Podcasts about Keith Devlin

It's easy to take growth for granted, for it to seem expected, inevitable even. Every person starts out as a baby and grows up. Plants grow from seeds into food. The economy grows. That stack of mail on your table grows. But why does anything grow the way that it does? In this hour, we go from the Alaska State Fair, to a kitchen in Brooklyn, to the deep sea, to ancient India, to South Korea, and lots of places in between, to investigate this question, and uncover the many forces that drive growth, sometimes wondrous, sometimes terrifying, and sometimes surprisingly, unnervingly fragile.Special thanks to Elie Tanaka, Keith Devlin, Deven Patel, Chris Gole, James Raymo and Jessica SavageEPISODE CREDITS: Reported by - Matt Kielty, Becca Bressler, Pat Walters, Sindhu Gnanasambandun, Annie McEwen, Simon Adlerwith help from - Rae MondoProduced by - Matt Kielty, Becca Bressler, Pat Walters, Sindhu Gnanasambandun, Annie McEwen, Simon AdlerSound design contributed by - Jeremy Bloomwith mixing help from - Jeremy BloomFact-checking by - Emily Krieger and Natalie Middletonand Edited by  - Pat WaltersEPISODE CITATIONS:Audio:“The Joy of Why,” (https://www.quantamagazine.org/tag/the-joy-of-why/) Steve Strogatz's podcast. Articles:“The End of Children,”(https://zpr.io/WBdg6bi8xwnr) The New Yorker, by Gideon Lewis-KrausBooks:Finding Fibonacci (https://zpr.io/3EjviAttUFke) by Keith DevlinDo Plants Know Math (https://zpr.io/bfbTZDJ8ehx5) by Chris GoleSingup for our newsletter!! It includes short essays, recommendations, and details about other ways to interact with the show. Sign up (https://radiolab.org/newsletter)!Radiolab is supported by listeners like you. Support Radiolab by becoming a member of The Lab (https://members.radiolab.org/) today.Follow our show on Instagram, Twitter and Facebook @radiolab, and share your thoughts with us by emailing radiolab@wnyc.org.Leadership support for Radiolab's science programming is provided by the Gordon and Betty Moore Foundation, Science Sandbox, a Simons Foundation Initiative, and the John Templeton Foundation. Foundational support for Radiolab was provided by the Alfred P. Sloan Foundation.

Anna and Paul discuss math, finance, geometry, finance bros, Piza, pizza, New Yawk, the Yankees, and making things accessible to the common man. Note: We refer to the author of "Finding Fibonacci" as “Kevin Devlin.” He is actually Keith Devlin. Follow @engineering_history_podcast on Instagram to keep up with our latest updates :) Further reading: The Man of Numbers: Fibonacci's Arithmetic Revolution By Keith Devlin Finding Fibonacci: The Quest to Rediscover the Forgotten Mathematical Genius Who Changed the World By Keith Devlin Fibonacci and the Financial Revolution By William Goetzmann  The Origins of Value: The Financial Innovations that Created Modern Capital Markets By William Goetzmann and K. Rouwenhurst   The History of Algrebra in Italy in the 14th and 15th Centuries. Some Remarks on Recent Historiography By Rafaella Franci  The Positional System and Base 10 | Mathematics for the Liberal Arts (lumenlearning.com)

About our GuestsKevin Moore is an experienced educator of young learners as well as a respected instructional leader. Presently, Kevin's attention and energies are consumed by two ventures of which he is a Co-Founder, Long-View Micro-School and The Number Lab. Long-View Micro School is a STEM focused, highly innovative, learner-centered educational environment thoughtfully designed for upper elementary and middle-school-aged learners.  Through his work at Long-View, Kevin is committed to impacting the educational landscape locally by adding to the diversity of schooling options for families in Austin Texas. In his work with The Number Lab, Kevin helps to design and facilitate professional development seminars for teachers who provide mathematics instruction to young learners. These seminars are meant to help teachers strengthen their own conceptual understandings of mathematics and inspire a culture of learning in their classrooms that engages learners as mathematicians. Kevin's work with The Number Lab connects him with educators throughout the United States and beyond.  Kaylie White is an experienced educator at Long-View Learning, where she strives to transform mathematics education by working with both young learners and educators from across the country. Kaylie designs and leads learning experiences for young mathematicians at Long-View Micro School — a STEM-focused, highly innovative, learner-centered educational environment designed for upper elementary and middle-school-aged learners. Through Long-View's teacher-facing work, Kaylie creates and facilitates professional development for teachers, including in-person workshops, Field Study Days at Long-View Micro School, and virtual coaching. She also leads the social media marketing for Long-View Learning. Kaylie is a bold, creative, and passionate educator who sees herself as a learner first. She eagerly works to collaborate with her team to continuously iterate and improve the learning experience for all. When she is not teaching and learning, Kaylie enjoys time with her husband and one-year-old son in Austin, Texas where they cook, hike, read, play soccer, and cheer on Austin FC.Follow their work: Instagram: long_view_learning School's instagram:  long_view_atx Website: long-view.com  Professional Development from The Number Lab (Long-View Team) Find Support from the team at https://www.long-view-learning.com/Show NotesAdrienne and Trae interview two master teachers in mathematics from Long- View Micro School in Austin, Texas. While Long-View is a progressive school, they have discovered the truth of dialectis in the classroom. While they do not formally consider their methods as classical, and their terminology may be different than common terms in classical education, they truly embrace the art teaching math dialectically. Teaching math is not about state standards or facts and formulas to memorize, but rather it is a discipline that is engaging, interesting, and helps students learn thinking and communication skills which are common to the goals of classical education. Some topics in this episode include: The high abilities of children to wrestle with big ideas and participate in deep and meaningful work The importance of a healthy community of learners with teachers as facilitators who will challenge and mediate students through meaningful ideas Children need opportunities to grapple with complex ideas so that they can learn the art of dialectics (Longview school is not classical and does not call it the art of dialectics, but that is inadvertently what is being discussed).  Real understanding emerges from the messiness of learning how to be precise with good language, with communication, and with tapping into creative ways of solving problems. Setting a school culture where learning is a process that everyone does together. .Books & Resources In This EpisodeA Mathematician's Lament: How School Cheats Us Out of Our Most Fascinating and Imaginative Art Form by Paul Lockhart and Keith Devlin  Visilbe Learning by John HattieDaring Greatly by Brené Brown Learner-Centered Teaching by Maryellen WeimerPlease Support us on Patreon_________________________________________________________Credits:Sound Engineer: Andrew HelselLogo Art: Anastasiya CFMusic: Vivaldi's Concerto for 2 Violins in B flat major, RV529 : Lana Trotovsek, violin Sreten Krstic, violin with Chamber Orchestra of Slovenian Philharmonic © 2022 Beautiful Teaching. All Rights Reserved ★ Support this podcast on Patreon ★

Mathematics is everywhere. We use numbers, quantities, values and measurements almost all the time. Counting and quantifying is part of almost everything that we do. An interesting question is how did it all start. When did humans start thinking mathematically and what is the origin of mathematical thinking. As we start tacking these questions, we stumble upon few more queries: how did our brain evolve to do mathematics; what are fundamental capacities that enable humans to do mathematical thinking; what are major milestones in the evolution of mathematical thinking and in the history of mathematical innovations; is mathematics discovered or is it invented. I invited Dr Keith Devlin to join me in this episode of Bridging the Gaps for a discussion that focuses on these questions. Dr Keith Devlin is the director of the Stanford Mathematics outreach project at Stanford University. His current research is focused on the use of different media to teach and communicate mathematics to diverse audiences. He has written 33 books and over 80 research articles. He is a World Economic Forum Fellow, a Fellow of the American Association for the Advancement of Science, and a Fellow of the American Mathematical Society.

Keith Devlin: Talking Media, Math, MOOCs | Steve Hargadon | May 8 2012 by Steve Hargadon

Keith Devlin is one of the world’s greatest advocates for mathematics. The British Mathematician  insists that maths in the 21st century depends on creativity. Devlin is the author of more than 30 popular science books; a university professor, as well as the co-founder and director of H-STAR, the Human-Sciences and Technologies Advanced Research Institute at Stanford University. His research focuses on the use of different methods for teaching mathematics to the general public.

School's In with Dan Schwartz and Denise Pope: "Learning Math skills for Life with guest Keith Devlin" Stanford Mathematician and NPR Weekend Edition “Math Guy” Keith Devlin talks about how learning math in the classroom is evolving and why it is more important for students to understand math concepts than it is to repeatedly solve equations. Originally aired on SiriusXM on September 1, 2018. Recorded at Stanford Video.

Keith Devlin, Stanford mathematician and NPR Weekend Edition “Math Guy," talks about how learning math in the classroom is evolving and why it is more important for students to understand math concepts than it is to repeatedly solve equations.

In this episode of The Wired Educator Podcast, Kelly interviews Dr. Jo Boaler about her amazing book Mathematical Mindsets: Unleashing Students' Potential Through Creative Math, Inspiring Messages, and Innovative Teaching. Dr Jo Boaler is a Professor of Mathematics Education at Stanford University and co-founder of www.youcubed.org. Formerly the Marie Curie Professor of Mathematics Education for England, a mathematics teacher in London comprehensive schools and a researcher at King's College, London. She is the author of eight books including What's Math Got To Do With It? (2015) and Mathematical Mindsets (2016). She is the recipient of the NCSM award for equity, the author of the first MOOC on mathematics learning for teachers and parents, a White House presenter and an advisor to the PISA team at the OECD. Mentioned in this episode: Book Creator is one of my favorite apps for any device! www.BookCreator.com Jo Boaler's book: Mathematical Mindsets: Unleashing Students' Potential Through Creative Math, Inspiring Messages, and Innovative Teaching. Here is a list of all of Jo's books! One of Jo's favorite mathematicians is Maryam Mirzakhani: Here she is in a 6 Set of Prints from NASA: Mighty Women in Science Poster Set. Two more of Jo's favorite mathematicians include: Steve Strogatz: Here is a list of his books. and Keith Devlin and his works. Jo used math counting sticks like these as a child and recommends similar to parents: Educational Math Counting Sticks. Jo cofounded: www.Youcubed.org a resource to inspire, educate and empower teachers of mathematics to transform their classroom. How to Learn Math: A free course for students by Jo Boaler. Leave a review for the Wired Educator Podcast here. Kelly has a new podcast title The Future Focused Podcast. Please give it a listen! Ask your superintendent to visit www.KellyCroy.com and request Kelly to be your opening day speaker. 

On this week’s BioTech Nation, “The NPR Math Guy”, Keith Devlin, tells us about Finding Fibonacci: The Quest to Rediscover the Forgotten Mathematical Genius Who Changed the World”. Then on Tech Nation Health, chief correspondent Dr. Daniel Kraft tells us about the winners of the Qualcomm Tricoder Xprize - StarTrek medicine isn’t fiction any more.

On this week's Tech Nation, “The NPR Math Guy”, Keith Devlin, tells us about Finding Fibonacci: The Quest to Rediscover the Forgotten Mathematical Genius Who Changed the World”. Then on Tech Nation Health, chief correspondent Dr. Daniel Kraft tells us about the winners of the Qualcomm Tricoder Xprize - StarTrek medicine isn't fiction any more.

In 2001, Stanford mathematician Dr Keith Devlin, also known as ‘The Math Guy’ on NPR’s Weekend Edition, set out to research the life and legacy of the thirteenth century mathematician Leonardo of Pisa, popularly known as Fibonacci. Leonardo introduced the Hindu-Arabic numeral system and arithmetic to the Western world, and thereby helped start a global, social and economic revolution. Devlin recounted Leonardo's story in a 2011 book titled The Man of Numbers: Fibonacci’s Arithmetic Revolution. In a simultaneously published companion e-book, Leonardo and Steve: The Young Genius Who Beat Apple to Market by 800 Years, he drew remarkable parallels between the careers of Leonardo and Apple’s Steve Jobs. His new book, Finding Fibonacci: The Quest to Rediscover the Forgotten Mathematical Genius Who Changed the World is a first-hand account of his experiences in uncovering the story, reconstructed from his project diary and notes, together with stories of three other contemporary scholars who were also motivated to find out about the long-forgotten medieval mathematician who did so much create the world we live in. This talk was held as part of the Sydney Ideas program on 3 October: http://sydney.edu.au/sydney_ideas/lectures/2017/keith_devlin.shtml

More at http://philosophytalk.org/shows/math-and-mind. How does a bunch of grey matter in our skulls have the ability to solve mathematical problems? Are we the only species that can? Does catching a baseball require doing calculations? Join John, Ken, and their guest, noted cognitive scientist and NPR's "Math Guy" Keith Devlin, as they discuss the many ways our minds can do the math.

Dr. Keith Devlin is a mathematician who’s also known as The Math Guy on NPR’s Weekend Edition. He has written several books explaining math to the masses. And he's also the co-founder and Executive Director of Stanford University’s Human-Sciences and Technologies Advanced Research Institute (H-Star). We spoke with Dr. Devlin about why math is difficult to understand and explain, how we tend to know more about mathematicians' lives than their work, and whether programs like Khan Academy help or hurt students.

A Stanford mathematician & Co-founder/Executive Director of the H-STAR Institue, Keith Devlin addresses insights into market segmentation and audience analysis gleaned from his work with the educational technology company BrainQuake.

A Stanford mathematician & Co-founder/Executive Director of the H-STAR Institue, Keith Devlin addresses insights into market segmentation and audience analysis gleaned from his work with the educational technology company BrainQuake.

Coding is not for everybody. We admit it. But we should all take at least a peek under the hood of the computers and devices that power our lives. It's empowering. Starting at a screen full of cryptic code is daunting, confusing, and might just well up some latent math anxiety. That's how New Tech City host Manoush Zomorodi felt, which is exactly why she decided to dive in head first. She signed up for a one-day computer programming intensive. This episode chronicle's how it went.   In short: It began a jumble of doubt and worry with baggage from high school math holding her back. "I am going to have to commit an act of coding to bring my anxiety level down a notch," she decided by late morning during the theory portion of the day. Yet within hours, Manoush had made a mostly functioning web app for her kids. "The mere act of making it myself made it less scary," she concludes.   Along the way she gains a greater reverence for the language of our machines and for the people fluent in them. Manoush wrote about this wild ride in more detail here, when a previous version of this show first aired.   Also in this episode:  Keith Devlin, author of "Introduction to Mathematical Thinking" and many other books, describes the kind of thinker that tech firms are desperately looking for. The new tech economy needs mathematicians, but he says, of the kind of math that is not so much about numbers, as problem solving and pattern recognition. These skills can be learned! If you liked this story, please click here to subscribe to our podcast on iTunes / RSS to find our other episodes. We're on Twitter too: @NewTechCity Now watch Manoush learn to code, despite her 10th grade math teacher!   (This episode is a longer version, with additional information, of our show that aired on January 8.)

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.

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.

Keith Devlin is a mathematician and executive director of H-STAR at Stanford University in Palo Alto, California. Krista Tippett spoke with him on July 11, 2013. This interview is included in our show “The Joy of Math.” Download the mp3 of the produced show at onbeing.org.

Mathematical equations are like sonnets says Keith Devlin. What most of us learn in school, he says, doesn’t begin to convey what mathematics is. And technology may free more of us to discover the wonder of mathematical thinking — as a reflection of the inner world of our minds.

Sol Lederman http://www.buzzsprout.com/5316/73938-keith-devlin-part-ii-inspired-by-math-17.mp3 Tue, 22 Jan 2013 00:00:00 -0500 2965 math, mathematics, inspiration full false Sol LedermanIn this podcas

Dr. Devlin and I discuss his "Introduction to Mathematical Thinking" MOOC (Massive Open Online Course) in great detail. 64,000 students registered for the very challenging course, although most didn't finish. What made the course challenging? How did grading work? How was support provided? What role did community play in the course? Why was this MOOC more like Facebook than Youtube? How might universities use MOOCs in the future to find the brightest students they might not find otherwise? How can MOOCs level the playing field in education? What's the next big thing for Dr. Devlin?

Keith Devlin concludes the course by discussing the development of mathematical cognition in humans as well as the millennium problems. (October 29, 2012)

Keith Devlin gives an overview of the history of mathematics. He discusses how it has evolved over time and explores many of its practical applications in the world. (October 1, 2012)

The Royal Mail says UK stamp prices are still among the best value in Europe, despite an imminent steep price rise. Tim Harford finds out whether this is true, and compares the price of postal services around the world. Plus, he finds out how, after being invented by Indian mathematicians, modern numbers became established in the ancient Arab world and then journeyed on to Europe in what was essentially the first maths textbook ever written, "Liber Abaci". Its author was Leonardo of Pisa, better known as Fibonacci. Tim speaks to Keith Devlin, author of The Man of Numbers, to find out more. This programme was first broadcast on the BBC World Service.

I interview Keith Devlin on a number of subjects: mathematics as a way of thinking, the role of video games, the importance of learning math in a historical context, the value of story-telling in teaching math, and more .... Plus, the most important thing that parents can do to help their kids who are struggling with math.

In the week scientists at the Large Hadron Collider announced that the most coveted prize in particle physics - the Higgs boson - may have been found, Tim Harford hears that the statistical significance is being mis-reported. Plus, the difficulties of cornering a market (especially when the commodity is a 1980s plastic doll). And, Tim Harford talks to author Keith Devlin about how Fibonacci revolutionised trade by introducing medieval businessmen to simple arithmetic.

Keith Devlin, Executive Director of the H-STAR Institute at Stanford University, discusses Leonardo and Steve: How Fibonacci Beat Apple to Market by 800 Years

Keith Devlin, Executive Director of the H-STAR Institute at Stanford University, discusses Leonardo and Steve: How Fibonacci Beat Apple to Market by 800 Years

Keith Devlin, Executive Director of the H-STAR Institute at Stanford University, discusses Leonardo and Steve: How Fibonacci Beat Apple to Market by 800 Years

Mathematician Keith Devlin discusses his collaboration with choral group Zambra. Plus dancer/mathematician Karl Schaffer, and the most important math discovery you've never heard of.

A conversation about the genesis of probability theory with mathematician Keith Devlin, author of The Unfinished Game: Pascal, Fermat and the Seventeenth-Century Letter that Made the World Modern.