Podcasts about lawrence berkeley national labs

Our guest in this episode is David Tench, a Grace Hopper postdoctoral fellow at Lawrence Berkeley National Labs, who specializes in scalable graph algorithms and compression techniques to tackle massive datasets. In this episode, we will learn how his techniques enable real-time analysis of large datasets, such as particle tracking in physics experiments or social network analysis, by reducing storage requirements while preserving critical structural properties. David also challenges the common belief that giant graphs are sparse by pointing to a potential bias: Maybe because of the challenges that exist in analyzing large dense graphs, we only see datasets of sparse graphs? The truth is out there… David encourages you to reach out to him if you have a large scale graph application that you don't currently have the capacity to deal with using your current methods and your current hardware. He promises to "look for the hammer that might help you with your nail".

Her Many Voices Foundation is delighted to present our January livestream with Isvari Maranwe, CEO of DG Sentinel and Co-Founder of Dweebsglabal. Isvari Maranwe is a former national security attorney who has written for the Boston Globe, spoken at TEDx talks, researched physics at CERN and the Lawrence Berkeley National Labs, and represented Fortune 500 companies and the U.S. government. The DG Sentinel is majority-minority, queer, and female led, and has staff from around the globe. We come from many different races, genders, sexualities, and backgrounds. Led by CEO Isvari Maranwe, she has a lifelong passion for diverse and authentic media and has been a columnist and author since she was 15 years old. The DG Sentinel Board includes best-selling authors, famous influencers, media giants, award-winning directors, and more.This conversation will be facilitated by Myrna James. James is a publisher, journalist, and interpreter of high tech. Her publication Apogeo Spatial illuminates how data from space is used to study the earth for the sake of humanity.Links https://dgsentinel.org/https://dweebsglobal.org/about-dweebs/Produced by Aicila Lewis. Hosted on Acast. See acast.com/privacy for more information.

In this episode of Lab to Startup, I speak with Shannon Ciston and Branden Brough. Branden is the Deputy director of Molecular Foundry at the Lawrence Berkeley National Labs and Shannon is the Director of the User Program. We explore various resources that Molecular Foundry offers like: World-class scientists with expertise across a broad range of disciplines and state-of-the-art instrumentation. How to get accepted to the program Cost to users (mostly free) Intellectual property rights from using their support Examples of startups that benefited from the program Learn more about Molecular Foundry: foundry.lbl.gov

My guest this week is Dr. Adam Arkin, our first interview outside of UCSF! Adam works across the Bay at Lawrence Berkeley National Labs and is a leader in the emerging fields of systems and synthetic biology. He has published more than 300 papers on a wide range of subjects and tells us about some of the large-scale initiatives he is currently leading and his fascination with viruses and bacteria.

In 1986, Cliff Stoll's boss at Lawrence Berkeley National Labs tasked him with getting to the bottom of a 75-cent accounting discrepancy in the lab's computer network, which was rented out to remote users by the minute. Stoll, 36, investigated the source of that minuscule anomaly, pulling on it like a loose thread until it led to a shocking culprit: a hacker in the system.

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.

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]. Hosted on Acast. See acast.com/privacy for more information.

We dig the Red Planet! And so does Curiosity. After a successful landing, and a round of high-fives at NASA, the latest rover to land on Mars is on the move, shovel in mechanical hand. Discover how the Mars Science Laboratory will hunt for the building blocks of life, and just what the heck a lipid is. Plus, how to distinguish Martians from Earthlings, and the tricks Mars has played on us in the past (canals, anyone?). Also, want to visit Mars firsthand? We can point you to the sign-up sheet for a manned mission. The catch: the ticket is one-way. Guests: •   John Grotzinger – Geologist, California Institute of Technology, and project scientist, NASA Mars Science Laboratory mission •   Jennifer Heldmann – Research scientist at NASA Ames Research Center •   David Blake – Principal Investigator of CheMin, a mineralogical instrument that is included in the analytical laboratory of the Mars Science Laboratory mission •   Rachel Harris – Astrobiology student at the NASA Astrobiology Institute •   Stuart Schlisserman – Physician in Palo Alto, California •   Felisa Wolfe-Simon – NASA astrobiology research fellow, Lawrence Berkeley National Labs •   Bas Lansdorp – Founder, Mars One

Simone Pagan-Griso, Postdoc Chamberlain Fellow at Lawrence Berkeley National Labs, works on the ATLAS team at CERN.TranscriptSpeaker 1: Spectrum's next [inaudible]. [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 2: Good afternoon. My name is Rick Karnofsky. Brad swift and I are the hosts of today's show. We are speaking with Dr Simone Simona, pic Ingreso of Lawrence Berkeley National Lab. [00:01:00] Simona is a physicist who is searching for the Higgs bows on which has also been called the God particle because it is the theoretical establish or have mass in the standard model of physics. This recording has been prerecorded and edited to Monet. Can you please tell us a little bit about what you do Speaker 3: that an experimental physicist? I basically work on understanding fundamental laws of nature in day, a smallest scale as possible and to understand which are the fundamental [00:01:30] constituents of matter and which laws, governor, these are the forces between them. And currently I work on an experimented, which is, uh, in um, Geneva, Switzerland, um, in the seminal laboratory and this experiment is called Atlas. And, uh, one of its purposes is actually to us, Mesh Protons are together to uh, investigate the nature of the fundamental Christy trends [00:02:00] of uh, the metal that we see around including to find the Higgs Boson. Is Macanese Alto almost widely accepted as never been proved experimentally. So it's really just a theory of this. Well, yes, very well motivated by just the theory and in doing this mechanism, what happens is that you introduce one more piece in these theory, we call them fields and this field basically [00:02:30] breaks down and give mass to these first careers. Speaker 3: But in doing this thing, one single piece remains the left. Okay. And uh, this small piece is suppose is what we are looking for is what is called the Higgs Boson. So if we see these, these expos on will be a very, very good indication that this mechanism is actually the one the natural have chosen and make things work as we see we some indications [00:03:00] or how it should behave. And which are the property of this particular in particular [inaudible] the key characteristic of this particular mass. We don't know in this theory it's mass is a free parameter if you want. We don't know what what you should AV. It could span in different ranges. However, we have both experimental constraints and a theoretical motivation to think that it's masses [00:03:30] in a well-defined range and this is the best way we can account for what we see in the end. Speaker 3: This was initially a quite wide range. It was initially searched the at cern and experiment, which was colliding electrons and anti electrons to search up to [inaudible] 2000 and increasing the energy because it was not fun and pushing it to harden harder. And what does increasing the energy do? Increase? That's [00:04:00] a very good question. The point is that in the end, energy and mass are back as Einstein teacher does are basically the same thing. So colliding them in electron anti electron at higher energy. We can procreate particle with higher masses basically. And the idea was try to create two collided higher energy because we didn't find any trees of the production of the heat. So they give an energy. So in mass it, it me, it meant that it was at higher masses that we couldn't [00:04:30] reach. So increasing the energy was the way to produce in a laboratory. Speaker 3: This particle after the year 2000 where this in this patio was not found, the collider was shut down because our new collider was under project to be built, which is still a large other collider that is now operating. And the search pastor to another laboratory which is located a r near Chicago. The fair made up that was still r a machine [00:05:00] which was basically colliding particle to create in laboratory heavy. Particular usually in nature are not easy to find. This was a little different. Particle was not colliding, electrons was colliding, protons and antiprotons. So cause the trends of the tones, this was done because in this way we could achieve higher energies in the collision. And the reason for that is just the protein mass is higher than the electron to collide is particularly to accelerate them [00:05:30] and to accelerate. And we use circular rings so we need to ban them and accelerate them. Speaker 3: But if they throw it too fast, you don't have enough bending power to to keep them in the ring. Right? So you need bigger and bigger drinks. Now with the protons you could with our relatively feasible ring, which is around the six kilometers in circumference, you could actually increased the energy by a lot. Can you please walk us through [00:06:00] what the standard model is? It basically has its really nice thing is that we, one equation, we can described how all the metrics that we see around behaves. I interact with other matters with all these forces at certain they sell tee shirts with this equation. Okay. Written down on the tee shirt and it's very compact form. And from there in principle you, you can know whatever happens or how matter's interacting, whatever different situation, [00:06:30] it turns out that we cannot solve that equation and if one can do it that we get a fixed price right away. Speaker 3: And if Nobel prize two probably, but we can try to find approximate solutions that and now the nice thing of the standard model is that the only thing you need to do to build this and our model is to write down in these equations the content of metal that you see around. So I say I just say I want [00:07:00] other recent electron. It doesn't tell me because why there is an electron, but I say I want to be at an electron. I'm human and Tau want to be quirks. Okay. But I don't specify that electrons can interact through light with other particles. So or I don't specify any force. I just write down the content of matters and then just applying and just requiring the, these equations are the same for [00:07:30] some symmetries. For different observers or around that. The easy example of like, I want the equation to be the same if I'm here or for me the other room. Speaker 3: Okay. So there are other symmetries that we can impose to this equation and just imposing this, the symmetry to start that is a question itself, does not satisfy these cemeteries. And the only way to satisfy these symmetries that pretty simple is that there are forces between these things that you've put in the theory. So it must be the electromagnetics, it must be [00:08:00] there or there was the theory wouldn't be symmetric in this transformation. This one, not one really nice thing. We didn't do steering, we didn't put by hand the forces that the full, all the forces that we see in nature, they come out just requiring asymmetry of this equation. Pretty nitrous symmetries and it comes out that if you do that, it's told it must exist. All the forces that we see. So this is one of the very beautiful things are of the standard one that why we believe [00:08:30] so much in this theory and why it worked. Speaker 3: So well. Many prediction of the standard model we're actually did, uh, from a theoretical point of view and then confirmed experimentally and did this also got the Nobel prize and gives them examples. Yeah. The WNC Boson started one of beautiful examples. We saw the worst there were, is trying to explain the objective of the case and why they happen. How did that happen [00:09:00] by the has several problem is doing based on their model, kind of unified all these treatments and a offered an explanation. But in order to that he had to introduce these forced carters that Dublin CBOs, which were as the photons bring light and bring electromagnetic force between two charged particles. These established the balls and chemigate this weak force between particles and can give rise to the case for the activity case. In order to do that, [00:09:30] they need to be, to act in a very short range. Speaker 3: And to do that the WNC both need to have a mass on the contrast of the Photon, which is masters and that's why it can travel as much as it wants. There was a kind of breaking ground prediction and uh, turns out that from nowhere energy experiments, which couldn't achieve that mass, they could any way measure other things, which made a very precise prediction of what [00:10:00] at the mess of the Dublin sibilance would have been. It's still at seven. They actually built an experiment to look for this particular, this keep an energy and they found it and that was noble price directly and yeah, that that was a beautiful example of how theory can go had experiments and, and you have example, on the other hand went for example in dark matter experiments found evidence of dark matter. While [00:10:30] no theoretical model was really seriously considering it as a possibility and we still don't know exactly what it is, right? So it's a very nice usually interplay between theoretical and experimental physicist in, in advancing the knowledge in this Speaker 4: [inaudible] you're listening to spectrum on l this week we are talking to Simona pink and zone about the search for the Higgs Bose on Speaker 3: [00:11:00] right now we know that the heeks particle must have a mass which is above 114 times 10 so the Proton and this bound comes from the lab experiment. We know that those who it's not in between what is kind of 155 to 180 times 70 times the muscle [inaudible] proud. We think that is unlikely to be heavier than [00:11:30] that because can measure other quantities, which can depend on the Higgs mass without directly producing it. This is kind of amazing. This is a pure quantum mechanical phenomenon, so that even if you don't produce actually a particle that can influence other phenomena, depending on the master analysis techniques to adopt are different because the properties of the particles change how much statistical, certain, Hey, do you need before you can exclude a mass [00:12:00] range or say, Hey, we, uh, we found the expose on. Yeah, that's a good question. Speaker 3: In the end, we count the number of coalition that we should be [inaudible] we think that he should, but we have other processes that are known and behaves in a similar way for claiming the discovery of the he expose on. We basically ask that the probability to be, uh, less than a 10 to the minus seven. So that means that even repeating, if, [00:12:30] if we repeated the experiment 10 millions times, only one of these times it would happen that the known processes we give rise to the number of events to explain what we see. We are getting very close in in starting refining, having enough data collected and enough knowledge of the data that we collect to be able to see if among the all the coalition that we record the Hicks person is produced or not. And how much data [00:13:00] are we talking about here? Speaker 3: Yeah, so the data in a larger than collider, we have 20 millions collision per second. However, in every collision of two protons, it doesn't always happen. The same thing. Different things can happen and what we look for is the result of this coalition. We have this theory, the standard model, which not only unifies all these forces but give really a precise prediction of what actually happens. [00:13:30] Even when you collide. For example, two protons, the heat exposed in is predicted to be produced only like a one over 10 billions, billion, billions. Yes. Of these conditions. And I'm the one and 10 yes. One in 10 billion. So valuable. Yeah. It's what we are looking for. All the data that we record from one coalition is about one megabyte and we cannot write that [00:14:00] much of 20 millions coalition per second on a disk. We just don't have the technology to do that and it will require an enormous disk space. Speaker 3: So one very active and difficult part of the experiment is try to decide in real time which of these collisions may be potentially interesting for what you're looking for or not. And we reduce them and write basically two, 300 of damage each second. How long does dates [00:14:30] to the text for you to get the data from? The experiments are happening in Geneva, so this is a very amazing thing and this is something that is only possible for the work of a lot of people, but usually data are get recorded. I send this a huge amount of data. There are people checking that every day. I mean while data is taking, everything is working properly. So all of them, they need to meet every day and decide what is was working, what was not, what had problems [00:15:00] and mark the data saying, okay, during these data I've had this problem during this, I had this one so that every one who analyzed can say, oh, I need this competent the detector. Speaker 3: So give me only the data. Which was working in which that you collected while this piece was working that that needs to be distributed worldwide when we analyzed and we'd be full doing that. It's not like you collect data, you analyze it itself. You also need some, some kind of processing [00:15:30] pre processing of this data and all this process usually takes are, are just few days really one week I would say I can brand my analysis based on data. Yeah. One thing that is maybe not, not obvious is why I need to process this data and this goes a bit in how these huge detector that right now, which are a black box for you. I mean I haven't explained anything about it, how it works and I mentioned [00:16:00] that it has many systems just to give you a feeling. I can tell you that a date, the systems that are closer to the interaction are the one that um, basically when the particle passed through them, they basically try to disturb the particle in the less possible. Speaker 3: So they are very thin part of material and they basically just just try to say, uh, to the electronic yet the particles pass through this point. So what you have [00:16:30] is kind of it creed all around several layers of grades, which will tell you a particular past here and other here. Sometimes they fail, they don't tell you that he passed. Sometimes they tell you that he's passed even if nothing was going on for noise of course. And so what you actually see when you record any event is are this huge amount of greets with points. And from that you need to figure out what does he mean? We mean how many particles were there, which trajectory did they, [00:17:00] they went through. And this is an highly non trivial task and this needs to be done in these. And from there we can start and saying, okay, if I see these kinds of particles, then it means that they originate from these other particle here and they have these energies. So I can, I know that this is not this process and you can do all this kind of infer things. So this needs to be done before the is analyzed and usually, yeah. Speaker 4: [inaudible] [00:17:30] you're listening to spectrum on k l x this week we are talking to Somalia and pink Ingreso about the search for the Higgs Boson theoretical particle of mass in the standard bottle of physics. Speaker 3: These experiments are very huge collaboration of people worldwide at center right now. Each of these experiments, [inaudible] experiment [00:18:00] is a collaboration of three thousands of people, which was needed to build the experiment to make it work, to still make it working right now. And when that eyes, what we see. So I'm very interested in just the scope of the project and how, how many people are working on it for such a fundamental question. When thinks that if we have an answer that could be potentially worthy of winning a Nobel prize. So who actually gets surprised if that's a very [00:18:30] good question. I think that of course, uh, in ob price I think is very much worth in this case, after all these years of searches, all the theorist working on building this theory of this Hicks Mechanism and these gander prediction of this particular of course worth a, a very good price and a noble price can be sweetened to that. Speaker 3: And as well as that, I think all the experimental [00:19:00] effort would may need a w is definitely worth a very good price. So I like to think that, uh, this price will be shared among all the people that worked along all these years. But of course it will happen that probably a representative, uh, of those will actually take physically the price. But I'm sure that, uh, it will happen that it will be felt as shared among all the thousands of physicist working on this [00:19:30] project. And what's it like for you as an individual scientist on a big team? How do you sort of carve out your own niche and how is you cannot, uh, enforce a strict cerotic across structure, right? You basically have [inaudible] you cannot appoint coordinators which can try to focus on day the work of many people. But every people is basically free to pursue his own research as he feels that is the better way to go. Speaker 3: It's never work that you do alone. It's something [00:20:00] that requires the work of several people. I worked on a similar thing in Chicago during my Phd [inaudible] a lot of experience in that and I tried to use the experience now too to improve things to push harder, our organized technique and understanding of our data at LHC. So there is plenty of room in which every person is contributing. I personally work, I'm like to work a lot on the analysis techniques [00:20:30] that are used to analyze what we see and to distinguish known processes from process that we are looking for. That is an extremely interesting field. Um, the reason for that is that we have a huge amount of information after this collision. Um, one that you didn't mention is that these detectors are huge [inaudible] yet us detector itself is kind of 45 meters long and 25 meters high. Speaker 3: So [00:21:00] there are some huge, uh, instrumentations and uh, each of the, this detector is made of various sub system which are, which have the, uh, goal of measuring different protests, processes of the known particles that comes out from the interactions. And being in a, this is a huge amount of information. Okay. And it's not easy. Um, you don't, you don't know exactly what happens, but you try [00:21:30] to reconcile from what you see what happened. And this is something, ah, that I tried to work a lot on in really just analyzing what they see and try to classify if you want the values coalition and try to understand what happened. And this field are made a lot of progresses and, and it's using very, very, uh, advances techniques. And, uh, it seemed interesting how, uh, many concerts [00:22:00] that were born in other science fields that computer science are actually merging in what we are using right now. Speaker 3: One of the nicer example are what are called narrow networks. So we're born in computer science are used a lot. For example, in, uh, our vision for the, for, uh, automation for robotics. Uh, and uh, we actually can use them to ah, to process the whole information that we have and try to classify [00:22:30] these events and to see how they look. Like we can use simulation of these events. We have a lot of people working, trying to simulate what what we expect to see in our detector, which been such a huge piece of instrument is not easy. And uh, using this simulation we can actually uh, make, uh, make new art tools like neural networks, which are tried to see what happened really in our detector and to see [00:23:00] if it is what we expect from a known process or from money x production. I have to say we are pretty close. We should be able to say something in a very short amount of time. We also know that thanks for joining us. Thank you for inviting me. Speaker 4: [inaudible] the regular feature of spectrum is to mention some of the science and technology events happening in [00:23:30] the bay area over the next two weeks. I'm joined for this calendar by Brad Swift Speaker 5: to preserve our planet. Scientists tell us that we must reduce the amount of co two in the atmosphere from its current level of 392 parts per million to below 350 parts per million. The organization three fifty.org is building a global grassroots movement to solve the climate crisis. Moving planet is a worldwide rally to demand solutions to the climate [00:24:00] crisis. Moving planet is a global day of action scheduled for Saturday, September 24th, 2011 the San Francisco Rally begins with a parade from Justin Herman Plaza, which is at the intersection of market street and the Embarcadero. The parade will head up market street to the Civic Center at 12:30 PM once at the civic center. There will be Speakers, music, food workshops and exhibits for details on all the Saturday events including the San Francisco rally. Go [00:24:30] to the website, three fifty.org and click on moving planet Speaker 2: Berkeley Ameritas professor Frank Shu will deliver a lecture entitled Nuclear Energy After Fukushima on Tuesday, September 27th at 6:00 PM at the Commonwealth Club's San Francisco office located on the second floor of five nine five market street. The media and public's reaction to the recent nuclear accident threatened to cripple the nuclear renaissance that is humanity's best hope for mitigating climate disruption. She will review how [00:25:00] light water reactors and the once through fuel cycle came to dominate the landscape for generating nuclear power today and we'll assess options for the future. A standard ticket for this event is $20 but emission is $8 for members and $7 for students with a valid ID visit, www.commonwealthclub.org Speaker 5: more information. What's right with Kansas. Learn how Kansas is climate and energy project is capitalizing on heartland values to change behavior [00:25:30] and reduce carbon emissions. A panel of Nancy Jackson, executive director, Kansas climate and energy project and Marianne Fuller from the Lawrence Berkeley labs. Environmental Energy Technologies Division will present the Kansas project plus be the first to see lbls video Kansas, which shows how the climate and energy project has become a Kansas mainstay. This will be Monday, October 3rd 7:00 PM to 9:00 PM this is a free event at the Berkeley Repertory Theater, [00:26:00] 2025 Addison Street in Berkeley, Speaker 2: exploratorium is hosting after dark and evening series for adults 18 and over. That mix is science, art and cocktails and mission to the exploratorium is included. Tickets are $15 or $12 for seniors, students or persons with disabilities and are free for members. On Thursday, October 6th from six to 10:00 PM this months after dark theme is again and again explore the fascinating worlds of reminiscence and repetition [00:26:30] and then backwards skate through your own nostalgia on their temporary roller rink. UC Berkeley professor of psychology, Art CIM, and Maura will explain the mechanics of human memory. The website for this event is www.exploratorium.edu/after dark and now for a couple of recent science news events. Here's Brad Swift. Speaker 5: Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. [00:27:00] The gamers achieved their discovery by playing folded and online game that allows players to collaborate and compete in predicting the structure of protein molecules. This is the first instance that the researchers are aware of in which gamers solved a longstanding scientific problem. After scientists repeatedly failed to piece together the structure of a protein cutting enzyme from an aids like virus they called in the folded players. The scientists challenged the gamers to produce an accurate model of the enzyme. The gamers did it and only three [00:27:30] weeks folded was created by computer scientists at the University of Washington Center for game science in collaboration with the Baker lab, a biochemistry lab at the university, figuring out the structure of proteins contributes to the research on the causes of and cures for cancer, Alzheimer's immune deficiencies, and a host of other disorders as well as work on biofuels. A paper describing the retrovirus enzyme structure was published September 18th [00:28:00] in the journal, nature, structural and molecular biology. The scientists and the gamers are listed as go authors Speaker 2: and in news related to this week's interview. Science reports that Israel has become an associate member of the European Physics Laboratory [inaudible]. They're the 21st member nation and the first new members since Bulgaria joined in 1999 this move is somewhat controversial. Sm Academics in the UK and South Africa. I wished to boycott collaboration due to Israeli Palestinian conflicts [00:28:30] but this ends a two year probationary membership and Israel will eventually contribute 1 billion Swiss francs to the project a year. Israeli representative to the certain Governing Council Eliezar revenue beachy states that he hopes this will inspire other Arab nations to join the effort. Speaker 4: [inaudible] music her during the show was attract [inaudible] Sean's divvy from David Lewis, Donna's self-published folk [00:29:00] and acoustic album. It is published under the creative Commons attribution license version 3.0 is available@wwwdotjamendo.com editing and production assistance for the show by Brad Swift. 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 [00:29:30] address is spectrum dot k a l x@yahoo.com join us in two weeks at this same time. [inaudible]. See acast.com/privacy for privacy and opt-out information.

Simone Pagan-Griso, Postdoc Chamberlain Fellow at Lawrence Berkeley National Labs, works on the ATLAS team at CERN.TranscriptSpeaker 1: Spectrum's next [inaudible]. [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 2: Good afternoon. My name is Rick Karnofsky. Brad swift and I are the hosts of today's show. We are speaking with Dr Simone Simona, pic Ingreso of Lawrence Berkeley National Lab. [00:01:00] Simona is a physicist who is searching for the Higgs bows on which has also been called the God particle because it is the theoretical establish or have mass in the standard model of physics. This recording has been prerecorded and edited to Monet. Can you please tell us a little bit about what you do Speaker 3: that an experimental physicist? I basically work on understanding fundamental laws of nature in day, a smallest scale as possible and to understand which are the fundamental [00:01:30] constituents of matter and which laws, governor, these are the forces between them. And currently I work on an experimented, which is, uh, in um, Geneva, Switzerland, um, in the seminal laboratory and this experiment is called Atlas. And, uh, one of its purposes is actually to us, Mesh Protons are together to uh, investigate the nature of the fundamental Christy trends [00:02:00] of uh, the metal that we see around including to find the Higgs Boson. Is Macanese Alto almost widely accepted as never been proved experimentally. So it's really just a theory of this. Well, yes, very well motivated by just the theory and in doing this mechanism, what happens is that you introduce one more piece in these theory, we call them fields and this field basically [00:02:30] breaks down and give mass to these first careers. Speaker 3: But in doing this thing, one single piece remains the left. Okay. And uh, this small piece is suppose is what we are looking for is what is called the Higgs Boson. So if we see these, these expos on will be a very, very good indication that this mechanism is actually the one the natural have chosen and make things work as we see we some indications [00:03:00] or how it should behave. And which are the property of this particular in particular [inaudible] the key characteristic of this particular mass. We don't know in this theory it's mass is a free parameter if you want. We don't know what what you should AV. It could span in different ranges. However, we have both experimental constraints and a theoretical motivation to think that it's masses [00:03:30] in a well-defined range and this is the best way we can account for what we see in the end. Speaker 3: This was initially a quite wide range. It was initially searched the at cern and experiment, which was colliding electrons and anti electrons to search up to [inaudible] 2000 and increasing the energy because it was not fun and pushing it to harden harder. And what does increasing the energy do? Increase? That's [00:04:00] a very good question. The point is that in the end, energy and mass are back as Einstein teacher does are basically the same thing. So colliding them in electron anti electron at higher energy. We can procreate particle with higher masses basically. And the idea was try to create two collided higher energy because we didn't find any trees of the production of the heat. So they give an energy. So in mass it, it me, it meant that it was at higher masses that we couldn't [00:04:30] reach. So increasing the energy was the way to produce in a laboratory. Speaker 3: This particle after the year 2000 where this in this patio was not found, the collider was shut down because our new collider was under project to be built, which is still a large other collider that is now operating. And the search pastor to another laboratory which is located a r near Chicago. The fair made up that was still r a machine [00:05:00] which was basically colliding particle to create in laboratory heavy. Particular usually in nature are not easy to find. This was a little different. Particle was not colliding, electrons was colliding, protons and antiprotons. So cause the trends of the tones, this was done because in this way we could achieve higher energies in the collision. And the reason for that is just the protein mass is higher than the electron to collide is particularly to accelerate them [00:05:30] and to accelerate. And we use circular rings so we need to ban them and accelerate them. Speaker 3: But if they throw it too fast, you don't have enough bending power to to keep them in the ring. Right? So you need bigger and bigger drinks. Now with the protons you could with our relatively feasible ring, which is around the six kilometers in circumference, you could actually increased the energy by a lot. Can you please walk us through [00:06:00] what the standard model is? It basically has its really nice thing is that we, one equation, we can described how all the metrics that we see around behaves. I interact with other matters with all these forces at certain they sell tee shirts with this equation. Okay. Written down on the tee shirt and it's very compact form. And from there in principle you, you can know whatever happens or how matter's interacting, whatever different situation, [00:06:30] it turns out that we cannot solve that equation and if one can do it that we get a fixed price right away. Speaker 3: And if Nobel prize two probably, but we can try to find approximate solutions that and now the nice thing of the standard model is that the only thing you need to do to build this and our model is to write down in these equations the content of metal that you see around. So I say I just say I want [00:07:00] other recent electron. It doesn't tell me because why there is an electron, but I say I want to be at an electron. I'm human and Tau want to be quirks. Okay. But I don't specify that electrons can interact through light with other particles. So or I don't specify any force. I just write down the content of matters and then just applying and just requiring the, these equations are the same for [00:07:30] some symmetries. For different observers or around that. The easy example of like, I want the equation to be the same if I'm here or for me the other room. Speaker 3: Okay. So there are other symmetries that we can impose to this equation and just imposing this, the symmetry to start that is a question itself, does not satisfy these cemeteries. And the only way to satisfy these symmetries that pretty simple is that there are forces between these things that you've put in the theory. So it must be the electromagnetics, it must be [00:08:00] there or there was the theory wouldn't be symmetric in this transformation. This one, not one really nice thing. We didn't do steering, we didn't put by hand the forces that the full, all the forces that we see in nature, they come out just requiring asymmetry of this equation. Pretty nitrous symmetries and it comes out that if you do that, it's told it must exist. All the forces that we see. So this is one of the very beautiful things are of the standard one that why we believe [00:08:30] so much in this theory and why it worked. Speaker 3: So well. Many prediction of the standard model we're actually did, uh, from a theoretical point of view and then confirmed experimentally and did this also got the Nobel prize and gives them examples. Yeah. The WNC Boson started one of beautiful examples. We saw the worst there were, is trying to explain the objective of the case and why they happen. How did that happen [00:09:00] by the has several problem is doing based on their model, kind of unified all these treatments and a offered an explanation. But in order to that he had to introduce these forced carters that Dublin CBOs, which were as the photons bring light and bring electromagnetic force between two charged particles. These established the balls and chemigate this weak force between particles and can give rise to the case for the activity case. In order to do that, [00:09:30] they need to be, to act in a very short range. Speaker 3: And to do that the WNC both need to have a mass on the contrast of the Photon, which is masters and that's why it can travel as much as it wants. There was a kind of breaking ground prediction and uh, turns out that from nowhere energy experiments, which couldn't achieve that mass, they could any way measure other things, which made a very precise prediction of what [00:10:00] at the mess of the Dublin sibilance would have been. It's still at seven. They actually built an experiment to look for this particular, this keep an energy and they found it and that was noble price directly and yeah, that that was a beautiful example of how theory can go had experiments and, and you have example, on the other hand went for example in dark matter experiments found evidence of dark matter. While [00:10:30] no theoretical model was really seriously considering it as a possibility and we still don't know exactly what it is, right? So it's a very nice usually interplay between theoretical and experimental physicist in, in advancing the knowledge in this Speaker 4: [inaudible] you're listening to spectrum on l this week we are talking to Simona pink and zone about the search for the Higgs Bose on Speaker 3: [00:11:00] right now we know that the heeks particle must have a mass which is above 114 times 10 so the Proton and this bound comes from the lab experiment. We know that those who it's not in between what is kind of 155 to 180 times 70 times the muscle [inaudible] proud. We think that is unlikely to be heavier than [00:11:30] that because can measure other quantities, which can depend on the Higgs mass without directly producing it. This is kind of amazing. This is a pure quantum mechanical phenomenon, so that even if you don't produce actually a particle that can influence other phenomena, depending on the master analysis techniques to adopt are different because the properties of the particles change how much statistical, certain, Hey, do you need before you can exclude a mass [00:12:00] range or say, Hey, we, uh, we found the expose on. Yeah, that's a good question. Speaker 3: In the end, we count the number of coalition that we should be [inaudible] we think that he should, but we have other processes that are known and behaves in a similar way for claiming the discovery of the he expose on. We basically ask that the probability to be, uh, less than a 10 to the minus seven. So that means that even repeating, if, [00:12:30] if we repeated the experiment 10 millions times, only one of these times it would happen that the known processes we give rise to the number of events to explain what we see. We are getting very close in in starting refining, having enough data collected and enough knowledge of the data that we collect to be able to see if among the all the coalition that we record the Hicks person is produced or not. And how much data [00:13:00] are we talking about here? Speaker 3: Yeah, so the data in a larger than collider, we have 20 millions collision per second. However, in every collision of two protons, it doesn't always happen. The same thing. Different things can happen and what we look for is the result of this coalition. We have this theory, the standard model, which not only unifies all these forces but give really a precise prediction of what actually happens. [00:13:30] Even when you collide. For example, two protons, the heat exposed in is predicted to be produced only like a one over 10 billions, billion, billions. Yes. Of these conditions. And I'm the one and 10 yes. One in 10 billion. So valuable. Yeah. It's what we are looking for. All the data that we record from one coalition is about one megabyte and we cannot write that [00:14:00] much of 20 millions coalition per second on a disk. We just don't have the technology to do that and it will require an enormous disk space. Speaker 3: So one very active and difficult part of the experiment is try to decide in real time which of these collisions may be potentially interesting for what you're looking for or not. And we reduce them and write basically two, 300 of damage each second. How long does dates [00:14:30] to the text for you to get the data from? The experiments are happening in Geneva, so this is a very amazing thing and this is something that is only possible for the work of a lot of people, but usually data are get recorded. I send this a huge amount of data. There are people checking that every day. I mean while data is taking, everything is working properly. So all of them, they need to meet every day and decide what is was working, what was not, what had problems [00:15:00] and mark the data saying, okay, during these data I've had this problem during this, I had this one so that every one who analyzed can say, oh, I need this competent the detector. Speaker 3: So give me only the data. Which was working in which that you collected while this piece was working that that needs to be distributed worldwide when we analyzed and we'd be full doing that. It's not like you collect data, you analyze it itself. You also need some, some kind of processing [00:15:30] pre processing of this data and all this process usually takes are, are just few days really one week I would say I can brand my analysis based on data. Yeah. One thing that is maybe not, not obvious is why I need to process this data and this goes a bit in how these huge detector that right now, which are a black box for you. I mean I haven't explained anything about it, how it works and I mentioned [00:16:00] that it has many systems just to give you a feeling. I can tell you that a date, the systems that are closer to the interaction are the one that um, basically when the particle passed through them, they basically try to disturb the particle in the less possible. Speaker 3: So they are very thin part of material and they basically just just try to say, uh, to the electronic yet the particles pass through this point. So what you have [00:16:30] is kind of it creed all around several layers of grades, which will tell you a particular past here and other here. Sometimes they fail, they don't tell you that he passed. Sometimes they tell you that he's passed even if nothing was going on for noise of course. And so what you actually see when you record any event is are this huge amount of greets with points. And from that you need to figure out what does he mean? We mean how many particles were there, which trajectory did they, [00:17:00] they went through. And this is an highly non trivial task and this needs to be done in these. And from there we can start and saying, okay, if I see these kinds of particles, then it means that they originate from these other particle here and they have these energies. So I can, I know that this is not this process and you can do all this kind of infer things. So this needs to be done before the is analyzed and usually, yeah. Speaker 4: [inaudible] [00:17:30] you're listening to spectrum on k l x this week we are talking to Somalia and pink Ingreso about the search for the Higgs Boson theoretical particle of mass in the standard bottle of physics. Speaker 3: These experiments are very huge collaboration of people worldwide at center right now. Each of these experiments, [inaudible] experiment [00:18:00] is a collaboration of three thousands of people, which was needed to build the experiment to make it work, to still make it working right now. And when that eyes, what we see. So I'm very interested in just the scope of the project and how, how many people are working on it for such a fundamental question. When thinks that if we have an answer that could be potentially worthy of winning a Nobel prize. So who actually gets surprised if that's a very [00:18:30] good question. I think that of course, uh, in ob price I think is very much worth in this case, after all these years of searches, all the theorist working on building this theory of this Hicks Mechanism and these gander prediction of this particular of course worth a, a very good price and a noble price can be sweetened to that. Speaker 3: And as well as that, I think all the experimental [00:19:00] effort would may need a w is definitely worth a very good price. So I like to think that, uh, this price will be shared among all the people that worked along all these years. But of course it will happen that probably a representative, uh, of those will actually take physically the price. But I'm sure that, uh, it will happen that it will be felt as shared among all the thousands of physicist working on this [00:19:30] project. And what's it like for you as an individual scientist on a big team? How do you sort of carve out your own niche and how is you cannot, uh, enforce a strict cerotic across structure, right? You basically have [inaudible] you cannot appoint coordinators which can try to focus on day the work of many people. But every people is basically free to pursue his own research as he feels that is the better way to go. Speaker 3: It's never work that you do alone. It's something [00:20:00] that requires the work of several people. I worked on a similar thing in Chicago during my Phd [inaudible] a lot of experience in that and I tried to use the experience now too to improve things to push harder, our organized technique and understanding of our data at LHC. So there is plenty of room in which every person is contributing. I personally work, I'm like to work a lot on the analysis techniques [00:20:30] that are used to analyze what we see and to distinguish known processes from process that we are looking for. That is an extremely interesting field. Um, the reason for that is that we have a huge amount of information after this collision. Um, one that you didn't mention is that these detectors are huge [inaudible] yet us detector itself is kind of 45 meters long and 25 meters high. Speaker 3: So [00:21:00] there are some huge, uh, instrumentations and uh, each of the, this detector is made of various sub system which are, which have the, uh, goal of measuring different protests, processes of the known particles that comes out from the interactions. And being in a, this is a huge amount of information. Okay. And it's not easy. Um, you don't, you don't know exactly what happens, but you try [00:21:30] to reconcile from what you see what happened. And this is something, ah, that I tried to work a lot on in really just analyzing what they see and try to classify if you want the values coalition and try to understand what happened. And this field are made a lot of progresses and, and it's using very, very, uh, advances techniques. And, uh, it seemed interesting how, uh, many concerts [00:22:00] that were born in other science fields that computer science are actually merging in what we are using right now. Speaker 3: One of the nicer example are what are called narrow networks. So we're born in computer science are used a lot. For example, in, uh, our vision for the, for, uh, automation for robotics. Uh, and uh, we actually can use them to ah, to process the whole information that we have and try to classify [00:22:30] these events and to see how they look. Like we can use simulation of these events. We have a lot of people working, trying to simulate what what we expect to see in our detector, which been such a huge piece of instrument is not easy. And uh, using this simulation we can actually uh, make, uh, make new art tools like neural networks, which are tried to see what happened really in our detector and to see [00:23:00] if it is what we expect from a known process or from money x production. I have to say we are pretty close. We should be able to say something in a very short amount of time. We also know that thanks for joining us. Thank you for inviting me. Speaker 4: [inaudible] the regular feature of spectrum is to mention some of the science and technology events happening in [00:23:30] the bay area over the next two weeks. I'm joined for this calendar by Brad Swift Speaker 5: to preserve our planet. Scientists tell us that we must reduce the amount of co two in the atmosphere from its current level of 392 parts per million to below 350 parts per million. The organization three fifty.org is building a global grassroots movement to solve the climate crisis. Moving planet is a worldwide rally to demand solutions to the climate [00:24:00] crisis. Moving planet is a global day of action scheduled for Saturday, September 24th, 2011 the San Francisco Rally begins with a parade from Justin Herman Plaza, which is at the intersection of market street and the Embarcadero. The parade will head up market street to the Civic Center at 12:30 PM once at the civic center. There will be Speakers, music, food workshops and exhibits for details on all the Saturday events including the San Francisco rally. Go [00:24:30] to the website, three fifty.org and click on moving planet Speaker 2: Berkeley Ameritas professor Frank Shu will deliver a lecture entitled Nuclear Energy After Fukushima on Tuesday, September 27th at 6:00 PM at the Commonwealth Club's San Francisco office located on the second floor of five nine five market street. The media and public's reaction to the recent nuclear accident threatened to cripple the nuclear renaissance that is humanity's best hope for mitigating climate disruption. She will review how [00:25:00] light water reactors and the once through fuel cycle came to dominate the landscape for generating nuclear power today and we'll assess options for the future. A standard ticket for this event is $20 but emission is $8 for members and $7 for students with a valid ID visit, www.commonwealthclub.org Speaker 5: more information. What's right with Kansas. Learn how Kansas is climate and energy project is capitalizing on heartland values to change behavior [00:25:30] and reduce carbon emissions. A panel of Nancy Jackson, executive director, Kansas climate and energy project and Marianne Fuller from the Lawrence Berkeley labs. Environmental Energy Technologies Division will present the Kansas project plus be the first to see lbls video Kansas, which shows how the climate and energy project has become a Kansas mainstay. This will be Monday, October 3rd 7:00 PM to 9:00 PM this is a free event at the Berkeley Repertory Theater, [00:26:00] 2025 Addison Street in Berkeley, Speaker 2: exploratorium is hosting after dark and evening series for adults 18 and over. That mix is science, art and cocktails and mission to the exploratorium is included. Tickets are $15 or $12 for seniors, students or persons with disabilities and are free for members. On Thursday, October 6th from six to 10:00 PM this months after dark theme is again and again explore the fascinating worlds of reminiscence and repetition [00:26:30] and then backwards skate through your own nostalgia on their temporary roller rink. UC Berkeley professor of psychology, Art CIM, and Maura will explain the mechanics of human memory. The website for this event is www.exploratorium.edu/after dark and now for a couple of recent science news events. Here's Brad Swift. Speaker 5: Gamers have solved the structure of a retrovirus enzyme whose configuration had stumped scientists for more than a decade. [00:27:00] The gamers achieved their discovery by playing folded and online game that allows players to collaborate and compete in predicting the structure of protein molecules. This is the first instance that the researchers are aware of in which gamers solved a longstanding scientific problem. After scientists repeatedly failed to piece together the structure of a protein cutting enzyme from an aids like virus they called in the folded players. The scientists challenged the gamers to produce an accurate model of the enzyme. The gamers did it and only three [00:27:30] weeks folded was created by computer scientists at the University of Washington Center for game science in collaboration with the Baker lab, a biochemistry lab at the university, figuring out the structure of proteins contributes to the research on the causes of and cures for cancer, Alzheimer's immune deficiencies, and a host of other disorders as well as work on biofuels. A paper describing the retrovirus enzyme structure was published September 18th [00:28:00] in the journal, nature, structural and molecular biology. The scientists and the gamers are listed as go authors Speaker 2: and in news related to this week's interview. Science reports that Israel has become an associate member of the European Physics Laboratory [inaudible]. They're the 21st member nation and the first new members since Bulgaria joined in 1999 this move is somewhat controversial. Sm Academics in the UK and South Africa. I wished to boycott collaboration due to Israeli Palestinian conflicts [00:28:30] but this ends a two year probationary membership and Israel will eventually contribute 1 billion Swiss francs to the project a year. Israeli representative to the certain Governing Council Eliezar revenue beachy states that he hopes this will inspire other Arab nations to join the effort. Speaker 4: [inaudible] music her during the show was attract [inaudible] Sean's divvy from David Lewis, Donna's self-published folk [00:29:00] and acoustic album. It is published under the creative Commons attribution license version 3.0 is available@wwwdotjamendo.com editing and production assistance for the show by Brad Swift. 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 [00:29:30] address is spectrum dot k a l x@yahoo.com join us in two weeks at this same time. [inaudible]. Hosted on Acast. See acast.com/privacy for more information.

Larissa Branin reports on a DOE-funded program that brings middle and high school science teachers to the Lawrence Livermore and Lawrence Berkeley National Labs each summer to give them hands-on experience as research scientists. This segment appears in the Fall 2010 edition of UCTV’s “State of Minds.” [Education] [Show ID: 20201]

Larissa Branin reports on a DOE-funded program that brings middle and high school science teachers to the Lawrence Livermore and Lawrence Berkeley National Labs each summer to give them hands-on experience as research scientists. This segment appears in the Fall 2010 edition of UCTV’s “State of Minds.” [Education] [Show ID: 20201]

Lawrence Berkeley National Labs explores three efforts: cheap solar energy, storing carbon deep underground, and energy efficiency in China. Ramamoorthy Ramesh discusses research to make photovoltaic cells using the most abundant elements in the Earth's crust -- materials that are literally as common as dirt. Nan Zhou expliores China’s energy use and the policies that have been implemented to increase energy efficiency and reduce CO2 emission growth. Curt Oldenburg discusses a strategy to reduce carbon emissions from coal and natural gas. Series: "Lawrence Berkeley National Laboratory " [Science] [Show ID: 19342]

Lawrence Berkeley National Labs explores three efforts: cheap solar energy, storing carbon deep underground, and energy efficiency in China. Ramamoorthy Ramesh discusses research to make photovoltaic cells using the most abundant elements in the Earth's crust -- materials that are literally as common as dirt. Nan Zhou expliores China’s energy use and the policies that have been implemented to increase energy efficiency and reduce CO2 emission growth. Curt Oldenburg discusses a strategy to reduce carbon emissions from coal and natural gas. Series: "Lawrence Berkeley National Laboratory " [Science] [Show ID: 19342]

Special web-only presentation from QUEST Radio. Fifty-five years after its construction, the Bevatron, a landmark particle accelerator at Lawrence Berkeley National Labs that helped pioneer physics discoveries and win several Nobel prizes, is about to be demolished.

Lawrence Berkeley National Labs just turned on a $27 million electron microscope. Its ability to make images to a resolution of half the width of a hydrogen atom makes it the most powerful microscope in The world.