that we can define it and get it all tied down scientifically and do it is now become part of our problem. But the idea that [00:12:00] we need to change and we know which direction to go, I think that's actually very clear within that change. Yeah. Does that relate to your idea of co-evolution? Is that sort of the basis of co-evolutionary thought or [inaudible] okay, so yeah, we haven't really laid that out. This was a thought experiment that I was in my own mind working in Brazil in the late seventies and I was very involved in sort of what's going on in the Amazon, gone onto [00:12:30] an Amazon planning team for Brazilian government and they were trying to optimally plan how things work, how could we develop the Amazon using science? And I was sitting there admits this process saying that's not the way development occurred in Europe. Speaker 4: That's not the way development occurred in the United States. There was a lot of experimentation and a lot of things didn't work and some things did work. Oh, that sounds like evolution at the time I was reading a lot of ecology and evolutionary theory and [00:13:00] was a friend of Paul aeroflex who was one of the cofounders of the idea of co-evolution species are primarily evolving in the context of each other, not to a fixed environment and what does that mean for how we think evolutionarily? And so yes, I began to try to understand or think about change in the human nature interaction in co-evolutionary terms. It's a pattern of thinking that sheds light on our predicament. But it's only [00:13:30] one pattern of thinking. So I don't say this is the answer, but it's very insightful. It's a pattern of thinking that says things are happening by experiment and that we should be experimenting more and be less certain about what we're doing. And what we've really done is set up a global system of everybody doing the same thing and we're not learning very much from it. And it's a very risky experiment. So I think if you understand change as an evolutionary process, you don't do what [00:14:00] we've done in globalizing the economy and trying to push that further and further and further. Speaker 1: Spectrum is a public affairs show on k Alex Burke. Our guest today is professor Richard Norgaard of UC Berkeley. In the next segment, he talks about the need for increasing diversity and experimentation in the world's economies. Speaker 4: [00:14:30] So the idea that industries and enterprises should try to become sustainable becomes an experiment. We're always experimenting. We have sincere corporations that are trying to go green. We have corporations that are greenwashing. Everybody's experimenting. But is the system as a whole set ups and those experiments are giving us the diversity we need from a systems [00:15:00] perspective and we're not doing that. And is that much easier to identify in the biological realm rather than in the technology economic world of manufacturing. And um, if economists were actually going out looking at how the world works more than we do, we, one of the beautiful things about biologists, they go out in the field and say, oh look, that's interesting. Yeah. I kind of spend very little time going out and say, wow, this industry is co-evolving [00:15:30] with that industry. Isn't this interesting? We tend to sit in our offices and smash data rather than actually try to observe. Speaker 4: I'm obviously, it's very difficult to observe economic phenomena today, uh, cause there's just so much of it happening and it's not as visible as it was say in the 19th century when industries were just emerging. Certainly there are applied and practical economists that are born at this. How are firms we configuring, how are they relating [00:16:00] to each other in different ways than the economics profession is the academic economics profession. Yeah. I think if we were to be more field oriented we would see co-evolution and maybe you'd be able to draw on it and learn from that. In terms of trying to alter the economic system and the path that we're currently on, given the ideological polarization, do you see a way that that could happen with the current polarization? I have great difficulties seeing it. [00:16:30] The common element unfortunately is we all need our share of material stuff rather than a discussion about what's the good life and how are we going to go forward. Speaker 4: The forward for both of them is more, it's more at the tension over who gets what. Until we get to a situation where we get beyond the stuff and use of energy to what makes a good life. I don't see that transformation happening, but I'm hopeful that it's creeping up somewhere [00:17:00] that those discussions are going on and that'll emerge somewhere. Certainly there are people talking about those things. I don't see it at the center we have now the two centers we have now two, can we create a world in which nations become less in tangled and we can get more experiments between them and then have some sort of a learning way between those different nations so that we retain our flexibility [00:17:30] and don't put all of our eggs in one basket. I guess that's the experiment I'm looking for and does the approach to climate change and global warming, is that an opportunity for the same kind of experimentation? Speaker 4: It may be the disaster that forces us into action. I don't know if you call that an or not, but a opportunity or disaster. It's certainly testing how well we understand complex systems and change with those systems [00:18:00] and I'm hoping we'll find a way to to make this adjustment, but we're not doing it very well now. It certainly seems that they're trying to stay within the growth paradigm so far in your mind until they abandoned that on some level or completely it's not really gonna pay off by my mind. Then again, growth is kind of tricky. What we don't want is a growth of impacts. We want a decline. We want to simplify the ways in which we're interactive with nature. Minimize the footprint. That's one way [00:18:30] to put it. Minimize the footprint so that's not a matter of growth or no growth, right? You could still have growth in the arts. Speaker 4: We could all cut each other's hair every other day and charge each other and the GDP would look fantastic. GDP is a very deceptive numbers just to measure market activity. If somebody wants to call that growth, that's okay with me, but what we really need to do is simplify and be less intrusive in the natural system. Similarly, looking [00:19:00] longterm and coming up with an experimental framework. The delta program that you were talking about and the delta in general being a mysterious black box that no one quite understands. Do you feel that there's a growing acknowledgement within the policy community that it's going to take years and years and years and a very dynamic approach to solve it? I think that's true. The Delta Reform Act of 2009 [00:19:30] is very supportive of science. It mandates that we use adaptive management. You know, it's acknowledging that we have to change our management as the times change. Speaker 4: It's legislation that says climate change exists and we need to bring climate change into our understanding of how we think of the Delta as right in the legislation. I mean that's unusual, you know, at least in the state of California already in a world in which we are acknowledging the system is changing [00:20:00] and we need to change with it. There's real complications as to how you get responsible public action and responsible private action in a changing world and a predictable world. You can say, if you do this, then this will happen. If you don't do it, you're responsible and changing world responsibility is really hard to assign and we still want responsible government. [00:20:30] We still want responsible managers, we want responsible enterprises, but how do you set up rules which you know need to change. If you know they need to change, then our agencies or private parties allowed to adjust before the rules are changed. You give it to see the problem. Structurally responsibility and a rapidly changing world are in conflict. This means we need a dramatic [00:21:00] increase in trust and that trust has to be based on actual actions that are based in scientific understanding of a changing world. How do we build that trust? It gets back to how do we collectively understand and learn together and live as a community together in a changing world, it's pretty dramatic transformation. Speaker 4: How do you see academic work addressing some of these [00:21:30] societal problems going forward? Is there a role? Of course, and of course academia is constantly changing and where the learning is taking place is constantly changing within academe. I guess I'd like to go back to this. You know, we're not a university where multiversity and Clark Kerr wrote a book on that almost 50 years ago. Yeah. How to become a university again. How to become a model for the experiment. We're actually in of trying to collectively understand [00:22:00] a very complex system. I think universities could play a very strong role in making an effort to actually change the system and the system of learning among students, and we're not even talking about that yet. We're still very much in the fractured disciplinary mode and if anything, maybe with the greater need for corporate funding for rich individuals help even more show going into the [00:22:30] disciplinary mode rather than the collective understanding mode. Richard Norgaard, thanks very much for coming on spectrum. Thank you very much for inviting me. It's great pleasure Speaker 2: spectrum shows are on iTunes here. This kid is simple link for you. The link is tiny url.com/k a l ex spectrum. Speaker 5: Now a few of the science of technology events [00:23:00] happening locally over the next two weeks. Vic, could I ski and I present the calendar on Tuesday, January 14th former NASA astronauts and Co founder of the B6 12 foundation. Ed Lou, well discuss protecting earth from asteroids. Why we may not see them coming at the Commonwealth Club of California, five nine five market street in San Francisco. Lou is pointed out that more than a million near Earth Asteroids are larger than the asteroid. That struck Siberia in 1908 [00:23:30] that one was about a thousand times more powerful than the atomic bomb dropped on Hiroshima and it was only about 40 meters across, yet it destroyed an area roughly the size of the San Francisco Bay area. Lou will discuss his mission to detect and track the million with the potential to destroy any major city on earth and how his B6 12 foundation plans to build, launch, and operate a deep space telescope with an infrared lens. The first private sector deep space mission [00:24:00] in history and mission will be $20 or $7 for students. For more information, visit Commonwealth club.org Speaker 3: on January 16th Dr Tom Volk will present a talk on the hidden romantic lives of fun guy. Dr [inaudible] is a professor of biology at the University of Wisconsin Lacrosse where he teaches courses on medical mycology, plant microbe interactions, food and industrial in Mycology, organismal biology and Latin and Greek for scientist. [00:24:30] Dr. Buck has also conducted fungal bio diversity studies in Wisconsin, Minnesota, Alaska, and Israel. His free public talk will be held on Thursday, January 16th from seven 30 to 9:30 PM and three 38 Koshland Hall on the UC Berkeley campus. Speaker 5: Basics, the bay area art and science interdisciplinary collaborative sessions is hosting talks center reception with exhibits on our watershed. Over 7 million of us live near the bays, [00:25:00] rivers and creeks that comprise the San Francisco Bay watershed. Professor Jay Lund will highlight and explore the ramifications of the urban bay areas, dependence on water from distant sources, environmental artists, Daniel McCormick and Mary O'Brien. We'll discuss what they term remedial art, surveying some of their watershed sculpture projects and professor Sarah Cohen will introduce us to sea vomit and other species as she spotlights aquatic diversity [00:25:30] in the bay accompanied by a string quartet. The show will be on Saturday, January 18th seven to 9:00 PM with doors at six 30 it's at the ODC theater, 31 five three 17th street in San Francisco. Admission is on a sliding scale so you can attend for free. You should visit Oh d C dance.org to make your reservation Speaker 3: the years first iteration of the monthly lecture series signs that cow will be held on January 18th [00:26:00] Christian Reichardt or researcher at UC Berkeley will speak about his research on cosmic microwave background radiation. Much of it connected in the South Pole. Cosmic background radiation is our most ancient form of detectable lights and carries the imprint of the big bang. It has been a crucial tool and exploring the beginning of our universe. For the past 20 years, scientists had been mapping this radiation using telescopes located in the South Pole. Dr Reichardt will discuss what is already known about the Big Bang, what the latest results from the South Pole could mean and what it's like to work at the bottom of the world. The free public talk will be held [00:26:30] on January 18th in room one 59 of Mulford Hall on the southwest edge of the UC Berkeley campus. The talk will begin promptly at 11:00 AM a feature spectrum is to present new stories we particularly interesting. Rick Karnofsky joins me for the news. Speaker 5: Oxford anthropologist, Robin Dunbar is famous for formulating the so called Dunbar's number. That's the maximum number of people with whom one can maintain stable social relationships with and it's about 150 [00:27:00] people he's published in the proceedings of National Academy of Sciences. This week. His article coauthored by Jerry Sarah Maki from Alto University in Finland and others reports on a study in which 24 students we're giving it an 18 month sell contract. Throughout the study, participants were given a survey to rank the emotional closeness of friends and family members. Perhaps unsurprisingly, greater emotional closeness rankings correlated with the frequency and duration of [00:27:30] cell phone calls. More surprisingly though was the number of people a person called and how much time they spent on the phone with them remained relatively constant. Even if the particular people they talk to May change. For example, the top three contacts typically get 40 to 50% of the time spent on calls. As new network members are added, some old network members either are replaced or receive your calls. The author's note. This is likely to reflect the consequences of finite resources [00:28:00] such as the time available for communication. That emotional effort required to sustain close relationships and the ability to make emotional investments. Speaker 3: A team of researchers at Lawrence Berkeley National Laboratory have used the inorganic material, vanadium dioxide, to create a micro sized robotic torsional muscle motor. The artificial muscle is a thousand times more powerful than a human muscle of the same size. The device can also hurt all objects 50 times as heavy as itself up to a distance five [00:28:30] times as long as its own link faster than the blink of a human eye within 60 milliseconds. A paper describing the innovative machine and its use of material phase transitions appeared in a recent issue of the journal. Advanced materials, the material and the robotic muscle. Vanadium dioxide is highly prized itself because its properties change with temperature. At low temperatures. It acts as an insulator, but suddenly I 67 degrees Celsius. It becomes a conductor. Additionally, upon warming the crystal instructure, the material will contract in one direction while expanding [00:29:00] in the other two. The multi-functionality of the material makes it a prime candidate for use as an artificial muscle, as well as helping to improve the efficiency in other electronic devices. Okay. Speaker 1: And the music heard during the show was written and produced by Alex Simon. Thank you for listening to spectrum. If you have comments about the show, [00:29:30] please send them to us. Our email address is [inaudible] spectrum dot k a l x@yahoo.com join us in two weeks at this time. Speaker 6: [inaudible]. See acast.com/privacy for privacy and opt-out information.

Richard Norgaard Prof Emeritus of Energy and Resources at UC Berkeley. Among the founders of ecological economics, his research addresses how environmental problems challenge scientific understanding and the policy process. Part one of two.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 3: [inaudible]Speaker 2: [inaudible].Speaker 1: Welcome to spectrum [00:00:30] the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Hi and good afternoon. My name is Brad Swift. I'm the host of today's show. Today we are presenting part one of two interviews with Richard Norgaard, professor emeritus of the energy resources group at UC Berkeley. Richard Norgaard received [00:01:00] his phd in economics from the University of Chicago in 1971 he was among the founders of the field of ecological economics. His research addresses how environmental problems challenged scientific understanding and the public policy process, how ecologists and economists understand systems differently and how globalization affects environmental governance. In today's interview, Norgaard talks about the origins of economic science defines [00:01:30] ecological economics and discusses certainty and uncertainty in science. Here's that interview Richard Norgaard. Welcome to spectrum. Thank you. It's a pleasure to be here. Would you describe how economic theory and the science of economics has been forged over time? Speaker 5: I hesitate to use that word science with economics, but like other patterns of thinking in in scholarly endeavors. It's a mix. There were the physiocrats [00:02:00] who basically were in admiration of physics and said, well, we ought to be able to think of the economy as a bunch of flows and they were on 1750 or so, didn't work out very well in the 19th century. As we knew more about energy, we had people more again from the physical side thinking about value, think about the economy as energy flows and we're still trying to do that well. What we really think of as sort of conventionally economics comes out [00:02:30] of moral philosophy and Adam Smith is sort of asking what makes a good society? How do people behave? And the markets have been around for Millennia. He took another look at markets and said, Gee, this is interesting to people acting in their own interests, make both of them better off. Speaker 5: And this was just a thought experiment. If that's true, then then what? Then what and any expanded that thought experiment, what does it mean [00:03:00] with Spec to the role of markets and the role of government? And that's been the dominant pattern. But what I would say thought experiments, if we look at what's going out out there and say she has it like this, if this this was happening, and then expand that to a more systemic understanding of the economy as a whole is not been by hard data collection and patterns emerging from the data though there is that element to it though, right? Reinforce the [00:03:30] thought. Oh to be sure. Malthus's thought experiment was one of the most important ever and he just thought, well, you know, it looks like agricultural production increases linearly and population increases geometrically and what does that mean? And that meant that you're going to come to the limits and clashes and war and bad behavior and and therefore abstinence would be good. Speaker 5: Late marriage would be good. And he definitely tried to back [00:04:00] that up with data. The data were very poor at the time. But yes, we've always tried to back up our thought experiments with data and sometimes that exchange changes how we think and makes our thinking more elaborate. But when I say we're different from other sciences in that we're less data-driven and more just pattern of thinking driven and then within the profession there are these various schools of thought to be sure we can [00:04:30] do get pressure to align yourself in some way. Where the school of thought, well I wouldn't say so much pressure, I would say it's, it's a desire or human desire for a sense of community and shared thinking and it's much more comfortable working with people who think like you do. And so there's pretty strong lines between people who think markets are most important and people who think power is most important sort of followers of Adam Smith or followers of Carl Marx. Speaker 5: But [00:05:00] yeah, there are times when, I guess you could say you feel the pressure, but it's more just the pressure of a community that and communities are good communities help us think together and dig deeper along a pattern of thinking. But of course they also keep you in the same Rut. And then we, if you become deviant, oh yeah. How are you treated at that point? Well and are you encouraged to be deviant? So anyway, so there are rankings of what's strong economics and what's weak economics. [00:05:30] And on the neoclassical side, the mathematicians have always had bigger Thrones than those who actually go out and study how the markets work. And then those who actually study the, the laws and regulations that determine how markets work. Those are referred to as institutional economists and for many years institutional economists, which are the lowest ranking, they studied the facts, they just studied history. Speaker 5: They weren't [00:06:00] high theorist, but of course it's, it's how, how laws get written that determine how markets work and not the mathematics. Early on in your career you've stepped out of the mainstream. I never was in the mainstream. I, I was out before I was in and I've always been out. I had a very strong experience as an 18 year old, 19 year old as a river guide in the Glen Canyon of the Colorado. And that's now under Lake Powell. And [00:06:30] I was one of a very small number of people who saw this area, but also saw it go under and I became a fairly committed environmentalist and then started thinking, well, I'm you know, 19 years old, I'm a sophomore, junior in college. What do I want to study, what I want to do in life? And I loved biology. I love geology, but nature is not the problem. We are. If we are, then what's the biggest thing? And it was not too difficult to say, well, it's, [00:07:00] it's our economy. It's how we think about our relationship with nature as determined by our economics and economic beliefs. And so I went into economics from the outside knowing that I was always on the outside. I don't recommend it. Speaker 2: [inaudible] you are listening to spectrum on k a l x Berkeley. [00:07:30] Richard Norgaard is our guest. He is an ecological economists. In the next segment, he defines it, logical, economic [inaudible]. Speaker 5: And what role do you think ecological economics has to play in shaping and informing policy? Well, we should probably describe ecologically economics a little bit first. And [00:08:00] I like to put it in a little bit in juxtaposition with environmental economics. Environmental Economics is basically a pattern of thinking that says things are left out of the economy or we don't get the opportunity to buy clean air. We don't get the opportunity to buy healthy environments and, and we just need to put everything in the market. And when everything's in the market, the market will be perfect. And so environmental economics is about [00:08:30] making the economy evermore inclusive by bringing more and more things into it. Ecological economics is not just an extension of economics. Ecological economics is a real effort to understand ecological systems and economic systems and try to understand where they may come into clash ecologies, basic premises, everything's connected to everything else. Speaker 5: And a basic premise of at least mainstream economics is that things can be divided [00:09:00] up and made into property and exchanged the one hand. The economic worldview is everything's divisible and ecological worldview. Everything is connected and that's a fundamental tension and human understanding of systems. And so at least to me is that tension that signifies sort of our ultimate limits of how we understand systems that's embedded in ecological economics. So how do you reveal that tension and then try [00:09:30] to have an impact on policy that would affect that tension. In Our world today is not set up that way. Our world today is set up that science brings answers and a better informed society can make better choices. But we also have sort of the idea that that we can have scientists inside of government that can say this is how things are, and then democracy is just about choosing between options. Speaker 5: [00:10:00] If you really see that fundamental tension all the way down and then science can't give answers and science can say, well look at the world as a divisible world. I see this. If I look at the world, isn't there connected world? I see this and it's up to all of us to then sort of get involved in the judgment process and the way policy is set up now it's very much in the context of a legislature that has certain roles and then the agencies that have certain roles and courts [00:10:30] that have certain roles and then policymakers are sort of in this process trying to set up options and pathways that if you follow ecological economics to its logical limits, we all need to be involved in this. And so I push ecological economics to discourse of democracy that we really need to think of democracy as a shared learning system, not as a vote counting system. Speaker 5: It's a process by which we all come to [00:11:00] better understanding and make compromises and that's very different than the way we think of policy and democracy and and science. Now the long step to their, and by no means do all ecological economists think this way. We do get involved in policy, but then it frequently comes into contradiction with sort of the fundamental problems of, of our understanding. Whenever you're in a system that's not where you think the system ought [00:11:30] to be, you're still stuck with these dilemmas of how do you intervene and, and transform the system. And so I myself get involved in and policy sort of positions and you know, you don't understand the nature of the world you're in unless you're engaged with it. You can't just sit back and say, well, I'm not gonna, I'm not going to engage until it's all set up. Right? So to be sure they're economists who don't see the tension and just say ecological economics ought to fit in the [00:12:00] policy process as it is, or ecologically economists who do see the tension and need to work or choose to work with the system to help transform it. Speaker 4: So in a sense, trying to build a consensus across the political world and just the general population as to the ongoing learning experiment that democracy could be. Speaker 5: Yeah, and we're so far from that now. We presumed that the enlightenment, everybody would become more educated. Everybody would be in a better position [00:12:30] to make rational decisions. But we actually created a world in which we have experts in various fields. We have a market system that divides us into very specialized tasks. And so our understanding is very fractured. And so partly the fact that economics is built on a divisible world has been used to create policy as further divided the world. And it's divided the world with through globalization to the point [00:13:00] where very distance from the production process of the materials, the clothes we wear, the food we eat. And so it's very hard to come to common understanding and make decisions collectively so that the system we devised as created serious problems for common understanding.Speaker 4: There seemed to be some people who are recognizing that more often and pushing back or asking for an alternative to that globalization [00:13:30] and division with this to hope, Speaker 5: this gives me hope, this, this division, this specialization, this fracturing of our sense of common understanding. Yeah, I see it in the drive for interdisciplinarity and the drive or you know, trying to understand the full effects of what we do, the and the bringing all the scientists together to understand climate change. As an example, I'm very involved in a process [00:14:00] in the California delta where we're trying to understand a complex system and we have procedures to try to bring in public input, but we still very much stakeholder staked down. We've got our positions and they're sort of a tension between the common understanding and let's just go to court. Let's sue each other. Let's battle it out. Let's you know I'm right, you're wrong. And that gets back to the community. I am mentioned with economists that you want to be in a shared [00:14:30] community, but if you've already got a shared community of laborers or shared community of capitalists or shared community of neoclassical economists, that's where you go back to and environmentalist are in a similar situation. Speaker 6: Spectrum is a public affairs show on KALX Berkeley. Our guest is [00:15:00] professor Richard Norgaard of UC Berkeley. In the next segment he talks about certainty and uncertainty in science. Speaker 5: Would the tension and increasing tension where systems potentially start to fail and common interest then gets galvanized by the failure of really large natural systems. Does the expression of risk management [00:15:30] start to bring people together? I think that's, that's a fair assessment of the situation where in that we have quested for certainty. John Dewey wrote a book on the quest for certainty and in the push for certainty we pretend we're actually reaching that certainty. And yet the very same time we're seeing that the uncertainty rules and sort of the story of climate science, it was always, well we don't know [00:16:00] this, we know none of this. We need to go back and build better and better models. And as we build better and better models, we, we learned how complex the system in is, is. And we can't really build in all the feedbacks of forest fires and uncertain events that are really contingent on particular things coming together particular time. Speaker 5: If we shift to what we don't know, that very powerful drive to be precautious and to come together and to slow the economy down. But that's also [00:16:30] like asking every scientist is say let's stress what we don't know instead of what we do know. And that's hasn't been, well the public hasn't asked that of scientists. Scientists aren't inclined to put all the emphasis in what we don't know. The whole system is sort of set up that science tells us this and then we can make a rational decision. And you know, you can imagine the climate deniers jumping on the scientific community. Well they do every time the scientific [00:17:00] community on climate becomes more specific and modifies what it knew before it gets jumped on. And so the tension is, is difficult. But yes, in the California Delta we're also in a situation where we really have to confess what we don't know and set up management systems to adapt to climate change, to invasive species to sea level rise and how the future's going to be unfolding is really unclear. Speaker 5: [00:17:30] But at the same time we have laws and legislation that say we have to write environmental impact statements and these environmental impact statements have to predict what's going to happen. And so we have a 20,000 plus page environmental impact statement for this Delta project. Is that information or is that just, you know, it's, it's, it's crazy. And so then is it kind of a general misunderstanding of science? Because really the flip side of science is the mystery and the unknown and that's really what drives a [00:18:00] lot of science is the unknown. And so it makes it so exciting. And so is it just that policymakers, general population only look to science for answers and don't want to deal with that whole mysterious side of science. I think, you know the mysterious side gets a little quasi religious sometimes and we tend to shy away from that. Speaker 5: But I think it's also just the way we've been set up in societies. This science has generated [00:18:30] a lot of technology. It's been technology generated out of just parts of what we know that then has consequences when we actually implement the technology. It changes us socially in the environment, but science has delivered lots of hard stuff. And then can we just extend that ability to understand the whole system and the answer does not look good and too says probably not. And that should then drive us to humility. [00:19:00] But when I went in and you get prestige for being a scientist, for coming up with answers, on the other hand, an honest scientist has to say, we're not holding it all together. We're not able to see the whole system and how do we understand the whole system? Who's going to understand the whole system and the level of understanding we have to have now is much greater as we have 7 billion going on, eight to 10 billion people, and [00:19:30] with the technologies we have today, we are intertwined with this system much more deeply and many, many, many, many more ways than humankind has historically. Speaker 5: And this has dramatically increased just the last 60 years. There's been a tenfold increase in economic activity. That's incredible. To have that kind of change and to think that it can continue, which is the paradigm that's, that will continue. It has to [00:20:00] have by the paradigm, but it, of course, that paradigm is has to be false and it's partly perpetrated by false economics or just reading a portion of what economists know, but that's inconceivable. But as we pushed this system harder, we have to understand it better and better and better and we're clearly not understanding it well enough. Now in your work, which tools and methods do you believe are the most important? I think I'm going to go back to those thought experiments. That's where the breakthroughs [00:20:30] come. Ways of reconceiving. What we're doing that gives us new insights that then help us change. Speaker 5: So Adam Smith's thought experiment gave us a much clearer understanding of what markets can do and we formulated a lot of our social organization along Adam Smith's ideas. We need new thought experiments that become equally popular somehow. [00:21:00] That's an issue because with markets we have stakeholders and with stakeholders then you get political power and then that reinforces existing system and how do we get a thought experiment within economics or ecological economics or from anywhere it comes that we'll reconfigure how we think about our relationship with nature to get us out of the system we're in now. Yeah. That's really the tool is I see it. That's what's been powerful in social theory. [00:21:30] The data collection, you know, fancy econometric analyses. Not so much model building and data driven stuff. Model building is good for understanding sort of the limits of how much you can understand and model building can be really good for bringing people from different disciplines together to have a shared project. That's fantastic, but as soon as you actually believe in your model, you're in trouble and that's [00:22:00] yeah, frequently happens. Speaker 3: Be sure to catch her Speaker 4: to have this interview with Richard Norgaard in two weeks. In that interview he talks about interdisciplinary problem solving. Speaker 6: Co-Evolution diversity and sustainability Speaker 4: [00:22:30] spectrum shows are archived on iTunes university. We have created a simple link for you to make it easy to find. The link is tiny url.com/k a l X. Speaker 6: [inaudible]. Now Speaker 4: the science and technology events happening locally [00:23:00] over the next two weeks. [inaudible] and I presented Speaker 7: the theme of January seconds after dark explore [inaudible] adult happy hour is sharing. Sharing isn't just about kids and toys. It's at the heart of some of the biggest problems facing all of us. Highlights of the evening include exploratorium social psychologist, Dr Hugh Macdonald, discussing the science of sharing the finer points of interviewing [00:23:30] with StoryCorps and a chance to share feedback on new exhibits about cooperation, competition, and collaborative problem solving. Admission do anyone 18 and over is $15 and is reduced for members visit exploratorium.edu for more information. Speaker 4: The life sciences division of the Berkeley Lab will hold a seminar on the effects that the deep water horizon oil spill in the Gulf of Mexico [00:24:00] had on the resident fish populations. Dr Fernando Galvez from Louisiana State University will speak about his research on the Gulf. Upon hearing about the spill in 2010 Dr Galvez and his team were actually able to take water and tissue samples from seven marsh habitats around the Gulf before and after the oil hit in order to assess the long and short term ecological consequences. He has more recently been investigating the [00:24:30] ability of the native fish to compensate for crude oil linking effects from the molecular level to physiological performance. The free public event will be held January 7th from four to 5:00 PM in room one 41 of the Berkeley lab building at seven one seven potter street in Berkeley. Speaker 7: The programs and policies director of the Oakland based National Center for Science Education. Joshua Rose now [00:25:00] well discuss the predecessor of the NC s e the Salsalito based Science League of America at the free Skype talk hosted by the bay area skeptics at Luphinia Cultural Center three one zero five Shattuck in Berkeley on January 9th at 7:30 PM the Science League was formed by Maynard Shipley, a science communicator and former shoe salesman to educate the public about evolution. More information [00:25:30] is that BA skeptics.org Speaker 4: the Henry Wheeler Center for emerging and neglected diseases. Annual symposium aims to strengthen connections between San Francisco Bay area scientists working on infectious diseases of global health importance and the broader global health research, product development and advocacy communities. The theme for the 2014 symposium is academia and the global health pipeline, [00:26:00] basic science, innovation and translation. The symposium features a dynamic list of invited Speakers from around the world, including scientists from developing countries. Participants include academic researchers from UC Berkeley, UCF, Stanford, UC Davis, as well as representatives from local biotechnology and pharmaceutical companies and global health nonprofits. The event will be held January 10th [00:26:30] from 9:00 AM to 6:00 PM in the lead cost Xing Center Auditorium. The event is free to attend, but you must register online at the center for emerging and neglected diseases website by January 6th to attend the symposium. A feature of spectrum is to present new stories we find interesting. Rick Karnofsky joins me for the news. Speaker 4: The December 23rd issue of nature news reviewed a preprint submitted to archive [00:27:00] by Notre Dame, astrophysicist David Bennett and a large team of collaborators that offers the first suggested report have an extra solar moon, extra solar planets have been found routinely. We now know of over a thousand that are detected by analyzing how it stars. Light, brightens and dims with time, but detecting the moon is exceedingly difficult. The team saw a smeared out brightness as if two objects had magnified the light. [00:27:30] The study is conservative and notes that their observations best fit a model of the moon with a mass smaller than Earth's orbiting the primary planet of a gas giant, but that other models may also fit while they don't fit as well. They have been observed in more systems. These include a lower mass star or brown Dorf orbit by a fast and small planet about the size of Neptune. Speaker 4: The team stresses that their study shows the power of micro Lenzing to survey such systems and helps [00:28:00] for a higher precision measurements from huddle. The UC Berkeley News Center reports that a team of UC Berkeley vision scientists has found that small fragments of Keratin protein in the I play a key role in warding off pathogens. Professor Susan Fleisig, an optometrist at the University of California, Berkeley says, what we know is people virtually never get corneal infections unless they're a contact lens wearer or unless they have very severe injury to the cornea. Professor [00:28:30] Fleisig, along with other UC Berkeley researchers recently discovered the proteins in the eye called Keratins. We're able to ward off bacteria to test this. Researchers introduced normal cells to bacteria, which predictably attacked and killed the defenseless healthy cells. But when small parts of Keratin proteins were added, the normal cells lived. Scientists have made an artificial version of a small part of the Keratin protein and tested it against different diseases. The proteins [00:29:00] destroyed bacteria that can cause struck throat, diarrhea, and staff. Further research is needed before isolated. Keratins can be used to fight bacteria, but it could be a low cost discovery that might change the way we treat and prevent infections. Speaker 2: [inaudible] music heard during the show was written and produced by Alex Simon. Thanks to Renee Rao for help with the calendar. Thank you [00:29:30] for listening to spectrum. If you have comments about the show, please send them to us via email or email. Address is spectrum. Duck klx@yahoo.com join us in two weeks at this same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Dr. Bea worked with the US Army Corps of Engineers, and Royal Dutch Shell around the world. His research and teaching have focused on risk assessment and management of engineered systems. He is co-founder of Center for Catastrophic Risk Management at UCB.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay [00:00:30] area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hey there and good afternoon. My name is Renee Rao and I'll be hosting today's show. Today. We present part one of two interviews with Robert B. Professor emeritus of civil and environmental engineering at UC Berkeley. Dr B served as an engineer with the U S Army Corps of Engineers, Shell oil, shell development, and Royal Dutch Shell. His work has taken him to more than 60 locations around the [00:01:00] world. His engineering work has focused on marine environments. While his research and teaching have focused on risk assessment and management of engineered systems, he's a cofounder of the center for catastrophic risk management at UC Berkeley. In part one, safety and risk management are discussed. Speaker 1: Bobby, welcome to spectrum. Thank you. Pleasure. You're part of the center for catastrophic risk management. How did that get started and what's the mission? What's the goal? Well, [00:01:30] it started on an airplane coming to California from New Orleans, Louisiana. In November, 2005 on the plate with me was professor Raymond c department, Civil Environmental Engineer. In the early days after Katrina, New Orleans flooding, there were still dragging bodies out, e Eric [00:02:00] and coming, our thinking was, well, why couldn't we help found a group here at Berkeley that would bring together interdisciplinary professionals both in the academic, in Ironman and outside to address catastrophic potential failures, disasters in two frameworks, one after they happen and two before they happen, after [00:02:30] the intent is not blame, shame or hurt, but rather to learn deeply how they happen so that then you can bring it back to prevention mitigation. So we got off the plane, I met with our Dean, Dean Sastry and said, could you tell us how to become a senator here at Berkeley?Speaker 1: I'll never forget it. He got up from his test, walked around to the other side, touch me on the left and right shoulders and said, your center. [00:03:00] That telephone center happened and today the center continues to exist under the leadership of Professor Carlene Roberts and continuing to address a wide variety of accidents that have happened. And once we are working to help not happen. Thank you. Berkeley and the funding is, there is an interesting question. Initially [00:03:30] we thought, well we'll turn to the university for funding. That was not as easy as some of us thought because university was already seriously stretched for funding, just funding itself. So at that point we turned two directions. First Direction principally because of my background was to industry and said, hey and a strength, would you fund research here [00:04:00] and return for your research funding. We'll give you great students with great research backgrounds and research results. Speaker 1: They became excellent funders. We turned to government homeland security for example, or the National Science Foundation. Similar responses. So the funding has come from both industry, commerce and government. Essentially all we had to ask university four [00:04:30] and it's been a precious resource to even ask for it. It has been space and support staff. Are there any of the centers projects that you'd want to talk about? There's I think two. One was a center for catastrophic risk management project at its inception sent bro, PG and e a disaster certainly to the people that were close to land one 32 [00:05:00] that exploded. We followed that disaster from the day it started and carried it all the way through the federal investigations at state investigations and drew from that very, very important lessons, preventative lessons. The other project that has been playing out sort of in sequence with it is in San Pedro, California, the San Pedro, low pressure gas [00:05:30] storage facilities. Speaker 1: It's in a neighborhood and you can see these large gas storage tanks. You can see roads nearby. You can see Walmart in shopping centers and schools and hospitals and homes and you'd say this sounds pretty dangerous. Founded back in the 1950s period. It's pretty old, kind of like Bobby in pre oh and worn out and [00:06:00] it's severed w we call risk creep, which means when they built the tanks and the facilities there, there weren't any people, there was a port to import the gas so forth. But suddenly we've got now densely packed, I'm going to call it political social community infrastructure system, which if you blow out those tanks, we've got big trouble. Houston, well we took on San Pedro in an attempt to help the homeowners that people [00:06:30] actually live there draw or call appropriate attention to the hazard so that they could get appropriate evaluation. Speaker 1: Mid Asian, we haven't been very successful. I think many people say, well, hasn't blown up. It's not gonna blow up. Other people who say, I think I smelled gas and an explosion is not far behind. And then you turn to the state regulation system and say, [00:07:00] well, who's responsible? Answer everybody. Nobody. And at that point it sinks back into the everyday activity of that community and our society. So one horrible experience. We learned a lot of lessons and I'm watching PG and e n r California Public Utilities Commission go through the learning experiences and they're obviously painful. But on the preventative side, art record is looking [00:07:30] pretty dismal. Yeah, that's tough. That's similar to the Chevron fire that was in Richmond and cause you're right, these things get built when they're far away and then developers build right up to them. Same with airports and all sorts of faculty. Speaker 1: Chevron refinery is what our latest investigation and it's got a story behind it because one of the stalwart sponsors at work that's been done by the center for catastrophic [00:08:00] risk management has been Chevron. In fact, they were a member of um, 10 years study that we conducted here concerning how organizations manage very high risk systems successfully. Chevron was one of the successful organizations. So when we saw Richmond go poof, boon, we said something's changed. [00:08:30] They had a sterling record for their operations here. What happened? Well, the story comes that this business of risk assessment management of these complex systems is one damn thing after another. And if you get your attention diverted like, oh, we need to make more money, you start diverting precious human resources working to achieve, say that he them [00:09:00] safety starts to degrade and at that point roasty Pintful only stay rusty so long at that point, poof, boom. Speaker 3: You're listening to spectrum on k a Alex Berkeley. Brad swift is interviewing Bob, be a civil and environmental engineer at UC Berkeley. In the next segment they talk about collaboration. Speaker 4: [00:09:30] Talk about some of the people you've collaborated with and the benefits that flow from Speaker 1: that kind of work. That's been one of the real blessings of my life has been collaboration. One of the things that dealing with complex problems and systems and most afraid of is myself. I'm afraid of myself because I know I'll think about something [00:10:00] in a single boy and I'll think about it from the knowledge I have and then all develop a solution or insight to how something happens. Given that set of intellectual tools and so learned to be afraid of myself and I get very comfortable is when I have people who don't think like me, who will in fact listen to me and then respectfully when I finished they say, [00:10:30] Oh, you're wrong. Here's why. And then of course out rock back and I say, okay, he explains more or less, let's get there. And what I have found in evitable Lee is I end up at a different point than where I started, which tells me the power of collaboration can be extremely strong as long as collaboration is knowledgeable and respectful. If it gets to be ignorance at work and it's disrespectful, you can expect Bob [00:11:00] to become pretty nasty. [inaudible]. Speaker 4: In reflection on your activities in civil engineering and in academia, does civil engineering need to change in some way or is there a subtle change happening that you recognize? Speaker 1: I think there's subtle change having and proud. I think I see it starting to sprout here at Berkeley. The change that's happening is that you struck on with your earlier question concerning collaboration. [00:11:30] So it turns out to be the power of civil engineering collaboration. We've actually got people in engineering working with people in political science, public health business. That is an extremely encouraging sign. As long as we can keep that collaboration going in the right directions. If you do that, do it well. Then this symphony of disasters and accidents, we'll hear that [00:12:00] music go down a lot. You sort of made famous, the civil engineering course one 80 and you're not teaching that anymore, right? That's correct. Did you pass it on to someone you know and give them the blessing? I tried to, yeah. C e one e engineering systems is what it was called, I think was teachable for me because of the experiences. Speaker 1: [00:12:30] I came here after 35 years, 36 years of industry work, and I've been working as laborers since I was 14 went to work as a roofer roofing crew in Florida. I'm not too smart, and so I was able to bring that background experience into the classroom and virtually turned the students loose, said we don't want you to do is first formed into teams. Well a year [00:13:00] at Berkeley, we tend to be what I call a star system student is independent. They gotta be the best in the class working together as something not encouraged. Well, I would say to hell with the star system, we're going to work as a team. So teamwork came in and that's because that hit very strong training through the Harvard Executive Master of Business Administration Program on teamwork and organization and that kind of stuff. So I brought that in and then said, well you have all this [00:13:30] technical stuff. Speaker 1: Get out of Berkeley, go out there and meet the real people, meet some real experts outside of the Berkeley experts and go solve problems. So essentially I turned them loose, but I kept him from hurting themselves. It worked beautifully. Well notice you can't then turn back to normal Berkeley faculty and say, teach it. It's not reasonable because he's not had that [00:14:00] experience. You could think about team teaching, but then you'd say, well ob, we have trouble with enough funding to teach with one person in a class, much less teen teaching. So I sort of agreed with myself to hope somebody remembers and when the university has more resources they could in fact return to these times of real life experience classes. The students that came [00:14:30] through that sort of experiences have made some remarkable contributions already. Good kids. Has anyone approached you about doing any of this online teaching? Speaker 1: Yes, and I steadily said no. The reason is a saying that I was given by a very dear friend and a collaborator, University of Washington, Seattle said a bomb. [00:15:00] Engineers want to believe the planet is not inhabited. We don't like people were antisocial. Go to a party and you can tell it immediately you were in a corner, you know, talking boring shop. Well let, don't want to contribute to e offline internet generation of engineers who do let her work with each other. I have all the liberating intellectual things in the classroom outside of the classroom. So [00:15:30] [inaudible] been very supportive. We need more human contact. Speaker 2: [inaudible]Speaker 5: spectrum is a public affairs show on KALX Berkeley. Our guest is professor Bob B of UC Berkeley. In the next segment they speak about safety. Speaker 2: Aw. Speaker 1: Is there anything that I haven't asked you about that you want to talk about? One of the things [00:16:00] that as I leave my career period in my career at Berkeley that makes me sad for Berkeley really got my attention during the Macondo disaster. Many good friends that I still have at DPE that were in fact involved in the causation of the accident kept saying, well, what we did we thought was safe. The thing that makes me say [00:16:30] is we still have a course to teach engineers what the word means and how to quantify it so that then people can look at it and say, this is acceptable. Those people could be from the school football or public hill. This kind of risk management not happening here. That's I had, and I can look forward. I think all of us can two continuing problems in this area because of a lack of appropriate [00:17:00] education. The engineering thinking in many cases is w explicit thinking about uncertainties, variability and is devoid of thinking intensely about the potential effects. Uh, human malfunctions. The engineer goes through a career of saying the weld will be done according to specifications. There's where it pumps up. [00:17:30] The engineers. Education is one a deals with an imaginary world. There is no significant uncertainty. You sorta by code specification or however inspection do away with that and things will be perfectly [inaudible]. Guess what? It's not the human factor, the human factor. Speaker 4: Given that there's always going to be that human factor [00:18:00] at risk management seems to be a quandary of the open-endedness of it. When do you feel you've done enough of it? When do you feel confident that you're ready to say, yes, I'm prepared for all circumstances? No one can know all things yet at the same time, you do as much as you can or what can you afford? Right. It comes down to the money side of it again. Yeah. I Speaker 1: love your question. I got on this while I was here, so I didn't come in here knowing this [00:18:30] one, when I came in to this risk assessment, management got into the depths of it. I had to do a lot of reading and reading. I was doing coming from many different industries and parts of the world said, oh well risk assessment and even a proactive think before predict cause like you were saying. But the falling that is, you can't predict everything, but they never said it. Okay. And the next thing you said was it's reactive [00:19:00] so that when something bad happens, you reflect on it, learn from it, and you manage the consequences. Well, I'm sitting here and by the way, I came here without a phd, but I got one, all of them white. I introduced interactive management and I'm sitting at home trying to think how to do something for a PhD dissertation that's new. Speaker 1: And I said, oh, there's proactive and there's reactive that gotta be interactive. How in the hell can I learn about this? And I end up working [00:19:30] with two pediatric emergency room management teams, a BB team, I call them [inaudible] into hospital Los Angeles, the other San Francisco general mortality rate, same number of beds in air emergency room wards was a factor of 10 higher in San Francisco. So we went and observed them, students with me, and we started interactive management. The baby can't tell you what's wrong with it [00:20:00] and yet the medical team has to be able to diagnose it, invoke corrective action to save the life and the success shows up in mortality. So we got deep into that and that entered interacted management. Hey, story goes on. We're working with commercial aviation, U S air, United Airlines and southwest airlines. U Us air comes to a confidential meeting and says, [00:20:30] well, we found out where we had five fatal accidents five years in a row. Speaker 1: We had given our flight crews instructions. They were to leave the gate on time without exception. Well, the five that had crashes did the checkout on the taxi out. Two of them found that they didn't have enough fuel to make the next airport unless they have tail. Winston. Of course they had headwinds. Well then experience in his interactive [00:21:00] management. The guy shows up at our doorstep here in Maine, sully Sullenberger and he's learning about what we have been learning. He's heard through u s air about this interactive management. Boy Did we carry him through it and boy did. He carry us through perfect example of how you can prepare a very complex hazardous system to succeed [00:21:30] in the face of failure. What they did that morning and he sent me an email that morning before they took off from the Guardian when they took all laws, both engines totally not predictable, did the scan or the alternative airports and what would happen if they didn't have enough flight path to make it turn toward the Hudson and pulled off. That was totally prepared for including design of back water back flow valves through the air intakes into [00:22:00] the Airbus. He knew what he was doing. Look at the flight inclination of the plane coming into the river. Looks like barefoot skiers toes up. Speaker 1: There's the power of the thinking so you do end up measuring safety just to, you said you never sure you got the spit on it or right. Something could happen out of the blue. Somebody walks across the street that's not supposed to. You then have to have the ability to get through [00:22:30] the system quickly and have the correct response. That's part of risk assessment management. Unfortunately, BP never learned it before the conduct so that when it really hit hard, it hit hard. That night they couldn't respond. They froze and they killed 11 people at White. Yeah, I read the report that you did on that and I was like potboiler. [00:23:00] It's really riveting stuff. Yup. Speaker 1: That's an amazing tale. Yeah, it makes me so overwhelming. Go sailing. You say all in the bay, Yo God, you know? Yeah. I'd taken the boat to Mexico taking the channel islands twice. I'm single handed sailor. Oh really? I've lost my ass once. Those exciting tale about [00:23:30] disaster preparation, I guess sailing alone is a good sort of a risk management hands on practice reason. You'd say, come on Bob, you got it. He's somewhat here, man. I've learned. When I say go, I can only sale, which means I can't think about Katrina or beat pea or San Bruno. I've got to focus totally on that boat and sailing. If not, I ask here quick. So it's a relief and that's why you do the [00:24:00] solo rather than have other people on board. Then you get sloppy, sloppy, and et cetera. Yeah, and so most of my sailing is done solo. Speaker 6: No [inaudible]. Speaker 3: If you're interested in the center for catastrophic risk management and it's riveting reports, visit the website, c c r n. Dot berkeley.edu [00:24:30] to listen to any and every past episode of spectrum for free. Visit our archive on iTunes university. The link is tiny url.com/calyx spectrum. Now two of the science and technology events happening locally over the next two weeks. Cheese, Yucca boss and I presented a calendar Speaker 7: this Tuesday, November 19th the SF ask a scientist's lecture series. [00:25:00] We'll present a talk by a neuroscientist, Adam Gazzaley and magician Robert Strong from ancient conjures to big ticket Las Vegas. Illusionists. Magicians have been expertly manipulating human attention and perception to dazzle and delight us. The team will demonstrate how magicians use our brains as their accomplices in effecting the impossible and explain what scientists can learn about the brain by studying the methods and techniques of magic. The event will take place on Tuesday, November 19th at 7:00 PM in Stanford's geology corner. Auditorium Room [00:25:30] Number One oh five and building number three 20 of Stanford's main quad. Speaker 3: This Wednesday, November 20th the UC Berkeley Archeological Research Facility will host a seminar on indigenous food ways and landscape management. Since 2007 a multidisciplinary research team has been working to implement an Eto archeological approach to explore indigenous landscape management on the central coast of California. This presentation includes results of a study associated with UC Berkeley Graduate Student Rob Casseroles, [00:26:00] dissertation research, which takes a historical ecological approach to integrating major sources of data, including fiery ecology of contemporary landscapes and results of macro botanical analysis of indigenous settlements. The event is open to all audiences and will be held on November 20th from 12 to 1:00 PM in room one oh one of the archaeological research facility on the UC Berkeley campus and now Chase Jakubowski with our new story. Speaker 7: This story is from the UC Berkeley new center. [00:26:30] CRISPR stands for clustered regularly interspaced short palindromic repeats for nearly two decades after Japanese researchers first discovered CRISPR in bacteria in 1987 scientists dismissed it as junk DNA, far from being junk. CRISPR was actually a way of storing the genetic information of an invading virus in the form of Palindromic DNA sequence. The bacteria used this genetic information to target the viral invader by chopping [00:27:00] it up with powerful CRISPR associated enzymes capable of cleaving its DNA molecule, just like a pair of molecular scissors. The mystery of CRISPR was resolved by Jennifer Doudna of the University of California Berkeley, a specialist in RNA about seven years ago. Downer was asked by a university colleague to look into this genetic particularity of bacteria and quickly became fascinated. The more we looked into it, the more it seemed extremely interesting. Professor Doudna [00:27:30] said then in 2011 she met Emmanuelle Carpentier of Ooma University in Sweden at a scientific conference. Speaker 7: Professor Carpentier told professor down a of another kind of CRISPR system that seemed to rely on a single gene called c a s nine both professors collaborated on the project and an August last year published what is now considered the seminal paper showing that cas nine was an enzyme capable of cutting both [00:28:00] strands of DNA double helix at precisely the point dictated by a programmable RNA sequence. In other words, an RNA molecule that could be made to order. It has worked beautifully on plants and animals. Professors Doudna and sharpen ta had found the holy grail of genetic engineering, a method of cutting and stitching DNA accurately and simply anywhere in a complex genome. I'm tremendously excited about the possibility of this discovery having a real impact on people's [00:28:30] lives. Maybe we'll offer the opportunity to do therapeutics that we've not been able to do in the past. Professor Doudna said her team is already working on possible ways of using the cas nine system to disrupt the damaging chromosomes responsible for down syndrome or the extra repetitive sequences of DNA that lead to Huntington's disease. What's exciting is that you can see the potential and it's certainly going to drive a lot of research to try to explore it as a potential human therapeutic tool. Speaker 3: [00:29:00] Mm. Don't forget to tune in next week to your part two professor B's interview. He and Brad Swift will discuss the California Delta and shoreline retreat. Okay. The music heard during this show was written and produced by Alex Simon. Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. [00:29:30] Our email address is spectrum KALX. Hey, yahoo.com join us in two weeks. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Chuck Frost, and Erin Fenley of the UCB Energy Office talk about their efforts to drive down electricity use on the Berkeley campus. This program will shift the onus for electricity use on each of the 28 Operating Units on Campus. Mypower.berkeley.eduTranscriptSpeaker 1: Spectrum's next. Speaker 2: Okay. Speaker 3: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, [00:00:30] a biweekly 30 minute program, bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Hello and good afternoon. My name is Renee Rao and I'll be hosting today's show. Did you know UC Berkeley has an energy office and an energy incentive program? Our guest on spectrum this week are Chuck Frost, the first ever energy manager of the UC Berkeley campus and Aaron family, the energy office communication specialist. [00:01:00] They talked with Brad swift about the programs the energy office has launched to drive down electricity use on the Berkeley campus. Here's the interview, Speaker 1: Chuck Frost and Aaron Fenley. Welcome to spectrum. Thanks for having us. Yeah, thank you. You work at the University of California Berkeley Energy Office. How did that come into being? Speaker 5: Well, the university hired a consultant to look at ways to save money on the campus. One of the things they came up with was to reestablish the energy [00:01:30] office. Speaker 1: Yeah. And that was about three or four years ago when bane consulting came in to check out what areas we could save money, um, on campus. And that was everything from payroll to energy management. So we dove in from there and it's part of operational excellence program. Actually through the energy management initiative we have created the energy office. We have also created an extensive outreach program which has its own goals and energy incentive program, which [00:02:00] has financial goals and then an energy policy which provides a framework. Speaker 5: Might there be, while the energy office actually tracks and monitors and assist the campus in reducing energy and we try to improve the building performance also. Is there anything that's really different the way your energy office is doing it that distinguishes you from other places? I think it's the number of dashboards we're using. We've got [00:02:30] almost a hundred installed on the smart meters and then also the incentive program or you could put the bill out into the campus. So the 28 operating units, if they beat their baseline or you will give them money. And this year we're giving them about $170,000 back to the campus, but it can go the other way starting next year and they could owe us two so it can go either way. It's a carrot in a stick. But out of the 28 opportunities this year, 20 received [00:03:00] money and two what Ellis and our goal is really to have no one, no HOAs and put the money back into the campus. Speaker 6: And how is it that you tie into the dashboard? Would the data, where do you collect the data? How do you tie it in? Speaker 5: Each building has a meter that monitors the incoming power to the building and that goes to an obvious is the name of the system. And then the pulse energy pulls off the obvious server to populate the dashboards [00:03:30] and kind of throws the bells and whistles on it. Speaker 6: Now are you able to use the data to reflect on the buildings efficiency its system? Speaker 5: It's actually can be used as a tool to identify when you have problems in the building. It's a, it'll throw up a flag. If you're doing too much energy after it learns you're building, it really knows how you'll drop. However, on a certain day and the weather and things like that, that's the model that is actually forms. It takes a few months to learn the building and actually it really a full seat, you know, a year. [00:04:00] And then once it identifies and learns and models who are building, then you can actually have threshold or limits that will flag your attention. If you have drawing too much or not enough, it can go either way. But that's a good indication. It's a lot better to have sub-metering in a building, but it's, it's very powerful just to have, you know, a smart meter in a building. And is there a move afoot to go to this sub-metering? Absolutely unfortunate. It just comes with a price and so it's very expensive. [00:04:30] But with the technology changing and wireless and things like that are being used a little bit more and I think it's coming down. So probably doable in the future. If you look at all the utilities on campus, we average between 30 and 35 million. That's for water, steam, gas and electricity. Speaker 1: And the electricity itself is about 17 yeah, Speaker 5: that's what he paid last year. Speaker 6: And so year to year as units start to save, you're able to give what back to them Speaker 5: when the, [00:05:00] the main meter at the campus drops down. That that's how we really determine and then we break it down into buildings, how much each of the buildings. But we actually look at the main meter also and then we are showing for the first time in a number of years where we actually did reduce and that an average of 2% creep was what we saw since the 90s Speaker 1: so so we can really avoid that creep by keeping the engineers in buildings. They've been divided into zones to work [00:05:30] in specific areas on the campus in order to understand the buildings, know what's going on there, work with the building managers in order to keep them tuned up so that the creep doesn't happen. Speaker 6: And that's the front line? Yes, it's the building engineers and building managers. Speaker 1: Well through the energy office there are stationary engineers, electrical engineers that are working in the zones with building managers in order to make that work happen. Speaker 5: So even though the skilled trades, Speaker 1: our goal goals a little bit different [00:06:00] than a traditional stationary engineer example where we're looking at kilowatts and BTUs, we want to help in any way we can and improve the building. But our focus is really energy. So we work with the shops but we have a different spin on it. So this past year a lot of the work that was very significant in reducing energy use was through variable fan drives. Yeah. Speaker 5: Both frequency drive. So anytime you can vary the flow on a large motor, whether it's pumping water pumping here you can [00:06:30] actually, once you reduce that substantial savings. So we saw a lot of opportunities and repairing dries, putting in new drives and things like that. Speaker 1: You kind of have more of a consultant role Speaker 5: in a sense. We like to say we're looking and um, some people will call it low hanging fruit. They don't cost a lot of money to invest in, but it could be scheduled changes. You could be heating and cooling at the same time. There's a lot, actually a lot of savings in those two areas and really don't have to spend a lot. You [00:07:00] just have to identify what I'm an example in this building we're in right now, it was a while ago, they actually had a painting project, so they wanted the fans to run 24 seven and it was one of the professors at notice will look at the dashboard and how come the energy use went up and it didn't go back down. So by him asking that question, we investigated and we found out that they had put all the fans in hand. There was no schedule to shut down at night so that that was about a $45,000 [00:07:30] avoidance would have been allowed to run the rest of the year. So those kinds of things, that's what the dashboard really helps a lot of people a lot of highest looking. So you can see what's going on and start asking the questions, why do I have this little blip of power? Why does it jump up like this? And the energy officer will go out and investigate it and sometimes it's just interviewing people. Sometimes it's walking through mechanical rooms and every building has a story. So you have to kind of dig into it. Speaker 7: [inaudible] mm, Speaker 4: [00:08:00] you're all sitting just spectrum on k a Alex Berkley. Our guests today are chuck frost and Aaron finally from the UC Berkeley Energy Office. In the next segment they talk about changing behavior to save energy Speaker 1: and what sort of outreach programs are you operating to try to just drum up support and awareness. We do have a energy management resource center right here in Barrows Hall Room One 92 [00:08:30] and people can stop by and pick up posters and flyers and light switch stickers can get information about saving energy, specifically in labs, residence halls and office spaces. You can also come there or email us@mypoweratberkeley.edu and set up a time to have our student team and we have an amazing student team who conduct surveys in offices, labs. We come in and take a nice observational survey [00:09:00] of what's going on in the spaces, um, leave stickers and materials to help that area find out more about what they can do. People here on campus are already doing so much to save energy, but there hasn't been a single place that we've gone to that we haven't found a few recommendations, uh, to give. So we provide personalized recommendations to that area. Then we post those on our website so they can be downloaded by the whole office or whole lab. And Speaker 5: would someone get involved if they're interested in becoming part of [00:09:30] the student team? Speaker 1: We just hired our student team for the semester, so all of our positions are filled currently. However you can stay in touch with us through our website and through Facebook where I post different internships that are available and they come up each semester. Yeah. Speaker 5: On the maintenance and new building side of things, there's obviously an ongoing maintenance that's required by all the buildings and are you folks involved in specifying improvements that could be [00:10:00] integrated into that maintenance process? We actually try to help with the maintenance too, but again we are looking at, everything we do has to be related to energy savings, so things like just clean filters. We'll save energy because there's less draw on the fans. It's an ongoing challenge, you know with the funding and things like that for an adequate maintenance, but it's improving and it's starting to turn, which is really good. It really needs to campus because of the age does [00:10:30] require a lot of maintenance on the different systems and things like that. And with new construction, do you get involved in decisions that are being made about what to put in the various buildings? That would be the policy that Aaron was mentioning earlier. We actually, with the new energy policy, we tried to insert ourselves pretty early into the design phases of the project. Actually in the very early design conception is where we want to be inserted. So we can talk about that. And are there [00:11:00] other sort of stakeholders, groups like yours that get drawn into that process Speaker 1: about energy efficiency or other things? Oh, other things? Well, I mean you could relate it to accessibility issues in a building. It's a very similar type of thing. You're going to build that in in the beginning too. Campus buildings these days, it's not going to be an afterthought and we want energy efficiency to be seen the same way. Speaker 5: And Are you, you're pretty much limited to off the shelf kind of technology at this point. There's no way for you to really work with anyone on campus [00:11:30] on creating some new technology that might, aren't working with certain groups. The Center for built environment, they're doing a research project right now on personal comfort units, which the focus is right at your desk and not a zone, the whole room. And they actually having some pretty amazing results. They have also a heating and cooling chair. So you actually heat the whole building just there as you need. And so the goal is to try to get people to trade in their heaters [00:12:00] that they've got underneath the desk that they bring in from home and they don't want anybody to know about that draw 1500 watts of power with one of these more efficient, uh, personal comfort units, which draw about 40 watts. So they're actually, I had one in my office and I, I hated to give it up, but they had to use it for the research, but it really works good. It's very interesting some of the work they're doing. Speaker 1: I also worked with some students in computer science in order to help us develop a mobile available [00:12:30] site for our dashboards because right now in pulse dashboards or flash and they don't display on mobile devices or tablets. So some of our computer science students help to develop an html version where we're showcasing about half the buildings that are available on pulse. However, you can access those through your mobile device now. And is it just a matter of time before you get them all hauled? The building's done that way. I certainly hope so. Yeah. Yeah. Yes, it is. An ongoing project. Speaker 5: [00:13:00] There is opportunity for innovation that you're finding within absolutely. The campus people are coming to you with ideas which you encourage them. Yes, definitely. Definitely. Yeah. That's exciting. That's the best part of my job actually is meeting some of the people I'd never get to meet otherwise are doing some really neat research and it's cutting edge and to look at the campus as a lab. It really is because of the diversity in buildings and we've got some buildings that are a hundred years old and [00:13:30] on the behavioral side, what sort of push do you make there and how successful is that? Speaker 1: We have been developing a lot of elements for our behavior change campaign, the my power campaign, reaching out to all of campus saying that everyone has a role to play in reducing energy use. We can all turn the lights off, we can all unplug things when we're done with them. We've put out about 10,000 stickers around [00:14:00] campus reminding people to shut the lights off, reminding people to turn their monitors off and those had been put up through student teams. They've also been put up through our power agent team, which is a group of very committed champions of energy efficiency here on campus. Most of them staff members, a few students. And they are also along with our engineers, some eyes and ears of the buildings on campus and they can keep us updated on things that are happening in those areas where they work and study. Speaker 5: [00:14:30] Oh, I'd like to say that we value anybody's input. And you know, I've had people that are gardeners or browns and I've had custodians and various groups that will say, you know, the light was on and you know, the buildings lights are on and things like that and brought it to her attention. So it's just everybody's health. We can do this. It's going to a group effort. Everybody's working together. Speaker 1: Absolutely. And anyone who wants to report any type of oddities [00:15:00] or anomalies and energy use, sending an email to my power@berkeley.edu gets our whole team's attention and we get back to everyone within 48 hours and get on the problem. So those types of reports have really helped us resolve some issues Speaker 6: other than electricity. You deal with natural gas. Steam is a big part of the campus as well. And how does water fit into that as issues? Speaker 5: Right now we're just focused on electricity, [00:15:30] they initial phase, but we will expand into it, you know, working closely with the sustainability office and, and water is very important in steam and yeah, Speaker 1: our dashboards even have capabilities of showing water usage and steam usage. But right now we're pretty single minded in our focus on energy efficiency and reducing permanently reducing the amount of energy we use on campus. But the campus does have a goal of reducing potable water use to 10% below 2008 levels by 2020 [00:16:00] and you can find out all about that@sustainabilitydotberkeley.eduSpeaker 3: [inaudible]Speaker 8: spectrum is a public affairs show on k a Alex Berkeley. Our guest are chuck frost and Aaron Penley in the UC Berkeley Energy Office. In the next segment they talk about new technologies and surprising collaborations. Speaker 6: And how does the steam system [00:16:30] here interact? It's shared, right? It's across a large group of the buildings or not because not all the buildings are on the steam [inaudible] Speaker 5: on the core, you know you have some remote buildings that have boilers and things like that and so you're not using electricity at all to develop the steam. Oh, that is correct. So it's just all, it's usually natural gas or gas to do that. Speaker 1: But isn't the steam a byproduct of the electricity production? Speaker 5: You're absolutely right. We have a cogent plant that does cause of the [00:17:00] turbine generate steam that we traditionally use and then we have on boilers that are kind of a backup to that now. Speaker 6: So that's then on top of the power you draw from PGNE the cogeneration. Speaker 1: We actually produce that energy and then sell it back to BJ to PGNE and then we buy it back. Speaker 5: We give 10 cents is the number we typically give because it's kind of a blend, an average of what we pay Speaker 6: [inaudible] I'm interested in the new technology that you're looking [00:17:30] at. Speaker 5: I think fault detection has actually been around for awhile with your control systems. You trended in the building and then you traditionally would analyze it, an engineer or somebody would look in and analyze it. So you automate that. And so what is really changed, and I think it's really good for the industry, the HVAC industry, is you've got people like Google and Microsoft and people that were never in the game before. Now I want to start mining the data from the buildings, analyzing that data for a fee and helping [00:18:00] with the fault detection. So it's a game changer at the industry. Probably in the last five years has changed more than it did 25 years before that. It's amazing. So we got new players in the game and wireless as well. Wireless is very big too. Yeah. The technology, Speaker 6: is it proving to be as reliable as copper wire? Speaker 5: I think it is. It's starting to be embraced by everybody. You have different technologies, ones that require repeaters and then you have mo technology, then self networking [00:18:30] and things like that. So even now we've got pilots going on that are pneumatic thermostats that are really wireless electronic thermostats that go back to a server and the pneumatic combined. And so that allows us to get down to the zone level to really control a building and really look for the energy. A zone would be like the room we're in now and then with the new wireless lighting that actually it looks at occupancy, it looks at a temperature. Also you can start pulling and really getting a good profile or [00:19:00] you're building when the energy is and when it's occupied and things like that. So those newer technologies are very promising. Speaker 6: Obviously you're going to drive the use and drive efficiency at cow and it's going to get harder and harder to reduce the use. Your Delta is going to get smaller and smaller. Where do you find new efficiencies? Speaker 5: We like to call it mining for Golden Nuggets and the nuggets are harder and they're deeper to find as you move forward, [00:19:30] that's for sure. But we've been working with a Berkeley national lab and also the Pacific Northwest National Lab and PGNE Energy Center and facility dynamics on ways to train our technicians to, to find those golden nuggets. So we're putting the technicians out in the field as we mentioned in zones in the learn the buildings and then they'll get the deeper look at the buildings once they understand the buildings, get more familiar with it. So that's where we're hoping to continue the process. But it is it, you're absolutely right. It's harder. You keep going in [00:20:00] whether you call a golden eye, gets her low hanging fruit, there's less and less. This orchard has been picked over pretty good. Speaker 6: This is what's the legacy of your data collection and distribution at this point? Speaker 1: Oh, right now we started April, 2011 and we are just now finishing up our first annual report that contains all of our, our data from the initiative since the inception, so that will be released as soon as it is approved. It is in its final [00:20:30] draft stage. Speaker 5: What was the biggest surprise for you when you started this process? I don't know if it was a surprise, but I was just amazed at how much of the small little pockets of research that are going on than it actually looking people coming forward. And I'd never heard of the before the center for built environment and just amazing what they had been doing for 20 years and they were a great group and they really understand building comfort and the looking at new technologies and things like that. So this personal comfort unit and [00:21:00] again David Color and computer science students, that was just an early surprised me. And then it would be looking at energy and buildings and some of the tools they've shown savings with lighting and just the smart apps they were developing and where they could track you through a building. They knew what you liked in lighting and and the environment and they could actually start to modify the building and the interface with the control system at the building over citrus in the Er. It was just amazing to me. It was a surprise. Okay. Speaker 9: And the biggest challenge going forward [00:21:30] in near term Speaker 1: for you guys is what? I think for me it's to keep reminding people that we're not done and we still have to keep remembering to incorporate energy efficiency into our daily actions. One of the most surprising and interesting things in this work has been seeing what people's attitudes towards energy efficiency are and some people believe that they're doing everything that they possibly can and we continually find that there's probably even more that [00:22:00] you could do somehow or another. So continuing to incorporate that into your daily work routine or your daily coming to school routine is very important. Speaker 9: Chuck Frost and Aaron Fendley, thanks very much for being on spectrum. Thank you for having us. Thank you so much and good luck with saving energy. Thank you. Speaker 8: [00:22:30] If you're interested in reducing energy use at cau, visit the website, my power.berkeley.edu there you'll find building dashboards and strategies for taking action. Speaker 3: [inaudible]Speaker 8: spectrum shows are also archived on iTunes university. We've created a simple link for you. The link is tiny url.com/cadillacs [00:23:00] spectrum here at spectrum. We like to highlight a few of the sides to technology events happening locally. Over the next few weeks. Brad swift and I Speaker 9: present the calendar. The last few days of the bay area science festival are this weekend tonight in San Francisco, science improv blitz where comics and phd students synthesize laughs for the sake of amusement and learning. This is happening at the south of Market Street Food Park [00:23:30] four 28 11th street from 7:00 PM to 8:30 PM this is a festival event and free discovery days at at and t park. A T and t park will become a science wonder and when Bay Area Science Festival Speaker 4: concludes again with the Free Science Extravaganza last year, more than 30,000 people enjoyed a nonstop program chock full of interactive exhibits, experiments, games, and shows all meant to entertain and inspire [00:24:00] with more than 150 exhibits or something for everyone to unleash their inner scientist. This festival grand finale is Saturday, November 2nd at the home of the San Francisco baseball giants at 24 Willie Mays plaza in San Francisco. It opens at 11:00 AM and runs until 4:00 PM Speaker 9: the Mathematical Sciences Research Institute and Berkeley City College will host a free public talk on verifying greenhouse gas emissions by Dr Inez Fung as part of the lecture series, not on the [00:24:30] test, the pleasures and uses of mathematics. Dr Inez Fung is a contributing author to the assessment reports of the intergovernmental panel on climate change, a scientific body under the auspices of the United Nations. Dr Fung will discuss how we measure and verify claims about emissions related to global warming. Dr Fung is a professor of atmospheric science at UC Berkeley where she has studied climate change for 20 years and has created mathematical models that represent [00:25:00] CO2 sources and sinks around the globe. The event will be held in Berkeley City College Auditorium on Wednesday, November six from 7:00 PM to 8:15 PM RSVP for the free event online@msri.org Speaker 4: the November installation of the monthly lecture series. Science of cow will focus on art inspired by science and mathematics. You see Berkeley Professor Carlos equin will speak about how math and computers [00:25:30] are being used to create new artwork every day. He will also try to answer the nearly insoluble question of whether art or science came. First. Professor sequined began his career at bell labs as part of the group that created the first solid state image sensor compatible with American broadcast television. He later joined the faculty at UC Berkeley where he eventually focused on the development of computer aided design tools for architects and mechanical engineers. Professor sequent has also collaborated with many artists over the years to make the most of computers [00:26:00] and the emerging rapid prototyping tools to create geometrical sculptures and a wide range of scales and materials. The lecture will be held at 11:00 AM on Saturday, November 16th in room 100 of the genetics and plant biology building on the UC Berkeley campus. The lecture is free and open to the public haired spectrum. We like to share our favorite stories about science. Brad Swift joins me for the news Speaker 9: science daily reports that scientists at the University of Wisconsin Madison [00:26:30] have constructed a three dimensional model of the so-called missing link, cold virus, Rhino virus c Rhino Virus C is believed to be responsible for up to half of all childhood colds and is a serious complicating factor for respiratory conditions such as asthma. Together with Rhino viruses, a n B. The recently discovered virus is responsible for millions of illnesses yearly at an estimated annual cost of more than $40 billion in the United States alone. [00:27:00] Because of the three cold virus strains all contribute to the common cold drug. Candidates that focused on rhinoviruses a and B failed antiviral drugs work by attaching to and modifying surface features of the virus. This highly detailed three dimensional structure for rhinovirus c will give pharmaceutical companies new targets for designing cold thwarting drugs. Speaker 4: UC Berkeley scientists have designed a satellite [00:27:30] that could detect large fires across the western United States by snapping a constant stream of photos of the earth below. Then scanning them for new hotspots that could indicate wildfires. The UC Berkeley teen described their plans for the satellite known as the fire urgency estimate or in geosynchronous orbit or flags. In the October 17th issue of the Journal. Remote Sensing Lego works by analyzing its infrared photos using a computer algorithm to detect differences in the land, especially bright lights [00:28:00] that may be fledgling fires. The program can analyze the entire west in minutes. Creators hope that the early detection of wildfires help to prevent loss of life and widespread damage that usually occur as a result of extensive wildfires. Researchers hope to raise the several hundred million dollars required to build the satellite through a combination of public and private means. Speaker 9: The Northern California chapter of the Society of professional journalists has awarded greater good science center editor in chief [00:28:30] Jason Marsh, uh, 2013, excellence in journalism award for his story. Why inequality is bad for the 1% a gripping look at how income disparity can negatively impact both the wealthy and the poor. Relying on cutting edge research. Jason's story illustrates the ways in which having wealth may adversely affect an individual's ability to be compassionate, understand social cues, and trust others. Those deficiencies can hinder social connection, a key part [00:29:00] of our happiness and our physical health. To read the article, go to the website. Greater good.berkeley.edu Speaker 7: [inaudible].Speaker 9: The music heard during the show was written and produced by Alex Simon Speaker 7: [inaudible].Speaker 1: Thank you for listening to spectrum. If you have comments [00:29:30] about the show, please send them to us via email. Our email address is spectrum dot klx@yahoo.com join us in two at this Speaker 2: time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

TranscriptSpeaker 1: Spectrum's. Next. Speaker 2: N. N. N. N. Speaker 3: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x, [00:00:30] Berkeley, a biweekly 30 minute program, bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Good afternoon. I'm Rick Karnofsky. Brad swift and I are the hosts of today's show. Today we're talking with doctors, Tonya Wilkie and Chris Rink of the Department of Energy Joint Genome Institute in Walnut Creek. They recently published an article entitled insights into the Phylogeny and coding potential [00:01:00] of microbial dark matter in which they have to characterized through relationships between 201 different genomes and identified some unique genomic features. Tonya and Chris, welcome to spectrum. Speaker 5: Thanks for having us. Thank you. Speaker 4: So Tanya, what is microbial dark matter? Speaker 5: We like to take life as we know it and put it in an evolutionary tree in a tree of life. And what this assists us is to figure out the evolutionary histories of organisms and the relationships between [00:01:30] related groups of organisms. So what does this mean? It's to say we take microbial diversity as we know it on this planet and we place it in this tree of life. What you will find is that there will be some major branches in this tree, about 30 of them, and we call these major branches Fila that are made up of organisms that you can cultivate. So we can grow them on plates in the laboratory, we can grow them in Allen Meyer, flask and liquid media. We can study that for CLG. We can figure out what substrates they metabolize, [00:02:00] we can figure out how they behave under different conditions. Speaker 5: Many of them we can even genetically modify. So we really know a lot about these organisms and we can really figure out, you know, how do they function, what are the genetic underpinnings that make them function the way they do in the laboratory and also in the environment where they come from. So now coming back to this tree of life, if you keep looking at this tree of life, uh, we will find at least another 30 off these major branches that we refer to as [00:02:30] Canada. Dot. Sila and these branches have no cultivators, representatives, so all the organisms that make up these branches, we have not yet been able to cultivate in the laboratory. We call these kind of dot, Fila or microbial dark matter. And the term dark matter. All biological dark matter has been coined by the Steve Craig Laboratory at Stanford University when they published the first genomes after a candidate, phylum TM seven. We know that dark matter is in most if not all [00:03:00] ecosystems. So we find it in most ecosystems, but to get at their complete genetic makeup. That's the key challenge. Speaker 4: Yeah. And if you, if you want to push it through the extreme, there are studies out there estimating the number of bacteria species they are and how many we can cultivate. And the result is all there. The estimation of the studies we can cultivate about, you know, one or 2% of all the microbial species out there. So basically nine to 9% is still out there and we haven't even looked at it. So this really, this major on culture microbes and majority is [00:03:30] still waiting out there to be explored. So that sort of carries on the analogy to cosmological dark matter in which there's much more of it than what we actually see and understand. Right. Speaker 5: So how common and how prevalent are, are these dark matter organisms? Yeah, that's a really good question. So in some environments they are what we would consider the rabbi biosphere. So they are actually at fairly low abundance, but our methods are sensitive enough to still pick them up. [00:04:00] In other environments. We had some sediment samples where some of these candidate file, our, actually what we would consider quite abandoned, it's a few percent, let's say 2% of opiate candidate phylum that to us, even 2% is quite abandoned. Again, you have to consider the whole community. And if one member is a 2%, that's, that's a pretty dominant community members. So I'd arise from environment, environment Speaker 4: and Chris, where were samples collected from? So altogether we sampled nine sampling sites all over the globe [00:04:30] and we tried to be as inclusive as possible. So we had marine samples, freshwater samples, sediment samples, um, some samples from habitats with very high temperatures and also a sample from a bioreactor. And there were a few samples among them that for which we had really great hopes. And among them were um, samples from the hot vans from the bottom of Pacific Ocean. The samples we got were from the East Pacific virus sampling side, and that's about 2,500 meters below the store phase. And [00:05:00] the sample there, you really need a submersible that's a small submarine and you can launch from a research vessel. In our case, those samples were taken by Elvin from the woods hole oceanographic institution and now you have a lot of full Canik activity and also the seawater seeps into the earth crust goes pretty deep and gets heated up. Speaker 4: And when it comes back out as a hydrothermal event, it has up to [inaudible] hundred 50 to 400 degrees Celsius. And it is enriched in chemicals such as a sulfur or iron. [00:05:30] It makes us immediately with the surrounding seawater, which is only about a two degrees Celsius. So it's a very, it's a very challenging environment because you have this gradient from two degrees to like 400 degrees within a few centimeters and you have those chemicals that uh, the organisms, the micro organisms could use blast. There is no sunlight. So we thought that's a very interesting habitat to look for. Microbial, dark matter. There were several samples. That's a to us. One of them is the Homestake [00:06:00] mine in South Dakota and that's an old gold mine that is not used anymore since 2002 but are there still scientific experiments going on there? It's a very deep mine, about 8,000 feet deep and we could all sample from about 300 feet. Speaker 4: And we were surprised about this Ikea diversity we found in those samples. There were a few Akia that were not close to any, I don't know another key out there for some of them. We even had to propose new archaeal Fila. Stepping back a bit, Chris, [00:06:30] can you tell us more about Ikea and perhaps the three domains of life? The three domains were really established by Culver's with his landmark paper in 1977 and what he proposed was a new group of Derek here. So then he had all together three domains. You had the bacteria and archaea and the eukaryotes, the eukaryote state. There are different one big differences to have the nucleus, right? They have to DNA in the nucleus and it also includes all the higher taxa. But then you have also their key and the bacteria. [00:07:00] And those are two groups that only single cell organisms, but they are very distant related to each other, the cell envelope, all. And also the cell duplication machinery of the archaea is closer to the eukaryotes than it is to the bacteria. Speaker 5: Yeah, and it's interesting, I mean Ikea, I guess we haven't sequenced some that much yet, but Ikea are very important too, but people are not aware of them. They know about bacteria, but Ikea and maybe because there aren't any RKO pathogen [00:07:30] and we'd like to think about bacteria with regards to human health, it's very important. That's why most of what we sequence are actually pathogens, human pathogens. So we sequence, I don't know how many strains of your senior pastors and other pathogenic bacteria, but archaea are equally important, at least in the environment. But because we rarely find them associated with humans, we don't really think about archaea much. Our people aren't really aware of Ikea. Speaker 4: Talk about their importance, Speaker 5: the importance [00:08:00] in the environment. So Ikea are, for example, found in extreme environments. We find them in Hydro Soma environments. We find them in hot springs. Uh, we, they have, they have biotechnological importance and not a lot of, quite useful in enzymes that are being used in biotechnology are derived from Ikea in part because we find them in these extreme environments and hot environments and they have the machinery to deal with this temperature. So they have enzymes that function [00:08:30] properly at high temperature and extreme conditions, really extreme on the commerce extreme or fields. And that makes them very attractive bio technologically because some of these enzymes that we would like to use should be still more tolerant or should have these features that are sort of more extreme. Um, so we can explain it them for a biotech technological applications. [inaudible] Speaker 6: [inaudible] [00:09:00] you are listening to spectrum on k l x Berkeley. I'm Rick [inaudible] and I'm talking with Kanya vulgate and Chris, her and Kate about using single cell genomics. You're expand our knowledge that the tree of life, Speaker 5: [00:09:30] so again, we called up a range of different collaborators and they were all willing to go back to these interesting sites, even to the hydrothermal vent and get us fresh sample. No one turned us down. So we, we, we screened them again to make sure they are really of the nature that we would like to have them and the ones that were suitable. We then fed into our single cell workflow. Can you talk briefly about that screening? There were two screens in waft. One screen was narrowing down the samples themselves and we received a lot more sample, I would say at least [00:10:00] three times as many sample as we ended up using. And we pre-screened these on a sort of barcode sequencing level. And so we down selected them to about a third. And then within this third we sorted about 9,000 single cells and within these 9,000 single cells, only a subset of them went through successful single cell, whole genome amplification. And out of that set then we were only, we were able to identify another subset. And [00:10:30] in the end we selected 200 for sequencing 201 Speaker 4: and how does single cell sequencing work? Speaker 5: So to give you a high level overview, you take a single cell directly from the environment, you isolate it, and there's different methodologies to do that. And then you break it open, you expose the genetic material within the cell, the genome, and then you amplify the genome. And some single cells will only have one copy of that genome. And we have a methodology, it's a whole genome amplification process that's called multiple displacement amplification [00:11:00] or MDA. And that allows us to make from one copy of the genome, millions and billions of copies. One copy of the genome corresponds to a few family or grams of DNA. We can do much with it. So we have to multiply, we have to make these millions and billions of copies of the genome to have sufficient DNA for next generation sequencing. Speaker 4: Are there other extreme environments that you guys didn't take advantage of in this study that might be promising? Definitely. Um, so we, [00:11:30] we created the list already off environments that would be interesting to us based on, you know, on the results from the last start in the experience we have with environmental conditions and the is microbes we've got out of it. So we're definitely planning to have a followup study where we explore all those, um, habitats that we couldn't include in this, uh, study. Speaker 5: So some examples of the Red Sea and some fjords in Norway and their various that were after Speaker 4: the, that the Black Sea is a very interesting environment too. It's, it's completely anoxic, high levels of sulfide [00:12:00] and it's, it's really, it's huge. So that's a very interesting place to sample too. And how historically have we come to this tree in the old days? And I mean the, the, the pre sequencing area, um, the main criteria that scientists use to categorize organisms whilst the phenotype. That's the, the morphology, the biochemical properties, the development. And that was used to put, uh, organisms into categories. And then with the dawn of the sequencing area, and that was [00:12:30] mainly, um, pushed by the Sanger sequencing, the development of the Sanger sequencing in the 70s. We finally had another and we could use and that was the DNA sequence of organisms. And that was used to classify and categorize organisms. Does a phenotyping still play a role in modern phylogeny? It still does play a role in modern philosophy in the, especially for eukaryotes. Speaker 4: Well you have a very significant phenotype. So what you do there is you can compare a phenotyping information with the [00:13:00] genomic information and on top of that even, uh, information from all the ontology and you try to combine all the information you have doing for, let's say, for the evolutionary relationships among those organisms in modern times, the phylogeny of bacteria, Nokia, it's mainly based on molecular data. Part of our results were used to infer phylogenetic relationships into the started. The evolutionary history of those microbes. We'll be, well do you have for the first time is we now have chine [00:13:30] ohms for a lot of those branches of the tree where before we only had some barcodes so we knew they were there, but we had no information about the genomic content and they'll seem to be hafted for the first time. We can actually look at the evolutionary history of those microbes and there were two, two main findings in our paper. Speaker 4: One was that for a few groups, the f the placement that taxonomic placement in the tree of life was kind of debated in the past. We could help to clarify that. For example, one group is they clock chemo needs [00:14:00] and it was previously published. It could be part of the farm of the spiral kids, but we could Cully show with our analysis that they are their own major branch entry of laughter or their own file them and a a second result. That's, I think it's very important that that's because they didn't share a lot of jeans with others. Bifurcates is that, that's, that's right. So if you placed him in a tree of life, you can see that the don't cluster close parakeets, they'll come out on the other side by out by themselves, not much resembling if the spark is there. And the second result was [00:14:30] that, uh, we found several of those main branches of the tree of life, those Fila the class of together consistently in our analysis. Speaker 4: And so we could group them together and assign super filer to them. One example is a sweet book, Zero Fila Debra Opa 11 or the one and Chino too, and also almost clustered together. So we proposed a super final name. Potesky and Potesky means I'm bear or simple. And we choose that because they have a reduced and streamlined genome. That's another common feature. [00:15:00] I'm Andrea and I, I have to say that, you know, looking into evolutionary relationships, it is, it is a moving target because as Tanya mentioned, especially for microbes and bacteria and like here, there's still so many, um, candidates that are out there for which we have no genomic information. So we definitely need way more sequences, um, to get a better idea of the evolutionary relationships of all the books. Your Nokia out there Speaker 6: [00:15:30] spectrum is a public affairs show about science on k a l x Berkeley. Our guests today are Tanya. Okay. And Chris Rink k you single cell genomics to find the relationships between hundreds of dark matter of microbes. Speaker 4: And can you speak to the current throughput? I would have thought that gathering up organisms in such extreme environments was really the time limiting factor. [00:16:00] But I suppose if you have this archive, other steps might end up taking a while. I will say the most time consuming step is really to to sort those single cells and then to lyse the single cells and amplify the genome and then of course to screen them for the, for genomes of interest for microbial like metagenomes [inaudible] that was a big part of the study. So actually getting the genomic information out of the single cells and if that can be even more streamlined than uh, and push to a higher or even more stupid level, I think [00:16:30] that will speed up the recovery of, of novel microbial dogmatic genomes quite a bit. Speaker 5: Well, we have a pretty sophisticated pipeline now at the JGI where we can do this at a fairly high throughput, but as Chris said, it still takes time and every sample is different. Every sample behaves different depending on what the properties of the samples are. You may have to be treated in a certain way to make it most successful for this application and other staff in the whole process that takes a long time is the key. The quality control [00:17:00] of the data. So the data is not as pretty as a sequencing data from an isolet genome where you get a perfect genome back and the sequence data that you get back is fairly, even the coverage covered all around the genome. Single cell data is messy. The amplification process introduces these artifacts and issues. It can introduce some error because you're making copies of a genome. Speaker 5: So errors can happen. You can also introduce what we call comeric rearrangement. That means that pieces of DNA [00:17:30] go together that shouldn't go together. Again, that happens during the amplification process. It's just the nature of the process. And on top of that, parts of the genome amplify nicely and other parts not so nice. So the overall sort of what we call sequence coverage is very uneven. So the data is difficult to deal with. We have specific assembly pipelines that we do. We do a sort of a digital normalization of the data before we even deal with the data, so it's not as nice. And then on top of that you can have contamination. So the whole process is very [00:18:00] prone to contamination. Imagine you only have one copy of a single cell, five Phantogram, one circle of DNA and any little piece of DNA that you have in that prep that sometimes as we know comes with the reagents. Speaker 5: Because reagents are not designed to deal with such low template molecules. They will call amplify, they will out-compete or compete with your template. So what you end up with in your sequence is your target and other stuff that was in was in the reagents or again, in your prep. We have very rigorous [00:18:30] process of cleaning everything. We you read a lot of things we sterilize, so we need to get rid of any DNA to not, um, to, to have a good quality genome in the end. And so that said, we have developed tools and pipelines at our institute now that specifically help us detect contamination. Sometimes it's not easy to detect it and then remove it. We want to make sure that the single cell genomes that we released at as single cell genome ABC are really ABC and not a plus x and [00:19:00] B plus k because accidentally something came along and contaminated the prep. And especially with candidate Fila, it's, it's fairly difficult to detect tech contamination because what would help us would be if we would have referenced genomes, we're actually generating this reference genome so we don't have a good reference to say, yeah, this is actually, that's our target organism and the rest is public contamination, so it's very tricky. Speaker 4: Are there other examples for [00:19:30] single cell sequencing being used on this many organisms Speaker 5: on this many organisms? No, not that I'm aware of. I know there's an effort underway and the h and p, the human microbiome project where they also identified there, they nicely call it the most wanted list, so they have the target organisms that are quite abundant in different microbiomes within the human body associated with the human body and they've been very successfully able to cultivate. A lot of them bring a lot of them in culture [00:20:00] and it may be easier for the h and p because we can mimic the conditions within the body a little bit better and more controlled. We know our body temperature and we know sort of what the middle year is in the different parts of our body. So it's a little bit easier to bring these organisms and culture than going to the hydrothermal vent and try and recreate these conditions which are extremely difficult to recreate. So that said, um, there are some that they are now targeting with single cell sequencing. So that's another large effort [00:20:30] that I know of that's specifically using single cell genomics to get at some of these reference genomes. Speaker 4: Can you get more out of this then? Sort of phylogenetic links? We found a few unique genomic features and one on one dimension is we found a recode. It's stopped caught on in, in two of those, a bacteria from the hot vans I mentioned earlier. And to give you a little bit of background, so, um, it's, we know the genetic information of each sale is and coded in its DNA, but in order to [00:21:00] make use of this genomic information, this genetic information has to be translated into proteins. And then proteins that could be enzymes that are employed in the metabolism to keep the cell going. And a dispensation is pretty universal between the three domains of life. The way it works, we have three basis in your DNA and three basis are called the core done. And each call is translated in the one amino acid. Speaker 4: So this way you'll build a chain of amino acids and then this chain is for a folder [00:21:30] and then you have your ready made protein. This call them triplet. This three basis also work for start and stop. So there are certain colons that tell the cell, okay, that's where you start a protein. And another called in to tell us the cell. So that's, that's where you enter prod and you're done with it. There are some slight variations, but in general does a universally called, is perceived between all three domains of life. And what we found was very interesting in two of those bacteria from the hot vans. Ah, those two caecilian bacteria, we found the [00:22:00] recording. So one of the accord on did not called for a stop code on anymore, but in the quarter's for an amino acid in that case, glycine. And that has never been seen before. Were you surprised by these results? Speaker 5: To us, they were surprising because they were unique and they were different. On the other hand, I have to say I'm not that surprised because we haven't, like Russ said, we haven't looked at heart yet and considering that we can only cultivate a few percent of all the microbial diversity that exists on this planet as far as, [00:22:30] as far as we know it, it's not that surprising that you find these novel functions and there's these unique features and novel genetic codes because it's really, it's a highly under-explored area. Speaker 4: It is very rewarding. But if you look in the future, um, how much is still out of the sequence? Of course we're interested in that. So we looked at all the files show diversity that's known, that's out there based on this, um, biomarkers that Tony mentioned earlier and we just compared it to the genomes that we have sequenced so far. And we really want [00:23:00] to know, so if you want to cover let's say about 50% of all the fall diversity that's out there, how many achievements do we still have to sequence and the number of the estimate was we need to sequence at least 16,004 more genomes Speaker 5: and this is a moving target. So this is as we know, diversity of today it and every day we sample my environments, we sequence them deeper and everyday our diversity estimates increase. So what we've done with these 201 it's the tip of the iceberg but it's a start. Speaker 4: [00:23:30] Well Tanya and Chris, thanks for joining us. Thanks for having us. Thanks for having us. Yeah. Speaker 6: [inaudible] that's what shows are archived on iTunes to you. We've queued a simple link for you. The link is tiny, url.com/calex Speaker 7: spectrum Speaker 8: irregular feature of spectrum is a calendar [00:24:00] of some of the science and technology related events happening in the bay area over the next two weeks. Here's Brad swift and Renee Rao here today. Majority tomorrow. Expanding technological inclusion, technological inclusion is not an issue for some of us. It is an issue for all of us. Mitchell Kapore, co-chair of [inaudible] center for social impact and a partner at Kapore capital. We'll moderate a panel discussion among the following [00:24:30] presenters, Jennifer r Guayle, executive director of Latino to Kimberly Bryant, founder of Black Girls Code Connie Mack Keebler, a venture capitalist with the collaborative fund. Vivek Wadhwa academic researcher, writer and entrepreneur here today. Majority tomorrow is free and open to everyone on a first come first seated basis. This is happening on the UC Berkeley campus in Soutar de Di Hall [inaudible] [00:25:00] Auditorium Monday October 7th at 4:00 PM Speaker 7: the second installment of the six part public lecture series, not on the test. The pleasure and uses of mathematics will be held this October 9th Dr. Keith Devlin will deliver a lecture on underlying mathematics in video games. Dr Devlin will show how casual video games that provide representation of mathematics enabled children and adults to learn basic mathematics by playing in the same way people [00:25:30] learn music by learning to play the piano. Professor Devlin is a mathematician at Stanford, a Co founder and president of Inner Tube Games and the math guy of NPR. The lecture will be held on October 9th at 7:00 PM in the Berkeley City College Auditorium located at 2050 Center street in Berkeley. The event is free and open to the public. Speaker 8: The Leonardo arts science evening rendezvous or laser is a lecture series with rotating barrier venues. October 9th there will be a laser [00:26:00] at UC Berkeley. Presenters include Zan Gill, a former NASA scientists, Jennifer Parker of UC Santa Cruz, Cheryl Leonard, a composer, Wayne Vitali, founding member of gamelons Sakara [inaudible]. This is Wednesday, October 9th from 6:30 PM to 9:00 PM on the UC Berkeley campus in barrels hall room 100 Speaker 7: how can we prevent information technology [00:26:30] from destroying the middle class? Jaron Lanier, is it computer scientists, Kim Poser, visual artist and author. October 14th linear will present his ideas on the impact of information technology on his two most recent books are title. You are not a gadget and who owns the future. The seminar will be held in Sue Taja, Dai Hall, but not auditorium on the UC Berkeley campus. Monday, October 14th from 11:00 AM to noon [00:27:00] and that with some science news headlines. Here's the Renee, the intergovernmental panel on climate change released part of its assessment report. Five last Friday. The more than 200 lead authors on their report included Lawrence Berkeley National Labs, Michael Warner and William Collins who had a chapters on longterm climate change productions and climate models. The report reinforces previous conclusions that over the next century, the continents will warm [00:27:30] with more hot extremes and fewer cold extremes. Precipitation patterns around the world will also continue changing. One-Arm Collins noted that climate models since the last report in 2007 have improved significantly as both data collection and mechanistic knowledge have grown using these models. Scientists made several projections of different scenarios for the best, worst and middling cases of continued greenhouse emissions. Speaker 7: [00:28:00] Two recent accomplishments by commercial space programs are notable. Orbital Sciences launched their sickness spacecraft on September 18th a top the company's rocket and Tara's from wallops island, Virginia. On September 28th the Cygnus dock did the international space station for the first time, a space x rocket carrying and Canadian satellite has launched from the California coast in a demonstration flight of a new Falcon rocket. The next generation. Rocket boasts [00:28:30] upgraded engines designed to improve performance and carry heavier payloads. The rocket is carrying a satellite dead kiss IOP, a project of the Canadian Space Agency and other partners. Once in orbit it will track space weather. Speaker 2: Mm mm mm. Mm Huh. Speaker 7: The music [00:29:00] heard during the show was written and produced by Alex Simon. Yeah. Speaker 3: Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Address is [inaudible] dot [inaudible] dot com Speaker 9: [inaudible]. See acast.com/privacy for privacy and opt-out information.

Amy Herr's research focuses on bioinstrumentation innovation to improve quantitative measurements in life sciences and translating that work to provide better clinical diagnostics. Amy is Professor of Bioengineering at UC Berkeley.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Mm MM. Speaker 3: Yeah. Speaker 1: Welcome to spectrum the science and technology show on k a l x [00:00:30] Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Good afternoon. My name is Renee Rao and I'll be hosting today's show. Our guest this week is Amy, her associate professor of bioengineering at UC Berkeley. Amy is a teacher and a researcher. Her research focuses on bioinstrumentation innovation to improve quantitative measurements in life sciences [00:01:00] and how to translate that work to provide better clinical diagnoses. She is a pioneer in the new field of proteomics. Brad swift and I interview Amy, her. Speaker 5: Amy, her. Thanks very much for coming on spectrum and welcome. Thank you. I'm very happy to be here. How did you become interested in bioengineering? So I am actually a trained mechanical engineer and I think what really peaked my interest in bioengineering was during graduate study in mechanical engineering. I realized that a lot of [00:01:30] the measurement and instrument challenges that exist that face engineering today really are in the life sciences. So this messy area where things are not necessarily tractable or well-described protein measurement is an area that I've been interested in for some time and I've been working on. And it's especially challenging from the perspective of designing instrument technology, measurement technology. What are protein biomarkers and what makes them elusive? Yeah. So protein biomarkers really is just sort of a catch [00:02:00] all phrase for indicators of disease state, um, indicators of living, organisms, response to treatment, just sort of indicators of what's going on in the organism at a particular time. Speaker 5: So there's many different types of biomarkers. You may have heard quite a bit about this genomics revolution and our use and understanding of information that's coming from nucleic acids. And what we're really looking for in Dow is building on what we've learned from our understanding of nucleic acids. How can we try [00:02:30] to understand proteins, which are the effectors of function, if you will, in living organisms and really try to use that information from proteins to understand all of these questions surrounding disease. So who has a disease, who might respond to specific treatments, who might not respond to specific treatments? How you are responding to specific treatments and in our mind it's released the next phase of what genomics has laid the groundwork for an area that we call proteomics. Can you give us a quick run through [00:03:00] of how molecular diagnosis works now and what new things you are trying to detect and what new information we can get from those? Speaker 5: I guess it has been striking to me as an instrument designer, innovator developer. If you take a look at our understanding of the role of proteins in disease right now, there's a treasure trove I would say, of information that's come out of basic discovery. So trying to understand what proteins are upregulated or downregulated or modified in [00:03:30] response to disease or treatment of disease. Right. So I would say there's definitely more effort that needs to be done in discovery, but we've done a lot of great work in discovery. A huge challenge and unmet need to use the engineering design terminology that exists right now is we have these potential indicators of disease or response to disease or prognosis, but very, very few of them have made it into a clinical setting into a diagnostic. Right now there are less than a hundred [00:04:00] different biomarkers that are being used for diagnostics. Speaker 5: That includes nucleic acids of DNA, RNA and proteins as well, just metabolites as well, right? So very, very few of the known existing bio molecules are being used in any way as a diagnostic measurement. And so there's really a huge gap right now between all of these promising markers that have been identified and those that are currently being used to make a diagnosis. So one of the things that we're [00:04:30] trying to do is to just build a basic framework for measurements that will allow people to make many, many, many measurements of a particular biomarker of potential interest so that you can look at many, many different patients' samples, many, many different disease states. We won't be really data limited. So the technologies that we use right now for a lot of these protein biomarkers to see whether or not the promising ones actually answer a clinical question, they're really rate limiting. Speaker 5: [00:05:00] They're really slow or they require a lot of material and in some cases this biospecimens these materials from patients are precious, hugely limited, right there, sparingly available. So we're just trying to think about ways that we can use these microfluidic architectures that require just tiny amounts of sample to run one measurement. How we can use those to scale up to make thousands of measurements. We're right now tens of measurements can be difficult and to make those measurements on, you know, a [00:05:30] microliter of sample from a patient as opposed to tens to hundreds of microliters. So that for us, this so-called biomarker validation question getting from yet this might work too. Okay, here are the clinical questions this marker can or cannot answer as the gap that we're trying to fill. Are you building these instruments? A major focus of my research group is looking at innovating new instrumentation, new technologies. Speaker 5: So by understanding the underlying physical principles [00:06:00] of the types of transport that we use. So electrophoresis and diffusion and by understanding unmet clinical or life sciences needs. So questions or challenges that currently exist out in life sciences laboratories or in clinical laboratories. We're basically trying to bring those two aspects together to develop new tools. All of the new tools that we develop are developed really to meet an unmet need either in the clinical setting or the life sciences setting and they're built with an understanding these underlying principles, but they all [00:06:30] have to be validated. So when we make a measurement with a new tool, we have to have some confidence in how well our measurement reflects our current understanding of the systems. And we typically do that by using conventional gold standard measurement technologies where appropriate. I think recently we've just come into this really interesting and exciting gray zone where we can make measurements that there really are no existing tools to be able to validate whether our measurement makes sense or not. And so we've had to put some effort and careful thought [00:07:00] into how do we validate our measurements using maybe indirect approaches so that we can say with some confidence the limits and the benefits of the tools that we're introducing. Speaker 4: You said earlier that a lot of your research comes from trying to meet the unmet needs of both the life sciences and the technological aspects. How do you go about picking which needs to meet? Do you find ones that you think, okay, well this is doable, or do you find ones that you think, maybe no one else can do this? I'm going to work on it? Speaker 5: Right. [00:07:30] That's a great question. So as an engineer, as an engineering designer, one of the first things that we do is really try to understand the world around us and try to understand how people approach existing problems, how they define those problems, why they approach them in a particular way. But I think this is one of the most exciting aspects of the work that we do. It's certainly true that if you get this first stage, this identification and understanding of unmet needs wrong, you're going to go down the wrong path, but if you get it right, you can make a huge difference in terms [00:08:00] of how people are approaching either science or medicine and our work is really translational in that way. So we're engineers and we're passionate about making excellent measurements and as you say, measurements that are currently not possible are the measurements that we're really looking to impact. Speaker 5: Measurements that are currently possible but needs significant improvement. We do focus on those as well, but when you can find a measurement that when you're talking to a biologist and explaining kind of what you can do and they look at you and say, oh my gosh, there's no [00:08:30] way I could do that right now, then you know you've hit upon something that's really important to at least consider further to fill a gap and unmet need that's out there at the present time. In many ways, I think it reminds many of us of why we chose to be engineers in the first place. I mean, certainly I can speak for myself and say I'm really excited about being able to make measurements that no one else can make. And understanding how those measurements, how good they are, how much more improvement they need, and maybe trying to understand the physics and think about [00:09:00] is something possible that we've discounted to date. But I think in many ways connecting with the end user also adds another layer of excitement and passion and motivation because you can really see how your work in the lab can make a difference in the world around us. Speaker 6: Aw. [inaudible] you're listening to spectrum k A. L. Alex Berkeley. Our guest today is Amy her in the next segment, [00:09:30] Amy talks about her lab at UC Berkeley. [inaudible] Speaker 5: how long has your lab been up and running? So my lab has been a, at Berkeley six years before I came to UC Berkeley. So I did my doctoral research at Stanford in mechanical engineering and then I loved a research and I wanted to continue doing research and so I worked for five years at a national lab and then coming to UC Berkeley was a big change in many ways, but I think [00:10:00] I'm working with an excellent team of, in many cases, junior colleagues here now, training them, postdocs and students just being invigorated every year with the fresh approaches that students, the frust questions that students ask about why are we doing some things in the way that we're doing them, or why is our understanding limited in this way as a faculty member? Just a huge source of inspiration and motivation over the six years. Has Your approach within the lab changed much? Speaker 5: Our lab has certainly changed. Yeah, [00:10:30] and I think as an individual, you as a researcher over the course of six years, certainly I will have also changed. You learn as you go and you learn on a technical level for sure. Absolutely. I would also say I've learned a lot from my groom to the students and the postdocs and the way that they approach problems. It's been just a fantastic honor to be able to work in bioengineering here at UC Berkeley with an amazing group of people who all come with different perspectives. And I've really pushed the research directions [00:11:00] in my group in ways that I couldn't have imagined six years ago. And they also come from very different disciplines as well, don't they? And has that mix changed for you over the six years? Yeah, that is absolutely true. So bioengineering, when I was in graduate school, which I'd like to think was in a long time ago, but it was, I finished almost a decade ago now. Speaker 5: It didn't even really exist. Right. It was just kind of starting and the graduate level widely at universities around the u s and globally as well. So most of the faculty, if you look at bio engineering, our formal training is [00:11:30] not in bio engineering. We're too old for that, I guess. And so the students who currently come to do doctoral study at UC Berkeley and with our partner institution, University of California, San Francisco, they all come with different backgrounds. More and more of them are coming with a biomedical or bio engineering undergraduate degree. But we certainly, you know, in my group alone have had students who have come from uh, aeronautics, chemical engineering, electrical engineering, chemistry, just a wide range of backgrounds. As someone who essentially [00:12:00] witnessed the genesis of an entire field of engineering and especially one that is so connected to the world. Can you tell us what that was like and how that's affected you? Speaker 5: Yeah. Seeing bioengineering starts really and become just the huge discipline in the really impactful area of research and study that it is today has been really inspiring. It's also does raise a lot of questions, questions about what is the appropriate curriculum for undergraduates who are studying. Bioengineering is something that [00:12:30] the faculty in my department, we talk about all the time. We try to refine our approach to this really, really important basic study that students undertake in their undergraduate years. Right? So there's that aspect of it wanting to make sure that we help them prepare themselves to be the best engineers possible when they leave UC Berkeley on the other hand, just seeing the huge advances that engineering is making in medicine and the way that it's changing the lives of people and has been for some time [00:13:00] for the better is really inspiring. I will say I often notice that students that I come into contact with here, they're really driven to make a positive impact in the world around them. Speaker 5: And I think that is really at the core of what engineers want to do. We want to understand, but we also want to make something, we want to make a positive impact with what we're doing and maybe I think in a very practical sense that's what an engineer is. I wanted to ask you a little [00:13:30] bit about what you've referred to the engineering mindset and I think it's a really interesting perspectives to want to maybe put us in that mind frame. Yeah, I think the engineering approaches to really just question question what you're observing, question what people are telling you. And so the engineering mindset I think is to be skeptical and to be observant, to not listen to necessarily what people tell you, but to use your own eyes and to discuss with peers or mentors [00:14:00] to try to understand and make sense of all of the different perspectives you're going to get when you're trying to understand the problem. Speaker 5: And so as engineers, we're always challenged with getting into kind of one way of thinking and that can push you down a path that could be productive. But if you really step outside and try to integrate a really holistic view of the world or the problem you're trying to understand, you might happen upon new approaches that users would never have dreamed of. Right? So there's that aspect. I think the engineering mindset is also to be objective. And in [00:14:30] our case in bio engineering, trying to be as quantitative as possible and to understand the limits and the advantages of being quantitative. And then certainly in bioengineering, there is a huge aspect of our mindset, which is to translate our solutions out into the world around us so that we can have a positive impact on society and the world more broadly. Spectrum is a public affairs show on k l x Berkeley. [00:15:00] Our guest today is [inaudible] Speaker 6: Amy her in the next segment, Amy offers advice to students interested in bio engineering. Speaker 5: Can you explain how you're using mathematics to reveal biological systems and create new medical applications? Yeah. One of the big things that we've seen lacking in instruments to make protein level measurements is any sort of quantitation, so a lot of the technologies [00:15:30] are just qualitative. You can see the presence of a particular protein of interest or okay, maybe it's higher presence in one sample versus another, but inherently in the way a lot of the conventional approaches, the conventional assays are run, there's very little confidence in being able to pull out exactly how many micrograms and material are present in a sample two it's hard to do comparisons between different samples except in a very qualitative way. What we're working on are technologies that are quantitative. [00:16:00] So that can allow you to pull out absolute mass level or concentration level information about how much protein is present in a particular sample. Speaker 5: And the hope there is that by doing that we can allow ourselves to create large databases of quantitative information about how much protein or particular form of protein is present under specific conditions. So you can imagine if you were doing a study, for example, on a particular biomarker [00:16:30] of interest, so prostate specific antigen, let's take, right. So if you knew that a particular isoform of this protein was present in certain cases, you could actually quantify how much is there. Enter that information in a database and a researcher say in Norway, who's also making similar measurements, but maybe on a different patient cohort could also upload their information. You can compare head to head. So these data sets could get bigger and bigger and bigger. And then potentially looking at questions of cell signaling [00:17:00] and in proteins that carry that signaling information. Perhaps integrating those quantitative levels of these particular proteins back into bioinformatics models that have been developed would lend insight into the exact response of a protein signaling pathway to a particular stimulation and give those bioinformatics models some actual numbers to work with as opposed to just relationships between specific proteins and are you building some of those models? Speaker 5: So a lot of what we do is collaboration with [00:17:30] specialists in protein signaling pathway models. So my lab is into bioinformatics lab, so we don't do a lot of that ourselves. But through our collaborations with the bioinformatics community, we know that quantitative levels of proteins at particular times is really important to these dynamic models. And so that's a major focus of our work as well. Speaker 4: It's interesting that you bring their PSA test up because I think that's been getting a lot of attention lately. I'd say look at more data. They're realizing it's not quite the silver bullet that people thought it was. [00:18:00] Are there any other examples like that that waste have completely overturned people's ideas of what we were seeing once we look at this large scale data? Yeah, Speaker 5: in particular a very striking example that you bring up the test for free versus total prostate specific antigen in blood. Right. And that's been used for many years as an indicator of prostate cancer. I think there are just three beautiful studies that have come out in the last year, one from UCF that have really pointed to the fact [00:18:30] that actually some of these PSA tests are really good at finding prostate cancer. They're just really bad at telling us if it's an aggressive or a slow moving prostate cancer. Right? So the prognostic information, how the patient is going to fare in the long run is just not there. So we're finding the prostate cancer, but we're not able to determine whether we should just watch full weights and see what happens or if we should actually embark upon some treatment. That's been a big interest of our group is looking [00:19:00] at specific diagnostic questions. Speaker 5: Who in the case of prostate cancer, can we improve prognostic information and trying to look at specific forms of the protein. So in this case, working with the researcher at Stanford Medical Center looking at different glyco forms of prostate specific antigen that may be more indicative of longterm outcomes for the patient. That in particular is a really interesting one for me because we started working with this researcher maybe six years ago before these big studies came out that showed the prognostic usefulness of the PSA [00:19:30] test was not so good and I definitely remember us submitting several proposals to funding agencies and basically getting the comments back that will we have an indicator for prostate cancer right now, we don't need another one. And so just even over the short time that we've been working on it, seeing that just turned on its head because of this ability to integrate all of this patient level information across countries and across different sites to try to understand how good is this test really have led us to realize it's not, as you [00:20:00] said, the silver bullet that we once hoped or thought that it was. I think that's a really good example. I think in some of those same studies, mammograms have also come out yet, right, is not necessarily answering the diagnostic questions that they hoped that that diagnostic would answer. What advice would you give to a young person thinking about bioengineering, about preparing for work in a multi disciplinary lab? Speaker 5: I think major advice that I would give to a young [00:20:30] person who's thinking about working in an interdisciplinary lab like those that you'll find in bioengineering, but also across the campus for sure. I know this interdisciplinary focus is something that permeates engineering right now and I think rightly so on many levels. Many of the problems that we're trying to solver so big are complex. That having these different inputs is just critical. I honestly think that is part of our community. We've not done a great job of communicating to either new engineers or people who are thinking about going into engineering and just this idea that [00:21:00] I can work on these really big challenges with teams of amazing people trying to have a positive impact through my work. I can get paid to do that. I can travel the world to do that. I can work on many different types of problems over the lifetime of my career. Speaker 5: Just an amazing career path really for anyone to consider. It's certainly very exciting and it certainly challenges you and it allows you to operate in these spheres that you would never imagine you could. So either with [00:21:30] different teams of people or just on problems that you maybe never even imagined you would come across. I think some of the advice I would give a undergraduate here at UC Berkeley, I would definitely urge them to seek out opportunities, clearly urge them to seek out mentors, so people who are maybe several years older than them, so people who are role models, who they might want to be like when they quote grow up. Right? We all have those people that we look for no matter how old we are. Look also for people around you who are maybe just a couple years [00:22:00] older than you, who have gone through a programmer or embarked upon research in a particular field and pick their brain about what worked for them and what didn't. Speaker 5: If they went back in time, what would they do differently or what are they so glad that they did? I think just finding these resources and making use of them and then paying it forward when your time comes and you have the experience to share insight with other people and advice is advice. You don't have to take it. But I do think it's certainly in my own career really helped me to listen to it and then weigh it for myself. [00:22:30] I think in an interdisciplinary field like bioengineering focusing on getting the rigorous fundamental understanding of engineering and the particular area that you're interested in is really key. Certainly advisees, I urge them to consider either a minor or some sort of emphasis material science, mechanical or electrical engineering cause it might help them out a little bit. But just making use of the resources that are around you and finding those resources is something I would urge students to do. I'd love to [00:23:00] know your favorite protein. Oh my favorite protein. I think actually right now it would be prostate specific antigen. Yes. Because there is so much controversy around it for sure. Yeah. So it was a good question. Sure. Amy, her. Thanks very much for coming on spectrum. Great. It was a pleasure. Thank you so much. Speaker 6: [inaudible] [inaudible] [inaudible] [00:23:30] [inaudible] Speaker 5: on the webcast of spectrum, we've chosen to include a new section of Amy's interview suitable. The more technologically inclined among us, she would discuss her exciting work inventing novel means of biological measurement. One other term I wanted to have you weigh in on is the term scale dependent physics and chemistry, and how is that important to your work? So [00:24:00] we are a bioengineering lab. We're an instrument innovation and development lab. So what we look at, or are there new ways to make protein level measurements that can inform our understanding or our approaches to disease? Right. And that's through this portal of proteins is indicators of disease. It's really interesting as you look at some of the basic fluid and material transport phenomenos. So things like diffusion or things like, in our case, we're interested in electro migration, so charged analytes. If you apply an electric field, [00:24:30] they're going to migrate, right? Speaker 5: They're going to go towards the cathode or the anode depending on their charge. These sorts of physical transport phenomena can really benefit from shrinking link scales. So in our case, we're interested in using tiny channels, so channels that hold fluids, liquids in particular channels that have a dimension about the size of a human hair. So they're very small. As you scale down channels to that size, you start to get some really beneficial properties that come out about the fluids. And then in particular, the use of [00:25:00] the electric fields benefits from those tiny channels because the channels have a very high surface area to volume ratio. So as you shrink a channel down, you get more and more surface area for a tiny volume. And that essentially means that if we apply a field, an electric field along a fluid that's in that channel, we can apply a very, very high fields and those high fields are going to make the fluid start heating something that's called jewel heating. Speaker 5: So in the electric circuits you have in your computer, for example, if you apply a field, you're moving electrons, not liquids, [00:25:30] but you're still getting this jewel heating because of the motion of those particles. As we have these really high surface areas, we can dissipate heat really effectively. So we can apply high, higher and higher fields than you could even say a millimeter diameter channel. Now we have channels that are microns in diameter, so orders of magnitude smaller and they cool very effectively. So that allows us to access a transport spaces that aren't accessible kind of in the macro scale. Speaker 5: So my [00:26:00] lab is really focused on taking fabrication approaches that have been developed for the semiconductor industry. So moving electrons around in tiny channels, if you will, and applying that with those sorts of approaches to now, not moving electrons but moving fluids, right liquids around. Um, and the reason we do that is because as we scaled the channels down, the channels that hold the liquids, we get beneficial properties. So heat dissipation is one of those beneficial phenomena. It really starts to [00:26:30] become more and more efficient as we scaled it. The dimensions, the cross section of the channel down. So in our case we like to use these tiny structures, these tiny fluid channels. Again, diameter of about if human here in cross section because it allows us to operate under really, really harsh conditions if you will. So at very, very high field strengths. In addition to that, another beneficial aspect of scaling down is much of the transport that happens inside these tiny channels really ends up relying on diffusion [00:27:00] as being the major mechanism of transport and diffusion a is very efficient over short distances, over long distances. Speaker 5: The scaling is not necessarily favorable and it might take you a long time for a molecule to diffuse a long distance, but as we use these techniques, these fabrication techniques to develop micro and Nano fluidic channels, those distances in those channels are tiny. So microns or nanometers and that means diffusion all the sudden becomes a very effective transport mechanism. [00:27:30] So we use these effective transport scalings these beneficial scalings to allow us to do things like mixing. So we can bring two analytes or two reagents in contact with each other and just rely on diffusion to get them to mix. Whereas in the macro scale we would want to stir or agitate the fluid in some way so we can use passive approaches and rely on diffusion to get effective mixing. Whereas on the macro scale we would have to have some sort of active stirring in order to get those, those species [00:28:00] to come together and react. Speaker 5: So are these techniques being applied to both your understanding of biological systems and in your applications that you're trying to build? It's a great question. So I think primarily a lot of the physical phenomena that we're using are really trying to drive towards efficient assays, efficient measurement technologies for specific applications. So for example, we might be looking at a particular protein mediated signaling pathway [00:28:30] and we might be really interested in different isoforms or different versions of proteins, the same protein, but maybe it has some sort of phosphorylation modification on it. Um, and by using these really efficient separation mechanisms like electrophoresis on the micro scale, it's electro migration properties, we can actually start to resolve species or separate them when if we were to use a less efficient architecture, we might not be able to separate them basically and tell them apart. So it allows us to in some ways [00:29:00] access information that sometimes is not accessible using conventional methodologies, conventional assays. Speaker 5: Um, but it also lets us get at looking at reactions for example, on timescales that you just can't do using macro scale techniques. So being able to look at very fine time points because we have really precise control of fluids using these micro architectures, these microfluidic channels. So there's kind of two answers. One, we want to look at specific proteins as related to clinical [00:29:30] questions. So those applications and in many cases we can do that more efficiently. But on the flip side, the fundamental understanding of biology, we might want to look at timescales that we can't measure box systems as well. Have you discovered anything really new and exciting with this novel level of precision? We have started to move into an area that's a little bit unknown and recently some of the work that's being generated in my lab and we're excited to be preparing now for communication to the broader technical [00:30:00] community is being able to look at protein signaling pathways on a single cell level. Speaker 5: So flow cytometry is one example of technology that exists that allows you to look at literally millions of individual cells and you've basically stained those cells with antibodies to a particular protein. So the cell is going to glow a particular color because the antibody has a floor for conjugated to it. The cell is going to glow as particular color of the antibody binds to an analyte of interest of a protein of interest in that cell. But the [00:30:30] problem is with flow cytometry, if you're looking for proteins that we don't have antibodies that are specific to them. So some of these isoforms for example, there's not an antibody that's just specific to a particular isoform. It's very difficult to to make a flow cytometry measurement or there's other cases, for example, with stem cell research or circulating tumor cells. We have so few starting cells that if you use flow cytometry, you're basically going to lose all of the material before you can make the measurement. Speaker 5: [00:31:00] So using these microfluidic architectures, we can um, do separations of single cells and be able to look at isoforms of particular proteins even if we don't have antibodies specific to one of the isoforms. If we have an antibody that's specific to all of the isoforms but we can resolve them from each other before we use an antibody to probe for them. Or if we have such a tiny starting population of cells like circulating tumor cells, we're going to be able to make measurements of the protein signaling pathways on those, you know, 10 or a hundred cells [00:31:30] that are of interest that we just can't do using conventional technologies. I should say. One of the major methods that my group has been working on over the last couple of years is this idea of western blotting. And this is a really powerhouse work horse analytical technique that's used in clinical and research labs all over the world. Speaker 5: Basically it's an assay that allows you to separate the protein contents of a particular sample, so to resolve species proteins by differences in molecular weight, for example, and [00:32:00] then it allows you to come in with an antibody that's specific to a target of interest and see at a particular molecular weight. Does this antibody recognize that protein? If so, most likely that is the protein that I'm looking for, that's my target or the candidate that I'm looking for. And so we've pushed in several different lines of inquiry, new ways to make this specific measurement. It's two measurements, molecular weight and this binding to an antibody or an immune regent of interest. We've really benefited from materials design, so developing [00:32:30] materials that we can change basically from molecular sieving matrices that are useful for the separation stage. Two materials that actually immobilize the of interest upon exposure to light and after we immobilize the proteins, we can come in with the antibody and probe to see if that particular band at that specific molecular weight is the target of interest. This is, I think, been really informative from the perspective of allowing us to design these systems to operate, say, at the single cell level [00:33:00] or to operate on clinical samples that are difficult to analyze using conventional technologies. Speaker 2: Mm MM. Speaker 3: Okay. Speaker 1: The music heard during this show was written in, produced by Alex Simon. Thank you for listening to spectrum. If you have comments about the show, please send them to [00:33:30] us via email. Our email address is spectrum dot k a l x hit yahoo.com join us into Speaker 7: [inaudible]Speaker 3: [00:34:00] probably. See acast.com/privacy for privacy and opt-out information.

Claire Kremen and Alastair Iles of ESPM at UC Berkeley, who ran the Berkeley Center for Diversified Farming. Next on their agenda is the Berkeley Food Institute, which will include College of Natural Resources, Goldman School of Public Policy, School of Journalism, Berkeley Law and School of Public Health.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute [00:00:30] program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hey there and good afternoon. My name is Renee Rao and I'll be hosting today's show. Our guest today, our professor Claire Kremen and Assistant Professor Allister isles in the Department of Environmental Science Policy and management at the University of California Berkeley. Claire Carmen focuses her research on conservation, biology and biodiversity. [00:01:00] Allister isles focuses his research on the intersections of science, technology, and environment that contribute to public policy, community welfare, environmental justice, and increased democracy and societal governance. Brad swift interviews the pair about their time as faculty directors of the Berkeley Center for diversified farming and the recent launch of the Berkeley Food Institute. This ambitious enterprise is a collaboration between the College of natural resources, the Goldman School of public policy, the Berkeley Graduate School of Journalism, [00:01:30] Berkeley Law School, and the school of public health. Allister isles is hearing impaired, so phd candidate Patrick Bower will be reading Alistair's answers during this interview. Speaker 4: In today's interview we have three folks, Claire, Carmen, Allister isles and Patrick Bower. Welcome to spectrum. Thank you. Thank you and a nod from Allister. I want to ask each of you, how were you drawn [00:02:00] to the study of sustainability and diversified farming Speaker 1: on native bees and how they contribute to crop pollination in California and it was really through my study of the bees and particularly of how bees respond to agriculture that I got interested in farming and that my eyes got opened to how unsustainable our current farming system is, particularly with its heavy reliance on monoculture. Speaker 4: [00:02:30] My background is in environmental policies and I've mostly worked on industrial chemical issues for a long time. I've also researched the consumption side of food starting with sustainable seafood. About three years ago, Claire was running a series of round tables on diversified farming systems and by a chance at a faculty lunch, she invited me to participate. I wasn't sure what it was all about, but I enjoyed learning about ecosystem services. I realized that agriculture has a major role to play. I'm making the planet more in the face [00:03:00] of many 21st century environmental dangers like climate change. Trying to change consumer behavior isn't going to be enough to achieve greater sustainability. We need to cover the whole food system and to find new connections across each part, so that's why I moved much more upstream into agriculture. Talk about the new Berkeley Food Institute that you've formed a cow. Speaker 4: How did it get started and what are its goals? We began with [00:03:30] a round table series on diversified farming systems or DFS about three years ago. I can't believe how far we've already come since then. The series was based on a seed grant from the Berkeley Institute of Environment. It had monthly meetings and spent an enormous range of topics from conservation, biology, consumer behavior, the health effects of pesticides on farm workers to policies for promoting DFS. At first, we weren't sure what our goals were. We had a vague idea that the round [00:04:00] table might evolve into a more institutionalized forum. Claire wanted to co-write a paper covering the results of the round tables, but it quickly became obvious that it was such a large topic that we needed a whole special issue. Do you even do justice to the topics? Fortunately we were able to persuade the ecology and society journal to accept our specialists. You plan. It was a lengthy process of assembling the various papers as students are coauthors on most of the papers. We believe strongly in promoting student research and Claire and I wanted [00:04:30] to institutionalize the round tables and that is how we can see to the DFS center. We realized that we couldn't manage all this new growth without hiring an executive director, which meant that we needed to start raising funds Speaker 1: and as we started looking into funding for the center for diversified farming and as we engaged both with donors and also with the top levels of the College of natural resources administration, it became clear that there was actually an opportunity to do something much bigger and much more far reaching [00:05:00] by partnering with the schools of journalism and of public policy. And that's because it's not sufficient to conduct the research that demonstrates the social and environmental benefits of sustainable agriculture or diversified farming systems. You really have to get the word out to a large public and you have to be able to influence key decision makers. So it makes a lot of sense for us to be partnering with journalism and Public Policy. Later on in the institutes development we also were joined [00:05:30] by other key actors, specifically the schools of public health and also the school of law. Speaker 1: So the goal of the institute is really a lofty one. We want nothing less than to be able through research teaching and outreach to be able to actually transform our current food system to one that is far more resilient, far more healthy and far more just how is the institute funded. We're funded this point by private individuals and also by family foundations [00:06:00] are their undergraduate and graduate degree programs within the institute? Not yet, but we are contemplating creating something called a designated emphasis for graduate students, which means several different departments combined together and create an additional degree program that graduate students can go through and we're also beginning to assess whether an undergraduate major makes sense. The first step we're taking already is to conduct an inventory of what's already [00:06:30] available on campus. There are quite a few different faculty that are already teaching courses related to the food system and so we're identifying all of these so that students can have access to this information. Those who are already interested in this Speaker 5: [inaudible]. Our guest today on Spec gem are Claire Allister Isles. In the next segment they talk about impediments to sustainable farming. Is k a l x Berkeley. Speaker 4: [00:07:00] What sort of collaborations will you be trying to foster with the institute? One of the key actions that the new institute will emphasize is nurturing new research and policy collaborations between faculty and students. Many parts of the food system are balkanized. They're divided up from each other and seldom communicate across disciplinary industry or supply chain segment lines. For example, urban agriculture policy makers might not think much about the sorts of foods [00:07:30] that city gardens are providing to poor minority neighborhoods. What we hope for is a set of collaborations that will cross disciplinary lines and that will address research topics that aren't being done but they could help bring about positive changes in the food system. Another thing that we are eager to look into is helping foster stronger connections with off campus actors such as farmers, food worker unions, government agencies and Bay area communities. This is where this would help inform the research being done on campus and where it might help enhance the ability [00:08:00] of these actors to work toward the transformation of the food system that Claire talked about. Some of our faculty already have off campus partners that they run research projects with citizen science or working with lay people and helping generate new science will likely be an important element, but not the only one. How directly will the institute be involved in actual farming or working directly with farmers? Speaker 1: We will definitely include growers on our advisory board and [00:08:30] also some faculty actually work with growers. For example, my work is all on farms owned by real people and so I work with growers on the kinds of experiments we're going to do and also on sometimes on land management that they're doing on their land. Speaker 4: What do you see as the impediments to the broad practice of sustainable agriculture and how can research and education help the impediments to sustainable agriculture legion? The most important impediment is arguably [00:09:00] the industrialized food system that we currently live in. The system is based on farming methods that include monoculture farming, the pervasive use of chemical and fossil fuel inputs, and an emphasis on increasing yields to the exclusion of other outcomes. The system is so entrenched that everyone who grows processes and eats food is caught in it. One example of how the industrial system discourages sustainable farming is the artificially cheap price of foods the food industry can externalize most environmental and social costs of producing food [00:09:30] by displacing these into farming communities, consumers and ecosystems. Public policies can Ivan this by promoting inappropriate subsidies for commodity crops and not properly funding conservation measures on farmland. Speaker 4: In turn, many farmers are trapped within a production structure or they have little room to adopt sustainable farming methods. They may have to comply with supply chain pressures such as contract farming that prescribes exactly what they should do on the farm or the rapid growth and market power of the agrifood corporations. [00:10:00] For decades, farmers have been struggling with the technological treadmill or they're obliged to adopt technological innovations such as pesticides and now GM seeds to be able to maintain their yields and cost structures in order to compete with other farmers doing likewise. Conversely, it can be very challenging for farmers to move to more sustainable methods. It is risky for farmers to try something new that they aren't familiar with and that requires them to develop new skills and knowledge. There has been a dramatic decline in the number of farmers in the u s [00:10:30] and there has been a trend of fewer new farmers entering the sector. On the positive side. These new entrants are more likely to use sustainable farming methods because they've been trained differently. Speaker 1: I think the broadest impediments are some aspects of our regulatory system and also market forces that encourage economies of scale sort of thing that make farmers have to get big or get out. For example, on the regulatory side, this new food safety modernization act is something that's going to impose [00:11:00] a lot of regulations on growers and that can actually disadvantage small growers. And sometimes it's the small growers that are the ones that are practicing more sustainable or more diversified forms of agriculture. But with this new food safety modernization act, they just might not be able to stay in business any longer. So the critical research that we need to do is to document the benefits and the costs and also the trade offs of different approaches. We need to be able to show what these benefits are so that we can hopefully have an influence [00:11:30] on some of the regulations. Speaker 6: Oh, you are listening to spectrum on k a Alex Berkeley. Our guests today are Claire Kremen and Alister aisles. Patrick Bower will be reading out and styles and series Alistair's hearing impaired. In the next segment, they talk about how they analyze farming. Oh, okay. Speaker 4: Would you explain [00:12:00] how you analyze an agricultural system for sustainability? Speaker 1: From an ecological perspective? What I find helpful is the concept of an agriculture that is regenerative. What that means, it's an agriculture that demands few external inputs and creates few wastes. Instead it tends to use the waste products that are produced in the production cycle as inputs, so for example, by composting waste materials or by integrating animals back onto the farm, growers can build soils. [00:12:30] These wells are then able to store water much more effectively protecting against droughts and they can also require, in that case, less water from external sources. Also, these oils can trap and filter nutrients leading to less nutrient waste and less pollution off site, and then such soils are also much more productive so they can lead to greater yields, so it's really a win, win, win, win. I can't really see any downside to farming like that. Speaker 4: In terms of the social and economic components [00:13:00] of an agricultural system, there are many possible measures that we could use. Social scientists have looked at measures such as the justice that is embodied in the system. That is as the agricultural system assuring justice for all the workers, growers in communities across the system. This justice could take the form of fair worker treatment such as paying farm workers better wages and preventing adverse health effects like heatstroke. It could also be limiting the exposures of farm workers in rural communities to pesticides. [00:13:30] Another measure is food security or the ability of consumers and communities, especially poor and minority people to gain access to enough nutritious and healthy foods to feed themselves. In the u s there are at least 40 million people who depend on food stamps to supplement their diets. Yet these people may not be able to afford healthy, sustainably produced foods. Speaker 4: Yet another measure is whether farmers able to sustain themselves through their work or whether they fall into greater debt to be able to stay in farming at all. Many [00:14:00] NGOs and food movements such as the food sovereignty movement would argue that the ability of farmers and communities to decide on what sorts of foods they want to produce and eat isn't an important outcome in and of itself. How has the understanding and measurement of sustainability changed over the years? You have studied it. Social scientists have only been thinking about sustainability for a fairly short time since about the early 1990s sustainable development as a discourse [00:14:30] first began developing in the late 1980s with the Brundtland Commission's report. Initially, social scientists were focused more on the rural sociology of agricultural production. They looked at issues in isolation and emphasized farmers only, but as more researchers began to enter the sustainability field, the focus shifted to thinking more holistically. They started to look at food supply Speaker 7: chains and commodities and how these shape the sustainability of farming. Researchers also began looking at how communities were defining sustainability [00:15:00] in their own terms. In 2000 Jack Kloppenburg led a very interesting study that surveyed a set of rural and urban communities for the sorts of words they would use to describe sustainability. More recently, social scientists have looked at how ecological and social sustainability are closely interconnected. Some of the most exciting new work is looking at the concept of socio ecological systems or how farmers are actively shaping farming landscapes and vice versa. Speaker 8: [00:15:30] Are there estimates or models that show the reductions in greenhouse gas that could be achieved in the conversion from industrial monoculture agriculture to sustainable agriculture? Speaker 1: This is actually something that's fairly well known. The production of synthetic fertilizers and pesticides is a really energy intensive process and so where it has been looked at, when people compare organic agriculture that avoids using those chemicals with conventional agriculture, organic agriculture [00:16:00] usually stacks up much better as far as greenhouse gas emissions, and this is true even though often organic growers have to perhaps use more fuel to do more cultivation practices on their lands, but it balances out because they're not using these energy intensively produced chemicals. Speaker 8: Biofuels were thought to be a sustainable source of energy and an enormous boost for agriculture as well. What are your thoughts on biofuels? Speaker 7: I've been looking [00:16:30] at the environmental and social effects of biofuels in the u s and Brazil for a few years now. Some years ago, biofuels were seen as a very promising technology that could help reduce greenhouse gas emissions, but in 2008 and a scientists called Tim searching gear sparked off a long debate about whether biofuels actually reduce greenhouse gas emissions and the overall picture. Some biofuels can actually lead to increased emissions because their production involves a direct or indirect cutting down forests to clear land for agriculture, which results in carbon [00:17:00] dioxide release. The upshot is that governments and NGOs now see biofuels much more skeptically. I think this is a positive development rather than uncritically embracing biofuels as a new development pathway. At the same time, the debate has now swung so much that people often don't distinguish between different types of biofuels. Biofuels are actually very diverse in their feedstock and production methods. Speaker 7: Most of the bad press is around corn ethanol in the u s and I think it's justified because as Michael Pollan, [00:17:30] for example, has written about the corn industry has created countless environmental problems, but there are what we call cellulosic feedstocks, grasses, agricultural crop, leftovers and trees and principle. We can have diversified farming systems that include these sorts of cellulosic crops as part of a fully integrated and diversified rather than having a few larger farmers and agrifood businesses dominate corn ethanol and thereby the biofuels industry. We could alternatively have many smaller farmers produce [00:18:00] grasses. For example. This is something that the new institute may look at. The challenge however is that cellulosic ethanol could easily succumb to the same industrialized monoculture model models we see for corn. So policy will have a very important role in the next decade and helping decide whether this will happen or not. Speaker 6: [inaudible] spectrum is a public affairs show. Hey Alex Berkley, our guests are clear come in and Allister isles, [00:18:30] they're starting the Berkeley food institute this fall and the next thing they talk about the scalability of sustainable farming and its impact on rural communities. Speaker 7: From your experience, what is the scale range of farms doing sustainable agriculture? Speaker 1: Even large scale farms are starting to incorporate sustainability practices into their businesses, which is really exciting, but it's a question whether they're truly sustainable. [00:19:00] As an ecologist, I don't believe that the practice of monoculture is compatible with sustainability. To have sustainability. We need more diverse farming systems when we have these diverse farming systems that can reduce the need for off farm inputs and also generate fewer ways. A good example of this is going back to pesticides and monoculture. When a grower grows a monoculture, they're pretty much forced to use pesticides. When you think about it, they're planting [00:19:30] a huge expanse of the same thing and it's kind of like laying out a feast for a pest species that can just go and rampage through that. And at the same time they've also eradicated the habitat that would have promoted the natural enemies that could've kept that past in check. Speaker 1: So then they really have no other recourse. They have to use pesticides and as I already noted, these take a great deal of energy to produce the results in greenhouse gas emissions. They pollute the surrounding environment. They can lead to unintended loss of biodiversity, of [00:20:00] non target insects. Also both subtle and not so subtle impacts on human health. When we do that, we can't really have a sustainable system, but on the other hand, we shouldn't conflate the practice of monoculture with scale because smaller farms can also practice monoculture and do sometimes practice monoculture and at the same time, perhaps larger farms can practice really diversified agriculture. It's not what I would think of as typical, but that doesn't mean it's impossible and I think it's important that we not limit [00:20:30] our imagination. We'd be able to imagine that a really large farm could be diverse, could be sustainable. Why not? Speaker 7: Does sustainability in any way limit the scale that can be achieved? Speaker 1: Well, I think it's an excellent question and we don't really have the answer to it. If we just look at what's out there, it seems like if you're at a larger scale, maybe that's going to be less sustainable in some ways, but it might be more sustainable in some other ways. There's certainly a relationship between scale ins and sustainability. If [00:21:00] we just look out at what's happening now, there can be unexpected twists. For example, very large companies may be able to develop sustainable practices of certain types such as efficiencies in distribution that small companies can't. On the other hand, smaller farms or companies might be better able to create the ecological complexity that we think is required to engender sustainable processes on farms. Also, when we think about it, some of these limits if do exist to creating sustainable systems [00:21:30] might relate not to biophysical limits, but to institutional arrangements or governance structures, business plans, et cetera. And again, they might be failures of our imagination to conceive of a better way of doing things. So I think it's really an excellent research topic. We need to study the successful models that exist out there at various scales and try to learn from them. Speaker 7: Are there studies that show the impact of sustainable agriculture on rural societies and economies and Willy Institute [00:22:00] undertake work in this area? Frankly, we don't really know what the answers may be. This is because there've been very few systemic studies done of the ways in which sustainable agriculture might benefit rural areas. And the 1940s a UC researcher called Walter Goldschmidt did a very important study and compared to rural towns in California that deferred in the degree of diversified farming and the degree to which they relied on industrialized farming methods. The town that you used more diversified from methods [00:22:30] showed significant gains of social and economic outcomes such as employment and community cohesiveness compared to the more industrialized town. Unfortunately, this sorta study hasn't been done. Again, as far as we are aware, thus the priority of the new institute will be to help sponsor a collaborative research project that updates this research and uses the tools and data that we now have to appraise whether and how diversified farming can provide greater benefits compared to the existing system. Speaker 7: What do you feel [00:23:00] are the best ways to encourage and enable young people to pursue farming? One of the most challenging obstacles we face in the food system today is that there is a rapidly aging farmer workforce. The average age of farmers in the U S is about 57 years, which is something you see in other industrial countries as well. There are widespread perceptions of farming as an acronystic and tedious. Many commentators think that many young people are unenthusiastic [00:23:30] about taking up farming for this reason. Farming is in the past. Therefore, one argument goes, we should invest more and more in labor saving technology to help offset the fact that fewer young people are entering farming in Australia. Where I come from, I heard about a farmer recently who just installed a $400,000 robotic system to milk cows. I don't agree with this sort of argument. To the contrary. Speaker 7: We are seeing a good number of young people take up farming in [00:24:00] both rural and especially urban areas. Farming seems to be a way to reconnect these people with a more sensory and experience rich life. There are tens of farmers schools that are developed across the countries such as the Alba Center near Salinas, where immigrant workers learn to be farmers and are given some support for entering the sector. This is one very powerful way to help new farmers provide training programs to help equip them for actual production, but they then face enormous problems and even getting a [00:24:30] toehold on the farming landscape because land can be very costly and very scarce. So they need financial help like loans and grants to sustain their first few years. At least. There's a new farmer network that has been pushing for bill and Congress to create this new institutional base, but unfortunately, so far it's not been very successful. Speaker 6: A big thanks to Claire Kremen at Alster Isles [00:25:00] for coming on to spectrum. I'll pass. Spectrum shows are archived on iTunes. You we've created a simple link for you. The link is tiny url.com/ [inaudible] spectrum. Now a few of the signs of technology events happening locally over the next few weeks. We kind of ski and I present the calendar. Speaker 3: On September 8th the UC Berkeley Botanical Garden will be hosting a workshop led by author [00:25:30] Amy Stewart, who wrote the drunken botanist, the plants that create the world's greatest strengths, a book that details the leaves, bark seeds, roots, flowers and fruit around the world that humans have contrived to turn into alcohol. Stuart will lead a walk through the garden to look at some of the typical plants that have been used throughout the ages. The workshop will be held in the garden from three to 6:00 PM on September 8th the first installment of the six part public lecture series, not on the test. The pleasures and uses [00:26:00] of mathematics will be held this September 11th past spectrum guests, Tony de Rose, a senior scientist and leader of the research group at Pixar animation studios presented a lecture on the use of mathematics in the making of Pixars animated films. Pixar animation is done entirely by computer and Dr. Rose will demonstrate how math and science helped create these stunning visuals in each Pixar film and explain the underlying computer technology, physics, geometry, and applied mathematics that made these pictures possible. [00:26:30] The lecture will be held on September 11th at 7:00 PM in the Berkeley City College Auditorium located at 2050 Center street in Berkeley. The rent is free and open to the public Speaker 7: this month. Science neat is on Tuesday the 17th the topic is fun guy here talks about mushrooms and bring your own mushrooms to have my colleges. Chris Green help you identify them. Science need is a monthly science happy hour for those 21 and over at El Rio bar [00:27:00] three one five eight mission street in San Francisco. Admission is $4 Speaker 3: here at spectrum. We'd like to share our favorite science stories with you. Rick Kaneski joins me for presenting the news. Speaker 7: Nature news reports that several journals have been caught in a scheme to artificially inflate their impact factors by strongly encouraging citations to other journals that were in on the scheme. The impact factor of journals is a measure of the average number of citations to recent articles [00:27:30] and is often used to compare the relative importance of a journal to the field. That is general is with higher impact factors are generally thought of more favorably than lower impact journals. The factors are calculated by Thomson Reuters, the company responsible for both end note citation software and the web of science literature database. Well, self citations have been caught in the past weeding out this collaborative gaming of the system is difficult and it can be costly for those journals [00:28:00] caught Thomson Reuters has suspended the impact factors of 0.6% of the more than 10,000 journals. They index a record percentage. In some cases, editors have been fired in others. Articles published in the suspended journals will not contribute to the rankings of universities responsible for them. Speaker 3: According to a UC Berkeley study published in the Journal proceedings of the National Academy of Sciences, blocking a certain enzyme can dramatically slow the ability of tumor cells [00:28:30] to multiply and spread to other tissues. Scientists have long observed that cancer cells metabolize lipids in particular ester lipids at higher rates than normal cells. The UC Berkeley team in activated a certain enzyme known as LPL glycerol phosphate synthase, or a gps that is critical to lipid formation and human breasts and skin cancer cells knocking out the enzymes, significantly reduced tumor growth and movement. The inhibitor has also been [00:29:00] tested in live mice, injected with Kansas owls too, promising results. While other studies have examined specific lipids, a gps appears to regulate a much broader portion of tumor growth and malignancy. Next steps will include developing a cancer therapy based on the age gps inhibitors. Speaker 5: Mm. The music heard during the show was written and produced by Alex Simon. We'd also like to thank Patrick Bower [00:29:30] first assistance during the interview. Thank you for listening to spectrum. Join us in two weeks at the same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Zoologist Toni Bodi is currently developing a genomic diagnostic screen for Alzheimer’s disease and is a founding member of the Berkeley Bio Labs new bio hacker space. Nature magazine.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Aw. [inaudible] [inaudible] [inaudible] [inaudible] [inaudible]. Speaker 1: Welcome to spectrum the science [00:00:30] and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi and good afternoon. My name is Brad Swift. I'm the host of today's show. Our guest is Tony Bodhi Hickerson, a zoologist who was part of a cognitive study of howler monkeys in Mexico. Tony is trying to organize a noninvasive [00:01:00] dolphin study in the wild using wireless network technology. She is currently developing a genomic diagnostic screen for Alzheimer's disease and is a founding member of the Berkeley bio labs, a new bio hackerspace. Tony talks about cognition, Alzheimer's disease, and creating a scientific community resource in the bay area. Rick Karnofsky and Renee Rau interview Tony on this edition of spectrum. Speaker 4: So welcome to spectrum. [00:01:30] I'm Rick Karnofsky here with Brad swift and Renee Rao. Our guest today on spectrum is Tony Bodhi, Hickerson and zoologist. Welcome to spectrum. Thank you for having me. Can you give us a little bit of a description of what you work on? Kind of a brief overview for the audience. That cognition is essentially the ability to receive and process information and the most abstract form. And we kind of think of it as mental processes, which can be both conscious and subconscious. [00:02:00] And so I do research on cognitive abilities of wildlife and at the moment I'm also working on an application in humans. What wildlife do you look at? Um, well I have looked at primates and I've been also involved in a dolphin project. So high functioning mammals. And how do you assess their cognitive abilities? Well, you can do behavioral studies, which is what I primarily do. Speaker 4: And of course just looking at the anatomy as well. So [00:02:30] I try to be as noninvasive as possible. I don't work in a lab with monkeys in a cage. I actually work in the wilderness and follow monkeys around all day. So where do you do that? I was doing that in Mexico for my last study with seven months and from Sunup I watched the sun come up and uh, the howler monkeys, which is a species that I was working on would call in the morning. That's how we'd find them. So we trek through the jungle and find them and then start our study. And it would usually last, well it would last until sundown. So depending on how many hours a like we had [00:03:00] [inaudible] Speaker 5: can you just walk us through what the study was and what you looked at in the howler monkeys and how you interpreted it? Speaker 4: Well, this study, I was a, the head field managers, so it wasn't my particular study, but I was managing all the data collection and uh, we were looking at two different species of Holler monkey. And they're hybrids. So there's hybrid zone in Mexico where both of these species, which we believe based on genetic evidence have been separated for about 3 million [00:03:30] years. They have different number of sex chromosomes. They're very morphologically different, are coming together and meeting successfully. They also have very different social structures and one group tends to be far more aggressive than the other one is much more communal. It has large groups up to 25 30 and the other one usually has three to five. So to see how behaviorly they come together and genetically they come together because in one cross if you have a female of a and a male of B, they can [00:04:00] have an offspring. But if you inverse it they cannot. So it's really interesting also genetically to see how things recombine. What kinds of data did you take? Oh, we took auditory, so we, they're hollow monkeys. So we had all their calls, which it changes from group to group and obviously from species to species. We also took a lot of behavioral information, affiliative, so like affection and aggressive behavior, like attacks and genetic [00:04:30] information through and study captures as well as fecal samples. Speaker 5: I'm just super curious about what it was like following the Heller monkeys and spending literally all day with them. You, Speaker 4: I started to go insane. You actually do. Um, no, it was a really profound life experience for sure. And I couldn't have designed a better project to be part of. Like if I had designed my dream project, it would have been this project. When I started this project, I didn't speak Spanish and [00:05:00] every single person in my team only spoke Spanish, so I learned Spanish very fast. But during the process of learning a second language, you have this inability to completely express yourself and it kind of makes you go insane. And then when you couple that with standing in the middle of like a really humid forest, you know, surrounded by mosquitoes and following monkeys running through the canopy. I got you about month five I think, and I realized that I started to go insane. [00:05:30] When I yelled at an ant out loud, I paused and just laughed hysterically to myself and realize that like this is the point where like I've reached my mental break. Then I'm yelling at ants and I need to get to a city as soon as possible. Speaker 2: Okay. Our guest today on spectrum is Tony Bodhi Hickerson, but she answers to Tony Bodhi in the next, she talks about her idea for a dolphin stone. [00:06:00] This is k a l x Berkeley. Speaker 4: And what do you do with the dolphins? Uh, the Dolphin project, uh, is not a field project, unfortunately at the moment. It's an education campaign for the international mantle project, which is responsible for all dolphin safe tuna that you've ever seen as well as the documentary, the cove. So they're very avid group on [inaudible]. [00:06:30] And so I was putting together a campaign to try and inspire people that they're really intense creatures and why maybe we should respect them. Speaker 5: You tell us a little bit about those abilities and why they're so intense. Speaker 4: There are three groups of mammals that have large brains that's great. Apes, elephants and marine mammals. And the dolphins came from a very different evolutionary path. So they have different [00:07:00] structures, which is also really interesting. They don't have the prefrontal Cortex, which is what we tend to associate with being human, the sort of emotional side of being human. But they have a very intense limbic system, which is also associated with emotions and bonding behavior and sexual behavior. Dolphins have sort of this mixed reputation of being very kind of aggressive and also being really altruistic almost in their actions. [00:07:30] So looking at not only the hard facts of the biological side of things of like what structures they have and what those abilities are, but also case studies of look at these sort of altruistic behaviors. So their ability to perceive the world around them and to react in an emotional state is potentially really profound. Speaker 5: And um, in your study to sort of understand all the ways that the Dolphin perceives the world and the way that it often feels these things, are you looking at the structures in their brains and seeing [00:08:00] the corresponding place where these thought processes and these perceptions happen? Or are you just observing behavior or are you doing both? Speaker 4: Well, hopefully both. So I'm currently designing a project, which is hopefully gonna do exactly what you just said. Our tools at the moment are very limited, especially because we want to be as noninvasive as possible. Animals don't react in captivity the way that they react in the wild. And obviously they don't have the same space or social structure to be able to do the same sorts of things. [00:08:30] There is an up and coming technology that I hope to apply to this sort of research which would allow biological data to be recorded in real time and it would be completely noninvasive. It would be almost like a sticker, so there'd be no puncturing. There would be no need for captivity. Hopefully we could even apply it with minimal stress to the animal and with that we could have gps data body, we could potentially record the vibrations from their echolocation [00:09:00] and also neurological data and this would be the first information of its kind to be able to correlate if there's an approach or an affiliative behavior between two individuals, what areas of their brain are actually being, you know, lit up and that could really profoundly affect what we know about their structure. Speaker 4: Yeah, that that is sounds really exciting. So it would be noninvasive. Do you know how that works? That must be really amazing. The technology that I'm, I'm hoping to work with [00:09:30] is a flexible microchip and I'm hoping to be working with some of the innovators to make it appliable to dolphins and something that would stick for up to a month. They should scan very quickly, so that is a restraint. I don't know as much of the engineering side of it because I'm not as much tech, but from my conversations with the people developing it, it seems like it might not be up to use for a year or two, but hopefully eventually we'll get [00:10:00] there and we'll have a better understanding of how one of the smartest animals on the planet. Thanks. Are other people currently doing anything more invasive? Captivity can be a very invasive process. How animals and captivity get in captivity are often from Dolphin Slaughters, which kill hundreds of their fellow pod mates to get a handful of dolphins because a live dolphin that is pristine, [00:10:30] you know mark free that goes into entertainment or goes into a laboratory studies. They get taken out and they get sold for hundreds of thousands of dollars and the rest of them get slaughtered and sold into the meat markets. Speaker 6: Mm MM. Speaker 3: You are listening to spectrum on k a l x Berkeley. Our guest today is Tony Bow-tie Hickerson. Tony is a zoologist. In the next segment she talks about diagnosing Alzheimer's disease. Speaker 4: [00:11:00] I actually wanted to ask you a little bit about the work you're doing with Alzheimer's and dice diagnostic work. Could you maybe tell us a little bit about how the process of diagnosing Alzheimer's works currently and what you're hoping to change about that? Well, there really isn't much in terms of diagnosis that's out for the general public. What I'm actually attempting to do, and initially it was for my own curiosity and you know obviously see the potential for other people to use it as [00:11:30] well. I wanted to test myself on this gene. So there is a gene called apoe e and there are three expressions of it and they account for about 95% of all Hymers, one of these types of accounts for 50% of all hammers. I can essentially locate this gene snippet out of the enormous strand of DNA and then look at their two spots where [00:12:00] the nucleotide is a certain sequence that I can tell you. Speaker 4: If that is type one, two or three of that apathy and off of that, they're very strong statistics that will tell you that you have a very high likelihood or very low likelihood of getting Alzheimer's by a certain age. And it's sort of a spectrum due to the fact that we're deployed. So we have two copies of this gene. So if you have this like really strong negative version and one positive version, you will [00:12:30] have later onset Ohio Hymers. Then if you have two really negative versions, but there are really strong numbers that tell us what your likelihood is. But what I would like to do is to make it something that's very accessible for everyone. I don't want to produce this and market it as some expensive tests that's going to just perpetuate this whole medical debt system. I want this to be something that people can access and know for themselves to be able to plan [00:13:00] for their own future and to be able to take care of themselves and their family members more effectively and responsibly. Speaker 4: So it's pretty similar to the aggressive cancer testing would you say? Or? Um, yeah, it's fairly similar. I haven't looked exactly at that one to see. I believe it is also a snip, which is like this single nucleotide change. So it should be very similar. Do you want to tell us a little bit about the process of you sort of isolating this gene? Did you go through and read the papers [00:13:30] and see that this gene was associated with it and develop the processes snippet on your own or I'm in the process of developing the process to snippet. So right now I'm troubleshooting the primer. So the, the molecule that you use to actually cut the DNA, what I have is currently binding to itself. So it is also binding to the site that I want it to, but it's also binding to itself. So I'm trying to sort that issue out. Speaker 4: It's a process that needs to be critiqued a bit before. I'm willing to, you know, expose more [00:14:00] people to the answers cause I want to make sure that it is very accurate before I would to give someone those sorts of answers. You're currently doing some form of genetic screening and you previously did all of these behavioral studies. It's quite a transition. So how, how did you make that transition? Well they're both in principle based on cognition, mental abilities and so all Hymers is the degradation of cognitive abilities, the degradation of being able to recall information as well as [00:14:30] the breakdown of even motor skills and language skills and so that is profoundly interesting to me to to understand where and how cognitive abilities act and then to understand how they're dismantled is the cycle of, of the process of understanding exactly how things work. A lot of times we figure out what parts of the brain do what based on lesion studies, which is causing and disruption. Speaker 4: The initial draw [00:15:00] to this was for my own curiosity. And that was sparked because my father has severe dementia. So I wanted to know for him, is this all Hymers or is it something environmental? And so I want to develop a test for him, for myself and for the public to know what's their likelihood so that they can plan for the future. Are there other differentiating factors you could look at as well besides this, besides this gene? So the gene is pretty profound and [00:15:30] it's significance in whether or not people get all hammers. But there's, there's also, you know, of course a lot of different factors and I should mention that like echoey is a specific kind of all hammers. It's not early onset and not all dementia is Alzheimer's. There's lots of ways to get dementia in old age. So this isn't like a yes, no test. Speaker 4: If you have a really great diagnostic and it looks like you're clear for this, it doesn't mean that when you hit 80 that you're not gonna have problems [00:16:00] still. You still have to take care of yourself. And a lot of studies have shown that simple things and everyone says this, but simple things like diet and exercise. If you exercise on a regular basis, you can break down a lot of these corrosive molecules that cause a lot of mental problems, cause a lot of cardiovascular problems and you have to keep your metabolism up to deal with this and your body will also, you know, work to heal itself. It's just really profound what control you have over your future. [00:16:30] Like I don't want to give people this test and say you're doing, I feel that you two have a lot more control than a lot of people want to admit over the future. And so take responsibility for yourself and take care of your body. Go exercise and eat well and have lots of friends and learn new languages and go travel. See the world Speaker 2: spectrum is a science and technology show on KALX Berkeley. Our guest [00:17:00] today is Tony Bodhi Hickerson in the next segment that Tony talks about, the new Berkeley Bio lab. Speaker 4: So you're involved in a biohacker space. Uh, yes. So actually as of last weekend we moved into a space in Valeho which is my n when the other core members lab on the, hopefully we will be also opening a space [00:17:30] in Berkeley eventually, but for now we're in relay hope and it's essentially like a hacker space, but it's in biotech in general and you pay a membership and you have access to the lab and the materials to do your own research, detached from corporate biases and the strains of academia. So we provide a space in the community to kind of teach each other and [00:18:00] to work in and we allow real hard science to take place and sort of a pioneer setting. What's the name of it and how does it compare it to bio curious and some of the other spaces in the bay area? Speaker 4: Sure. The name of the lab is going to be Berkeley bio labs. Some of the other entities that will be occurring within this lab is a June cell technologies. We're trying to be much more accessible in that our membership [00:18:30] is only going to be $100 a month, whereas a lot of other bio spaces are $2,000 and up a month. I think that having more spaces isn't necessarily a bad thing. We tend to be a little bit more focused on regenerative medicine and stem cell research, so people who are more focused along that lines might be more attracted to work with us, but certainly weren't. We're not discriminating against people who aren't in stem cell research or regenerative medicine. That's just what we tend to do. I shouldn't ask you if you could [00:19:00] tell us a little bit more about the projects that are happening in the space now. Speaker 4: At the moment, we haven't even opened up yet. We were literally still moving all of the giant centrifuges and automated robots. And so right now I'm is my project as well as John's London, which is one of the founding members of the biohacker lab and he works in regenerative medicine and stem cells. [00:19:30] And once we kind of get settled and open our doors, we'll hopefully be screening lots of potential innovators to come and join our project and not necessarily his project but you know, whatever inspires them to try and you know, make a difference. And what will that screening process look like? It'll honestly be very personal. We're going to just meet with people one on one and see what they're interested in doing, what they have done and what they want to see in the future. It's much more about the people and [00:20:00] their drive to do something than the letters after their name. Speaker 4: We all feel that someone who's really driven to take the four or five years after a bachelor's and do their own research potentially has a lot more to offer than someone who might not know what they want to do in his just signing up for pastry. Cause they feel like it's the next step. So we're definitely open to pioneers, innovators and people who are willing to scrap to make a change. How are you getting the word out about the a space? [00:20:30] Well, actually the, the first thing that has happened so far on the 24th I believe it was, we had a paper written about us in nature. And so that was the first real publicity, and this is the second. So the article was called biotechnology independent streak. If anyone cares to look it up in the July 24th issue, it's gotta be super expensive to have all of the high mated robots and the giant centrifuge. Speaker 4: How are you financing [00:21:00] the space? All of the equipment is already owned by John. He's been working in biotech for quite some time and it has accumulated a very impressive stock of machinery and equipment and he's more than happy to share, to enable other people. He's been really phenomenal and assisting me and getting into a lab space, she's really enabled me to be able to do research that I would never be able to do on my own. And he's doing that for hopefully a lot of other people and so [00:21:30] I would hope to perpetuate that and help people get into it and start making a difference. What do you anticipate the future of the hackerspace pain? Well, we hope that we find lots of driven people who want to come and we are overflowing with scientists until we need to open up another space. I would love to see this be a scientific movement. Speaker 4: Science is all about curiosity. It's about having a question and figuring out how to find the answer and I think that that's [00:22:00] something in our education system that a lot of times is not really taught. People are taught facts, they're not taught. How do you figure facts out? You know? It's not about memorization. It's about teaching yourself how to think. How did you get into science? I have always been profoundly curious, but actually I started out as an art major and about two and a half years in I got called into my advisor's [00:22:30] office and I said, you can't take any more science classes. Told me you filled up all your electives and another semester. And if you take another science class, then we're going to kick you out of the fine arts school. So I said, okay. And I put in an application at another university and switched into science because I thought it was completely absurd that they would hinder me from taking science classes, but it was just a curiosity to understand how [00:23:00] the molecular and biological world works. Understand, you know, how life happens and how stars are born. It's something that I don't understand why every single person doesn't have this profound emotional response to understanding all Tony, thanks for joining. Yes, thank you. Speaker 2: Oh, [inaudible]. If you can not always catch spectrum broadcasts, know that shows are archived [00:23:30] on iTunes university, we have created a simple link to the archive just for you. The link is tiny url.com/calyx spectrum. No, a few of the science and technology events happening locally over the next two weeks. Rick Karnofsky and I present the calendar. Speaker 3: Tuesday. August 27th the UC Berkeley Botanical Gardens [00:24:00] will host a guided butterfly walk. Join Sally Levinson, the gardens resident caterpillar lady on a walk through the amazing collections of the botanical garden in search of butterflies to register for a butterfly walk, which is free with admission email garden@berkeley.edu the butterfly walk will be held from three to 4:00 PM on Tuesday, August 27th at the UC Berkeley Botanical Gardens. At this month, [00:24:30] actual science, you can learn how the properties of diamonds are uniquely suited for scientific research. Christine beavers is a research scientist based at the advanced light source at Lawrence Berkeley National Lab. Her specialty is crystallography, which is the determination of 3d structures of molecules from crystals using x-rays. Actual science will be on Thursday, August 29th at 6:00 PM [00:25:00] at actual cafe six three three four San Pablo Avenue in Oakland and mission is free. UC Berkeley is holding its first monthly blood drive of the school year on August 29th you can make an appointment online, but walk-ins are also welcome. Speaker 3: You are eligible to donate if you are in good health way, at least 110 pounds and are 17 years or older. The blood drive will be on Thursday, August 29th in the Anna had [00:25:30] alumni house on the UC Berkeley campus. It will last from 9:00 AM to 3:00 PM you can make an appointment or find more information at the website. Red cross.org using the sponsor code you see be wonder fest and ask a scientist present the neuroscience of magic on Wednesday, September 4th at the [inaudible] street food park, 48 [00:26:00] 11th street in San Francisco. You CSF professor of neuroscience, Adam Gazzaley and the comedy magician, Robert Strong. We'll lead discussions from ancient conjurers t quick handed con artists, two big ticket Las Vegas illusionists magicians. Throughout the ages, I've been expertly manipulating human at attention and perception to dazzle and delight us. [00:26:30] Of course, you know that the phenomenon of cognitive and sensory illusions are responsible for the magic, but you've got to admit it still kind of freaks you out when some guy in a top hat defies the of nature right in front of your eyes. The event is free. Now, two news stories. Speaker 3: Berkeley News Center reports a new theory by fluid dynamics experts at the University of California Berkeley shows how Zombie vorticies [00:27:00] help lead to the birth of a new star reporting in the journal Physical Review Letters, a team led by computational physicist Philip Marcus shows how variations in gas density led to instability, which generates the whirlpool like vorticies needed for stars to form. The Zombie reference is an astronomical nod to pop culture and because of the so called dead zones in which these vorticies exist, this new model has caught the [00:27:30] attention of Marcus's colleagues at UC Berkeley, including Richard Klein, adjunct professor of astronomy and fellow star formation expert, Christopher McKee, UC Berkeley professor of physics and astronomy. They were not part of the work described in physical review letters but are collaborating with Marcus to put the Zombie vorticies through more tests. Science daily reports the identification of what may be the earliest known [00:28:00] biomarker associated with the risk of developing Alzheimer's disease. Speaker 3: The results suggest that this novel potential biomarker is present in cerebral spinal fluid at least a decade before signs of dementia manifest. If our initial findings can be replicated by other laboratories, the results will change the way we currently think about the causes of Alzheimer's Disease said Dr Ramon true? Yes. Research professor [00:28:30] at the CSIC Institute of Biomedical Research of Barcelona and lead author of the study that was published in annals of neurology. This discovery may enable us to search for more effective treatments that can be administered during the preclinical stage. These C S I c researchers demonstrated that a decrease in the content of micro chondrial DNA in cerebral spinal fluid may be a preclinical indicator [00:29:00] for Alzheimer's disease. Furthermore, there may be a direct causal relationship Speaker 6: [inaudible].Speaker 1: The music hub during this show was written and produced by Alex Simon. Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Address [00:29:30] is spectrum dot k. Alright. yahoo.com join us in two weeks at this same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Joan Ball is a UC Berkeley Grad student in the College of Natural Resouces. Peter Oboyski is Collections Manager & Sr. Museum Scientist at the UC Berkeley Essig Museum of Entomology. www.notesfromnature.orgTranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible] [inaudible] [inaudible] [inaudible] [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hey there and good afternoon. My name is Renee Rao and I'll be hosting today's show. Today we get to hear about an exciting citizen science project from Joanie Ball and Peter Oh Boyski. [00:01:00] Joni is a UC Berkeley graduate student in the College of natural resources where she focuses her research on dragonflies. Peter is a collections manager and senior museum scientist at the UC Berkeley Asig Museum of entomology. They spoke to Brad Swift about the new cal project. The ASIG is collaborating with Zooniverse to run the cal bog website, which allows anyone with an internet connection to help digitize the vast collection of bugs specimens in nine California natural history museums [00:01:30] just over 3000 citizens, scientists have joined the project today. We'll learn more about cal vogue and bugs in general in today's interview, Speaker 4: Joanie Ball and Peter O. Boyski, welcome to spectrum. Thank you. Thank you. Let's talk about the cal bug project that you're both part of and how did that get started? What was the genesis of the project? Speaker 1: So Quebec started in 2010 as a collaboration of the major entomology collections in California. And [00:02:00] as a group, the collections were awarded an NSF grant to database their entymology collections through this program called advancing digitization of biological collections. And the goal is to digitize over 1 million specimens. The purpose is to capture the collection information from the labels, like the species name, when the specimen was collected, who collected it and when it was collected. Speaker 4: So the ECIG museum is an insect collection at UC Berkeley and our collections go back about a hundred years. [00:02:30] And these represents the research of our faculty and students over that period of time. And it's a representation of what's lived in California all this time. So each one of those specimens in the museum is a data point. It tells you what lived where at what time. And so the problem is it's all locked up in these specimens. It's on these tiny little labels sitting in a museum somewhere. And nobody has access to this information. So the point of this project is to make that data available to, to the research community, into the public cause this all [00:03:00] goes online free to everybody to look at. So that's the big point of this is to make this a hundred years of of data available to people, researchers and to do this, you know, is it's a pretty overwhelming task. Speaker 4: Now, other museums have done this before with their vertebrate collections. For instance, the Museum of vertebrate zoology here on campus, they've already database their entire collection and they're able to do wonderful things with it. They're looking at distributions of different species and what time of year they occur. But entomology museums have lagged behind just [00:03:30] because of the sheer volume of specimens that we have. We have orders of magnitude more specimens than some of these other museums and we just thought that was too big of a job and nobody wanted to tackle that job. But now with this funding from the National Science Foundation, we feel like, okay, we can take a shot at this now let's take a stab at it. How big is the collection? Well, we don't actually know, but uh, when you multiply how many specimens per drawer and all the jurors that we have that comes out somewhere around five to 6 million specimens that we have in our collection, and that's [00:04:00] just a USAC, that's just the ecig museum and then combine that with the eight other institutions that we're working with. We're talking tens of millions of specimens among all of us. So to do the 1 million is just a, you know, the tip of the iceberg, but it's a place to start. Speaker 1: In the beginning of the project, we were hiring students to enter the data manually directly from the specimens themselves, but we found that that was taking a really long time. So we started taking photographs of the specimens, which is [00:04:30] beneficial in that we then have a record of both the specimen itself and the labels so we can go back and check specimens later. People can also enter this data from the images from wherever they are online. That's how we've started this notes from nature project where we have an interactive database now for people to enter. The specimen data online. As of this morning we had to over 2,790 people entering data. We're approaching 170,000 [00:05:00] total transcription people entering data online through this project, which started just a few weeks ago. Speaker 4: Wow, that's impressive. It is. Have you tried to calculate how many people you think need to volunteer to help? So when we initially started this project, and we are even in the planning stages, we thought, well how long would it take us to actually database? Just our collection alone. You look at the amount of staff that we have in the budget that we [00:05:30] have, and we figured at least a century to do this in house. So we hired some students to help us out, take some of these images, and they started doing the database for us, but we realized, okay, that cut it down to maybe half a century. It's still, that was going to be too long. We needed more help in having these images that you can be sitting online anywhere in the world and jump online and help us transcribe these images. So that was a huge step forward. It's incredibly simple step to take, but it was a very important one. And how did that idea bubble up? Well, we heard about Speaker 1: Zooniverse, which does a citizen [00:06:00] science organization that creates these web interfaces. In particular, we saw this project called old weather. What this project did was enter weather records from ship logs from World War One. The purpose is to improve climate models for the oceans in that time period. So we knew we wanted to do something similar with with our images. I submitted an application to them. What won them over I think was the actual photos of our specimens with the [00:06:30] pen sticking through them. They're really impressed with that and that's also something that the citizen scientists really like as well. They really enjoy seeing the actual pictures of the insects. Speaker 5: [inaudible] you're listening to spectrum. I'm KLX Berkeley, I guess today are Joanie Ball and Peter Boise from the Calvin project. In the next segment they discuss how they choose which specimens to begin at. Speaker 6: [00:07:00] Talk a little bit about the people at the ECIG that keep it all going. Speaker 4: Yeah, we do have a pretty limited staff in the museum, but I have to say the real work gets done by the undergraduates. These are either volunteers or work study students and they put in endless hours and they're the ones who are taking these images that were putting up online without them work just doesn't get done on campus. They really are the, the workforce of this campus. Speaker 6: Going back to the involvement of the citizen scientists, the transcription [00:07:30] work that they do, how would you characterize who's good at it? What sort of person would enjoy this? Do you have a sense of who that is or do you think people should just try it and see? Speaker 1: Does anyone who's curious and has little time to help out? But it tends to be people who are really enjoy contributing to something. Speaker 4: Yeah, it is an opportunity to be part of a larger community. People enjoy that and I think some people are surprised when they, they like it. So some people just log on, Eh, it's okay. [00:08:00] And some people, it just doesn't do it for them. But they took a look and now they know. But other people, they kind of surprise themselves like, oh, this is actually kind of fun. And in a way you're following an expedition. You can see where these things are coming from, what year they were collected. We had some really funny comments about one of our professors who is still actively collecting. Somebody suggested perhaps he's a vampire because he's been collecting for 50 years and the specimens are still coming in. So a little observations like that and people just, they become part of our community without even knowing it. Speaker 1: Yeah, and some people [00:08:30] who never really had an interest in insects before find themselves now more interested in what's around them. One woman mentioned that as she was driving and insect splattered on her car and she was trying to identify it or you know, suddenly she had this new appreciation for insects, which was pretty neat. Speaker 6: How are you choosing the million specimens start? Speaker 1: Uh, well actually one of the groups that we've decided to focus on [00:09:00] start with are the dragon flies. The reason for that is that we have good collections for them over the hundred years where we have our collections. They've been well collected over time. They're pretty charismatic group. They're also used as biological indicators for stream ecosystem health. So that's one of the groups that we're focusing on. We're also focusing on certain insects that are used in applied research like pollinators or biological control agents. What are the, some of the other groups, Speaker 4: the approach we use to slicking [00:09:30] the groups where groups that we have well-represented in the museum, groups that have some significance regarding global change, whether it be land use change that be climate change, changing the way water is distributed. So which groups are more sensitive to that. That might give us some indication of of what's happened in the past. The other criteria and we use was places where we have longterm collections because museums have some biases in them and we have [00:10:00] to recognize that when we do this kind of research people when to a particular place at a particular time because there's something interesting there for them. So some places we have fewer collections over the years, other places we have nice longterm data sets. So we also focused on locations where we knew we had nice longterm data. That makes sense. Yeah, so collecting is ongoing. Speaker 4: It is consumer. We continually collect the museum specimens. The insect collection comes from a number of sources. The most common [00:10:30] is research that's done right here on campus. Professors, students who are doing research projects, they deposit what we refer to as voucher specimens in the museum. So you write a publication that says you found this species at this place. Somebody else reads it and says, well that sounds odd. I don't think that thing occurs there. Well, you have to be able to go back to that specimen and look at it. Oh yeah, sure enough, there it is. I wouldn't believe that. So we have to voucher these specimens in a museum. So that's a large part of where our collection comes from. In 1939 professor ESIG, [00:11:00] the namesake of our museum, had this idea to start the California insect survey. UC Berkeley is a land grant school, which means we owe a certain responsibility back to the community, to agriculture, to forestry, to the urban ecosystem. Speaker 4: And we need to be able to answer questions. But if we don't have representatives of the insects that are out there, then it's much harder to answer the sort of questions. So that was his logic in launching the California Insec survey, sending professors and students all over the state. And that was in 1939 [00:11:30] so our collections go back earlier than that, but that's where the real boost began in our collections. So from that point on, we've had regular collecting trips. People in the museum, professors, other folks will go out and collect all over the state and then deposit their material. Another source of our specimens, our donations, there's a lot of hobbyists, enthusiasts that aren't necessarily professional entomologists, but they enjoy butterflies or beetles or whatever group. At some point when have their family and their kids and they've got these big boxes taken [00:12:00] up a lot of space in their house. They said, well, Geez, you know, I really like having these here, but yeah, maybe I should give them to a museum somewhere. So I get a lot of that kind of stuff as well. Just in the past couple of years we've had, I don't know about 10,000 donated specimens, which has been really nice. We don't do much in the way of trading there. There are museums out there that'll buy and sell specimens, but because the main interest of our museum is answering questions about California, we can go out and get most of that stuff ourselves. Speaker 5: [00:12:30] Our guest today on spectrum are Joanie, Baal [inaudible]. In the next segment they talk about how cal bug is already affecting research. This is k LX Berkeley. Speaker 4: So how is the end product affecting research do you think from pre digitization and now post digitization? [00:13:00] How are people able to leverage what they have in a database now that they couldn't do previously? Speaker 1: I am doing research using the Jag and fly collections from a few different angles. One of my projects is to resurvey sites that were originally sampled in 1914 for Jag and flies. So this collector clearance, Hamilton Kennedy went around California and Nevada collecting dragonflies that in 1914 and create a list of species [00:13:30] for all of the sites that he visited, which turns out to be around 40 sites throughout the region. The problem was he didn't include the dates that he visited these sites. That information is on his specimen. So I use the collection to reconstruct the dates that he went to these specific sites. And then I revisited those sites on the same day. And now what I'm doing is I'm comparing my surveys to the original surveys that were done in 1914 to see how things like species richness and that proportion of habitat [00:14:00] generalist versus specialist and some other community metrics have changed over that time period. Speaker 1: Another project that I'm working on will be using all of the museums specimens for dragon flies and I'll be comparing communities for different counties for the different time periods throughout that hundred years that we have collections. So I'm looking to see which time periods have enough specimens for a comparison. For example, there was a lot of collecting activity in the 70s there's a lot of current [00:14:30] collecting activity through another group, actually dragon fly enthusiast group who report their sightings, so I'm using their sightings for current species distribution throughout California. One of the last projects that I'm working on is creating species distribution models, which is something that a lot of ecologists are doing right now with historical data. The museum collections are points for that. You can create a latitude and longitude for where you find individual specimens throughout time. I'm using these to [00:15:00] look at changes in species distribution over recent decades in relation to factors like climate and land use. So I started analyzing some of the changes in the dragon fly communities based on the resurvey and some of the things that I'm finding so far is are that communities are becoming more similar throughout this survey. Previously you might find much more different species of at different sites, whereas now you're finding a lot of the same things over and over again. So we're seeing kind of a homogenization [00:15:30] of Jag and fly communities. Speaker 4: A lot of researchers have come to the museum to do similar sorts of studies to Joanie's where they're looking at one species. It's distribution over time. And that meant coming into our museum, looking at our specimens, typing that up, they would bring that home and put that into their database, write up a report on that. But that didn't always end up back in our database. And there's only one species at a time. So the advantage to what we're doing now is we can look at whole communities at a time Joanie's case, the whole dragon [00:16:00] fly dams will fly community rather than looking at one species at a time. So you couldn't do that before without one of these larger databases. We keep thinking in terms of the research, which is one of the main reasons why we're doing this, but there's a lot of practical outcomes for the general public as well. Speaker 4: For instance, maybe you're a fly fisherman and you're going up to this particular drainage basin or this river and you want to know what, what's flying up there? I want to know what kind of flies I should be tying. So at some point in the future you'll be able to pull up in our database and see, well what's flying at that time of year in that area? Or you find a spider in your [00:16:30] house and you want to know what kinds of spiders are found in my area, you should be able to go to our database and find that. Or yeah, you're a farmer and you're thinking about rotating to some new crop that you haven't planted before and you want to know what kind of pests should I be worried about? What things feed on this plant in this area? So those are the kinds of questions that other folks outside of the museum community should be able to use. And like I say, this is all freely available online once it's all been database. So this is, you know, it's not just for us, it's for everybody. Speaker 4: What ends up [00:17:00] being the most diverse species of insects. If you were mentioning dragonflies aren't really all that diverse. Beatles. There's a famous geneticists Haldane. When asked, what has he learned in his studies about the creator? Said the creator had an inordinate fondness for beetles. Certainly beetles are the most species rich out there, and within the Beatles, the weevils, a lot of these are very hosts specialized, and so for every species of plant out there, you may have several species of weevil that specialize on them. So [00:17:30] it said that if you were to take one of every species, take a black tail deer, a blue whale, a sequoia tree, every species of insects out there and lined them all up, four out of 10 would be a beetle. So 40% of the diversity of the macro diversity. Now, when I say this to people who study bacteria and viruses, they say, ah, yeah, well, I see. Okay, you right, you're right. There are, there's a lot out there with that, but of multicellular animals and plants, the insects, certainly out number, most other things. Speaker 3: [00:18:00] I'm Renee Rao and you're listening to spectrum. Today's guest are Jody ball and Peter Boyce. In the next segment, they discuss the importance of entomology. This is Kayla Berkeley. Speaker 4: What is the most studied insect? The more charismatic things, as you might guess, get a lot more attention. Butterflies get a lot of attention there. Show either out during the day, they're conspicuous, they don't hide [00:18:30] themselves. It makes them easy to study and for hobbyists to notice them. The more obscure things, the tiny, the brown, the cryptic things that are much more diverse but are much harder to study and there's far fewer people that actually study them. It's just human nature. Yeah. We were attracted to some things that we find aesthetically pleasing and other things that we don't. It takes a special kind of person to look at them. We call them entomologists. Speaker 4: Within the current environment. Are [00:19:00] Insects ascending or is, are they struggling or is it case by case? Very much case by case and again, the more charismatic things we know a lot more about, I know of about 20 species that are listed as endangered in California. 14 of those are butterflies. Then there is a large [inaudible] three pretty charismatic beetles, lion of grasshopper, so these are all pretty conspicuous sort of things. A lot of them are endangered because of habitat loss. They specialize in a particular plant that only occurs in a particular habitat and especially meadows. [00:19:30] So many meadows had been turned into grazed plots or housing developments or golf courses. There's been all kinds of lawsuits around what to do with this meadow and that sort of thing, but there's probably a lot more out there that have become very rare that we just don't know about it because nobody has looked at them in any great depth. Speaker 4: That said, some of the things we do also promote some insects. Certainly our agriculture is this great field of food for not just us, but for insects as well, so some pest species where we consider them past, you know, they're just trying to live, they flourished. There's other things [00:20:00] prescribed burning where you open up a habitat and let the new vegetation grow back in. There are some insects that specialize on that. Unfortunately, the things that specialize in more stable habitat, say old growth forest, they're having less of a good time about it because those habitats, once you disturb them, it takes a long time for them to get back into balance. So yeah, it's a case by case basis. Somethings are doing well, others are not. Speaker 1: The other thing that we're seeing is like in many other groups, habitat generalists are really expanding because they can [00:20:30] live in a variety of different environments and they're more tolerant to changes in the habitat so they can even live in urban areas. So a lot of the habitat generalists are really expanding while the habitat specialists are more likely to be declining. Speaker 4: So I think to some extent we've talked about it, but is there anything specific about the importance of studying insects that you want to mention? Well, we like to think that humans rule the world and [00:21:00] uh, but you know, if our species was to disappear tomorrow, the world would probably go on. Okay. Maybe even better. But if insects were to disappear tomorrow, most ecosystems would collapse pretty quickly. And so I think that's a pretty compelling reason right there to look at them. The act as pollinators, they're recycling nutrients, they're keeping plants and checks are the plants don't over run the world. They're keeping other insects and checks so they don't overrun the world. It kind of keeps things in balance. The act as food for a lot of other organisms. So they're, they're, uh, one of [00:21:30] the most important components of the ecosystem. And to me that's enough reason to study them. Speaker 4: But beyond that, their biology, their behavior sometimes just fascinating to just sit by a pond and watch a dragon fly. It's, it's just amazing to see how they move and how they can move. I mean, they've inspired so many things. I think the, uh, the helicopter was inspired by dragonflies. It's the same kind of design, you know, beyond that, their physiology, there's just so many things about them that are fascinating. And that's where I came from in all of this as an undergraduate, I was an electrical [00:22:00] engineering major for three years and finally realized that biology was really my passion. By coincidence. My first entomology professor got his phd here at Berkeley in entomology and this is at the University of Connecticut. He's the one who got me excited about it. For me, every day of that classroom was just fascinating. Everything I learned was telling me about this world that has been all around me my whole life, but I've never noticed it. Speaker 4: And then all of a sudden somebody opened my eyes [00:22:30] and I just started noticing more and more and it just fascinates me. I mean it's, it's 20 something years later. I still am just as fascinated today as I was before. But I think some of the more obvious things are things like pollination. Our crops depend on having pollinators in with colony collapse disorder going on with the honey bees. What does that mean? So there's a lot of very compelling reasons too, is to study insects. But I think for most of us it's because we love it. They're just fascinating. Great. Joanie ball and Peter o Boyski. Thanks [00:23:00] very much for coming on spectrum. My pleasure. Thank you. If you think you might want to get involved with cal bag. Here's Peter with some more information about how to do that. There's a number of websites where you can find information about us. The ECIG museum. If you go to our website, ecig.berkeley.edu I'm the collections manager, Peter Boyski and you can contact me directly. Gordon Deshita is one of the coordinators of our project. He's on that website as well. There is a cal bug website, get's cal bug.berkeley.edu [00:23:30] and that also has information about the project. Okay. Speaker 2: [inaudible]Speaker 5: the science and technology events happening globally over the next two weeks. Brad switch will join me in presenting the calendar Speaker 3: next Monday. The California Academy of Sciences will host a lecture [00:24:00] by Dr. Anthony [inaudible] Guerra and associate professor of physics at UC Santa Cruz. Dr. Guerra will speak about the evolution of models that scientists use to understand and study the universe. For over two decades, scientists have been refining the standard model they currently use with new data. In light of this, the concept of inflation has been revised in many cases, inflation completely upends. Our picture of the large scale structure of the universe and suggests that the universe may not actually have a beginning. [00:24:30] An object of such enormous size and complexity can only be described as a multi-verse. Dr. Guerra will walk through the development of these ideas and describe other aspects of the multi-verse that scientists wish to test. The lecture will be held on Monday, August 5th at 7:30 PM in the California Academy of Sciences. Planetarium tickets will be available online@calacademy.org Speaker 6: the August East Bay Science Cafe Presents Huta Greys Hammer Phd, [00:25:00] a science officer at the California Institute for Regenerative Medicine, the state stem cell agency that manages bond funds dedicated to support basic translational and clinical stem cell and regenerative medicine research in California. Her research background is in the study of embryonic development, elucidating how the cells of mouse and chick embryos assemble into functional organs. Udo will explore the power of the promise and the problems [00:25:30] of stem cells. That's Wednesday night, August 7th, 2013 in the Cafe Valparaiso, 41 30 Solano Avenue in Berkeley from seven to 9:00 PM Speaker 5: on spectrum. We also like to cover science stories, so we found particularly interesting. Brad swift flew join me in presenting papers. Speaker 6: A multidisciplinary team at the University of Texas Southwest Medical [00:26:00] Center has found that measuring the oxygenation of tumors can be a valuable tool in guiding radiation therapy, opening the door for personalized therapies that keep tumors in check with oxygen enhancement in research, examining tissue oxygenation levels and predicting radiation response. University of Texas southwest scientists led by Dr. Ralph Mason reported in the June 27th online issue of magnetic resonance in medicine [00:26:30] that countering hypoxic and aggressive tumors with an oxygen challenge, which amounts to inhaling oxygen while monitoring tumor response coincides with a greater delay in tumor growth in irradiated animal model. The next step is clinical trials to assess tumor response to radiation therapy says Dr. Mason. If the results are confirmed in humans, the implication for personalized therapies for cancers could mean fewer radiation treatments [00:27:00] or perhaps one single high dose treatment. In some cases, the simple addition of oxygen to stereotactic body radiation greatly improves response. The key is to identify those patients who will benefit Speaker 3: an android app released Monday. Allow smart phone owners to donate their phones, computing power to scientific research around the world. The app was developed by the Berkeley Open infrastructure for network computing or Boy Inc a project [00:27:30] that is best known for developing similar software for personal computers. The app install software that allows the charging phone's processing power to be used to analyze data or run simulations that would normally require expensive supercomputers. The app supports a variety of projects ranging from a program that searches radio telescope data for spinning stars called pulse eyes to one that searches for a more effective aids treatment through a community grid points creator. David Anderson [00:28:00] noted that the computing power of the nearly 1 billion android devices currently being used around the globe exceeds that of the world's largest conventional super computer. The app is currently available at the android app store, but I found you should keep an eye out as Anderson's next project maybe to design a version compatible with apple systems. Speaker 2: Okay. [00:28:30] [inaudible] [inaudible] music in the show is written produced by Alex Simon, edited by Renee Brown. Speaker 5: [00:29:00] Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Our email address is spectrum, Doug K l x@yahoo.com join us in two weeks at this same time. Speaker 2: [00:29:30] [inaudible] [inaudible]. See acast.com/privacy for privacy and opt-out information.

Arash Komeili cell biologist, Assc. Prof. plant and microbial biology UC Berkeley. His research uses bacterial magnetosomes as a model system to study the molecular mechanisms governing the biogenesis and maintenance of bacterial organelles. Part 2.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible] [inaudible]. Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hello and good afternoon. My name is Renee Rao. I'll be hosting today's show. Today we present part two of our interview with a Rosh Kamali. Dr [inaudible] is a cell biologist and associate [00:01:00] professor of plant and microbial biology at UC Berkeley. Previously on spectrum, he discussed his work with magneto tactic bacteria. Here's Dr Camilia explaining why these bacteria so interesting. Speaker 4: We work with a specific type of bacteria. They're called magneto is tactic bacteria and these are organisms that are quite widespread. You can find them in most aquatic environments by almost any sort of classification. You can really group them together if you [00:01:30] take their shape or if you look at even the genes they have, you can't really group them into one specific group as opposed to many other bacteria that you can do that, but unites them together as a group is that they're able to orient in magnetic fields. And some along magnetic fields Speaker 3: today. In part two of his interview, Dr [inaudible] explains how these discoveries might be applied and discusses the scientific outreach he does in our community. Here is Brad swift interviewing a Kamali, Speaker 4: [00:02:00] so how is it that you're trying to leverage what you're learning about the magnetic zone? You're trying to apply it in any way. Are you still really in the pure research mode? I think we're starting to move out or at least branch out to try to do some applications as well. This has been a really, one of the areas of research that's been the most active, or at least the most thought about for Magna [inaudible] bacteria for the last 40 years or so of that people have been working on it. You have two [00:02:30] features of the magnesiums that immediately can be thought of as being very useful for applications, but one is that they're making something that's nanometers size. Very small is magnetic and it has very, very irregular dimensions, quite free of impurities. So you can make magnetic particles in the lab and people have gotten very good at it actually, but it's often very hard to control some of their features. Speaker 4: Maybe contaminants can kind of bind my net [00:03:00] particles pretty easily. And then on top of that you have to sort of use certain types of chemical conditions that are not so favorable. Maybe the Ph has to be a little bit high or chemicals that you don't want to use. And that's one of the reasons why the bacteria are so great. Right? Then as I said, they make an Organelle in this case to magnetism. So then within this tiny 50 nanometers sphere, they can just make what is otherwise a toxic condition inside of that and make this magnetic particle. But the cells are [00:03:30] growing in relatively harmless growth media at 30 degrees centigrade. So you can make magnetic particles under what are not toxic conditions because the bacteria are taking care of that inside of the cell. So that's one of the reasons people have been really fascinated by them. Speaker 4: So how can we take these sort of perfect crystals out of these bacteria and apply them to something else? The other aspect of it that's really important to recognize is that it's not just that the bacteria are randomly making magnetic particles. [00:04:00] They actually have a whole set of genes that they're used to build a magnetism and build the magnetic particle. So the ability to make a magnetic crystal is in coated in jeans, so you can not only extract the magnets out of these bacteria to use it for applications. Maybe you can extract the genes and put them into another organism and now give that other organism the capability to make magnetic nanoparticles. They're [00:04:30] magnetic properties, mixed them, really useful for many different kinds of applications. One of them, they can be potentially contrast agents for magnetic resonance imaging or MRI. When you get an MRI, does a lot of structures that are easily seen, but a lot of things are sort of invisible to the MRI and if you had a little magnetic particle in that region, you'd be able to see it better. One idea is can we put the genes as we learn more about them, can we sort of gather [00:05:00] up a minimum set of genes that are sort of sufficient to make a magnetism and a magnetic particle and then just put those into some other cell types and then see if that's enough to make a magnetic particle and that settle and they can we track it by MRI or something so that that's actually the focus of a grant that we recently got with a few other groups on campus. As a large collaborative grant, Speaker 4: how will you start to [00:05:30] prove that concept? I think we're taking many parallel approaches for it. You know, both to show the utility or the different ways that you would have to image them. One group is working on essentially technologies for imaging, magnetic nanoparticles and animals, and then we are sort of at the very other end of the spectrum and the collaboration, we're trying to say, we think we have a set of genes that are sufficient. This process, let's start taking baby steps [00:06:00] and move them to other types of cells, whether they're bacteria or other cells. And see if we can produce magnetic particles in those cells. Are other collaborators they're focusing more on, well, if we know these genes, can we start transferring them to mammalian cells and then in animal studies we could track cells using magnetic resonance imaging. Each group has focusing on a different aspect of the project. Speaker 4: Some of the other applications are really fascinating too. There's one where [00:06:30] particles hold their magnetic properties very stably and if you give a very strong magnetic field then you can kind of flip the dipole moment of the crystal. You can do this back and forth, keeps switching it, and if the pulse is switching faster than the dipole man can flip on the magnetic protocol. The difference in energies essentially released as heat. We can in that way heat the particle. There's a lot of anticancer treatments to try to essentially have the particles adhere to [00:07:00] a tumor and then heat the particles using this method. Just have the heat of the particles, kill the cells locally. There's been quite a few papers on it and some of these types of studies are in clinical trials to see how effective that could be for different kinds of tumors. Speaker 4: Yeah. Bacteria seems to get used that way. More and more to go into a tumor and linger just on the tumor and continue to just be very local in terms of very specific. And that's, you know, [00:07:30] local drug delivery or local attacking of tumor cells would be something that's very, this bacteria have this great access that other organisms don't have. If you can localize them and direct them. And that's sort of some, there's some other work which I think is also really interesting is to thinking about the magna detected bacteria as a vehicle for delivering drugs. You know, one of the things you can imagine is that you could guide them with a magnetic fields so you can have them guided to some [00:08:00] areas in the body by an external magnetic field. And there's definitely some people who are working on that. Can they move the bacteria through vasculature to a certain area because they can swim along magnetic field. Speaker 4: So if you want to localize it somewhere, you would have to instigate that field there. Yeah, exactly. To direct it. Right. The stuff I was telling you about with the heat treatment, I think all of that is trying to, right now at least because there's not much known about how to target the bacteria, they work with kinds of tumors that are accessible [00:08:30] so that you could inject the particles into the tumor directly directly to the tumor as opposed to try to do a systemic thing. Yeah, exactly. But you can imagine that maybe one benefit of the is is that they are surrounded by biological membrane and you can have proteins on them and people have done this pretty, you can display specific proteins on the surface of magnesiums, so then you could customize your, I need a zone to have affinity for certain types of proteins [00:09:00] or certain types of cells. Some proof of concept of that has been done for sure. Speaker 5: Mm MM. Speaker 3: Our guest on spectrum today, is it rush Molly, I cell biologist and associate professor at UC Berkeley. In the next segment. Dr Camelli speaks more about some of his collaborative. This is k a l x Berkeley. [00:09:30] [inaudible]. Speaker 4: The work you're doing with a sequencing is a lot of it. Trying to catalog everything. Keep track of what's, what sort of explain the sequencing side of what you're doing. The sequencing side, we are fortunate that the organism that we work with is in pure culture. Our lab rat essentially has been already sequenced by someone else. When we sequence, [00:10:00] it's more to make sure if we're going to put some gene fusion into the bacteria or that what we have is correct. Our sequencing is relatively limited. We are trying to branch out more and say nowadays technologies for sequencing the whole genome are much more accessible, affordable, certain types of genetics that we do where we try to delete genes or randomly mutate them. Then we can just start identify what's changed by going back and just sequencing the whole [00:10:30] genome or the bacteria. We are doing a little bit of that. Speaker 4: We do it on campus very accessible and affordable, but it's really something that was unthinkable even five, six years ago that you could do this on a large scale, do it affordably. And it could be a pretty routine tool in research. Sorry, I mean it's a really exciting, actually you're not gonna necessarily have to be restricted to these lab rats that do represent some of the general features of the process you're interested [00:11:00] in, but not the diversity of fitness necessarily. And so you can say, instead of studying just one organism, maybe I can study many other ones. There's still a lot that I can do with my model system in the law that I can't do with some of these other unconventional organisms, but they're at least visible to me. Their genes are visible to me and I don't have to isolate them away from everybody else to get an understanding of [00:11:30] what their genetic makeup is and where they are. Speaker 4: And for things like microbiome studies is revolutionize the whole field. They were, they were always just looking at such a small sliver of what they could isolate. Yeah. And now you can look at everything, you know, they can do lots of really interesting experiments like what's on your fingers, what's on your, you know, how's your right hand different from your left hand and microbial content. Yeah. You know, so that's really interesting. Yeah, it gets very refined. Is synthetic [00:12:00] biology involved in what you're doing in some way? Yeah, definitely. So what I was telling you about the applications, you know, essentially, I mean synthetic biology, I guess there's different ways of defining it. For me, you have inspiration from some biological system and now you're trying to extrapolate that and put it in a new context to do something new or something different than it normally does. Speaker 4: Though. What I was telling you about this, this project that we have on campus or does not support [00:12:30] it by the Keck foundation to put the magnetism genes into other organisms, but that's essentially synthetic biology. So yeah, we are really relying on that and trying to see if we're going to move these genes, how are they going to be more, how can we customize them so that they work better in the new organisms they go to? Can we add on things to them or take things away and doing this using synthetic biology essentially that it would fall under the category of synthetic biology. Sort started like mixing and matching genes and in [00:13:00] new contexts that you wouldn't have naturally. And what sort of safety protocols do you have to abide by in your research? For? For our research, we are working with something that's non-pathogenic that's quite harmless. Speaker 4: We follow the, the university has pretty strict guidelines for even for nonpathogenic organisms. Anytime you're working with recombinant DNA, even those things I was telling you where we are making a fluorescent protein fusion, we really [00:13:30] have to be careful about how we get rid of things and you know, don't just dump it down the drain. Safety-Wise. We don't really use anything harmful in the lab. I think maybe you're getting more into like what do you do with the hybrid organisms somehow and there we have to be, you know, we're always careful about how we dispose of materials. Eat cultures are always killed by bleach or heating before we dispose of it. You know, often people [00:14:00] say imagination runs wild with them. Right. You know? Yeah. And a lot of that has to do with fiction. Yeah. Books and movies and things. But I think it's important to sort of sort of what prompts me to ask. Speaker 4: And I think a lot of times maybe scientists think about that too late, you know, so, so maybe it may not be the first thing you say. That'd be the first thing you think about. And then it may also, it may not be in your training expertise or whatever to even know what would be dangerous. So I, I, [00:14:30] is that something that the university is helping with in the sense of certainly providing those kinds of resources to you so you don't have to be expert, right? We don't. Yeah, exactly. How can you be, and also you know, we have to comply with not just handling of biological organisms, but just how the lab functions. We have not only have to comply with university rules, but we have federal rules for worker safety, city rules that are different. So we have five or six different sort of safety protocols that we have to [00:15:00] abide by and we do get inspections once a year and I know people who work with animals, they have even more extensive things. I'd have to go through a whole separate set of protocols to just the sort of ethical treatment of the animals approved by independent boards and things like that. And the funding agencies have a lot of rules, so they give us money, but they expect us to follow certain types of rules. Speaker 2: [inaudible] [00:15:30] you're listening to spectrum on k a Alex Berkeley. Our guest is a Raj Chameleon. In the next segment he speaks about his work on outreach to the broader public [inaudible] [inaudible] [inaudible] Speaker 4: I noticed you've got a Twitter account. I do, yeah. And is that sort of part [00:16:00] of an outreach effort on your part to get the community involved or people interested in what you're doing? How do you view outreach going forward for your projects? Yeah, so the Twitter thing is you'd asked me that outreach are fun and I think it's both. It's not anonymous. You can be social, my name, you can find it. We have one for the lab also, which not very active at all by mine. A lot of people that I follow are other scientists. I think it is not known so well that there are many scientists on Twitter and there's great outreach [00:16:30] because often is a great way to share new findings and research or things that are exciting to people or having a discussion within the community, but this all accessible. Speaker 4: None of it is anonymous, so you can really see that. It's also fun obviously. For example, I encourage people to look out there. There's a lot of great science writers who take research findings and they in science blogs turn it into very accessible stories to understand the latest developments in research for [00:17:00] outreach. We try to do a lot of things. Members of my lab go out to, there's different events where scientists can interact with the community. I've done a few microbiology experiments with my son's classroom and you know, kindergarten, first, second grade. For me it's been really eye opening to do that because you see you all, sometimes you think what you're doing is so inaccessible on out there. But when you go and just talk to people you see that they can get really excited about, especially kids, [00:17:30] kids can get really excited about micro was, which is kind of funny because it's not something they can see and they really only heard about bad germs. Speaker 4: They've only heard about things that can hurt them and it's just great to go out there and talk about things that are good germs and on their bodies and everything. So we do a little experiment where we take the little auger played, which has the growth for the bacteria. They put their little fingerprints on it or they can see over the course of few days, bacteria grow on there. They washed her hands and they can see that that changes whether they can grow, [00:18:00] and I do the exact same experiment. I teach undergraduate microbiology lab here. You know, the questions that the undergrads ask are almost exactly the same questions that the third graders ask. So it's great to see that they have the insight and the excitement to learn about science. It just has to be, I think, encouraged and followed up more as they go through schooling. Speaker 4: I think another reason for us to go and do outreaches to just sort of, I get more excited about my work when I go and talk to other people and see that it's not so out there [00:18:30] and the university provides a lot of chances for us to do outreach to it. I mean, just recently we had cal day. There was lots of science on campus. Other blogs that you follow because you'd want to mention some colleagues at Berkeley have blogs, but I think people are more active through Twitter than they are through blogs. The scientific American blogs in general are pretty good. You mentioned the Keck Foundation that's brought together this collaboration that you're going to try to do the applied research on. Are there other collaborations [00:19:00] that you're trying to pursue? Yeah. You know our work, we rely on a lot of collaborations mainly because the bacteria do this really amazing thing of building these magnetic particles and we're always just like the example I told you about with the more high resolution electron microscopy where we were able to see something that we hadn't seen before. Speaker 4: There was a lot of people who were interested in imaging magnetic particles. They're developing instruments all the time that you would be able to look at these things in new ways and [00:19:30] we can't build the same instruments, but it ends up being a really great interaction all the time to find these groups that are developing technologies for imaging bacteria or imaging particles and then see how what we've learned can be applied to their technologies. One great collaboration we've had recently is with the walls worth group at Harvard and they have these, essentially there is a way you can treat diamonds so that there's certain defects on the surface of the diamonds and then you can detect magnetic [00:20:00] fields close to the surface of the diamond can actually essentially image these bacteria that we've worked with sitting on the surface of these diamonds because of their magnetic properties. Speaker 4: It's been great for us because working with them, hopefully we're able to fine tune some aspects of their technique to then study the magnetic particles and the magnetic chains in a different way than we had been so far and learn new things. Basically at any given point we might have seven or eight active collaboration's going on. [00:20:30] A lot of it on our part is not that difficult. We just provide a sample of the bacteria and then they work on it and if it goes somewhere then we go and get more involved in the collaboration. You start iterating with them. Yeah, exactly. This Keck collaboration was out of a brainstorming session. Went from there and we have another collaboration. Also synthetic biology that was just funded by the office of naval research and that's between two or three groups that are in different universities. We had always just talked here and there to each other and all of a sudden we realized that we could do something [00:21:00] together. Speaker 4: And that's how that came about. It's a huge part of science I think is even more now with funding situation and you have to really look for more creative ways of doing your science and your sense is that the funding environment is dwindling. Is that good? Yeah. Yeah. I think it was already bad and the sequester just sort of pushed it down even further. For example, you look at NIH, the amount of money is that increasing, which means it's not keeping up with inflation. So your purchasing power is much less and then all of [00:21:30] a sudden the sequester takes out a few percentages off of what was getting funded to you. So I think both the success rates for getting a grant and the amount of money that you get from that grant are lower. Even if you're lucky enough to be able to get the grant. What you could do with the money is less than before. Obviously, you know, I'm biased, but I don't think it's that great. You're essentially sacrificing the next generation of scientists, limiting [00:22:00] it, limiting it big time. Speaker 4: Was there anything that you wanted to mention? One thing I was going to say is that we've talked a lot about these bacteria, but obviously the visual is the easiest way to really appreciate what they do. And we have a, on my lab website, we have a page of videos where you can see how these bacteria migrate along magnetic fields and you can see images of them and you can see the structures within the solid with the magnesium. So clinic. So, so people go to [inaudible] [00:22:30] lab.org they can actually see videos of the bacteria. Great. Yeah, that'd be good. Yeah. Arash Kamali. Thanks very much for being on spectrum. Thank you so much. This was a lot of fun. Speaker 2: [inaudible]. You can follow Rajkot Maley on Twitter at micro magnet or you can watch them. Fantastic [00:23:00] sell videos on his website Oh Maley, that is k o n e I l I e lab.org and now a few of the science and technology events happening locally over the next few weeks and Rick chronicity joins me in presenting the calendarSpeaker 3: this Monday. The California Academy of Sciences will host a talk by Dr. John Jenkins, [00:23:30] senior research scientist at the Seti Institute. Dr. Jenkins will speak about NASA search for other habitable planets. In 2009 NASA launched the space cough known as Kepler into orbit in order to survey our own region of the Milky Way. Kepler's has been looking for planets that are similar in size and distance from a son to our owners. In those four years. The probe has collected data on over 190,000 stars and confirmed over 130 new planets. Dr. Jenkins [00:24:00] will discuss the exciting you dated that capital has provided as well as a few of the technical and scientific challenges that went into building a vessel at Kepler. He will also give a brief overview of tests. NASA's next mission to detect earth's closest cousins. This event will be held Monday, July 15th at 7:30 PM in the planetarium of the California Academy of Sciences. Go to cal academy.org to reserve a ticket in advance. Speaker 6: The theme for July is adult science, happy hour science, [00:24:30] neat. His brains, brains, grains, everything you've always wanted to know about your brain and more. There'll be talks in demos on memory, truth and tricks, neurobiology, human brains, a sheep brain dissection and illusions. Science neat takes place at the El Rio bar. Three one five eight mission street in San Francisco and mission for those 21 and over is $4 this month's [00:25:00] science need is on Tuesday, July 16th with doors at six and then talks at six 30 Speaker 3: every Sunday. This month the UC Berkeley Botanical Gardens will be hosting special be explained explainer lectures about the importance of wild bees in the care and maintenance of all gardens and especially in the native California Habitat. The botanical garden also features and amazing collection of plants from nearly every continent. Although there is a focus on plants that thrive in our Mediterranean climate. [00:25:30] The Asian, Californian and South American collections are currently blooming. The garden will be open from 9:00 AM to 5:00 PM most days. Although bee explainer tours are only offered from 11 to one 30 on Sundays, admission is $10 for adults and $8 for students. Speaker 6: On Saturday, July 20th at 11:00 AM Dr Steve Croft. We'll give the free public science at cal lecture on snacking gorgeous and cannibalizing the [00:26:00] feeding habits of black holes. Learn about the latest telescopes and how they are giving more information about how black holes grow and merge. Steve Leads the science at cal lecture series and as an assistant project astronomer working on large radio surveys and transient and variable astronomical sources. He helps commission the Allen Telescope Array for science operations and develop data analysis pipelines. He is an expert in the use of data at [00:26:30] a wide range of wavelengths from many different telescopes. The talk is@dwinellehallroomonefortyfivevisitscienceatcaldotberkeley.edu for more information and now Speaker 3: spectrum brings you some of our favorite stories in science and technology news. Rick Kaneski joins me again for the news science news summarized an article published on July 3rd in the proceedings of the royal society a about how surface [00:27:00] tension can lead to upstream contamination. Sebastian BN. Connie observed this when watching the preparation of Argentinian Montay t when hot water was poured from a pot into a container of leaves below some of the tea leaves float upward against the force of gravity and upstream of the water flow being Kinney and his colleagues from the University of Havana and from Rutgers showed through both experiments and simulations. [00:27:30] The particles can flow upstream several meters and up central meter high waterfalls because the downstream flow of clean water creates a gradient. What the container of t or other particles lowering the surface tension of the water, the particles are thus pulled into the clean water which has a greater surface tension. Speaker 3: The team also demonstrated that these results could have practical applications such as through the discharge of a standard pipette in other lab work [00:28:00] or in the simulated release of waste into larger scale channels. Indiana University scientist have transformed mouse embryonic stem cells into key structures of the inner ear. The discovery provides new insight into the sensory Oregon's developmental process and sets the stage for laboratory models of disease, drug discovery, and potential treatments for hearing loss and balance disorders. A research team led by ear. He has Chino Phd and Russi Holton. A professor [00:28:30] at the school of Medicine reported that by using a three dimensional cell culture method, they were able to Koch stem cells to develop into inner ear sensory epithelia containing hair cells, supporting cells and neurons that collectively detect sound had movement and gravity. The researchers reported online Wednesday in the journal Nature, Karl Kohler, the papers first author and a graduate student at the medical school said the three dimensional culture allows the cells to self [00:29:00] organize into complex tissues using mechanical cues that are found during embryonic development. Additional research is needed to determine how exactly inner ear cells involved in auditory sensing might develop as well as how these processes can be applied to develop human inner ear cells. Speaker 7: [inaudible] music heard during the shows witness produced by Alex. Thanks to Rick krones for contributing [00:29:30] to our news and calendar section and to Rene Rao for editing systems. Thank you for listening to spectrum. If you have comments about [inaudible] about Speaker 3: the show, please send them to us via email Speaker 1: or email address is spectrum. Doug k a l x@yahoo.com join us in two weeks at the same time. See acast.com/privacy for privacy and opt-out information.

Paul Piff, social psychologist and post-doc scholar in the Psychology Dept at UC Berkeley, studies how social hierarchy, inequality, and emotion shape relations between individuals and groups. Paul Piff received PhD in Psychology from UCB May 2012.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible].Speaker 1: Welcome to spectrum the science and technology show on k [00:00:30] a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Good afternoon. My name is Brad swift and I'm your house today. In today's interview, Renee Rao and I talk with Paul Piff, a social psychologist and postdoctoral scholar in the psychology department at the University of California, Berkeley. Paul's studies house, social [00:01:00] hierarchy, inequality and emotion shape relations between individuals and groups. Paul piff received his phd in psychology from UC Berkeley in May, 2012 onto the interview. Paul Piff, welcome to spectrum. Thanks so much for having me on. It's a pleasure. I wanted to have you talk about your research. Psychology is such a big field. How does your research fit into that? Speaker 4: Psychology is a big field. Lot of people are psychologists center interested in a lot [00:01:30] of different questions as they relate to people and organisms and why different kinds of organisms do the things that they do. The brand of psychology that I'm really interested in is called social psychology. So what I do is as opposed to having people lay on a couch and talk to me about their problems, I study what people do around others in the reasons for what they do. So I study emotion. That's one of the focuses of my work. I've also recently gotten really interested in [00:02:00] the effects of inequality and specifically how a person's levels of wealth and status in society shapes the ways that they see the world and behave toward other people. As a social psychologist, you take a question that's of interest to you, like how do the rich behave compared to those that are poor. And then you think about how you would design experiments in different kinds of studies to look at that using a very quantitative approach. So as a social psychologist, I design a lot of studies where people literally [00:02:30] come into the lab. There's something happening where I can observe what they do without their necessarily knowing, and I use that to infer basic motivations behind people's behavior. Speaker 3: Can you explain then some of your methods, maybe an example of how you're set up Speaker 4: study, study. So a lot of the work that I've been doing relates to this basic question of how money shapes behavior. So how do people who have a lot of money behave differently toward others from those who don't have [00:03:00] as much money? One of the things that I was interested in studying for example, is how does the amount of money that you have shaped how generous and helping you are toward other people. In social psychology, we call that general category of behavior, pro social behavior or altruism. What makes people behave in ways that help another person out, even if that means they have to do something kind of costly. So let's say I'm interested in looking at levels of generosity, a lot of different ways in which people can be generous toward one another in everyday life. [00:03:30] But I want to study this in the lab. Speaker 4: And so one of the ways that we can do that is using a standard task where we can have someone engage in it and see how generous they are. And one of the tasks that I'll use is called the dictator task. And for instance, in one study in this dictator task, I give someone literally $10 and I say, you can keep all these $10 10 single dollar bills or you can decide how many of these dollar bills you want to give away, if any, [00:04:00] to another person who's totally anonymous that you've been paired with in this study. And I tell them they'll never meet this other person, the other person will never meet them. And I just measure how many of those dollars they're willing to give away. Another thing I do before they come into the lab is measure what their income is. So I can look at how generous they are, how many of these single dollar bills they're willing to give away as a function of how much money they have. Speaker 4: And that's one of the assessments that I used in one area of study to look at levels [00:04:30] of giving levels of generosity in the simple task as a function of how much money people have. So there's rational economic models that would say that if you have a lot of money, that the utility of those $10 is somewhat diminished because you have more money in the first place. So you would predict that as a rational actor, a person who has more money is going to give more money away cause $10 means less. That's the opposite of what we find. In fact, people who make under $15,000 [00:05:00] a year give significantly more on average six to $7 away then to someone who makes 150,000 to $200,000 a year. So we found incredible differences. And so a lot of my work over the last five or six years, and this is in collaboration with other people in my lab, is to try to document why it is that these really notable differences emerge between the haves and the have nots and what the psychological underpinnings of those differences are. But that's an example of a kind of study that will run Speaker 2: [00:05:30] [inaudible]. Our guest today is Paul Piff, a social psychologist. Paul is talking about how he designs his research studies. This is k a l X. Berkeley. Speaker 5: I have a question about the dictator test. Do you find any sort of other correlating variables in between just wealth and lack of [00:06:00] wealth? Do you find education has difference or how people made the wealth? Can you draw a sort of a causal line between saying this person has more and this makes them less empathetic or this person being less empathetic maybe has led to them being wealthier? Speaker 4: The dictator task has been used a lot and there are a lot of correlating variables that we know about already. Age correlates, religion correlates, ethnicity correlates, and so if I'm interested in the specific effects of wealth, I have to [00:06:30] account for those other things and I do so controlling for a lot of other variables. Wealth above and beyond a person's race, their age, what religion they are, how religious they are in the first place. Wealth has a specific effect, but the question that you're getting at I think is a even bigger one, which is how do I know whether it's wealth that causes someone to do something or is it people that are say a little more selfish with their money, who become wealthy in the first place? [00:07:00] And that is a really important question. And I think one of the insights that we've had from a lot of the experimental work that we've done, I can literally take someone whose quote unquote poor, make them feel rich and show you that making them feel wealthy temporarily in the lab actually makes them behave more unethically, which suggests that there's at least in part a causal direction between having money, feeling like you have money and that subjective experience. Speaker 4: It's psychological [00:07:30] experience causing you to behave in some ways that are a little more entitled, a little more self-serving. Now there's an another important question, which is if these differences do exist between those that have and those that don't, are they fixed? Are they rooted? Is that just a fact of life that we have to accept and sort of move on from, or are they sensitive to changes and if they are, what are the kinds of things that you can do to move people's behavior around or to make certain people in society a little more empathetic [00:08:00] without necessarily getting into the details? There are a lot of things that can be done in a lot of my work looks at specific variables that you can manipulate, even through subtle interventions that get people who had a lot more money to behave in ways that are a lot more compassionate and a lot more empathetic. And one of the lessons that I've learned from this work is that it's not that difficult. So it's not that people who have money or necessarily corrupt in any way, but that there's a specific psychological experience associated with privilege [00:08:30] that gets you to become a little more disconnected from others. A little more insular from others in that certain patterns of behavior flow as a result, but those patterns can easily changed. Speaker 5: Can we talk about some of the tweaks that you use to sort of bring about those changes? Speaker 4: Sure. One of the things that I'm really interested in right now is if it's the case that upper status individuals are more likely to behave unethically, then what are some subtle interventions that could be [00:09:00] done? Like a little ethics reminder course at the beginning that, so I've run this where I basically had people do sort of a 10 minutes ethics training program where I remind them about some of the benefits of the rules and how cooperating with others can ultimately bring about gains for the whole group, including yourself. And I see how that basic values intervention changes their patterns of unethical, the downstream. But now in one of the studies that I ran, I just wanted to look at helping behavior. [00:09:30] What makes a person want to help out another? So in this study, the way that I designed my test was I had one group of participants sitting in the lab and about 15 minutes into the study, it's the room bursts. Speaker 4: Another person. Now this is appearing visibly distressed. They're worried, they're sweating, they're anxious, they apologize for being late, and they introduce themselves as their partner in the study. Now there is an experimenter standing there who says, it's so great that you're late. Why don't you go ahead and see yourself in this other room? [00:10:00] And they turn to the participant and ask the participant if they'd be willing to give up some of their own time to help out this other person who would otherwise have to stay on for a lot of extra time to complete all of the tasks that they need to complete. And so that's our measure of helping behavior. How many minutes people are willing to volunteer to help out this other person who's actually a confederate. There's someone we've trained to be late to appear distressed, et cetera. They're an actor. All right. Speaker 4: So in one condition we find that Richard people give [00:10:30] way fewer minutes than poor people paralleling all the other results. But we had this other condition that I think is really revealing in that condition. Before they received in the lab about 15 minutes earlier, they watched a 46 second long video. And in that video, it was just a quick little reminder of the problems of childhood poverty. And it was a video that we'd designed to elicit increased feelings of compassion. Now, in that group, 15 minutes later, when [00:11:00] the people who had seen that video were sitting in a lab and we're introduced to that confederate and asked if they'd be willing to help them out, there were no differences between the rich and the poor in our study. So essentially that quick little reminder of the needs of others made wealthier people just as generous of their time to help out this other person as poor people suggesting that simple reminders of the needs of other people can go a long way toward restoring that empathy gap. And so the interesting question [00:11:30] to me is what are the ways in which in everyday life we can remind even those in the upper echelons of society, of the needs of other people in the small benefits that can be incurred through small and even sometimes trivial acts of kindness toward another person. Speaker 4: You are listening to the on k Speaker 2: a l x Berkeley. Our guest today is Paul. Pissed in the next second [00:12:00] he talks about his collaboration with Facebook. [inaudible] Speaker 5: try not to talk about how psychology seems to be a field that's accessible, not only in terms of mechanics and just finding the work, but also more understandable for a layman or for everyday people. Then most sciences, I think it's one of the most popular majors in colleges across the u s and can you sort of talk about the broad appeal that psychology has and why you think that might [00:12:30] be? I think Speaker 4: that observation rings true. I think psychology is something that's accessible and that that accessibility and the understandable illness of the content is what makes it kind of relatable and popular in the kind of work that we do. It's a positive and a negative. So what I mean by that is everyone who's engaged with others or interacted with others who are, has a sense of how people behave is a, an intuitive psychologist. We're all psychologists. [00:13:00] We all make decisions based on what we think is gonna make us happy. What's gonna make others happy? What's the kind of relationship that's meaningful to me? We all run these kinds of experiments. In fact, the life is sort of like a psychological experiment to run on a single person, 5 billion people at a time or whatever the population of the earth is. So we're all intuitive psychologists. But what that means is for the work that we do, if we find something or generate a finding, it's either obvious. Speaker 4: So someone could say, Oh yeah, you had to run a study [00:13:30] to do that. I've known that all along. Or if it doesn't conform to your worldview, you're wrong. You've run the study incorrectly. So the question is, are we actually convincing people or revealing new insights about how the mind works to others such that our awareness and understanding of psychology is increasing? Or are we simply just telling people what they knew all along or telling them things that they feel like is just flat out wrong? And that's something that I've wondered about myself. To what extent our findings are convincing people or informing people of things that they don't [00:14:00] intuitively experience in their everyday lives. Speaker 5: Do you want to talk about what you're doing with Facebook? I know you're, yeah, we can talk about Facebook in an ongoing collaboration with Facebook. So maybe you should tell us a little bit more about that Speaker 4: with Facebook. Dacher Keltner, who's a psychology faculty member here at Berkeley and Amelianna, Simon Thomas, who's the science director of the greater good science center, also at Berkeley, and I have been working with a team of engineers [00:14:30] at Facebook to put very, very simply make Facebook a more compassionate place. Now, when we started working with Facebook about 12 months ago, that was what was post to us. Help us make Facebook a more compassionate place. What does that mean? How do you do that? Well, what's become clear to me is that there are a lot of opportunities on Facebook and elsewhere to build little tools to make interactions between people and online. A little more sympathetic and a little more empathetic. [00:15:00] So here's an example. A lot of people on Facebook post photos. What that means when photos are getting posted is that there's the possibility that you're going to encounter a photo that you don't like. Speaker 4: And what Facebook found was that people were encountering these photos and just submitting reports to Facebook saying, hey, there's something seriously wrong with this photo. Facebook needs to take it down. And more often than not, people were reporting photos that had been posted by a friend of theirs. Very rarely do these reported photos actually violate [00:15:30] Facebook's terms of services. So Facebook can't do anything about it. And what we thought and what we've done is in the context of a photo being posted that you don't like, maybe this is a photo of your child that you think shouldn't be up at violates your privacy. Maybe it's a photo of you at a party in a some kind of revealing pose that you think is embarrassing. It doesn't really matter. But what we've done is tried to, for instance, give people tools to express why that photo is problematic, not to Facebook but to the person who posted [00:16:00] it. Speaker 4: And so now there's a series of things that pop up on the site. If you're having a problem with something that someone's posted that basically gets you to think about your experience, be a little bit mindful about the feelings that you're experiencing and be a little more mindful in how you express those feelings to the other person. That puts the photo up and when we just looked at the data recently, what we found is that by identifying the particular reason why you're finding that photo problematic and expressing that to the other person gets [00:16:30] them to be a lot more empathetic, a lot more sympathetic and really importantly a lot more likely to take the photo down. So we're actually trying to resolve disputes and conflicts on Facebook and there are a lot of other directions that this work is taken. We're dealing with bullying with the team at Yale, we're doing all sorts of other things that basically relate to what makes people get along or not get along in an online context. Speaker 5: I think the other question that I was trying to get at but didn't quite get to is how you think interactions [00:17:00] on platforms like the Internet, if they are fundamentally different than people interacting face to face or in a laboratory and why you think that might be the case? Speaker 4: Yes. What I mean by that is there's no single answer to the question and I think it's too early to tell. I think that online interactions are expressions of fundamental psychological tendencies, much like real world interactions are. So I don't think that things unfolds [00:17:30] online that wouldn't unfold in the real world, but does that mean that certain things are going to be accentuated or emphasized or magnified in an online setting? I think that's true as well. So I think online interactions are a certain kind of context where dynamics and fold that aren't fundamentally different from other kinds contexts in everyday life, but in which you might see certain kinds of patterns emphasized or magnified. Speaker 2: [00:18:00] This is k a l x Berkeley. The show is spectrum. Our guest is Paul Piff, a social psychologist. Speaker 4: Do you see a future in collaboration between brain studies and psychology? Absolutely. So that that future is now, I think a lot of psychologists who [00:18:30] incorporate brain imaging and brain data, FMR data into their papers, into their studies. This is the direction that even my work is beginning to move into. So I feel like the opportunities for collaboration are definitely there and in fact they're unfolding now. There's a lot of neuroscience that's less interested in quote unquote psychology and more interested in say biology, but there's a lot of social neuroscience, a lot of brain research that's done that's specifically motivated and [00:19:00] oriented around understanding why people feel the things that they do. What does emotion look like in the brain? What drives basic behavior patterns? So absolutely, I think that those opportunities are there, and this is a, an incredibly exciting developing area of the science. Speaker 4: One of the things in the fifties and sixties when BF Skinner and behaviorism was all the rage, is that behaviorism and the quantification of behavior gained traction [00:19:30] because it was argued that you can't look inside the black box. And if you can't look inside the black box, which is people's brains, people's minds, then the only thing you can study is behavior. And if we're interested in a science of behavior, then the only thing we can measure is what a person does or what a rat does or what a pigeon pecks at. But what neuroscience has allowed us to do is take a look at what is happening in that so-called black box. And if you put someone's brain in [00:20:00] a magnet in, scan it and see what's happening in the brain when you're showing them, say, images of another person's suffering, well then you're getting a sense of what compassion looks like neuro anatomically. Speaker 4: And that's a really exciting and incredible opportunity for understanding how basic psychological experiences are rooted in the brain and how basic anatomical structures in the brain can illuminate how psychology works. So I think the [00:20:30] opportunities are bi-directional. If I might, let me just add one more thing, which is one more insight that I think is interesting to me that social psychology seems to have been moving in the direction of, or psychology and there are about 80 or 90 years of research documenting the extent to which people stick to their groups. People are antagonistic potentially toward other groups. There's a history of violence in the human tradition or the history of humanity as sort of a history [00:21:00] of violence and that's given a lot of psychologists the perspective that people are in a way born to be sort of self-serving, especially if you look at behavior from an evolutionary framework, then it makes sense that people would do anything they could to get themselves ahead of the pack and get their groups ahead of the pack of other groups. Speaker 4: And what I think is a really important insight, and this is in part a movement that's been inspired by people like my advisor in graduate [00:21:30] school, Dacher Keltner, toward understanding that people are a lot more complicated than that in that a lot of the driving motivation to behavior is not just what gets you ahead, but also how you can help other people. So in a way, compassion and altruism we're learning is hardwired into the brain and that's a really puzzling thing because it's hard to fit that specifically into an evolutionary framework. But put generally [00:22:00] what I think we're learning about what motivates people is not just that people are motivated to get ahead, but the people are really driven to make others around them happy and to serve other people in ways that benefit others. And that insight has inspired 30 years of the most hard-hitting social psychology that I know of and it's also given rise to just a different kind of conceptualization of what makes people do the things that they do. Paul Piff, thanks very much for coming on spectrum. [00:22:30] That was a lot of fun. Thanks again for having me. On and I'd be happy to come on any other time. Great. Speaker 2: [inaudible] spectrum is archived on iTunes university. To find the archives, do a search in your favorite browser for iTunes Dash and view space k a l x space spectrum. The feature of spectrum is to present new stories we find [00:23:00] interesting and a coolio and Renee route present the news. Speaker 6: A National Institute of Health funded team of researchers at Stanford University have created an entirely transparent mouse brain. This new process known as clarity by its inventors will allow scientists to explore the neural networks and their natural 3d arrangement without having to slice the brain or severing any neural connections. Additionally, the process preserves the delicate biochemistry of the brain, which will allow researchers to test [00:23:30] chemicals affecting specific structures as well as to examine past brain activity. While the breakthrough is not part of the Obama Administration's recent brain exploration initiative, the senior author on the paper, Dr Karl Deisseroth, was involved in the planning of the initiative. Speaker 1: Well, some moderations do need to be made for the more complex human brain. The Stanford lab has already produced transparent human livers, hearts and lungs. You see Berkeley researchers and the integrative Biology Department just came out [00:24:00] with a study showing the positive effects of stress in studies on rats. They found that brief stressful events caused stem cells to branch into new nerve cells that improved the rats. Mental performance. It is important to differentiate acute stress and chronic stress. Chronic stress elevates levels of stress hormones that suppress the production of new neurons, which impairs mental performance. Associate Professor Coffer Characterizes [00:24:30] the overall message of this study as stress can be something that makes you better, but it is a question of how much, how long and how you interpret or perceive it. We'd like to mention a few of the science and technology events happening locally over the next two weeks. Rick Karnofsky, Julian and Renee arou present the calendar. NASA astrobiology researcher and Lawrence Berkeley fellow in residence, Felisa Wolf Simon is delivering tonight. Future Friday's [00:25:00] lecture at the Chabot Space and science center at 10,000 Skyline Boulevard in Oakland. She'll be discussing the chemical elements that can support microbial life on earth. Drawing from molecular biology, biochemistry and physiology. Admission is $23 in advance. Visit shabbos space.org for more info this Saturday come to the UC Berkeley campus for the [inaudible] Speaker 6: bears annual kal day. Over 300 lectures, workshops [00:25:30] and presentations will be available with topics ranging from how the interplay of light with the atmosphere can create rainbows to a demonstration from the first laundry folding robot. Rosie Cal Day's tomorrow April 20th held on the UC Berkeley campus and open to the public events. Begin at 8:00 AM go to [inaudible] dot berkeley.edu Speaker 1: false schedule of events April 22nd through April 26th is national parks week. During this week, [00:26:00] admission to all US national parks is free. Put on your hiking boots and visit the nearest national park to you. Speaker 6: On April 27th Berkeley High School will host the day long Alameda County apps challenge contestants are asked to create apps that will address community needs. Using Alameda county open datasets apprise of $3,000 will be awarded to the most inventive and user friendly app. Well, second, third and honorable mentions will also be meted out. Alameda county [00:26:30] invites participation from residents of all skill levels and age groups. The apps challenge is part of a nationwide movement to increase transparency and implement open data policies in governmental organizations. The event be held at Berkeley High School Speaker 1: in downtown Berkeley from 8:00 AM to 7:00 PM on Saturday, April 27th it costs $15 to participate with discounts for students and seniors. There has been a rapid spread of sudden oak death pathogen [00:27:00] referred to Assad over the East Bay hills, specifically in north Berkeley and Montclair. Professor Matteo Garber, Loto, head of the UC Berkeley forest pathology and my collegey lab has been tracking the spread through annual area surveys. Garber Lotos team is looking for volunteers to help conduct annual spring surveys to find diseased trees. There will be several training sessions for volunteers in the bay area. The Berkeley session is on Saturday, April 27th at 1:00 PM [00:27:30] on the Berkeley campus in one 59 Mulford Hall. For other training sessions in the bay area. Searched the web for sod blitz project, but first after dark at the new exploratorium in San Francisco. [inaudible] on Thursday May 2nd after dark is the exploratorium monthly evening program for adults 18 and over. Admission for non-members is $15 in addition to the museums regular exhibits, there will be live music films and [00:28:00] the lectures. The theme this month is home and you can hear about how an empty warehouse on pier 15 was transformed into the explore Torrens new home. Karen [inaudible]. We'll discuss the human microbiome and Ron Hitchman. We'll talk about what makes earth and other goldilocks planets just right for sustaining life. For more information, visit the exploratorium.edu Speaker 6: on Friday May 3rd the San Francisco ASCA scientists lecture series [00:28:30] will host a workshop on crafting the perfect science story. Editors of the science writer handbook will share personal stories of working in the field and address questions about building sustainable science writing careers. The May 3rd event will begin at 7:00 PM in San Francisco's bizarre cafe. More details can be found online at ask a scientist, s f.com Speaker 2: [inaudible] [00:29:00] a character in the show is by lost on a David from his album, folk acoustic and available by it. We have Commons license 3.0 and attribution editing assistance provided by renew route 90 spectrum. If you have comments about the show, please send them to us. [00:29:30] Our email address is spectrum lx@yahoo.com join us in two weeks. Same time [inaudible]. See acast.com/privacy for privacy and opt-out information.

Flaminia Catteruccia discusses the molecular basis of mating and reproduction in Anopheles gambiae mosquito. Her research provides insight into the mosquito reproductive biology to better develop vector control. Catteruccia is Associate Professor of Immunology and Infectious Diseases at the Harvard School of Public Health.TranscriptSpeaker 1: Spectrum's next. Speaker 2: [inaudible] [inaudible] [inaudible] [inaudible] Speaker 3: [inaudible].Speaker 2: [inaudible].Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews, featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 4: Good afternoon. My name is Brad swift and I'm the host of today's show. Our interview is with Dr Flaminia cutthroat Chia associate professor of immunology and infectious [00:01:00] diseases in the department of the same name at the Harvard School of Public Health. She is also an associate professor at the University of [inaudible] in Italy. Malaria is a leading cause of death in tropical and subtropical regions. The plasmodium parasite that causes malaria is transmitted by the biting of female [inaudible] mosquitoes. Dr Cutthroat Chias group studies the molecular basis of mating and reproduction in both the female and male of [00:01:30] four species of mosquito. They are looking for the most effective and robust strategies to frustrate mosquito reproduction. Overall, they aim to provide insight into the reproductive biology of this malaria vector, which until recently remained largely unstudied. So the new targets for vector control can be developed. And Dr Cutolo Chia was in the bay area recently for a conference and I was able to arrange an interview Flaminia Katja, welcome to spectrum. [00:02:00] Thank you. What'd you give us an overview of your current Speaker 3: object? Yes, sure. So my research group is based at the Harvard School of Public Health, uh, is working on, uh, the biology of the mosquitoes that transmit malaria in Africa. And mother is still a massive problem for tropical and subtropical countries, but in particular for Africa as it scales almost a million people every year and infects not 200 million people [00:02:30] every year. So it's a massive social and economical problem and malaria is transmitted by mosquitoes. So we believe that if we can stop mosquitoes from transmitting malaria, then we can solve a big problem for the countries that are affected. Three particular, my group focuses on studying some aspects of the mosquito biology that are important for malaria transmission and will focus on reproduction on how mosquitoes reproduce, what makes them fertile. Because [00:03:00] at the end of the day, our goal is to develop novel methods to control mosquito populations. And we think that we could control them by introducing sturdy to international populations as an alternative to what's already been done now, which is mainly based on the use of insecticides to kill them. Speaker 3: And, but they have to be quite targeted ways to use the insecticides by pushing these insecticides on mosquito nets. So that mosquitoes that try to bite on night while people are asleep and the nets get killed [00:03:30] or through sprays or insecticides inside and house walls to kill mosquitoes at arresting indoors. But these methods are not sufficient to stop moderate transmission. And also mosquitoes are becoming resistant to the action of insecticides, which means they're not killed anymore and they change their behavior rather than biting at night inside houses to start by the outdoor and during the day so that insecticides can not get to them anymore. So our thought is our instead is on the idea that, uh, rather than killing [00:04:00] mosquitoes, we can sterilize them so that then there'll be fewer mosquitoes out there. They can transmit malaria and then eventually malaria transmission will stop. Speaker 3: And so we study how mosquitoes reproduce, what's important for their reproductive biology. And we have three major avenues or research. The first one is we try to understand what's important for reproduction because one tracking aspects of reproduction in the malaria mosquitoes is that the females have sex only once in their lives and after that they [00:04:30] completely switch off. They're not interested in more. And so this is quite a vulnerable step in the life cycle of our mosquito because it happens on once. So we are very much interested in understanding what is it that happens to females, what's the switch that completely abolishes that their receptivity to compilation. Because in principle, if we could understand what are the refactoring is as a call to further copulation, then we could induce the same mechanisms in variant females [00:05:00] and trick them into thinking that they've made it. And so they would make any model contributed to the next generations. Speaker 3: So that's a big area of our research where we try to understand what happens to females after copulation after sex so that we can identify what are those factors that change that behavior so that we can induce them. The second area or research and studies is a more translational side. We are interested in developing tools to induce the reality [00:05:30] in male mosquitoes. One idea of control is based on the release of males that are sterile. This males will of course try to find females to have sex with them and eventually those fund them. But there'd be no project coming out of these compilations. And so if we keep doing this over and over again, if you keep releasing sterile males, then we can sterilize most of the females that are natural populations and so the population will crush. And so with malaria [00:06:00] transmission, and so we are trying to find ways to serialize males in a genetic way, introduce genetic stability rather than using irrigations or chemo sterilizations as it's done for other insects. Speaker 3: Because it's important that whatever we do to fertility, it doesn't affect biology. The general biology of this mosquitoes and their behavior and also their fitness and that of competitiveness in terms of meeting and normally irritation or chemo sterilizations, those [00:06:30] can cause severe fitness costs to these mosquitoes. And so we got a little more subtle than we tried to study. So the mosquito DNA and understand what are the factors that are important for my facility so that we can interfere specifically with those factors. And so develop a male mosquito that is sterile and then we can release in the field. So that's our second area of research. And then a newer area research that we're interested in is in understanding what's the impact of what we do in terms of malaria transmission in particular, in terms [00:07:00] of what would be the impact of these measures on the ability of the female to transmit malaria. Speaker 3: Because if we introduce sterility in a population, how does that effect the partial development within those females? We don't want to develop mosquitoes that are sterile, but at the same time that are better at transmitting malaria. And so one new aspect of our research is trying to understand what's the link between reproduction and mosquitoes and Parkside development inside the female. So this [00:07:30] is broadly what our love is doing. Why is it that malaria is so lethal? Well, the mother has been eradicated from large parts of the world, has been eradicated from the u s from Europe and we are actually quite close already getting malaria in Africa as well in the fifties and sixties with the use of insecticides use a queening. And so drugs to kill the precise insecticides to kill mosquitoes. But unfortunately [00:08:00] those programs were stopped because of a number of reasons. And within a few years the number of Americans really went back to what it was before these programs were even started. Speaker 3: So one of the problems with malaria said it's a very dynamic disease from one single case, you can have tens and hundreds of secondary cases that can spread very quickly. So it's very difficult to control. So the synergy between the mosquito and the malaria [00:08:30] is the enabling factor in principle is a preventable and curable disease. It shouldn't be so deadly. However, our ability to control it in the countries where it's presence at the moment is limited by logistic reasons, lack of hospitals, lack of resources, and the fact that the mosquitoes are very efficient at transmitting the parasite. [inaudible] Speaker 4: [00:09:00] you were listening to spectrum on KALX Berkeley. Our guest today is Flaminia Qatari Chia molecular entomologist at the Harvard School of Public Health, researching mosquito reproduction as a way to combat malaria. How long has your project been going? We've been working on it for six [00:09:30] years. So that's kind of new. Yeah. And does it have a length of time or is it pretty open ended? Speaker 3: It's open-ended until I get funded. It's the funding. Yes, yes. Always is, isn't it? Yes. And of course, until it's relevant release, I think the funding will be there until this was a breakthrough. Yeah. A solution. Yes. Yeah. Yeah. And Udall, was that a completely empty niche? No one was doing that. So we are really the first ones looking at reproductive biology in this mosquitoes from a molecular [00:10:00] and genetic point of view. Most of the studies before us were performed at the ecological level. So there's actually quite a lot knowing about the ecology of reproduction, but not much known about genetic factors and the pathways that are important for fertility. That's something that is completely new. So whatever we find is novel. So it's exciting for us, but at the same time, we have to do everything you know, is, we have to start from scratch. So it's more challenging maybe Speaker 4: once [00:10:30] the mosquito has ingested the parasite, the malaria parasite from a human, how does it interact with the mosquito? Speaker 5: Okay. Speaker 3: The parasite has a complex life cycle inside the mosquito vector, and it takes a few days to complete from when the mosquito ingests the parasite. When the mosquito can inject the parasite into the next person, it takes about 12 days. And that's the time that the press site needs to go through different developmental stages. [00:11:00] And so once some mosquito takes sliders infected, then the process will have to leave the blood environments. There'll be a stage that happens inside the mosquito midgut and then the prosight will have to leave as quick as possible. Uh, the makeup before he, it gets killed by the mosquito enzymes, digestive enzymes particular, and then it'll have to find its way to the salivary glands, which are these tissues where saliva is produced by the mosquito. And once it reaches the Salami Glands, then [00:11:30] it can be injected into the next person because during blood feeding, the female will inject a little bit of saliva into the team of the person that is this biting. Speaker 3: And so during that process the process can be transmitted. Actually most mosquitoes don't even live long enough for the proceeds to develop. So that's a major roadblock or process in development. Is there any thought to trying to alter the parasite itself? There's a lot of research on modifying [00:12:00] the mosquito so that rather than allowing person development, they'll kill the parasite. And of course there's a lot of research on finding drugs that can kill across sites in people that are infected. And there is research on malaria vaccines as well. We don't have a vaccine yet. There is a vaccine that is now in Stage three trials that could be promising in combination with other control measures. It's quite clear that malaria will not be defeated by using a single measure. So [00:12:30] the use of insecticides, possibly the use of sterile males, hopefully combined with the use of drugs to confirm [inaudible] in people and hopefully also without, without vaccine that could be effective for awhile. We will need all these measures to control the spread of the disease. Speaker 4: How large your group is, is the group that's working on your project. Speaker 5: Okay. Speaker 3: My group is composed by about 10 people at the moment. Speaker 4: And what are the different scientific disciplines you've brought together [00:13:00] with that group? Speaker 5: Yeah, Speaker 3: well it's a combination of molecular biology and genetics and biochemistry. Also evolutionary biology, big of ecology as well. Speaker 5: Okay, Speaker 4: and within the group, how do you orchestrate the workflow of all that? How do you decide which thing you're going to focus on at what point in time Speaker 3: to go ahead and go forward with the research? Oh yeah, those are actually tough decisions sometimes because there is so much [00:13:30] that we can be doing, just so many different ideas. It's circulated in the lab and sometimes it's difficult to prioritize them. So in general, we do discuss ideas all together. I can come up with some ideas and then we discuss, uh, with the group and some we like the brainstorming and then more ideas emerge. And then we focus on what's more important according to our priorities. We always have to make choices. We tried to have projects that are most solid in a way that we [00:14:00] know will give us results quite quickly. And then at the same time also establish longer term projects for maybe bigger goals. So it's a combination of all the two. Speaker 4: What is the life cycle of this mosquito? Speaker 3: So the mosquitoes we work on, um, anopheles mosquitoes that, that are not fillings are the only mosquito, second trust mates, uh, malaria to humans and draw about 30, 40 and awful in species that transmit malaria. And we study in particular, um, our mosquitoes called [00:14:30] Anopheles Gambiae and that's the most important vector in Africa and therefore the most important actor in the world. But we also start in some other mosquitoes out important vectors in other parts of the world. We are now interested in southern American vectors, Asian vectors. So we have four different mosquito species in our lab for comparative studies and Life Cycle is from a female that is, I've been intimidated by a male. Then this female will need to feed them blog to develop eggs. And that's the step that is exploited [00:15:00] by the plasmodium parasite of malaria to be transmitted. And so the female will feed on blood preferentially on, on men, on humans. Speaker 3: She will develop her eggs and then the eggs will be fertilized by the sperm that is transferred from the male. The eggs will be laid water, so the eggs will hatch and give larvae. And then a pupa will with form that doesn't feed. And then after two days and adult will emerge from the PUPA. And so our, as a, as that [00:15:30] little step, males and females will have to find each other for copulation and then the female will have to block feed again. And so that the cycle can start all over again. So overall from egg to egg is about a couple of weeks. The Life Cycle Speaker 2: [inaudible]Speaker 6: this is k a l x Berkeley. The show is spectrum. Our guest is Flaminia [00:16:00] [inaudible]. She's working to eradicate malaria. Speaker 2: [inaudible].Speaker 3: Is there a side effect to affecting the mosquito population so thoroughly? Yeah, that's a very good question. What are the possible effect on the ecosystem of mosquitoes? Useful for anything? Do we need mosquitoes in this world? And these are very good concerns, very reasonable concerns. [00:16:30] However, the Fallon sets targeting fertility is a very specious Pacific control measure. Unlike the use of insecticides where you kill everything that comes in contact with insecticide, if you use mosquitoes to eradicate mosquitoes, that's a very selective way to do that. It's a very specific way to do that. So I think that the effects on the ecosystem will be very marginal, but of course that's something that will have to be followed and would have to be monitored, will be a very insane eco-friendly way to reduce monitor transmission because you would, [00:17:00] we would only target those pieces that cosmic me [inaudible] thousands of mosquitoes species on the planet and only 20 or 30 I at transmitting malaria so we wouldn't kill all mosquitoes and we would only have to target those that ugly at transmitting the disease. Speaker 3: With the mosquitoes that you're growing in the lab, how are you feeding them? We feed them differently depending on their developmental stage, so we, the larval stages, the early stages, we feed them with fish food or cat food and for the adults [00:17:30] we feed them with sugar solutions that both the male and the female will feed on. So it's water mixed with sugar and then the females, we have to feed them on bloods for egg developments, we feed them with blood that we buy from blood banks. So we've completely eliminated the use of animals for that, which is we are very pleased with. Speaker 4: Do you feel you're close with the sterilized male part of the project and do you have plans to try to take it to the next level? Speaker 3: Yeah, we, we are thinking [00:18:00] a lot now about how we can make our system more effective because the way we in use steroids in this males, it's very inefficient in the lab. We need more than a day's work to get 20 or 30 males that are sterile to how do we scale this up. We really need to push and hopefully we can work with engineers and find the best way to scale this up and do the automated way that can be much more effective. Speaker 4: [00:18:30] You're continuing to pursue the female side of it. Speaker 3: The female side of it is what's more exciting for us in a way because there's more biology behind it, but we're also very much interested in understanding what are the determinants of fitness in the males because when we make them sterile, we'll still need to make sure that there will be competitive for meetings with feel females. And so apart from studying the biology of reproduction in females, we're also very much interested in that in what makes a meal good [00:19:00] meal, a fit meal that will have good chance of success once it's released. So yeah, that's why we are studying both male and female reproductive biology. We are not just selling waist to induce 30 but also what are the determinants of fertility? Speaker 4: If you succeed in creating a sterilized male or a female that doesn't lay eggs, do you have a plan or is there a plan for how to introduce them into the wild [00:19:30] or is that something that would need to be developed when the time comes? Speaker 3: We don't have a plan as such, but we are starting to think about a plan in terms of the logistics of it. There is a lot of know how that comes from the release of sterile males for targeting other insects, species, insects, pieces that are mainly agricultural pests like fruit flies, Milo flies, school worms, potato. We will do that. Old insects that cause the via damage [00:20:00] to the agriculture. It's a drug programs and based on the release of millions of sterile flies all over the world really. And so all the issues concerning the mass production of these insects, the packaging and the distribution of these stallions, six to the places where they're needed and then the release, all those issues have already been sorted out for other insects and so in principle shouldn't be too difficult to transfer that expertise onto mosquito work. It [00:20:30] should be feasible. We don't have the expertise in ourselves, but working in collaboration with the people that have it, that should be possible. I'm optimistic that that could be done without huge efforts. Speaker 4: Are you teaching as well as doing your research? Speaker 3: Yeah, I have some teaching to do is not massive. I mainly teach postgraduate students and I teach while they work on, so it's infectious diseases. My teaching load is not very big. Maybe it will get bigger in the next few years because [00:21:00] I've just started a year ago and I'm enjoying it. I enjoy teaching postgraduate students very much because they're small groups and normally they're very interested, very dedicated and also they ask amazing questions. So it's actually quite fulfilling. I know that some of the Harvard students are just brilliant, so it's a different experience from what was used before. I like it very much. Yeah. But I really prefer doing research. You know, it's, it's like that's my first, uh, my [00:21:30] top priority is to do good research, but of course we have a mission to encourage the next generations to get into science and getting into research. I like the idea of contributing to that. Flaminia Katya, thank you very much for coming on spectrum. Welcome. Good luck. Thank you. Speaker 7: I'm gonna [inaudible] Speaker 3: um, Speaker 6: if you would like to hear a previous [00:22:00] spectrum show, they are archived on iTunes university, go to the calyx website, calix.berkeley.edu. Click on programming, select news, scroll down to spectrum and that section. There's a link to podcasts or send us an email@spectrumdotcalyxatyahoo.com and I'll send you the link. Speaker 2: [inaudible]Speaker 8: [00:22:30] a feature of spectrum is to present news stories we find interesting. When the news are Renee Rao and Rick Karnofsky, Speaker 9: the UC Berkeley habitus will play host to the first ever dreambox a three d printing bending machine. By the end of this month, the machine will allow users to take advantage of three d printing technology without paying steep up front costs for the machinery [00:23:00] to use. The machine users will first choose an item model within Dream Boxes Catalog upload one of their own via the web. Next, the print command is given and the order is sent to a cloud based print queue before being directed to the vending machine. Once the item has been created, it is put into a locker with a unique unlock code that is texted to the users. The creators estimate that each use of the printer will range from two to $15 on average depending on the complexity of the object and the materials used. Speaker 8: [00:23:30] A team from New Castle University reported in science that honeybees are three times more likely to remember a learn floral scent when they are rewarded with caffeine. Caffeine occurs in coffea and citrus species and to be pharmacologically Speaker 9: active but not repellent to the bees in higher concentrations. It is known to be toxic and repellent due in part to the bitter taste, but in lower concentrations that occur in nature. It offers a reward. [00:24:00] The team also applied caffeine to the brains of the insects and observed that it increased activity aiding the formation of longterm memories. Speaker 2: [inaudible].Speaker 9: A [00:24:30] regular feature of spectrum is dimension. A few of the science and technology events happening locally over the next few weeks. Rick and Renee present the calendar this March nerd night. East Bay will feature UCB associate Professor Matt Walker on Sleeping Memory Guy Branum on the invasion of Canada and the Chabot space and science centers. Jonathan Bradman on the night sky. This will happen Monday, March 25th at the new Parkway Theater in Oakland. Doors will open at seven show begins at eight. [00:25:00] Tickets are available online for $8 and all ages are welcome. Past spectrum guests, Michael Isen will be speaking to the Commonwealth club on the subject of reinventing scientific communication. While most scientific literature is now online, it remains as inaccessible to the public as it was centuries ago. With the physical limitations of print journals replaced by expensive publisher paywalls, [inaudible] who cofounded the Public Library of science. [00:25:30] We'll discuss the scientific journals and new open access models. Tickets are $20 or $7 for students with valid id. Speaker 9: The talk is on Wednesday, March 27th in San Francisco. There is a reception@fivethirtyandthetalkstartsatsixpmvisitcommonwealthclub.org for tickets and more info this April 2nd the ASCA scientist lecture series. We'll discuss tiny creatures with the ability to invade your body, [00:26:00] hijack your cells, change your DNA, and modify you physically and behaviorally to suit their own devious goals. Jack Mackarel, director of the Center for discovery and innovation in parasitic diseases will lead the talk on the parasitic organisms that live among and inside us. Some of the world's most pernicious diseases are caused by these supreme sophisticated organisms, but according to evolutionary biologist, parasites have also played a significant role in shaping the human species. The event will be held Tuesday, April 2nd [00:26:30] at 7:00 PM in Soma Street food park near the corner of 11th and Harrison. Leonardo art science evening rendezvous or laser has several talks this month. Speaker 8: Jess holding explains the use of light and other natural phenomenon to explore perception. NASA is Chris McKay will speak about the curiosity. Mars mission, USF Vagina and Nagarajan presents embedded mathematics in women's ritual [00:27:00] art designs in southern India. She'll talk about the geometry of rice powder paintings. Finally, Nikki, you Layla will discuss the mechanics and construction of marionettes. Laser takes place@stanforduniversityonaprilfourthfromsevenpmtoninepmmoreinformationaboutthelaserseriescanbefoundonthewebatleonardo.info.Speaker 9: That's pretty good. Tuesday, April 16th in the Tuscher African Hall, Mary Roach [00:27:30] will lead an unforgettable tour of the human insides. Questions inspired by our insides are taboo in their own ways. Why is crunchy food so appealing? Why doesn't the stomach digest itself? How much can you eat before your stomach burst? Can Constipation kill you? Did it kill Elvis? Roche will introduce her audience to the scientist who tackle these questions. She will then take the audience through her experiences in a pet food taste test, lab of bacterial [00:28:00] transplant and alive stomach. This lecture will take place Tuesday, April 16th at 7:00 PM in San Francisco for more information and to get tickets in advance, go online to cal academy.org Speaker 2: [inaudible] [inaudible] [00:28:30] music card during the show is by Lasonna David from his album folk and acoustic made available by a creative Commons license 3.0 attribution. Special thanks [00:29:00] to David Dropkin for helping set up the interview. [inaudible] thank you for listening to spectrum. If you have comments about the show, please send them to us via our email address is spectrum dot klx@yahoo.com join us in two [00:29:30] weeks at this same time. The [inaudible] [inaudible] [inaudible]. See acast.com/privacy for privacy and opt-out information.

In part 1, investigator with the Howard Hughes Medical Institute Michael Eisen talks about his research, the field, and both experimental and computational biology. Eisen is Associate Professor of Genetics, Genomics, and Development in UC Berkeley's Dept. of Molecular Biology.TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible]. Welcome to [inaudible] Speaker 1: section, the Science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews [00:00:30] featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Good afternoon. My name is Brad Swift. Thanks for tuning in. Today we are presenting part one of two interviews with Michael Eisen and associate professor of genetics, genomics and development in UC Berkeley's department of molecular biology. Iceland employs a combination of experimental and computational methods to the study of gene regulation [00:01:00] using the fruit fly Drosophila melanogaster as a model system. Isen and his colleagues have pioneered genomic approaches in modern molecular biology and our leaders in the emerging field of computational biology. In part one, Michael talks about how he got started in biology and how his research has evolved onto the interview. Michael Isen, welcome to spectrum. Thank you. My pleasure. Would you give us a narrative of how you initiated your research and how your research has [00:01:30] changed to what it is currently? Speaker 4: Okay. Actually, I grew up in a family of scientists. My parents were both biologists, so I always had an interest in biology. But as a kid, my talents were primarily in math and I was a heavy duty math geek and went to college expecting to be a mathematician and took this freshman calculus class and all the hardcore math geeks tuck. And I did fine. I did well in the class, but [00:02:00] there were several people in the class who were clearly a notch better than me in a way that I think you only can realize and you know, basketball and mathematics at the age of 18 that you're not destined to be the best. And I think math is a field where if you're not the best, it's just kind of boring. And so I stayed as a mathematician and math major in college, but I started increasingly taking a lot of biology classes and had more or less, you know, realized that biology was what really captured my, my attention and [00:02:30] my heart. Speaker 4: And so I went to graduate school but had the idea that I'm interested in biology, but I'm really good at math. So there must be some way of combining these two things. And so I entered a graduate program in biophysics, which is sort of a place where people who are interested in biology maybe haven't taken all the prereqs for a normal biology department but also have a quantitative background go cause. And so, you know, in the way that people sort of drifted into things, I drifted into working on protein structure and [00:03:00] did my phd studying the evolution of the proteins on the surface of flu viruses and using a combination of experimental work and I would hesitate to call it mathematics. It was really just sort of kind of physics and it's, it's a lot of data. You generate a lot of raw data, you generate a lot of data on the coordinates of individual protein molecules and things that they might bind to. Speaker 4: And so it was very natural to start using computers in that work. You know, my background was not in computer science. I programmed as a kid [00:03:30] because my grandfather bought me a computer and I taught myself how to program and I wrote programs to, you know, keep track of baseball statistics and other things like that. In College, I basically never programmed anything in the math department I was in. It was considered not math that you were touching a computer. And so I didn't really do anything with computers until I got to graduate school when you started seeing all this data coming down the pipe. But I wasn't particularly interested in structural biology and I discovered that through six years from graduate school that [00:04:00] although I liked doing it, it wasn't intellectually satisfying, was too small. You're working on one sugar bound to one protein in one virus and I was having trouble seeing how that would expand into something grand and whatever. Speaker 4: You know, the ambitions of, uh, of a graduate student wanting to do something big. And I got lucky in the way that often happens in that my advisor had a colleague he knew from an advisory board. He sat on and he was coming into town because his brother was getting some honorary degree [00:04:30] and I met him in his hotel room, Austin. And he had with him, uh, glass microscope slide onto which had been spotted down little pieces of DNA, each of which corresponded to one gene in the yeast genome. So it's about 6,000 genes in the yeast genome. And you could see them because there was still salt in the spots, but it was a very evocative little device. You could sort of hold it up in front of the sun and you could see the sun sort of glittering on all these little spots. Speaker 4: You could just see the grandness of [00:05:00] the device. Didn't know how people were using them. I didn't know what they would be used for. I didn't know what I would do with them, but I was sort of drawn in by the scale of it all. The idea that you could work on everything at once and you didn't have to choose to work on just one little thing and disappear into a little corner and study. Just that. And so my advisor said, oh, you really should go do this. They need someone who's, you know, understands biology, but can deal with the computational side of things. It's clear that this was going to generate a lot of data [00:05:30] and that, you know, he was right. I mean this was a field that really was in great need of people who understood the biology but could work well in the quantitative computational side of things. Speaker 4: So I packed up and moved to Stanford with a short stint as a minor league baseball announcer in between. Really it was just a very fortuitous time to have gotten into this new field. I mean, the field was really just beginning. So this was in 1996 the first genomes been sequenced, they were microbes, there's bacteria and yeast [00:06:00] and so forth. And we were just getting our first glimpse of the scale of the kind of problems that we were going to be facing in genomics. But what I loved about this device, which is a DNA microarray, it's the sort of became a very hot tool in biology for a number of years was that it wasn't just a computer, it wasn't just data in a computer. It actually you were doing to do experiments with this. I'm interested in biology cause I liked living things. I like doing experiments, I like seeing things and I didn't want to just disappear with someone else's data and [00:06:30] analyze it. Speaker 4: So I went to Stanford to work on these and it really was just this awesome time and we were generating huge amounts of data in the lab and not just me. There were, you know, dozens of people generating tons of different types of experiments and so forth. And we lacked any kind of framework for looking at that data constructively. You couldn't look at those experiments and figure out by looking line by line in an excel spreadsheet at what gene was expressed, at what level and what condition. It just wasn't [00:07:00] the way to do it. And so my main contribution to the field at the time was in bringing tools for organizing the information and presenting it visually and being able to interact with that kind of incredibly complicated data in a way that was intuitive for people who understood the biology and allowed them to go back and forth between the experiment in the computer and the data and really try to make sense of what was a huge amounts of data with huge amounts of information, but something nobody had really been trained to [00:07:30] look at. And so it was there that I really realized kind of the way I like to do science, which is this constant back and forth between experiments on the computer. In my mind and in what I try to teach people in my lab. There's no distinction between doing experiments on the bench or in the field or in a computer that they're just different ways of looking at biology. Speaker 3: This is spectrum line KALX Berkeley. Today, Michael [00:08:00] I's associate professor at UC Berkeley explains his research in developmental biology. Speaker 4: On the basis of that time at Stanford, I got a job at Berkeley and what I did when I started my lab at Berkeley was really tried to focus on one problem. I mean I had been working on a million different problems at Stanford where we had a huge group and a million different people working on, and I was sort of moving around from problem the problem and helping out people with their data or thinking of different experiments. And when I came to Berkeley, I really [00:08:30] wanted to focus on one problem. And the problem that had intrigued me from the beginning of working on the microarray stuff was figuring out how it is that an animal's genome, which is the same essentially in every cell in the body, how it instructs different cells to behave differently, to turn on different genes and to acquire different properties. And so partly because of the influence of people here at Berkeley who were working on fruit flies, I switched my research program to work on [inaudible] when I started my lab at Berkeley, the genome of that [00:09:00] had just been sequenced and I liked working with animals. Speaker 4: I like having something that moves around and you know, had some behaviors and so the lab started to work on flies and pretty much since then that's what we've worked on. That's sort of the story of how I got to where I am. So your research then is you're looking at flies over time? Yeah, I mean, I mean I see how the genes are expressed. I'd say we're looking at classified more as developmental biology in the sense that we're looking at how genes are expressed over time during the lifespan of a lie. To this day, [00:09:30] we can't look at a newly sequenced genome and say, oh well this is what the animal's going to look like. That is, I couldn't tell you except sort of by cheating and knowing, comparing it to other genomes. If I, you gave me a fly genome, I look at it, I wouldn't know it was a fly or a worm or a tree or it's just the way in which the organism acquires it. Speaker 4: Things that make them interesting, their form, their appearance, their function. We have just the tiniest scratch of understanding of how that works. And so it's, for me, the most [00:10:00] interesting problem in biology is how do you get in a complicated structure like an animal out of a single cell. And how is that encoded in a genome sequence? I mean it's a fascinating mystery that I thought, you know, when I first started doing this I thought we'd have solved that problem by now. Not Easily. You know, because we had all this new data, we had the genome sequences we could measure. And a lot of what my lab does is actually measure which genes come on when, during development and try to understand for individual genes where that's been encoded in the genome [00:10:30] and how that happens. And I just sort of figured, well, you know, the problem for all these years was not that the problem was that hard. Speaker 4: We just didn't have the right data to look at this problem. And now we can do these experiments. I can sequence the genome of a fly and in a day I can characterize which genes are turned on when during development. And I sort of naively thought, well, we'll just sort of put it into a computer and shake things up and be clever and we'll figure out how these things are related to each other. And I mean now it's laughable that I would've ever thought that, but it was a very, very complicated thing. It's a process that's [00:11:00] executed by very complicated molecular machines operating in a very complicated environment or the nucleus and it, you know, we really don't understand it very well. We've learned a lot, but it's not a problem. We really understand. And so what is it that you've accumulated in terms of knowledge in that regard? Speaker 4: What do you think you've learned? A small amount of this is coming from my lab, but this is a whole field of people looking at this. But that we know the basic way in which that information is encoded in the genome. [00:11:30] We know that there are tuneable switches that can turn genes on and off in different conditions. And we know basically what molecular processes are involved in doing that in the sense that we know that there are proteins that can bind DNA in a sequence specific manner. So they will stick only to pieces of DNA that contain a motif or a particular code that distinct for each of these factors. In flies, there's several hundred of these factors and for humans that are several thousand of these factors that bind DNA in a [00:12:00] sequence specific manner, and they basically translate the nucleotide sequence of the genome into a different kind of code, which is the code of proteins bound to DNA. Speaker 4: And we know from a million different experiments that it's the action of those proteins binding to DNA that triggers the differential expression of genes in different conditions. So if you have a particular proteins, these are called transcription factors. If you have one in a cell at high levels than the genes [00:12:30] that are responding to that factor will be turned on in that cell. And if there's another cell where that protein isn't present, the set of genes that responds to it won't be turned on. So we know that as a general statement, but working out exactly how those proteins function, what it is that they actually do to turn a gene on and off, how they interact with each other, what conditions are necessary for them to function. All of those things are, I wouldn't say we know nothing about it, but they're very, [00:13:00] very poorly understood. Speaker 4: A lot of this sort of simple ideas that people had of there being a kind of regulatory code that looked something like the protein code that we're, you know, amino acid code that people are familiar with, right, that there'll be a genetic code for gene regulation. The idea that that's true is long disappeared from our thinking in the sense that it's much more like a very, very complicated problem with hundreds of different proteins that all interact with each other in a dynamic way. Something bind recruits, something else. [00:13:30] The thing it recruits changes the coding on the DNA and essence to a different state and then that allows other proteins to come in and that somehow or another that we still really don't understand. You eventually reach a state where the gene is turned on or turned off depending on what these factors are doing and you know, while there's lots of models for how that might function, they're all still tentative and we're getting better. The techniques for doing these kinds of experiments get better all the time. We can take individual pieces of or Sophala embryo [00:14:00] and sequence all the RNA contains and get a really complete picture of what's turned on when the technology is improving to the point where we can do a lot of this by imaging cells as amazing things we can do, but still the next level of understanding the singularity in our understanding of transcriptional regulation is still before us. Speaker 3: Spectrum is on KALX, Berkley alternating Fridays today. Michael [inaudible], associate professor at UC Berkeley [00:14:30] is our guest. In the next section, Michael describes the challenges his research poses Speaker 4: and is the task then the hard work of science and documenting everything's, yeah. Mapping a little bit about just observing. I mean, I'm a big believer in observational science that what's limited us to this has been just our poor tools for looking at what's going on. I mean we still hard to visualize the activity of individual molecules within cells, although we're on the precipice [00:15:00] of being able to do that better. So yeah, it's looking and realizing when the paradigms we have for thinking about this thing are clearly just not sufficient. And I think the fields get trapped sometimes in a way of thinking about how their system works and they do experiments that are predicated on some particular idea. But you know, usually when you have an idea and you pursue it for quite a long time and it doesn't pan out, it's because the idea is wrong. Speaker 4: And not always, but I think the transcriptional regulation field has been slow to adapt [00:15:30] to new sort of models for thinking. Although that is changing, I think that there's a lot of activity now and thinking about the dynamics of DNA and proteins within the nucleus. You know, we tend to think about DNA as kind of a static thing that sits in the nucleus and it's a, it's sort of read out by proteins, but really much more accurate as to think of it as a living kind of warned me like thing in the nucleus that gets pulled around to different parts of the nucleus and where it is in the nucleus is one way in which you control what's turned on and off. And I think people are really [00:16:00] appreciating the importance of this sort of three-dimensional architecture of the nucleus as a key facet and controlling the activity that there's, the nucleus itself is not a homogeneous place. Speaker 4: There is active and inactive regions of the nucleus and it's really largely from imaging that we're learning how that's functioning and you know, we as the whole field and are there lots of collaborators and people who are doing work? Yeah, I mean I'd say oh yeah. I mean it's a, it's an active feeling. Pay Attention to [00:16:30] oh yeah. So it's an active, if not huge field and not just in flies. I mean, I think it's transcriptional regulations of big field and in particular in developmental biology where amongst scientists we're interested in how animals develop. It's long been clear that gene regulation is sort of sits at the center of understanding development and so people interested in developmental biology and have long been interested in transcriptional regulation and I think everybody's got their own take on it here. But yeah, it's a very active field with lots of people, including several other people at Berkeley who are doing really [00:17:00] fascinating stuff. Speaker 4: So it's not out in the wilderness. This is not the hinterlands of science, but it's um, it's a nice field to work in about appropriate size. Our annual meetings only have a thousand, a few thousand people. It's not like some of these fields with 25,000 people. I can realistically know all the people who are working on problems related to ours and I literally know them and I know what they're doing and we sort of exchange ideas. So I like it. It's, it's nice community of people. [00:17:30] Is the field driving a lot of tool development? Absolutely. I say, this is something I really try to encourage people in my lab and people I trained to think, which is when you have a problem, you should be thinking not what am I good at? What can I apply to this problem? What technique has out there that would work here? Speaker 4: But what do I need to do? What is the right way to solve this problem? And if someone else has figured out how to do it, great, do it. But if they haven't, then do it yourself. And I think that this applies sort of very specifically [00:18:00] to doing individual experiments, but also to this broader issue we were talking about before with this interplay between computation and experiment. I think too many people come into science graduate school or wherever, thinking, well, I'm an experimentalist or I'm a computational biologist or whatever. And then they ask a question and then the inevitably hit the point where the logical path and pursuing their question would take them across this self-imposed boundary. Either you're an experimentalist who generated data and you're not [00:18:30] able to get at it in the right way and therefore, you know what you really need to be doing is sitting at a computer and playing around with the data. Speaker 4: But if you view that as a boundary that you're not allowed to cross or you're incapable of crossing, you'll never solve it because it almost never works. You almost never can find somebody else no matter how talented they are. Who's as interested in the problem that you're working on as you are. And I think that's a general rule. Scientists should feel as uninhibited about pursuing new things even if they're bad at it. It's certainly been a mantra [00:19:00] I've always tried to convey to the people in my lab, which is, yeah, sure, you come in with a computer science background and you know you're a coder and you've never picked up a pipette or grown a fly. But that's why the first thing you should do in the lab is go grow flies and vice versa. For the people who come in perfectly good in the lab but unable to do stuff in the computer, the first thing you should do is start playing around with data on the computer and it doesn't always work and not everybody sort of successfully bridges that gap, but the best scientists in my mind are ones who don't [00:19:30] circumscribe what they're good at. Speaker 4: They have problems and they pursue them. When something like visualization, is that a bridge too far to try to embrace that kind of technology? I've always done that. I mean I almost every time I do an analysis in the computer, I reduce it to picture some way or another. You know, because of the human brain, no matter how fancy your analysis is, the human brain is just not good at assimilating information as numbers. What we're good at as thinkers is looking at patterns, [00:20:00] finding patterns and things, looking at looking at images, recognizing when patterns are interesting and important, and there's a crucial role for turning data into something the human brain can pull in. And that's always, for me, one of the most fun things is taking data that is just a string of numbers and figuring out how to present it to your brain in a way that makes some sense for it and the refinement of it so that it's believable. Speaker 4: Yeah, and so then you can do it over and over and over and get the same result. Yeah, and all, I mean it is one of the dangers [00:20:30] you deal with when you're working with, when you're relying on human pattern recognition is we're so good at it that we recognize patterns even when they don't exist. There's a lot of statistics that gets used in modern biology, but often people I think use it incorrectly and people think that statistics is going to tell them what things are important, what things they should be paying attention to. For me, we almost entirely used statistical thinking to tell us when we've fooled ourselves into thinking something's interesting, you know, with enough data and enough things going on, you're going [00:21:00] to find something that looks interesting there and having a check on that part of your brain that likes to find patterns and interesting things is also crucial. Speaker 4: You know, I think people understand that if you flip a coin three times, it's not that we are trying to land on heads, but they have much, much harder time thinking about what happens if you flip a coin a billion times. We're struggling with this in biology, this transformation from small data to big data, it taxes people's ability to think clearly about what kinds of phenomena are interesting and aren't interesting. [00:21:30] Big Data is sort of the promise land now for a lot of people. Yeah. I'm a big believer in data intrinsically. If you're interested in observing things and interested in understanding how they work, the more you can measure about them better. It's just that's not the end of the game. Right? Just simply measuring things that doesn't lead to insight. Going from observing something to understanding it. That's where the challenges and that's true. Whether you're looking at the movement of DNA in a nucleus or you're [00:22:00] looking at people by a target, right? Like the same. It's the same problem. Speaker 3: This concludes part one of our interview with Michael [inaudible]. On the next spectrum, Michael Eisen will explain the Public Library of science, which he [inaudible]. He will give his thoughts on genetically modified organisms and a strategy for labeling food. He discusses scientific outreach and research funding. Don't miss him now. Our calendar of science and technology [00:22:30] events happening locally over the next few weeks. Rick Karnofsky and Renee Rao present the calendar Speaker 5: tomorrow, February 9th from noon to one wild Oakland presents nature photography basics at lake merit. Meet in front of the Rotary Nature Center at 600 Bellevue Avenue at Perkins in Oakland. For this free event, learn to get more out of the camera you currently have and use it to capture beautiful photos of Oakland's jewel lake merit. [00:23:00] Bring your camera and you'll learn the basics of composition, camera settings, but photography and wildlife photography. Okay. Your instructor will be Dan. Tigger, a freelance photographer that publishes regularly in Bay Nature and other magazines. RSVP at Wild Oakland dot o r G. UC Berkeley Speaker 6: is holding its monthly blood drive. This February 12th you are eligible to no-name blood if you are in good health way, at least 110 pounds and are 17 years or older. You can [00:23:30] also check out the eligibility guidelines online for an initial self screening if you're not eligible or you prefer not to donate blood. There are other ways to support campus blood drives through volunteering, encouraging others and simply spreading the word. You can make an appointment online, but walk ins are also welcome. The blood drive will be on February 12th and the alumni house on the UC Berkeley campus will last from 12 to 6:00 PM you can make an appointment or find more information at the website. [00:24:00] Red Cross blood.org using the sponsor code you see be February 13th Dr. Bruce Ames, senior scientist at the Children's Hospital Oakland Research Institute will speak at a colloquium on the effects that an inadequate supply of vitamins and minerals has on aging. Speaker 6: Dr Ames posits that the metabolism responds to a moderate deficiency of an essential vitamin or mineral by concentrating on collecting the scarce proteins [00:24:30] to help short term survival and reproductive fitness, usually at the expense of proteins important for longterm health. This is known as triaged theory. Dr Ian Discuss ways in which the human metabolism has evolved to favor short term survival over longterm health. He will also present evidence that this metabolic trade-off accelerates aging associated diseases such as cancer, cognitive decline, and cardiovascular disease. The colloquium will be on February 13th from 12 [00:25:00] to 1:15 PM on the UC Berkeley campus in five one oh one Tolman hall February 16th the Monthly Science at Cau Lecture series will hold a talk focusing on the emerging field of synthetic biology, which applies engineering principles to biology to build sales with new capabilities. The Speaker, John Dabber is a mentor in the international genetically engineered machines competition or ai-jen and a UC Berkeley professor, [00:25:30] Dr Debra. We'll discuss the new technique created in J key's link's lab to make low cost drugs to treat malaria. He will also introduce student members of the UC Berkeley Igm team who will discuss their prize winning project. The free public event will be on February 16th from 11:00 AM to 12:00 PM will be held on the UC Berkeley campus in room one oh five of Stanley hall Speaker 5: on Tuesday the 19th how long now and Yearbook Buenos Center for the Arts Presents. Chris Anderson's talk [00:26:00] on the makers revolution. He describes the democratization of manufacturing and the implications that that has. Anderson himself left his job as editor of wired magazine to join a 22 year old from Tijuana and running a typical makers firm. Three d robotics, which builds is do it yourself. Drones, what based collaboration tools and small batch technology such as cheap 3d printers, three d scanners, laser cutters and assembly. Robots are transforming manufacturing. [00:26:30] Suddenly large scale manufacturers are competing, not just with each other on multi-year cycles are competing with swarms of tiny competitors who can go from invention to innovation to market dominance. In a weeks today, Anderson notes there are nearly a thousand maker spaces shared production facilities around the world and they're growing at an astounding rate. The talk is seven 30 to 9:00 PM at the Lam Research Theater at the Yerba Buena Center for the arts at 700 Howard Street in San Francisco. Speaker 5: [00:27:00] Tickets are $15 for more information, visit long now.org now to new stories presented by Renee and Rick. The Federal Communication Commission has released a proposal to create super wifi networks across the nation. This proposal created by FCC Chairman Julius Jenna Koski, is it global first, and if approved, could provide free access to the web in every metropolitan area and many rural areas. The powerful new service could even allow people [00:27:30] to make calls for mobile phones using only the Internet. A robust public policy debate has already sprung up around the proposal, which has drawn aggressive lobbying on both sides. Verizon wireless and at t, and t along with other telecommunications companies have launched a campaign to persuade lawmakers. The proposal is technically and financially unfeasible. Meanwhile, tech companies like Google and Microsoft have championed the ideas sparking innovation and widening access to an [00:28:00] increasingly important resource. We can add this to the growing list of public policy debate over our changing and complex relationship with the Internet. Speaker 5: A team at McMaster university as reported in the February 3rd issue of nature chemical biology that they have found the first demonstration of a secreted metabolite that can protect against toxic gold and cause gold. Biomineralization. That's right. Bacterium Delphia, [00:28:30] a seat of [inaudible] take solutions continuing dissolve the gold and creates gold particles. This helps protect the bacteria from absorbing harmful gold ions, but it also might be used to harvest gold. The researchers found genes that cause gold, precipitation, engineered bacteria that lack these jeans and observed that these bacteria had stunted growth and that there was no gold precipitation. They also extracted the chemical responsible [00:29:00] for the gold mineralization naming it delftibactin a, the molecule creates metallic gold within seconds in Ph neutral conditions at room temperature. Gold exists in extremely dilute quantities in many water sources and the bacteria or the metabolite might be used to extract gold from mine. Waste in the future. Speaker 3: [inaudible] the music her during the show is by Luciana, David [00:29:30] from his album foam and acoustic, released under a creative Commons license, 3.0 attribution. Thank you for listening to spectrum. If you have comments about show, please send Speaker 1: them to us. Our email address is spectrum dot k a l x@yahoo.com join us in two weeks at this same time. Speaker 2: [inaudible]. See acast.com/privacy for privacy and opt-out information.

Pioneers in Engineering is a UC Berkeley student-run project that provides STEM outreach in local high schools. PIE sponsors and supports a Spring semester robot competition. Guests include Vivek Nedyavila, Andrew Vanderburg, and David Huang. pioneers.berkeley.eduTranscriptsSpeaker 1: Spectrum's next Speaker 2: [inaudible].Speaker 1: [00:00:30] Welcome to spectrum the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Hi and good afternoon. My name is Brad swift and I'm the host of today's show. Our interview is with representatives of Pioneers and engineering, also known as Pi, [00:01:00] a UC Berkeley student run project. Since 2008 Pi has been doing stem outreach in bay area high schools, Pi sponsors and supports and annual spring semester robot competition, high school teams design, build and operate robots over seven weeks culminating in a thrilling final competition at the Lawrence Hall of Science Pineys UC Berkeley students to be mentors during this year as robot competition. Each [00:01:30] team gets a set of mentors to encourage and guide the team, helping them to realize their potential, explaining Pi, the stem outreach they do and why you may want to join our Vivek Nay Diallo Vala, Andrew Vanderburg and David Hawaiian onto the interview. I want to welcome you all to spectrum. And would you introduce yourselves and tell us what your major is? Speaker 1: Hi, my name is Vivek. I'm a UX major, electrical engineering and [00:02:00] computer sciences. I'm a junior. Speaker 4: I'm Andrew. I'm a senior physics and astronomy major. Speaker 3: Hi, my name is David. I'm a fourth year apply math and computer science major. Andrew, can you explain the history and goals of Pioneers and engineering? Speaker 4: Sure, so pioneer's engineering was founded in 2008 by Berkeley engineers. The general idea is that while there are a lot of good robotics competitions that provide science outreach to high school students, [00:02:30] a lot of them aren't very good at providing outreach to the students who need it. Most. The ones in the underprivileged schools. So pioneers in engineering or pie as we like to call it, is focusing on trying to provide that outreach. So we try to make it more sustainable so that they don't have to pay as much money every year and they don't have to have corporate sponsors. And we also try to make it more friendly so that they don't have to go out and search for their own mentors. They get their own mentors from UC Berkeley and we provide [inaudible]. Speaker 1: [00:03:00] And how did you decide on robots as the focus of your engineering challenge? Speaker 4: I think that robots are kind of a gimmick. They're cool, they're exciting and they have a lot of pop culture and references. But the lessons that we teach them could be applied to engineering, all sorts of different things. Perhaps we could do a science competition and get the same teaching out of it. Robots just provide something exciting. They provide a hook and they provide a climactic final competition where they can [00:03:30] have their robots, you know, compete head to head. [inaudible] Speaker 1: there is a certain kit aspect to what you're doing with the robots in terms of a known entity. A constraint. Speaker 4: Yeah. So we um, give them a very well-defined kit of parts which they can use so they don't have to start from scratch because building a robot from basic electronic components and pieces of metal or plywood is really hard. So we give them a good start. We give [00:04:00] them a kit which they can build upon. They don't have to do all of the electronics. They don't have to do a lot of the tedious work, but they can do something really cool with them in the end. Speaker 1: What's the funding source that you use for this competition? Speaker 4: We see corporate sponsorships. We go to companies like Google, Qualcomm, Boeing, and we ask them if they can support us, if they can. We advertise for them. We put their logos on our banners and our tee shirts [00:04:30] and they also get deductions for supporting charitable causes. [inaudible] Speaker 1: and are you a club? What is your organizational status? Speaker 4: We are technically a project of Tau Beta Pi, which is the engineering honor society and our finances and our organization go through them. Many of our members have or no, not affiliated with Beta Pi. They are recruited by us Speaker 1: beside the robot competition. Are there other projects within Pi [00:05:00] that you're working on? We have a team that actually goes to a high school called Ralph Bunche High School in West Oakland and this team does a program called Pie prep for these kids in which they have 13 or 14 modules of stem outreach kind of and they basically teach them cool things about science and technology and a little bit about robotics and physics and stuff like that and it's, it's once a week. It's intended to be fun and just spark their interest and also give them [00:05:30] a little bit of theoretical knowledge. This has been going very well this semester and from the results in the surveys that we've been taking, we're most likely gonna ramp it up next fall to even more schools. The exact number, we're not sure, but it's going to continue ramping up in the next few years and hopefully touch in the realm of 1314 schools in the area. We're hoping that this is going to be a very successful program and also inspire more interest in our robotics competition for the so we can have something good going on in the fall. It's [00:06:00] something in interest spring so it's like a year round kind of thing. Speaker 3: This is spectrum on k a l x Berkeley. Today's topic is pioneers in engineering. Three representatives from Pi join us. They are Vivek, Andrew and David. Andrew. How is it that high school's become involved in the [00:06:30] competition? Speaker 4: We do a lot of recruiting into high schools who fit our core mission, the ones who probably wouldn't be able to compete sustainably and the other robotics competitions that are out there. So we contact teachers and the sciences and we ask them if they're interested and if their students are interested in putting together a team and then they apply for a team and if we have room we'll take them. Speaker 3: What is the limit on teams? You have a capacity issue. Speaker 4: Yeah. We have a limit of about 20 teams could be up as many as 24 this year and the limitations [00:07:00] are put in place by our ability to produce kits and to provide mentors for them. We would rather have a good competition with 25 teams than one that stretched too thin with 35 Speaker 3: and do schools stick with it. Speaker 4: There is a core group of schools who seem to be building up somewhat of a legacy. They'll come back year after year. We actually just had our first student who is a four year high school participant in Pi Join Pi as a staff member [00:07:30] in college. Speaker 3: Great. That's the goal, right? In a way that's sort of the ideal. Andrew, when the teams are picked, they're picked by the teachers at the high schools. Speaker 4: The teams are I guess collected by the teachers at the high school, but they're based on interest. We've in the past tried to limit the number of people on the team, but we're moving away from that because um, we have a lot more mentors than we have in the past. Speaker 3: How do you try to keep the parody of the experience within [00:08:00] the teams and the resources that they have access to the equipment, the time spent? How do you, how do you try to balance all that? Keep everybody kind of on the same level. Speaker 4: So there are teams who have access to a machine shop in their high school and we can't provide that to everyone. But we do provide as a basic set of tools to anyone who wants them. We loan them out if they want to go to the high school and work with their team. And sometimes the high schools come to UC Berkeley and they can use our tools and our workspace in O'Brian Hall [00:08:30] in north side, we also try to ration the experience level of the mentors. We tried to provide the more experienced mentors to the less experienced teams. As a general rule, we try to provide equal experience and different types of engineering to each school. So each school should hope to have a mechanical engineer or someone who's mechanically inclined and someone who is electrically inclined or programming inclined. Speaker 1: And the number of mentors per team. Last year it ranged between four to six [00:09:00] of AVEC. Talk about your experience as a mentor on the robot competition. My experience at Ralph Bunche high school mentoring and was a series of ups and downs. But in the end it kind of culminated in something special. So started off with a few weeks of mentorship prep by um, Andrew and his mentorship team. They prepped us for what we would encounter a little bit of the social aspect of the kids, but mostly about the uh, technical mentorship. Ralph [00:09:30] onto high is a rather underprivileged high school in West Oakland. There were only three of them in the team and we had to struggle with people dropping out, people coming in because of the small size of the team, small quarrels that were involved, a lot of social issues that we were not as equipped for as mentors coming from UC Berkeley. Speaker 1: Um, not to mention the social barrier itself of where we have all come from in our lives compared to where these kids have come from. And [00:10:00] it was a really interesting experience for me because I actually have had a little bit of experience with kids from underprivileged backgrounds and the experience that I had in pulling my mentorship team into it with me trying to get everyone on the same page with these kids to not get frustrated with them, to not unequivocally say something and like have it mar the rest of our mentorship semesters. So it was a journey and it ended up being very rewarding, um, in the sense that [00:10:30] we got second place in the robotics competition and this team of three kids who were definitely the underdogs and it was just, you know, one of those quintessential underdog stories. They ended up getting second place and I was super proud of them. Speaker 1: So very rewarding experience. David, tell us about your experience last year as a mentor. I think the biggest and rather pleasant surprise, uh, during the tournament was at discrimination the week before and during the actual [00:11:00] tournament at the end of the season. The atmosphere was just absolutely incredible. We had, um, PAC has of spectators. We had epic music classing in the background and in both hers mining hardware. We had the scrimmage and the Lawrence Hom signs where we had to file tournament. The stage was very well prepared and when each team sent up their team members send their robot on the stage to compete. It gives you the feeling that you're these [00:11:30] stars on stage, sort of like maybe no gladiators in ancient Roman stadiums where you're the center of the attention of everyone around you and really at some level I feel like that's where colleges should be about is motivating students, motivating students, intellectual growth and also highlighting their achievements and I think in that sense Speaker 5: the Pi robotic competition has totally exceeded my expectation. I remember seeing a couple up the high school students [00:12:00] who ended up winning the competition, just crying on the stage and joy. I have no doubt that it had been a parade and really life changing experience for them. Speaker 3: Spectrum is on KALX Berkeley alternating Fridays. Today, we are talking with Vivec, Andrew and David about pioneers in engineering Speaker 1: as your involvement [00:12:30] in Pi giving you some insights into where you might want to go with your major. Speaker 4: My involvement in Pi has really been my first major experience in teaching and it turns out that teaching is a lot harder than you would think, especially teaching some of the difficult concepts that we have to do so quickly in our decal. It turns out that trying to break down the concepts into logical chunks and presenting them in a logical way is almost as hard, if not harder than learning them yourself. [00:13:00] So I found that teaching and learning to teach was a really good experience for me and it will help me presumably as I graduate and go to Grad school [inaudible] Speaker 1: because are you thinking of being a teacher? Speaker 4: I'm thinking of being hopefully a professor in the future. I hope that my experience in Pi will give me a leg up from working on that and hopefully make it easier for my students to learn in the future. Speaker 3: [inaudible] David, anything. Yeah. Speaker 5: So I try and Pi as a part of my effort to explore [00:13:30] more in computer science, which I started taking classes last year and I have to say during the course of last semesters tournament, I really enjoy working with the staff member, other fellow UC Berkeley students and Pi. And I also really enjoy working with the high school students on my team to the extent that, uh, I'm starting to look more and more into the idea of working at a technology startup. And I'm also fairly sure I'm going to do computer science as a second major along with math. [00:14:00] And so in that sense, I think it's really solidify my interests in this field. Speaker 1: VEC, how has pi affected your plans for the future? I've actually had, I guess in the last few weeks to think about this very seriously. And through talking with a number of people in Pie, I'm very, very inclined to do something kind of like this as a job in the future. Like being scientific outreach. Yeah, exactly. Scientific kind [00:14:30] of stem education. Stem outreach. Yeah. So there's um, a company called sparkfun that we have grown closer to over the last year and this is kind of exactly what they do. They have a sparkfun kit circuit skit and it's a solderless circuit skit where they can bring it to elementary, middle school classrooms and have these kids play around with circuits. They want to fund a trip across the nation teaching stuff like this to little kid. Just seeing things like this happen in the world makes me really rethink, do [00:15:00] I just want to become a fabrications engineer or something or like do I want to be a programmer or do I need something like this without there the risks are higher, but the reward, the potential reward is greater. Yeah, that's, that's how it's changed my outlook. What sort of a time commitment is there to being a Pi staffer or a mentor? Speaker 4: So being a mentor, we ask that you attend a two hour day call once a week. We ask that you mentor your teams [00:15:30] for at least two hours a week. And we also ask that you do a five minute progress report so that we know how your teams are doing. So if you add in transportation time, it's probably adds up to about six to eight hours a week of time commitment. That won't be distributed evenly necessarily because there'll be weeks where you have weekend events, which lasts all day. But I think that most peer mentors have found that the time commitment really isn't a problem because by the time that the time coming and gets large, [00:16:00] you really want to be there and it's a lot of fun. Speaker 1: And then for staff, so I know this isn't the time for staff to get involved or are you always looking for staff or is it really just at the fall? Speaker 4: So we're always looking for staff. We do need mentors more than staff at this moment, but as a staff member, the time commitment is probably larger, probably order of 10 hours a week for the seven or eight weeks around the competition. At other times it's less, more [00:16:30] of a year long job than this intense seven week period as it would be for a mentor. Speaker 1: Andrew, if you want to become a mentor, what's the process? Okay. Speaker 4: For people who are interested in being mentors to the high school students, we are going to have a mentoring decal which starts in early February. On February 4th that decal will run from six to 8:00 PM on Mondays and Thursdays. And it's once a week. You choose one of those two times and uh, you come to that, you learn [00:17:00] about robotics and then we scheduled for a seven week period starting in March time for you to go to your high schools every week. That's flexible, depends on your schedule, on the high school schedule. The final competition will wrap up around April 28th Speaker 1: and the kind of people you're looking for talk about who can be a mentor, Speaker 4: right? So we accept mentors from every background. We believe that our decal will teach them the basics that can get them [00:17:30] to help their high school students out. And we also believe that learning about engineering is not the only purpose of Pi. We think that other students from other backgrounds can contribute just as much as engineers can because in the end it's not just about teaching them to be engineers, it's about teaching them to go to college, what it's like to be in college, what it's like, enjoy learning and some of our best mentors in the past have not been engineers. Speaker 6: [inaudible]Speaker 3: [00:18:00] pioneers in engineering on spectrum detailing their stem outreach. This is k a l X. Speaker 6: [inaudible].Speaker 3: Do you all find Pi to be a real supportive community for your own personal interests as well as the collective interest of doing the competition and start with the Vac, right. [00:18:30] Then we'll go around. Speaker 1: For me it's the spirit of kind of like self-expression. You're doing something very special for these kids. It's a form of giving someone else what I had when I was a kid in the form of my dad or in the form of other people in my life who influenced me towards engineering and to motivate kids or like allow them to have that confidence in themselves. To go towards stem and at least higher education, one of the main goals of Pie. [00:19:00] Don't be afraid to apply to college and stuff like that. That form of self expression and just kind of helping these kids and self fulfillment through that, that the perk that I get, Speaker 4: I feel as if Pi is a really supportive community because even though the going is often tough as a staff member, there's a lot of pressure because he wants to deliver a good competition to the students. Everyone's willing to help each other out. And I think that it's a really good community to have around you because [00:19:30] even though we're all doing a lot of work and sometimes we can get stressed, we remember that we have each other and that we're all working towards a common goal, which is to give these students a good educational experience. And that's something that a lot of them don't get in school. Speaker 5: So coming from the perspective of surf a semi insider outsider, uh, as a pass mentor, um, I think Pi has given me the opportunity to meet a lot of other people who are similarly interested in science and engineering [00:20:00] from the perspective that these are wonderful things to learn about and to see happen in everyday life instead of just something that you learned together job. And going along that perspective, having met all these really interesting people, empire has given me more social avenues to while to hang out, for instance, for Thanksgiving or just took walk around campus and to know that there are all these people around me who are also likewise striving for a similar goal. And that's comforting to know. Speaker 3: [00:20:30] Vivek, Andrew and David, thanks very much for being on spectrum. Thank you. Thank you for having us. Speaker 2: [inaudible] now our calendar of local science and technology events over the next two weeks, Renee Rao and Ricardo [inaudible] present the calendar. Speaker 7: [00:21:00] Okay. Dr. Shannon Bennett, associate curator of microbiology at the California Academy of Sciences. We'll be hosting a lecture by HIV expert, Dr Leo Weinberger, who will discuss the engineering of a retro virus to cure HIV. While progress has been made in controlling the virus with heavy cocktails or combinations of drugs, more virulent and resistant varieties continue to arise, Weinberger will explore his idea of using the same virus that causes the disease to deliver [00:21:30] the cure. The event will be held at 12:00 PM on Saturday, January 26 tickets will be on sale at the California Academy of Sciences website, $15 for adults and seven for students or seniors. Martin Hellman, Speaker 8: the co-inventor of public key cryptography is presenting the free Stanford engineering hero lecture at the Long Engineering Center at Stanford on Tuesday, January 29th from seven to 9:00 PM [00:22:00] with reception after his talk on the wisdom of foolishness, explorers, how tilting at windmills can turn out. Well in the 1970s Homan was competing with the national security agency who had a much larger budgets than he had, and it was warned that the NSA may classify any accomplishments he made. Despite this with help from Whitfield Diffie and Ralph Merkle, Hellman spearheaded systems that are still used to secure Chileans of dollars of financial [00:22:30] transactions a day. Visit www. That's certain.com for more info Speaker 7: east based first nerd night of 2013 we'll feature three Speakers, Daniel Cohen, a phd candidate in the joint UC Berkeley UCLA program. We'll speak about the theme of collective behavior, discussing the mechanism for everything from hurting sheep to sell your cooperation. Andrew Pike, a u Penn geologist by trade has also been [00:23:00] a contender in the competitive rock paper, Scissors League of Philadelphia. He will discuss some of the surprisingly complex strategies to the game. Lena Nielsen, the Innovation Director at the Bluhm center for developing economies at UC Berkeley. We'll explore technological solutions to extreme global problems that are also financially feasible. The event will start at eight but doors open at seven the event is held on January 28th at the new parkway located at four seven four [00:23:30] 24th street in Oakland. Science fans of all ages are welcome and can purchase the $8 tickets online. Speaker 8: On Tuesday, February 5th at 6:00 PM the Felix Block, a professor in theoretical physics at and the director of the Stanford Institute for theoretical physicist, Leonard Susskind is talking to the Commonwealth Club of San Francisco located at five nine five market street. The presentation is entitled the theoretical minimum, [00:24:00] what you need to know to start doing physics Susskind. We'll discuss how to learn more about physics and how to think more like a scientist. He will provide a toolkit to help people advance at their own pace. The cost is $20 to the public, $8 to members and $7 to students. Visit www that commonwealth club.org four tickets. Speaker 7: UC Berkeley's center for emerging and neglected diseases will hold its fifth annual [00:24:30] symposium this year. A variety of Speakers will present their work in various areas of infection and host response. The theme of the symposium, the keynote Speaker, dawn Ghanem will explore new developments in malaria drugs across the world. Sarah Sawyer, another Speaker. We'll discuss what typically keeps animal viruses from infecting humans. Other topics will include emerging African biomedical research on HIV AIDS, mycobacterium [00:25:00] tuberculosis, and new testing protocols for infectious diseases in developing countries. The symposium will be held in Stanley Hall on the UC Berkeley campus on February 11th from 9:00 AM to 5:00 PM it's open to anyone who registers@www.global health.berkeley.edu Speaker 2: [inaudible]Speaker 8: [00:25:30] the two news items [inaudible] that can Renee, university of Cambridge researchers published an article in Nature Chemistry on January 20th that indicates DNA conform not only the classic double stranded Helix, but also structures that are made from four strands. It's been thought that these square shaped g quadroplex structures may form in the DNA of cells, but this paper is one of the first to provide evidence that they do exist [00:26:00] in human cells. They forum when four Guanines make a special type of hydrogen bond. Speaker 8: The telomeres that protect Chromosomal DNA are Irish and Guanine and research points to quadroplex formation. And there is evidence that suggests quadruplex formation could damage these Tila mirrors and may play a role in how certain genes contribute to cancer. The team created a simple antibody that stabilizes these g quadroplex structures and showed how the structures are [00:26:30] formed and trapped in human DNA. When describing the long term goals of the research, the team told science daily that many current cancer treatments attack DNA, but it's not clear what the rules are. We don't aware in the genome some of them react. It can be a scattergun approach. The possibility that particular cancer cells harboring genes with these motifs can now be targets and appear to be more vulnerable to interference than normal cells is that thrilling prospect. Speaker 7: Okay. A joint [00:27:00] UC Berkeley Duke University Study of couches across the nation reveals a disturbingly high percentage of our sofas contained noticeable levels of toxins. 102 couches in 27 states were examined in this study. Of these 41% were found to contain the chemical chlorinated Tris, a known carcinogen. 17% of the couches also contain Penta BDE, which can cause hormonal disruptions. While chlorinated Tris was banned [00:27:30] from use in children's clothing in the 1970s it continues to be routinely used by companies seeking to make foam furniture more fire resistant. Currently, California State Law requires a certain degree of flame retardancy, but does not require that the types or amount of chemicals used to achieve this be disclosed. Well, most cotton will or down catches are naturally flame resistant. Any foam catches will almost certainly require added chemicals to meet current standards. Last June, [00:28:00] Governor Jerry Brown advised the state legislature to reform flammability standards for furniture. Once the new regulations are adopted, the chemical free couches should be available. Speaker 2: [inaudible] [inaudible] [inaudible]. The music art during the show is by on a David from his album folk and acoustic released under [00:28:30] a creative Commons license 3.0 attributes. [inaudible] [inaudible] [inaudible] [inaudible]. [00:29:00] Yeah. Thank you for listening to spectrum. If you have common staff to show, please send them to us via email. All right, email address is spectrum dot klx@yahoo.com join us in two weeks. This same time. Speaker 9: [inaudible] [00:29:30] [inaudible] [inaudible]. See acast.com/privacy for privacy and opt-out information.

Three members of The Berkeley Science Review (Editor-in-chief Sebastien Lounis, Web Editor Adam Hill, and BSR Author Lindsay Glesener) talk about the printed Review and the digital blog. They describe how the BSR has changed their view of science.TranscriptSpeaker 1: Spectrum's next. Speaker 2: Mm hmm. [inaudible]. Speaker 1: Welcome to spectrum the science [00:00:30] and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Good afternoon. My name is Brad Swift. In today's interview, Rick Karnofsky talks with three contributors to the Berkeley Science Review. The review is a student run by annual magazine that publishes in fallen spring. The review is also started, a blog that publishes four times a week to augment [00:01:00] the magazine. Our guests, our blog editor, Adam Hill, editor in chief Sebastian Lunas and author Lindsey Glasner. They talk about how it all gets done and what it means to them to do it. Here is Rick with the interview. First of all, welcome to spectrum. Thank you. Thanks. Thanks for why don't you introduce yourself Speaker 4: then what you do for the BSR and also what your research here at cal says. Hi, my name is Sebastian Lunas. I'm the editor in chief of the Berkeley Science Review and I'm also a fifth [00:01:30] year phd student in the graduate group in Applied Science and technology. At UC Berkeley. I do my research at the molecular foundry up at Lawrence Berkeley National Lab in Delia Milan's group and focus on studying nanocrystals of transparent conducting oxides. Great. Speaker 1: Uh, my name is Lindsey and I'm a writer for the BSR in the upcoming issue. I'm a graduate student in the physics department with a little bit of luck. I'll be graduating this December getting my phd and I work at the Space Sciences Laboratory [00:02:00] for Dr Bob Lynne. We build instruments that go on rockets, balloons and satellites to look at the solar system and sometimes things outside the solar system. Speaker 5: Yes sir. Right. For the blog. Is that right? I will be, yes. Okay. My name is Adam Hill. I am the editor of the PSR blog and we sort of work in tandem with the magazine to both keep people aware of the BSR in between issues and also to independently promote science and issues of [00:02:30] science education. Great. And your research here at cal? I am in Charles Harris's group in chemistry where I use ultra fast lasers to look at the dynamics of organic metallic catalysts. Okay. So can someone tell me a little bit about the Berkeley Science Review? Speaker 4: I'll take that one. So the Berkeley Science review is UC Berkeley is General Interest Science magazine. It's written, edited, produced entirely by UC Berkeley graduate students and it comes out twice a year. Basically the goal [00:03:00] of highlighting and showcasing and the cutting edge research that's going on at Berkeley, as well as taking a look at UC Berkeley science community and science history and doing so in a way that is accessible to a general audience. So it's not a technical publication, it's not a peer reviewed journal, it's a a general interest science magazine and it's written with the aim of being able to be picked up by anyone on campus and get an exciting look at what's going on at Berkeley. Part of the mission is also to help train editors and authors [00:03:30] through the process of putting together a professional level publication. And we're able to do that because we only publish two issues a year. So it gives us sort of a six month cycle to actually spend some time and work out really high quality content for the magazine as well as a really visually appealing layout. How long has the Berkeley Science Review been around? The science review was started in 2001 man, it's been producing two issues a year since then, so we're, we're going on 23rd issue coming out [00:04:00] this fall has a blog band active for that of the block's been around since Speaker 5: 2010 and a gold team was responsible for starting the blog since then. I think it has grown significantly in scope and readership. And how do you attract readers to both the magazine and and the blog for the blog in particular, we found that social media is one of the best routes to getting significant readership. Speaker 4: In terms of the magazine, I guess to answers, we generally just print as many as we can [00:04:30] and get them all over campus. And what's your approximate circulation? That we typically print between two to 3000 copies per issue and we distribute those across campus and then to a couple of local organizations and coffee shops around campus. Then we have a small number of subscribers, but we sort of know based on the fact that our magazine sort of disappear very quickly that we are getting a significant on our readership, but we're actually conducting a readership survey this fall to sort of get a better idea of how people actually come across the magazine, how many people are reading it, what their sort of [00:05:00] demographic makeup is, and we've also been trying to do a better job over the last year or so of integrating our magazine content with the blog. Speaker 5: And where should people look for that survey? Speaker 4: The magazine will have a prompt in it probably on the inside of the front cover with the link to the survey. We don't want people that haven't read the magazine to be filling out the survey and skewing our results. So if you do pick up the magazine interview. Yeah, exactly. If you do pick up the magazine, [00:05:30] please fill out the survey and let us know who you are. We're very interested and we'd love to hear from you. Lindsey, how did you come to volunteer as a writer? Yeah, my history with the Berkeley Science review is very short. Up until last spring, I was one of those people who would pick up the magazine when I sighed in the places on campus, but I also saw a call for pitches that was advertised to a lot of the departments. I think the particular place I saw, it was graduate student mailing Speaker 1: list in the physics department [00:06:00] and it offered the opportunity to pitch a story for the Berkeley Science Review. And I thought, well, I've got something interesting to write about. So I sent in a pitch and it was accepted. And what was your pitch? The idea for my story was inspired by my phd project, which is a project to put solar, observing x-ray instruments on a NASA rocket. And I thought it might be interesting not only from a scientific perspective, but there's also a bit of a humanist aspect to the story because I thought [00:06:30] people might want to know about what it's like to build one of these experiments and what it's like to go to a launch facility and an actually launched the rocket and once I got a little deeper into the topic, another thing that came into it was Berkeley's long history of building experiments like these. It really goes back to the beginnings of NASA, the whole thing developed together. And so that aspect kind of started taking over the story and became very important to it. Speaker 4: And then from there you just decided to volunteer to write for the blog [00:07:00] as well or, Speaker 1: well I think we've decided that it would be organic to have some blog entries as well because this is a project that is going to launch with any luck on November 2nd so without the timing would be appropriate to have a story about the project and then to have updates on did it launch, what's happening with the project throughout the fall. Speaker 4: This is sort of an example of how we're trying to really integrate the magazine and the web content where it's where it's organic to do so. We figured since it was an ongoing project, [00:07:30] it was a perfect opportunity to sort of transition people right from reading the magazine to reading posts on the blog and sort of integrate those two. Oh, that's great. And it's also worth mentioning that I think there's a significant cross section of the readership who don't necessarily encounter the magazine on campus, but who do read it on our website that said science review.berkeley.edu and do you have your entire back catalog online? We do. We're in the process of fully introducing the very earliest issues as actual searchable texts right [00:08:00] now their catalog in sort of a reader format where you can read them that way, but we're sort of moving towards making them more indexable and more accessible. Speaker 4: And is Lindsay's volunteer story typical? Do you normally draw authors from your readership? I would say her story is typical in that she received an email through somebody, one of the departmental email lists and that's how we do a lot of our outreach for authors. Uh, we have our own active email list that we reach out to when we do a call for pitches, but we also spray them out through the departments [00:08:30] and I would say most of our authors come from that outreach effort. A good proportion of them have read the magazine before. We've been making an effort this year to also get in touch with a lot of the first year students on campus. A lot of our writers are more senior Phd Students, but I think there's also a huge opportunity for first year Grad students that aren't bogged down their research to get involved. Speaker 6: [inaudible] this [00:09:00] is spectrum on k a LX Berkeley. Today's guests are from the Berkeley Science Review and it's Gluck. Speaker 1: How was writing for the BSR different or similar to writing for other publications? It's very challenging. I've spent the last six years getting used to scientific writing for publications or for my colleagues, and it was surprisingly [00:09:30] difficult for me to write for the BSR. I imagine that sort of a common story because it's a broader audience or, yeah, when we're writing for scientific publications, we use very specialized language with carefully chosen words that are really specific, but they're meant for people who already know what those words mean and are very comfortable hearing them and using them. I think when you're writing for a broader audience, you have to choose your words just as carefully or maybe even more so, but you [00:10:00] have to focus less on being so specific and accurate and more on whether the words will be understood and whether they'll be interesting. Speaker 1: Usually when I'm writing a scientific article, I don't need to worry about it being interesting. Hopefully. Interesting enough to site, I shouldn't mention that. In the magazine we have, I serve a number of different formats, so we have a number of different lengths of articles ranging from short little snapshots that are three or 400 words, two feature-length articles like the one that Lindsey wrote, which are typically two [00:10:30] to 4,000 words, sometimes even slightly longer. And so Lindsay jumped in as a first time author with, with one of the features with which I think are quite challenging. I think she did a great job. It was definitely a big barrier to getting started. When I first sat down to try to put some of my ideas on paper, I found it extremely challenging. After things had gotten rolling and I got feedback from the editors, which was very helpful. Speaker 1: Then it became a lot easier. Can you describe that editorial process a little bit more? Well, let's see. So we go through several drafts. So before [00:11:00] the first draft I had met with the first editor for my story. His name is Alexis and she and I had talked about our ideas for the story, which directions we thought it should take, kind of what topics we wanted to put together for the first draft and then I wrote that first draft and that was the one that for me was really challenging to get something down on paper. Then after sending that to her, she circulated it amongst some of the other editors and several of them gave me feedback on it, give me ideas, [00:11:30] pointed out which parts of the draft they thought were interesting, which ones needed more development or just weren't as relevant and then working from that and building it into a second draft is where I got a lot more inspired and writing. It became much easier at that point. It was definitely a fun article to write, although it was difficult because in order to write it, I got to delve a bit into the history of the laboratory. I work at the Space Sciences Laboratory and conduct [00:12:00] interviews with people who are around for some particular pieces of that history. So I don't want to make it sound like writing this article was a huge ordeal that I hated. It was actually a lot of fun. It was just putting the words on paper that I found very difficult at the beginning. Speaker 5: Did you find yourself interviewing a lot of faculty members who you might not have otherwise been interacting with for the piece? Speaker 1: I didn't interview anybody that I didn't know already. Ours tends to be a very intimate community where people know [00:12:30] each other, but I did have conversations with people that I probably wouldn't have talked with otherwise. So a couple of the people that I interviewed were people that I know quite well and have had conversations with before or maybe work with. And some of them were people I knew of but hadn't really ever had a chance to chat with them. And so hearing their stories about building rocket experiments when they were students was very interesting. Speaker 5: Did want to comment on that because I do find that, [00:13:00] uh, both in the case of the blog and the magazine itself, I think one of the best parts of both is the part that gets people out there and talking with scientists either in their field or tangentially related fields with whom they might never otherwise be interacting. It's very easy to get stuck in this little world of your advisor, the couple of students with whom you work on your project, you know, maybe a couple of friends who you see for beer each week. But beyond that, a scientist world can get very [00:13:30] narrow if you're not being proactive in avoiding that. And I think that both the blog and the magazine can really open new experiences to people who are writers and editors in terms of interacting with people in other disciplines or with people of significantly different ages within their own discipline who they might never have otherwise met. Speaker 1: On that note, I also wanted to say a couple of things that had occurred to me too. If you were talking and I wanted to talk about the [00:14:00] value of writing for the BSR for the authors as well as getting information out there for the public. I think this is a really useful thing for the authors who write for both the magazine in the blog in two aspects. I was thinking first about my personal experience and at the stage I'm at in my graduate student career, which is hopefully near the end, you get very zoned in on one particular subject. You kind of managed to convince yourself that this is the only thing in the world that matters [00:14:30] and you spend all your time on that and you can get a little burnt out on that. So for me at the time I started writing for the BSR, it was great to kind of force me to open up my mind a little bit and put my own project in the context of its historical perspective and also the perspective of the community. Speaker 1: It was a great way for me remind myself that there are connections to the community and that I'm not working in this kind of void. This black box down in the basement at the lab. The other thing I was [00:15:00] thinking when you mentioned how you're trying to get a lot of first year authors involved is that that could be really influential for them in choosing a thesis group. I know in the physics department it can be a little bit daunting because you have so many choices of which research group to work with, which particular topic to specialize in and I think a lot of first year physics students are just a little bit lost in that vast parameter space. So by writing for the BSR, I think that would probably encourage them [00:15:30] to find a whisper something they're interested in and start talking to people about it and I could definitely see that leading to them choosing that group to do their thesis work with Speaker 6: [inaudible].Speaker 4: Today's guests on spectrum are Adam Hill, Sebastian Lewis and Lindsay Glasner from the Berkeley Science Review Speaker 6: [inaudible].Speaker 4: [00:16:00] So the print publication is free? Yes. Is your entire budget from cal or do you get outside contributions? We do get quite a bit of funding from cow to the graduate assembly, which provides us with quite a bit of funding and then we also work with our printer. They have a relationship with an advertising agency who then in turn provide the suite of ads that are relevant to a science oriented publication that we are able then to put into our magazine. And how is the editorial stuff [00:16:30] selected each year or each issue or however frequently you guys change things up? It's basically whenever someone decides to leave and we put out a call for applications for the editorial staff, so most editors stay on for two to four issues, which is good because it helps with institutional memory and you get people that are more experienced that are able to coach. Speaker 4: The more junior editors talked about authors and editors. What about art? I mean the BSR is usually a very beautiful publication. [00:17:00] Sure. Where does that all come from? The layout staff. The BSR is sort of the unsung hero of the magazine and one of the most exciting experiences as an author and as an editor is about halfway through the process. We have a meeting with our layout staff where they first show us the designs they've come up with for various articles in the magazine and working with just the words for for quite some time. And then coming in and seeing it actually displayed in a magazine format that looks incredibly professional and is very well designed is incredibly exciting. So the way it works for the magazine is we [00:17:30] have a team of about 10 layout editors and an art director. We don't require the layout editors to come in with an experience. This is sort of another one of the examples of how the BSR is able to take people that are excited about learning about how to do layout, how many to do design and because of the timescale of the magazine, Speaker 5: it gives people enough time to learn those tools and working in an interactive team where they're going to get a lot of feedback on what they're doing and how it looks. And end up with a really amazing product. [00:18:00] What's that editorial process for the blog? Look back, we published four times a week with a crew of about a dozen authors at the moment, so we'll tend to go about a month between publications for an individual author and they'll come to me with some sort of idea. Can I write about pesticides in farming and California is efforts to insist on labeling GMO foods or something like that? You know, I'll say absolutely and the, the main interaction that I have at the [00:18:30] early stage of the process is regulating tone. Actually they're coming at it from the right viewpoint and coming at it from a balanced viewpoint where what they'll have at the end of writing this reporting more than opinion, although we also do have a category for opinion, but I like to try to avoid any ambiguity between the two. Speaker 5: Sure. I think that's an issue that a lot of blogs face is that it can be difficult to separate the editorial standpoint of the blog. Ours is basically scientists' cool from the editorial [00:19:00] standpoint of the individual authors, which can often be very specific and very passionate. Then I'll often not have particularly significant amounts of feedback or interaction with the authors until just a couple of days before their blog is scheduled to go up at which point we'll start hashing things together and seeing it in the digital format is a great way to really get a feel for how a blog post is going to come together part because you can't necessarily know how a blog reads till things like hyperlinks are in place. [00:19:30] Then we'll tend to hang it back and forth making changes when things are going well. We wrap up about the night before the blog post goes up and then the next morning we'll send it up and relate it. To your point earlier about, um, how the BSR has helped you as a researcher have a little bit more breadth than you might as a Grad student. Do you see it changing how you go forward after you leave cows, start your postdoc or whatever? Speaker 1: I think it wouldn't lead me to make decisions differently [00:20:00] after I graduate. Otherwise I don't exactly know what's on their highs and yet for me, but it gives me a little more inspiration about my field. So in that aspect, I suppose it could have a really powerful effect because the decision that I'll be faced with when I graduate is decision that many of us are faced with when we finished our PhDs, which is do you want to stay in academia? Do you want to switch to an engineering job where you can potentially make a lot more money and have a lot more say in where you live, who you work for, that sort of deal. [00:20:30] So inspiring students at a point in their graduate career at which they're about to make that decision, I think is a really good thing. So reminding them of some of the inspiring and motivating things about the field they're in could help to keep them there. The other interesting issue whenever we have anyone involved in science Speaker 7: outreach who are themselves scientists on the areas, how they see the rest of the scientific community looking at their science outreach. So I think Brad Vojtech who was on the show earlier talked about this tweet [00:21:00] of Damocles. You're always waiting until your outreach efforts like sabotage your actual career in some way. Did you have any reservations before for writing to our broader audience? Speaker 1: I would say personally, no. I didn't have any reservations about it. I think that there is a sort of pervasive fear about that in the scientific community. Like if you do too much scientific outreach then people will think that maybe you're not serious about the thing that you're actually working on. And I think that's mostly false. I hope that [00:21:30] people don't actually have that view, but I would say that pretty common. Certainly an anxiety that people have. Yeah, I think so. And there probably is some reason for it as well. I would not want to do scientific outreach to the point where I was not putting out scientific publications because especially as a woman, you want to make sure that people know you can do the work as well as do the outreach about it. I think that some of the barriers between people doing scientific research and doing scientific [00:22:00] outreach are starting to come down a bit. Speaker 1: At my laboratory we're starting to see more and more people who are working both on hard science and doing outreach as well. In particular, a friend of mine is now splitting her time, roughly 50 50 between those two things. And so she's hired by both departments at our lab. So I think any stigma about those things or at least starting to to come down and be resolved. So what should people interested in volunteering for the BSR do? [00:22:30] They should contact us by email, I think is typically the best route for both. So the email address for the Berkeley science if you blog is science review blog@gmail.com and for the magazine or for the BSR as an organization in general. It's the science review@gmaildotcomishouldalsomentionthatmostoftheinformationabouthowtogetinvolveddesirewebsiteatsciencereviewdotberkeley.edu well Lindsey, thanks for joining us. Thank you very much. Cool at all. [00:23:00] Well, thank you both for joining. Yes, thank you. Thank you very much. Speaker 2: Okay. Speaker 1: Regular feature of spectrum is to mention a few of [00:23:30] the science and technology events happening locally over the next few weeks. Here are Lisa kind of itch Renee Rao and Rick [inaudible] with the calendar. They should both space and science center is starting their next season of night school tonight on third Friday of the month Speaker 7: from seven to 11:00 PM Chabot opens their doors to adults 21 years in over with drinks, music, planetarium shows, telescope viewings and more. Number admission is $5 and general admission is $12 [00:24:00] visit www.chabotspace.org for more information. That's c h a, B o t space dot o r g. Remote Speaker 8: islands have been heralded as natural labs with some spectacular cases of rapid evolution in proliferation of species on November 17th at 11:00 AM in the genetics and plant biology building room 100 science at cal presents professor Rosemary Gillespie, director of the ESIC Museum of entomology [00:24:30] at UC Berkeley. She will address one of the most puzzling features of the high diversity of species on remote islands with her lecture entitled vagrant and Variability Evolution on remote islands. Science at cal is a series of free science lectures aimed at general audiences. On November 20th a museum of Paleontology at UC Berkeley will host a lecture by a university scientist, sue sumo Tomia, who will lead presentations on current research practice talks and discussions on topics [00:25:00] of paleontological interest. Coffee and snacks will be available. The lecture will be held in 1101 of the valley life sciences building on the UC Berkeley campus from 11 to 12:00 PM the new and wildly successful nerd night. East Bay will be held on Tuesday, November 27th at the Stork Club, 2130 Telegraph Avenue in Oakland, doors open at 7:00 PM and the three lectures begin at 8:00 PM you must be 21 and the emission is $8. [00:25:30] Join Calyx DJ eye on the prize and hosts in Davis and Rick Karnofsky for this scientific salon in Oakland Uptown district, Speaker 7: the Stanford Linear National Accelerator Laboratory. Slack is celebrating their 50th anniversary on Wednesday, November 28th at 7:00 PM in the Oshman family JCC Cultural Arts Center located in Jessica Lynn, Sal Townsquare at three nine two one Fabian way in Palo Alto. [00:26:00] The Commonwealth Club presents the event that is $5 for students, $10 for members and $15 for all others. Nobel Prize winner and director of Meredith's, Burton Richter and scientist Norbert Holt comp. We'll discuss how the accelerator has made cutting edge advancements from particle to astrophysics, advanced energy science and more. Sac has discovered two fundamental particles prove that protons are made of corks and shown how DNA directs protein fabrication. For [00:26:30] more on this event. Visit Commonwealth club.org now two news stories with Rennie Rao and Rick Karnofsky Science Daily has recently summarized an article by researchers at the Israel Institute of Technology published in nature materials on a novel way of splitting water into hydrogen and oxygen associate professor of material science and engineering. Abner Rothschild noted that their method of trapping light and the ultra thin films of ferric [00:27:00] oxide is the first of its kind. These rust films are about 5,000 times thinner than standard office paper and are inexpensive, stable in water, non-toxic and can oxidize water without being oxidized to get around poor transport properties. The team uses resonance, light trapping indifference between forward and backward propagating waves enhances the light absorption in quarter wave or in some cases deeper sub wavelength [00:27:30] films amplifying the intensity close to the surface, allowing charged carriers created by the light to reach the surface and oxidize water. This is a promising step into harvesting solar energy and storing it as hydrogen. Speaker 8: UC Berkeley's greater good science center has launched an interactive, shareable online gratitude journal through November. People in the campus community are invited to participate in the cal gratitude challenge by keeping a two week online [00:28:00] gratitude journal. The website was made both to conduct research and educate people about the powers of gratitude in their lives both before and after a 14 day period. Participants are asked to fill out surveys intended to measure traits like resilience, attachment tendencies, and happiest the projects designers are hoping for around a thousand participants. The website is located@thanksfor.org that's t h n. X, the number four [00:28:30] [inaudible] dot org Speaker 2: [inaudible]. The music or during the show is by Los Donna David from his album folk and acoustic released under creative Commons license 3.0 [00:29:00] attribution. [inaudible] [inaudible]. Thank you for listening to spectrum. If you have comments about the show, please send them to us via email or email address is spectrum@klxatyahoo.com [00:29:30] join us in two weeks at this same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

The Voyteks created the Brain Systems, Connections, Associations, and Network Relationships engine, or brainSCANr. The tool is used to explore the relationships between different terms in peer reviewed publications. http://brainscanr.com/TranscriptSpeaker 1: Spectrum's next Speaker 2: [inaudible].Speaker 1: Welcome to spectrum [00:00:30] the science and technology show on k a l x Berkeley, a biweekly 30 minute program bringing you interviews featuring bay area scientists and technologists as well as a calendar of local events and news. Speaker 3: Good afternoon. I'm Rick Karnofsky. Brad swift and I are the hosts of today's show. We're speaking with Jessica and Bradley Vojtech. Jessica is a designer and a developer who earned her master's of information management and systems here at cal and has [00:01:00] worked on several UC Berkeley websites. She's also working on the future of science education through projects like ned the neuron. Brad is in NIH, N N I g m s postdoctoral fellow at ucs f. He got his phd from cal. He's a prolific blogger and Zombie expert. The void techs are here to talk about brain systems, connections and associations and network relationships or brain scanner. This website helps people explore [00:01:30] how neuroscience terms relate to one another in the peer reviewed literature. They've documented their project in our recent journal of neuroscience methods paper. Speaker 4: Brad and Jessica, welcome to spectrum. Thank you for having us. Thanks. Can you tell us a little bit about brain scanner? Actually, I was at a conference here at cal hell by the CSA, so the cognitive science student association and Undergraduate Association here at cal that they had several neuroscientists and cognitive scientists come and give presentations and I was one of those people. I [00:02:00] was on a panel with a Stanford cognitive scientists at the end of the day. It was a Q and a. We got into a question about what can be known in the neurosciences and I had mentioned that the peer reviewed neuroscientific literature probably smarter than we are. There's something like 3 million peer reviewed neuroscientific publications and I was saying that that is just too many. There is no way for anybody to to integrate all of those facts and I said if there some automated or algorithmic way of doing that, we could probably find some neat stuff out and he disagreed with me pretty strongly on the panel [00:02:30] and I sort of stewed on that for awhile. Speaker 4: That ended up becoming the brain scanner project actually, which is using text mining to look at how different topics in the neurosciences relate to one another. We had conversation about this and I had just started about six months before my a master's program at the School of Information. So all of the stuff that he was saying really jived with what I was learning. So we got together after that. We talked about it off and on sort of over dinner and stuff occasionally, but I think it was [00:03:00] right around won't. Right, right before we found out you were pregnant. Right, right around Christmas when we first actually sat down together to work on it and that was just a random evening. We didn't have, well, we didn't have a baby at the time, so we didn't have much else to do. Brad was working on this thing and he said, you know, I've been working on this all day. Speaker 4: I'm trying to get this algorithm to work and see if we can get any results out of this. And I kind of challenged him. I said, I can do that faster than you can started taking my course. I had [00:03:30] all of these new skills that I just wanted to kind of show off. And I did. She actually beat me. You guys were both sort of where we were. We're basically coding. Yeah. We're sitting on the couch. Not really cause we weren't actually doing it together. We are using two different competitor competing. Exactly. So who do you see as the audience for brain scanner? Well I know the answer to that someone. Right. So I have colleagues who tell me a lot of Grad students actually mostly a who say that they use it as a stop for [00:04:00] searching. The peer reviewed neuroscientific literature. So pub med, which is the surface run by the National Library of medicine, which is part of the national institutes for health index is a lot of these peer reviewed biomedical journals. Speaker 4: Their search engine is quite good but it returns just textual information. You know, you just, you see the 20 most recently published papers or you know, however you want to sort it related to the search term or of interest. Yeah. So basically anybody who wants to create an app can get access to this data. You have to follow certain [00:04:30] rules, but otherwise you can get the information out of this database easily. In a, in a sort of standard format, we provide a graphic or a visualization layer on top of the search so you can put in one of these search terms and you can see here are the topics that relate to it very strongly in literature. Statistically speaking, you know, uh, by that I mean here are the words or terms that show up a lot in papers with the term memory for example. We also then list the papers that are related and you can see the full list of terms and [00:05:00] how it relates to different topics and things like that. Um, if I want to look at a brain region and say, okay, what are the other brain regions that are related to this can really quickly visually see that based upon these 3 million publications that we, we searched through Speaker 2: [inaudible]Speaker 4: you are listening to spectrum on k a l x Berkeley. We're talking to with user interface developer, Jessica Vojtech. And neuroscientists, Bradley Wojciech about brain scanner Speaker 2: [inaudible]Speaker 4: [00:05:30] do you see other potentially valuable ways you can harness PubMed's data or other reference sources? Yeah, absolutely. So one of the aspects actually of the paper that we published was ways to address that, that very question. Uh, initially we tried to publish the paper just as a here's a, here's a resource or one of the editor's version on that rejected the paper, said, you know, what, what can you do with this? And a, of course, you know, this is something we've been thinking about. And [00:06:00] so I tried to build a proof of concept. So one of the, one of the things that we showed statistically speaking that you can do with this, does the data they call hypothesis generation or semiautomated hypothesis generation. And this works off of a very simple idea. Um, it's almost like recommend their algorithms and um, like linkedin or Facebook or something like that. Speaker 4: You know, it's like if you know this person, you might know this person, kind of a friend of a friend should be a friend idea. You know, Rick and I, I know you and you know Rick, maybe you have a friend named Jim. And so statistically speaking, [00:06:30] Jim and I might get along right because you and I get along and you, and he'd get along, especially if I and Jim get along. And so you can go through algorithmically and say, you know, in the literature if Migraine for example, which is the example you give in the paper, uh, is strongly related to a neurotransmitter Serotonin, which I didn't know before we made the website actually, um, that in the medical literature there's a whole serotonin hypothesis from migraines I guess because Migraines respond to, uh, antidepressants, which are usually serotonergic drugs. So anyway, Serotonin [00:07:00] and Migraines are very strongly related and neuroscientists know a lot about the basic physiology of Serotonin, where in the brain is expressed and things like that. Speaker 4: And so on the neuroscience side, we know that Serotonin is very strongly expressed in, in a brain region called the striatum, which is sort of deep frontal part of the brain. And, uh, there's thousands of papers that talk about Serotonin and Migraines and Serotonin in this brain region, the striatum respectively, but there's only 19 papers or something like that to talk about that brain region and migraines. [00:07:30] And so statistically speaking, maybe we're missing something here, right? Maybe just nobody's really looked at this connection between migraines in that brain region. Maybe there aren't papers published on it because people have looked and there's nothing there. But, uh, that's why it's somewhat automated. You can go through this list of recommended hypotheses and you as an expert, I can go through that list and say, oh, some of these are nonsense. Or Oh, that's, that could be interesting. Speaker 4: Maybe. Maybe we should look into that. So it gives you a low hanging fruit basically. Yeah. And so that would be something [00:08:00] eventually I would like to build into the site. Are you continuing to analyze new papers as they enter in pub med? We haven't rerun it for awhile. I think there's something on the order of 10,000 new papers published every month in the neurosciences. But when you're standing in the face of 3 million, it's sort of drop in the bucket. So we, we worry running it every month or two. Um, but the results really don't change very quickly. Right. It's pretty stable. So yes, we, we should actually [00:08:30] run it again. It's been about six months or so. If you guys actually like, well I mean as a or perhaps how, you know, the ideas in the literature might change. For instance, that's actually something that I did do. Speaker 4: Um, I eliminated the searches to just bring the regions, so how different brain regions relate to each other across time. So I did a search for all papers published up to like 1905, which wasn't very many. Of course not in your, you know, you have an exponential increase in the number of being published. Okay. But then again, I ran it again for all papers published to like up to 1935, [00:09:00] 55, 75, 95 and you know, 2005, right? Uh, or 2011. And you could actually see how our understanding of how different brain regions relate change over time. And that was kind of neat. Um, if I was going to be a little bit statistically, uh, stronger about this, what I should have done in the original paper, and I didn't think about it until after we republished it was I should've run the semiautomated hypothesis generation algorithm, uh, on a limited amount of data. So I test data set up to like say 1990 [00:09:30] and then found plausible hypotheses from that Dataset and then run it again on the entire thing and see, you know, if we had found new things. And you know, if that corroborated what we've learned in the last 22 years. Speaker 2: [inaudible]Speaker 5: you're listening to spectrum on k a l x Berkeley. We're talking with Brad and Jessica Vojtech about brain scanner. They're a site to show links [00:10:00] that may exist between brain structures, cognitive functions, neurological disorders, and more as data mined from the academic literature. Speaker 2: [inaudible]Speaker 4: I mean this is a side side project for us. Yeah, Speaker 1: it was two weeks in $11 and 50 cents. And what did that go to? Um, coffee and coffee. Yeah. [00:10:30] Um, no it, it went into the Google app engine server time. So we actually were able to use Google app engine to distribute the processing, which is also what made mind my code a little bit quicker to run through all of this data. Speaker 4: I was doing single queries at a time and because we have 800 terms in the database and we have to do how every term relates to every other term, it's 800 squared,Speaker 1: try to buy two essentially. And then there's the roundtrip between between his your machine and the um, [00:11:00] pub met database. So, you know, you're making requests, you're making requests, making requests anyway. It was maybe three days, three days or four days. And I was able to do it in about two hours by um, putting it into the cloud and using app engine. So that $11 and 50 cents went to paying for the service and agree to say a hundred squared divided by two minus 800 a lot. So do you want to talk about how that dictionary of keywords was generated? Speaker 4: Initially I [00:11:30] had wanted to try and figure out how brain regions relate this. This grew out of my phd work actually at Berkeley. I worked with Professor Bob Knight who used to be the head of the neurosciences institute, Helen Wells neuroscience here. And my phd thesis was looking at how to brain regions, the prefrontal cortex and the Basal Ganglia related to working memory. And as I was standing for my qualifying exams, I was trying to figure out, okay, what are the brain regions that send inputs to [00:12:00] [inaudible], which is one of the parts of the Basal Ganglia and where he dies this ride in project two. And in order to figure that out, I spent, I don't know, two months off and on three months off and on over at the biomedical library here, digging through old, uh, anatomical papers from the 1970s and basically drawing little hand-drawn charts to try and figure out how these things connected. Speaker 4: And it really surprised me. It was frustrating because you know, here we are in, well, when [00:12:30] I was doing this, it was like 2008 right? And all I wanted to know is how different brain regions connect. And I was like, why can't I just go to a website and say, okay, striatum, what are its inputs and outputs? Like we have that information, right? Why can't I do that? Um, and so anyway, that was one of the motivating factors for me also. And there's actually a paper published in 2002 called neuro names. And then this researcher was trying to create an ontology of, of brain region names Ryan. So the terms that we use now in 2012 aren't necessarily [00:13:00] the same that people were using back in 1900 when they were first describing the basic anatomy. And so you have some Latin names for brain regions. Speaker 4: You have modern names for brain regions, you have names for different groupings of brain regions. So I referred earlier to the base like Ganglia, uh, and that is composed of, you know, maybe five different brain regions. And if I talk about three of those brain regions, uh, can I give examples? Is the putamen and the Globus Pallidus, uh, Globus Pallidus is actually contained [00:13:30] of two separate ones. And the putamen and Globus Pallidus if you combine them together or known by one name. But if you combine the putamen with the striatum, that's a different name. And so you actually have these weird venn diagram overlapping naming Schema. Speaker 1: There's a significant vocabulary problem, which is the term that we use in the information sciences. Basically the fact that you have multiple names for the same thing and you have the same name for some different things. So you know this venn diagram idea. Um, so yeah, [00:14:00] if you're going to use a very simple search algorithm, you have, you can't do it, you wouldn't, you're not going to get all of the results. So, um, I think our system tries to solve that vocabulary problem a little bit. Speaker 4: And then there's actually a researcher, um, Russ Poltrack drag, who used to be a faculty of neuroscience at UCLA and I think he's in University of Texas now. And he actually tried to create an ontology for cognitive term. So in cognitive science and psychology and cognitive neuroscience, you know, we have terms like working memory [00:14:30] and attention and in they're trying to create a whole ontology for how these different things really. So like working memory as part of memory, which you know, in memory also contains a longterm memory. And so we'll use his first attempt as a dictionary as well. And then we went to the NIH website and they've got a listing of all these different kinds of neurological disorders and we use that. So we pulled a bunch of publicly available data basically and use those dictionaries as our starting point. Speaker 1: And then we [00:15:00] also took suggestions from the people on our website almost immediately we started getting requests for more and different terms. So you had the, when you find two keywords that appear in a paper together, you assume that they're actually related. Can you comment on if people might have demonstrated that they're not actually related, how does that affect your system? Like some, like an instance in which, uh, it says this brain region is not connected to this other [00:15:30] brain region, right? Um, yes, we have assumed that there's a publication bias that if there is not a connection then someone does not publish a paper about that. Speaker 4: Okay. And negative publications or negative findings go very under reported in the scientific literature. Speaker 1: Right. So we're hopefully taking advantage of that. Hopefully the law of large numbers means that our data is mostly correct and it does seem to be that way. The example that Brad gave, uh, with the Allen Brain Atlas, [00:16:00] that there is certain corroborating evidence that seems to suggest that this is a, at least plausible connections. There's obviously no one say that better. No, that's perfectly scientifically accurate. I tend to get a little bit specific when I'm talking about this kind of stuff. Speaker 4: Is there already some sort of bias that might drive certain kinds of papers up? If the paper has a lot of buzzwords, perhaps it suddenly becomes more important. Do you 100% yes, absolutely. There are always [00:16:30] hot topics. Uh, and that shows up for sure Speaker 1: only because there's more papers published on that subject. We don't currently have a any kind of waiting per paper. Speaker 4: Yeah. Like when you go into the website and you'd do something like, um, there's a brain region called the Amygdala and you know, it'll be very strongly associated with fear. And so that's actually one of my concerns is problem getting these biases. So, you know, there's a lot of literature on this brain region, the Amygdala and how it relates to fear, but it certainly does a lot more than just processing fear, [00:17:00] right? It's this general emotional affective labeling sort of idea that anyway, that's, that's neuroscience specific stuff, you know, and brain region called the insula and disgust or love or you know, these other kinds of strong emotions. And so yeah, it definitely reflects certain biases as well. And we, we try and quantify that even to an extent a little bit. So again, using the Allen Brain Atlas data, we show from our Dataset, what are the top five brain regions that express or that are related to dopamine, for example. Speaker 4: And in the real human brain, what are the top five brain [00:17:30] regions that express dopaminergic related genes? And you can actually see that there's a very clear bias. So one of the regions that expresses dobutamine very strongly is very hard to study. Neuroscientifically speaking. It's, it's deepen deep part of the brain. It's hard to get any, it's very small, so you can't get it from like brain scanning expresses a lot of dopamine, but people don't study it and we can actually quantify then some of these under-studied relationships, right? We're like, here's a brain region that we know expresses a lot of dopamine, but there's a a hundred papers only and another [00:18:00] brain region that's very sexy and too about domain has 10,000 papers. Right? So our system shows you an example well of the current state of scientific literature. So it's not necessarily 100% correct, but it reflects what scientists think as a whole at this point. Yeah, I agree. And we try and be very careful about that in the paper and in talking about it like we are right now Speaker 2: [inaudible]Speaker 5: [00:18:30] you are listening to spectrum on k a l x Berkeley. We're talking with user interface developer, Jessica Vojtech and neuroscientist Bradley Vojtech about brain scanner. Speaker 2: [inaudible]Speaker 4: I was really surprised you. I taught neuro anatomy for three semesters here at Berkeley and you know, so I know the anatomy pretty well. And on your first ran it, I had one of those like yes, kind [00:19:00] of moments like I can't believe this work because it really does find all of these clusters really nicely. And that was a very pleasant surprise because technically speaking it couldn't have been any other way. Like it just has to, you know, I mean these topics co-occur a lot, so it should be that way, but it's always nice to see something like that work. Brian, I wanted to ask about the journals that you sent the paper off too. How did you pick them? Art Of picking a journal where to send a paper. It's actually really hard. So certain journals get [00:19:30] more readership than others. And then there's the open access factor. Speaker 4: So I'm, I'm a big open science, open data advocate and so I try and shoot for that. I had forgotten, there's actually sort of a, a very wide protest of Elsevier, which is one of the publishing companies right now. And the journal that published my papers and Elsevier Journal, but, uh, I had signed the petition and I was part of that Nash shortly thereafter. That would have impacted my decision had I been thinking about it. Yeah. And yeah, so it's mainly a balance between readership and expectation and you sort [00:20:00] of get a feel after publishing a few papers of what editors are looking for. And so yeah, I am the one that has experience with navigating the academic publishing environment. Yeah. So yeah, we sent it out to a lot of journals and, uh, mostly it didn't pass editorial review, which means that there's an editor that decides whether or not conceptually it will be interesting for their journal to publish it once got center review at a journal and they're like, well, it was sort of torn. Speaker 4: There were four reviewers, four pure reviewers, [00:20:30] and two of them were fairly enthusiastic and the other two are like, this is cool, but so what? Right. Um, and the general consensus was it didn't fit with the theme of the Journal. The Journal of neuroscience methods point really well and your reviewers are very, and um, actually there's a figure at the end of the paper where we did some integration with the Allen Brain. Alice Paul Allen, one of the co founders of Microsoft who is a cuisine heir, has put half a billion dollars into this institute. [00:21:00] Initially the goal was to map, uh, the expression of all of these different genes in the human brain, in the mouse brain, and they made all that data publicly available. And so we use that as a test data set. So we said, okay, where are these different, uh, neurotransmitter related genes actually expressed in the brain and what does our system think about wearing the brain? These neurotransmitters are, there's a week but significant correlation between the two, which suggests that our system reflects actual reality to a certain extent at least. [00:21:30] And that was a suggestion I got from one of the peer reviewers and that was really good. It was a lot of extra work, but it ended up being a really good addition to the paper. Speaker 1: But both of you guys are involved in science education and science outreach. So I was hoping you can comment on that. I'm actually starting a project with a friend of mine building a neuroscience kids books. So we're going to teach neuroscience to elementary school kids with an electronic ebook featuring the neuron. Yes, featured his name is ned the neuron. He's a pure middle cell and he works in the motor cortex of the brain. [00:22:00] And is the neuroscience focus partly driven by bad or do you have any sort of personal interest in as well? I do have a personal interest in and I, I, you know, obviously it's convenient that my husband is a neuroscientist, but actually the character and the original story idea is my partners who's also a neuroscientist and phd in neuroscience here at cal here at cal. Speaker 4: Yeah. I get this question a fair amount. Like why do I do blogging and outreach and things like that. So there's actually a few answers to that. One I find blogging, uh, helps me [00:22:30] do better science. If I have to figure out a very simple way of explaining something, then I feel like I understand it better. It's sort of like one of the best ways to learn something is by trying to teach it. Right. I had a very strange path to academia. I actually got kicked out as an undergraduate from the university. I had to sort of beg my way back in because my grades were pretty low. You know, a couple of people help me out along the way and that were pretty important to me. And I think a lot of Grad students have this experience where they, they feel like they don't belong there in in sense that like, oh [00:23:00] my God, I'm not smart enough to do this. Speaker 4: You know? And when I look at the resumes or cvs of, you know, tenured faculty here at Berkeley, right? It's just paper after paper and award and amazing achievement and you're just like struggling to even understand how to write a paper and it seems just like this daunting, intractable problem. And so because of that, I actually have a section in my CV where I actually list every time a paper has been rejected. I've actually had graduate students tell me that. That's been kind of Nice to see that you know, you see somebody who's doing pretty well and you see that, you know, in order to get there [00:23:30] you sort of have to slog through a lot of crap. Speaker 1: Did you plan to work together some more? I think so. You know, we're obviously working together to raise a son right now. We actually were talking on the way over here about trying to implement some of the ideas we've Speaker 4: been talking about that people have suggested. I think we could definitely do that. Yeah, there's definitely a lot of overlap. I'm very interested in dynamic data visualization and that's something that Jesse's is obviously getting quite quite good at and so I'd [00:24:00] like to start doing that for a lot of my research papers as well. Brad and Jess, thanks for joining us. Oh, thank you very much for having us. Thank you so much for having us. Speaker 2: [inaudible]Speaker 6: and now for some science news headlines. Here's Renee Rao and Brad sweet Speaker 2: [inaudible]Speaker 7: [00:24:30] the Berkeley new center reports researchers at the University of California Berkeley are gathering evidence this fall that the Feisty Fox squirrels scampering around campus or not just mindlessly foraging for food but engaging in a long term savings strategy to track the nut stashing activity. The student researchers are using GPS technology to record all of the food burials and in the process are creating [00:25:00] an elaborate map showing every campus tree building and garbage can. Miquel Delgado a doctorial student in psychology heads the squirrel research team in the laboratory of UC Berkeley, psychologist Luchea Jacobs. The research team is replicating the caching experiment on humans by timing students as they burry Easter eggs on campus and try to find them. We're using humans as a model for squirrel behavior to ask questions that we can't ask. Squirrels still got us said the group has a cow squirrels website to promote their work. Speaker 6: [00:25:30] UC Berkeley professor of cell and molecular biology and chemistry. Carolyn Bertozzi has won the 2012 Heinrich Violin prize. Professor Bartow Z has founded the field of bio orthogonal chemistry. In her groundbreaking approach, she creatively exploits the benefits of synthetic chemistry to study the vital processes within living beings. Professor Dr Volk Gang Baumeister, chair of the board of Trustees of the Heinrich Violin Prize says of Professor Berto z. [00:26:00] Her breakthrough method to identify sugar patterns on the cell surface is a milestone for our understanding of the functions of sugars in health and disease and paves the way for novel diagnostic and therapeutic approaches. Speaker 3: Irregular feature of spectrum is a calendar of some of the science and technology related events happening in the bay area over the next two weeks. Brad swift and Renee Rao join me for this. The second annual Bay Area Science Festival is wrapping up this weekend. [00:26:30] Highlights include art in science and gallery gala showing the intersection of image and research tonight at the Berkeley Arts Festival, Gallery Science superheros tonight at the Tech Museum in San Jose and discovery days at at and t park tomorrow November 3rd from 11:00 AM to 4:00 PM last year more than 21,000 people showed up to this free event this year. There are more than 150 exhibits. Visit Bay area science.org for more information about any of these [00:27:00] great activities and to see their regular calendar of science goings on. Speaker 6: Big Ideas. Berkeley is an annual innovation contest that provides funding, support, and encouragement to interdisciplinary teams of UC undergraduate and graduate students who have big ideas. The pre-proposal entry deadline is 5:00 PM November six 2012 all pre-proposals must be submitted via the online application on the big ideas website. Remember there are big idea advisers to help students craft [00:27:30] their pre-proposals. You can drop in at room 100 Blum hall during scheduled hours or email advisers to schedule an appointment at another time. Check the big ideas website for advisor times or to make an appointment. There will also be an editing blitz November 5th from five to 8:00 PM in room, 100 of bloom hall advisors and past winters will be available to provide applicants with valuable last-minute insights and advice on your pre-proposal. This is a great opportunity to hone your proposal and get support from those [00:28:00] who know what it takes to build a successful big idea. The big ideas website is big ideas.berkeley.edu Speaker 7: on November 8th the center for ethnographic research will hold a colloquium to understand cancer treatment trajectories using an array of ethnographic data. The Speaker Daniel Dohan and associate professor in the Phillip r Lee Institute for Health Policy Studies. We'll discuss this research about inequality and culture with a focus on cancer. He will focus on his most recent study which examines how patients [00:28:30] with advanced diseases find out about and decide whether to participate in clinical trials of new cancer drugs. The event, which is free and open to the public, will be held from four to 5:30 PM at 25 38 Channing waySpeaker 2: [inaudible]Speaker 5: the music you [00:29:00] heard during say show was spend less on and David from his album book and Acoustic, it is released under a creative Commons license version 3.0 spectrum was recorded and edited by me, Rick Karnofsky, and by Brad Swift. Thank you for listening to spectrum. If you have comments about the show, please send them to us via email. Our email address is spectrum dot k a l x@yahoo.com [00:29:30] join us in two weeks at this same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.