Stay ConnectedWelcome to Science Fare! In this show, scientist and writer Susan Keatley talks with scientists about their latest research, and draws connections between the research and high school science learning standards.
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Copyright: © Susan Keatley
Pat Brown talks about his path to becoming a physician and scientist, the importance of a bench-to-bedside-back-to-bench approach in drug development, and targeted cancer therapy. Using his work in leukemia as an example, Pat talks about how changes at the level of DNA sequence change proteins and can lead to the development of cancer, and how scientists can use this knowledge to develop specific cancer treatments.
Works cited in this conversation:
The Emperor of All Maladies: A Biography of Cancer by Siddhartha Mukherjee
Janet Rowley and her work on cancer genetics
FLT3 inhibitors: a paradigm for the development of targeted therapeutics for paediatric cancer, in the European Journal of Cancer, March 2004
The biology and targeting of FLT3 in pediatric leukemia, in Frontiers in Oncology, September 2014
Episode highlights:
*Susan introduces Pat [1:58];
*Pat talks about his journey to becoming a physician and scientist focusing on pediatric leukemia [5:08];
*What is leukemia? Pat gives us an overview [8:46];
*Why leukemia has been at the forefront of cancer research and treatment [11:58];
*Pat’s early research and clinical work in leukemia [13:38];
*When, how, and why cancer treatment shifted from a one-size-fits-all approach to something more targeted [15:45];
*Some of the specifics of Pat’s work — what is FLT3? Why is it important in leukemia? [21:12];
*Pat’s work in developing clinical trials for treatments for children with leukemia — bench to bedside and back again [28:00];
*Success with the small molecule lestaurtinib, a first-generation FLT3 inhibitor [30:10];
*Pat’s group partnered with another company to produce a monoclonal antibody that could target FLT3 [31:12];
*Main challenge with both treatments (and challenge with all cancer therapies) is cancer developing resistance to treatment — people try to prevent resistance with multimodal treatments [32:20];
*Leads to the idea of personalized therapy — in each person, what are the genetic characteristics driving the cancer and can those be targeted with a cocktail tailored to that person? [35:40];
*Liquid biopsy’s potential in helping us see solid tumor cancers earlier and more comprehensively [36:58];
*Pat’s reflections on working in “translational medicine” — as a physician and a scientist — and the importance of bedside to bench as well as bench to bedside [39:21];
*How working as a scientist in academia is different from working in industry [43:25];
*What Pat is working on now, and his hopes for a decade or two out [50:04];
*High school science portion of the episode — Focusing on leukemia as an example, Pat tells us how changes in the DNA sequence of a gene can result in cancer. This connects to one of the Next Generation High School Science Standards in Life Science, which states that students should be able to construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells [55:23];
*Pat shares a memory from high school science [1:02:43];
*Pat’s advice to high school students today who are interested in science [1:04:05]
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Focusing on leukemia as an example, Pat Brown tells us how changes in the DNA sequence of a gene can result in cancer. This connects to one of the Next Generation High School Science Standards in Life Science, which states that students should be able to construct an explanation based on evidence for how the structure of DNA determines the structure of proteins which carry out the essential functions of life through systems of specialized cells.
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Naomi Oppenheimer and Matan Yah Ben Zion talk about their path to becoming physicists and their latest work — a look at the diffusion of a substance made of repulsive particles.
Most often when high school students learn about diffusion, the assumption is that the particles feel no attractions to each other. When you place a drop of dye into a flask of water, the dye spreads. Microscopically, the particles of dye and water bounce off each other due to thermal motion but we assume they experience no significant attraction or repulsion to each other.
But what happens if the particles DO repel each other? It turns out that this often the case, in scenarios ranging from collections of proteins to groups of people. Naomi and Matan studied diffusion in this scenario, and they share their findings here and the implications for larger questions.
Papers cited in this conversation:
Compact Expansion of a Repulsive Suspension in Physical Review Letters, June 2024
Bustling through the physics of crowds in Knowable, November 2024
Lane nucleation in complex active flows in Science, March 2023
Scientist bios:
Naomi is an assistant professor of Exact Sciences in the school for Physics and Astronomy at Tel Aviv University. She is interested in complex fluids, statistical mechanics, soft matter, and biology-inspired physical systems. She uses theoretical analytical tools, numerical simulations, and a dash of experiments. Some of her research achievements include predicting the effect of protein concentration on membrane viscosity and understanding why crumpled paper is shapeable, and her future directions include studying heterogeneous materials in biology and for next-generation functional materials.
Matan is an assistant professor of artificial intelligence at the Donders Center for Cognition at Radboud University in Nijmegen in the Netherlands. Matan’s research focuses on natural computation and collective behavior. He uses a combination of applied physics, statistical mechanics, artificial intelligence, and materials science to explain collective behavior in nature and to realize it in robotic swarms. Some of his research achievements include programmable self-assembly on the sub-cellular scale, developing a synthetic swarm or micro-swimmers on the cellular scale, and designing decentralized learning in robotic swarms.
Episode highlights:
*Susan introduces Naomi and Matan [1:28];
*How Naomi and Matan became scientists and ended up working together [3:25];
*What is regular thermal diffusion? [10:45];
*How Naomi and Matan got the idea to look at diffusion in a repulsive substance [15:52];
*What did they think they might see? [18:32];
*Repulsive particles are ubiquitous [20:20];
*How theory, simulations, and experiments came together in this work [25:15];
*How the expansion of a repulsive substance difference from normal diffusion [29:25];
*Why are the results significant and what new questions do they raise? [36:53];
*Relevance of this work to thinking about crowds of people [40:20];
*How this work helps broaden how students think about diffusion [44:30];
*Naomi and Matan share memories from high school science [48:00];
*Naomi and Matan give advice to high school students interested in studying science [51:18]
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Season 2, Episode #4.
In this mini episode, Naomi Oppenheimer and Matan Yah Ben Zion talk about their path to becoming physicists and their latest work — a look at the diffusion of a substance made of repulsive particles.
Most often when high school students learn about diffusion, the assumption is that the particles feel no attractions to each other. When you place a drop of dye into a flask of water, the dye spreads. Microscopically, the particles of dye and water bounce off each other due to thermal motion but we assume they experience no significant attraction or repulsion to each other.
But what happens if the particles DO repel each other? It turns out that this often the case, in scenarios ranging from collections of proteins to groups of people. Naomi and Matan studied diffusion in this scenario, and they share their findings here and the implications for larger questions.
If you like this episode, stay turned for the full length interview in a few days!
Scientist bios:
Naomi is an assistant professor of Exact Sciences in the school for Physics and Astronomy at Tel Aviv University. She is interested in complex fluids, statistical mechanics, soft matter, and biology-inspired physical systems. She uses theoretical analytical tools, numerical simulations, and a dash of experiments. Some of her research achievements include predicting the effect of protein concentration on membrane viscosity and understanding why crumpled paper is shapeable, and her future directions include studying heterogeneous materials in biology and for next-generation functional materials.
Matan is an assistant professor of artificial intelligence at the Donders Center for Cognition at Radboud University in Nijmegen in the Netherlands. Matan’s research focuses on natural computation and collective behavior. He uses a combination of applied physics, statistical mechanics, artificial intelligence, and materials science to explain collective behavior in nature and to realize it in robotic swarms. Some of his research achievements include programmable self-assembly on the sub-cellular scale, developing a synthetic swarm or micro-swimmers on the cellular scale, and designing decentralized learning in robotic swarms.
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Our guest today is Dr. Leo Otterbein, a professor of surgery at Beth Israel Deaconess Medical Center and Harvard Medical School. Leo’s research group focuses on the role of carbon monoxide as a therapeutic agent in medical applications ranging from organ transplant to infection to cancer. Inhaled carbon monoxide is currently in numerous FDA trials based in large part due the research in Leo's lab over the past decade. Leo is also chair of the Beth Israel Deaconess Medical Center (BIDMC) Institutional Animal Care and Use Committee. As the site miner for the BIDMC Center for the Integration of Medicine and Innovative Technology and member of the Boston Biomedical Innovations Center Technology Assessment and Development Group, Leo mentors and provides specialized expertise in entrepreneurial start-up ventures for innovative technologies. Leo trains graduate students, post-doctoral fellows, surgical residents, and junior faculty in basic research, grant proposals and career guidance.
On the episode, we talk about the myriad possibilities of carbon monoxide (yes, carbon monoxide!) in medicine, ranging from its use in organ transplantation, cancer, wound care, and sickle cell anemia.
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Season 2, Episode #2.
Dr. Dan Hatfield is a senior public health researcher at FHI360 with 15 years of experience developing, evaluating, and replicating community and behavioral interventions promoting healthy eating and physical activity, particularly in children, adolescents, and families. Previously, as a Research Assistant Professor at Tufts University, he served as principal or co-investigator on 13 federal and foundation-funded research grants, and he taught graduate courses in behavioral theory, health communications, and public health. His subject-matter expertise spans diverse domains, including nutrition, physical activity, obesity prevention, health communications, and theory-based intervention design.
Dan talks with us about the opportunities for and barriers to programs that aim to get communities more physically active.
Highlights of the episode:
*Susan introduces Dan [0:56];
*Dan’s background and path to becoming a scientist [2:08];
*Dan talks about the more and less well known benefits of physical activity [7:27];
*Some of the impediments to getting individuals and communities active [12:37];
*Dan’s work in helping to establish physical activity programs in a community in East Boston [18:11];
*Dan’s current NIH study in partnership with New York Road Runners [29:13];
*Dan’s hopes for the next 5 - 10 years for getting more people moving more [30:39];
*Was there a time when people in the US were moving a lot more? [34:46];
*High school science section — Dan talks about how when solving a problem, you determine the “necessary qualitative and quantitative criteria and constraints for solutions,
including any requirements set by society,” (From the Technology and Engineering Massachusetts standard HS-ETS1-1. Analyze a major global challenge to specific a design problem that can be improved.) [37:12];
*Dan shares a memory from high school science [44:20];
*Dan gives advice to high school students interested in studying science [46:04]
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Season 2, Episode #1.
Mike Shelley is an applied mathematician who uses modeling and simulation to better understand the physics and biology of complex systems. He is the director of the Center for Computational Biology, which is part of the Flatiron Institute — the scientific research arm of the Simons Foundation located in NYC. He also co-founded and co-directs the Courant Institute’s Applied Mathematics Laboratory at New York University.
Today, Mike is going to talk about elucidating how things in the cell find their proper place. Most listeners likely know that the cell is the basic unit of life, and within the cell are important structures like, for example, the nucleus which holds the DNA, and the ribosomes, where proteins are made. There are other structures that are actually transient, like the spindle, for example, and yet are crucially important for cell division — the process of making new cells.
Mike and his colleagues have done extensive work to understand how the spindle and related structures form, get in the right place, and stay in the right place for successful cell division. His work is a beautiful example of how physics and biology together help solve problems and push forward our understanding of the complexities of life.
Papers mentioned in this conversation:
“Forces positioning the mitotic spindle: Theories, and now experiments,” 2016, Bioessays
“Laser ablation and fluid flows reveal the mechanism behind spindle and centrosome positioning,” 2023, Nature Physics
Highlights of the episode:
*Susan introduces Mike and today’s topic [0:56];
*Mike’s background and path to becoming a scientist [2:50];
*The art of biophysical modeling and how it’s different from mathematical modeling [6:52];
*The technological and computational advances that have strengthened modeling [9:20];
*What is the spindle and why is it so important? [15:36];
*Different sets of forces have been proposed as key drivers in positioning the spindle — how was Mike’s group able to combine experiments and biophysical modeling to determine that pulling forces were predominant? [18:00];
*An earlier review paper from 2016 suggested that pushing forces were predominant — how changes like this are part of the scientific process [27:08];
*Other scientific problems Mike is excited about [28:45];
*High school science section — Mike talks about how understanding forces in the cellular world is quite different from what we see in the typical macroscopic world of the physics classroom with its ramps, balls, pendulums, etc. [32:18];
*Mike shares a memory from high school science [40:02];
*Mike gives advice to high school students interested in studying science [42:15]
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In this episode, I give a quick summary of the interview with Christie del-Castillo Hegyi and Jody Segrave Daly that aired on Science Fare on Monday, June 17, 2024. Christie and Jody are the founders of the Fed is Best Foundation and authors, along with Lynnette Hafken, of the forthcoming book, Fed is Best.
In today’s episode, we talk about:
*The Next Generation High School Science Standard entitled, “Engaging in Argument from Evidence.” In this standard, high school students are asked to evaluate the claims, evidence, and reasoning behind currently accepted explanations or solutions to determine the merits of arguments. I ask Christie and Jody how their work demonstrates this standard. [3:33];
*The advice Jody and Christie would give to high school students interested in science [14:50]
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In this episode of Science Fare, I interview Christie del-Castillo Hegyi and Jody Segrave-Daly, founders of the Fed is Best Foundation and authors, along with Lynnette Hafken, of the forthcoming book, Fed is Best.
Links mentioned in the episode:
Fed is Best Book
New York Times Parenting article on How to Deal with Low Breastmilk Supply
Sibling study on breast- and formula-fed babies and outcomes (appearing in Social Science & Medicine, 2014)
In the interview, we talk about:
*Christie’s and Jody’s experiences that led them to start the Fed is Best Foundation [4:15];
*The Fed is Best book and dispelling the myth that every mother makes enough milk to feed her baby [15:30];
*Dispelling the myth that supplementing a baby is at odds with breastfeeding [22:15];
*Dispelling the myth that baby formula harms babies [28:45];
*The sibling study on breast-and formula-fed babies and outcomes [34:45];
*Postpartum mental health and breastfeeding [39:50];
*Practical feeding guidance in the Fed is Best book [43:05];
*The impact of the Fed is Best Foundation on policy and public attitudes [46:15];
*Where to find the Fed is Best book [54:45]
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Lisa Ammirati, high school science teacher and chair of the science department at Abington Friends School talks to us about her career as a science teacher and strategies to integrate classroom curriculum with events in the broader world.
In this conversation, we talk about:
*Lisa’s career in teaching [3:25];
*What it’s like being a department chair [4:58];
*What is uniquely special about teaching 10th grade chemistry [6:30];
*What Lisa has done in her classroom to connect the curriculum to the broader world [8:35];
*Why the Flint, MI chemistry unit worked so well [10:22];
*What are some challenges teachers face in connecting classroom curriculum to the broader world? [17:43];
*Why is it important to do this? [20:40];
*What can public school teachers, who may be more constrained in their curriculum, do to link the classroom to world events? [24:40];
*How can a podcast like best help in the effort to draw connections between the high school science classroom and the world of scientists and what they do? [27:50]
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Jill Herschleb, senior director of cell biology at 10x Genomics, talks about her path as a scientist and her work in building the tools that have helped make single-cell genomics the robust and flexible technology it is today.
Here is an informative video on single cell genomics and its use in the effort to make a comprehensive human cell map (aka, the Human Cell Atlas).
In Part 2 of this conversation, we discuss:
*the idea of a cell as a test tube in single-cell genomics, and setting up massively parallel (millions and millions!) experiments [1:58];
*the Human Cell Atlas is a Human Genome Project-type effort, but with throughput that dwarfs that of the 1990s [4:00];
*Single-cell perturb-seq — the evolution of the classic mutant screen [5:25];
*Mechanics of how single-cell analysis works —partitioning via droplets [8:30];
*Implications for drug discovery and development [9:40];
*How do we analyze all these data? [12:35];
*How scientist communities are changing [20:00];
*What Jill’s job at 10x Genomics is like [21:05];
*What trouble-shooting as a scientist at a biotech company looks like [26:00];
*Jill’s advice on how to progress in a scientific career [29:14];
*Connection to a California state high school science learning standard on engineering design [32:08];
*Jill’s memory from high school science — her AP Chemistry teacher conveying both the difficulty and possibility of doing well on the AP exam [36:51];
*Jill’s advice to high school students interested in science — first, science is fun, and remember that! make sure to find the joy in it, in whatever way, when it gets hard, and second, keep your eyes open to all of the various ways you can be a scientist. [40:13]
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Episode #8.
Jill Herschleb, senior director of cell biology at 10x Genomics, talks about her path as a scientist and her work in building the tools that have helped make single-cell genomics the robust and flexible technology it is today.
Here is an informative video on single cell genomics and its use in the effort to make a comprehensive human cell map (aka, the Human Cell Atlas).
In Part 1 of this conversation, we discuss:
*How Jill got interested in science as a kid [2:30]
*Jill’s grad school realization that scientists could build tools, and that was what she wanted to focus on [4:15]
*Jill’s path after graduate school, and the many opportunities for scientists beyond academia [6:05]
*Jill’s role at 10x Genomics [10:15]
*Prelude to single-cell genomics: next-generation sequencing (NGS). What is it and why it is important? [14:20]
*How did NGS lead to single-cell genomics? What is single-cell genomics? Moving beyond the limits of hypothesis-based research with single-cell genomics [18:45]
*One example of an important discovery from single-cell genomics: the pulmonary ionocyte and its role in Cystic Fibrosis [28:00]
*The necessity of more data at this resolution — the single cell — to make important discoveries [32:30]
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At the halfway point of Season One of the Science Fare podcast, let’s have a listen to this special High School Science highlights episode — a collection of clips from previous episodes when the scientists link their work to the high school science learning standards. We have Hashim Al-Hashimi (Episodes 1 and 2) talking about how complexity evolves, Jamie Morton (Episodes 3 and 4) talking about the scientific process and feedback in biological systems, and Kelly Knudson (Episode 5 and 6) talking about how strontium gets into bones.
Specific timestamps:
*Hashim Al-Hashimi: New York state high school curriculum in Life Sciences disciplinary core idea: “Although DNA replication is tightly regulated and remarkably accurate, errors do occur and result in mutations which are also a source of genetic variation.” How can we think about mutations and the evolution of variation in terms of a sweet spot between evolutionary fitness and peril? [2:10]
*Jamie Morton: In the Maryland state high school curriculum under the topic of The Nature of Science, students are expected to master the idea that “scientific inquiry is characterized by a common set of values that include logical thinking, precision, open-mindedness, objectivity, skepticism, replicability of results, and honest and ethical reporting of findings.” How did the study on autism and microbiome incorporate some of these values? [9:50]
*Jamie Morton: Also in the Maryland state high school curriculum, we have the Life Science learning standard that says, “Feedback mechanisms maintain a living system’s internal conditions within certain limits and mediate behaviors allowing it to remain alive and functional even as external conditions change within some range. Feedback mechanisms can encourage through positive feedback or discourage through negative feedback what is going on inside the living system.” Can we talk about the microbiome and autism in these terms? [14:25]
*Kelly Knudson: In the Arizona state high school curriculum, in the Chemistry section of the learning standards, students are asked to “explain how the structure of atoms relates to patterns and properties observed within the periodic table.” How does the way Strontium gets into bones relate to this idea? [17:30]
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Part 2 of the conversation with Kelly Knudson, professor of Anthropology in the School of Human Evolution and Social Change at Arizona State University, and director of the Center for Bioarchaeological Research and the Archaeological Chemistry Laboratory, who talks to us about archaeological chemistry, her path as an archaeological chemist, and about a paper she and others published in PNAS entitled “Feasting and the evolution of cooperative social organizations circa 2300 B.P. in Paracas culture, southern Peru,” in which the chemical isotope data help determine where objects at a feasting site came from, and from there, lead to inferences about the evolution of social complexity at the site.
We discuss:
*What Kelly and her colleagues learned about where the objects at the site were from [2:45]; about 25% of objects coming from significant distances, and interpret that to mean the feast-goers were coming from significant distances [3:00];
*Were the results expected? Surprising? [3:54];
*What kinds of distances are we talking about, and how does the concept of distance today differ from what it may have meant in the past? [6:30];
*How the archaeological and chemical data come together [9:30];
*What happens when the archaeological and chemical data conflict? An example [12:45];
*How the field of archaeological chemistry has changed since Kelly was in graduate school [16:49];
*What excites Kelly the most about archaeological chemistry research — trying to understand what people’s lives were like the past [17:40];
*Connection to an Arizona state high school science learning standard on how the structure of atoms relates to patterns and properties observed in the Periodic Table [19:10];
*Kelly’s memory from high school science — an AP Bio project that was her first “field” experience and how much she loved it [23:45];
*Kelly’s advice to high school students interested in science — explore, be attuned to what interests you, be open to new paths and opportunities that open up [26:00]
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Episode #5.
Kelly Knudson, professor of Anthropology in the School of Human Evolution and Social Change at Arizona State University, and director of the Center for Bioarchaeological Research and the Archaeological Chemistry Laboratory, talks to us about archaeological chemistry, her path as an archaeological chemist, and about a paper she and others published in PNAS entitled “Feasting and the evolution of cooperative social organizations circa 2300 B.P. in Paracas culture, southern Peru,” in which the chemical isotope data help determine where objects at a feasting site came from, and from there, lead to inferences about the evolution of social complexity at the site.
We discuss:
*A brief intro to archaeological chemistry [1:28];
*Kelly’s background and path to a career in archaeological chemistry [2:47 ];
*Importance of getting into the field and having mentors in her early career [7:10];
*Kelly’s job now: direct the lab (12,000 archaeological samples analyzed to date!), admin and budgeting, teaching, mentoring students in the classroom and in the lab [7:55];
*Introduction to the PNAS paper on feasting and using archaeological chemistry to infer how far the people at the feast traveled to get there [14:10];
*When archaeologists may need to use chemistry to help determine where objects at a site are from [15:30];
*What are isotopes? [17:50];
*How to use Strontium isotopes (Sr-86 and Sr-87) to figure out where objects are from [19:47];
*Objects found at the site — cotton textiles, bottle gourds, corn, llamas, etc — and why this looks like a feast versus everyday food consumption [23:20];
*Using guinea pigs to make Strontium isotope maps in Peru [27:20]
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Part 2 of the conversation with Jamie Morton, scientist and founder of Gutsy Analytics, who talks about his June 2023 paper in Nature Neuroscience entitled, “Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles,” in which Jamie and 42 other authors re-analyzed prior datasets to discover new connections between the human gut microbiome and autism.
For a primer on the human microbiome, check out this 2020 review piece that appeared in Nature Medicine: “Current understanding of the human microbiome.”
We discuss:
*Implications of this work for future studies on autism — how to get at causality [2:55];
*Importance of longitudinal studies [3:40];
*Clinical trials done via sampling kits [5:40];
*Has the human microbiome changed over the past decades? [7:10];
*Microbiome research going forward, beyond autism [9:00];
*Microbiome and differential responses to drugs [10:45];
*Historical context -- when did scientists start talking about the microbiome seriously? [11:30];
*Connection to Maryland high school science standard on the nature of science [13:00];
*Connection to Maryland high school science standard on feedback in biological systems [17:40];
*Jamie’s memory from high school science — preparing for a robotics competition [20:27];
*Jamie’s advice to high school students interested in science — importance of multidisciplinary work [23:01]
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Jamie Morton, scientist and founder of Gutsy Analytics, talks about his June 2023 paper in Nature Neuroscience entitled, “Multi-level analysis of the gut-brain axis shows autism spectrum disorder-associated molecular and microbial profiles,” in which Jamie and 42 other authors re-analyzed prior datasets to discover new connections between the human gut microbiome and autism.
For a primer on the human microbiome, check out this 2020 review piece that appeared in Nature Medicine: “Current understanding of the human microbiome.”
We discuss:
*Introduction of the terms “human gut microbiome” and “autism” [1:20]
*Jamie’s background as a scientist [4:05];
*How this study got started at the Simons Foundation [5:37];
*Jamie’s interest in autism [7:18];
*Genesis of the research [8:10];
*What is a meta-analysis? [10:47];
*Importance of analyzing previous datasets [11:20];
*Deciding on what kinds of data to focus on [12:30];
*Bringing together different kinds of data to build a functional architecture [14:22];
*Computational modeling ins and outs — batch effect correction, age and sex matching to avoid confounding [15:09];
*Associations between data and autism [18:31], including the surprising overlap between microbial and human pathways [21:15];
*Causality or association? [23:45];
*FMT paper: “Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota."[24:42];
*What is FMT and what does it do? [25:09];
*Overlap between paper’s research and FMT study — additional validation [27:54]
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Here is Part 2 of the conversation with Hashim Al-Hashimi, professor of biochemistry and molecular physics at Columbia University, who talks about his March 2023 paper in the Proceedings of the National Academy of Sciences (PNAS) entitled, “Turing, von Neumann, and the computational architecture of biological machines,” in which he writes about an opportunity for better understanding biological problems: seeing biological molecules as computing machines.
We discuss:
*Quick recap of Part 1 [1:05];
*DNA polymerase and its transition states (spoiler alert: it’s like Pac-Man) [1:57];
*The different shapes, or contortions, of biomolecules can be seen as computing transition states [5:52];
*Right now in biology, there is a lot of focus on protein structure, and too little focus on the protein’s program [7:25];
*Not all computers (and therefore biological molecules) are Turing machines — computer scientists have developed a hierarchy of computers [8:27];
*The simplest machine is the finite state machine, with no external memory, and so the states are a form of memory [8:37];
*Computation as anything that follows instructions to solve a problem [10:30];
*Push-down automaton as the next computer in the hierarchy [11:00];
*Bounded tape computer as the next [13:00];
*How to begin building transition tables for biological molecules? Exploit the growing database of structures, to start. [14:00];
*Weakness of transition rules: they don’t include time information, critical to doing something like simulating a cell [16:00];
*Moving forward and building momentum around the effort to build transition tables [18:00];
*Quantum computing and its potential future role in determining transition states [19:50];
*Could we use this in the future to simulate complicated systems, like clinical trials, for example? [22:02];
*Relevance to a particular New York State high school science “disciplinary core idea” in the life sciences: “although DNA replication is tightly regulated and remarkably accurate, errors do occur and result in mutations, which are also a source of genetic variation,” [25:09] and how we can think about the ‘sweet spot’ of errors for evolving complexity but not harming an organism (or a computer!) [26:00];
*Hashim’s memory from high school science in Wales [32:35];
*Hashim’s advice to high school students today interested in studying science [34:30]
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Hashim Al-Hashimi, professor of biochemistry and molecular physics at Columbia University, talks about his March 2023 paper in the Proceedings of the National Academy of Sciences (PNAS) entitled, “Turing, von Neumann, and the computational architecture of biological machines,” in which he writes about an opportunity for better understanding biological problems: seeing biological molecules as computing machines.
In Part 1 of our conversation, we discuss:
*Hashim’s background as a scientist [1:05];
*Prelude to the problem: the late Nobel laureate Sydney Brenner’s idea that we are drowning in data [3:55];
*How Hashim got involved in this research [5:25];
*John von Neumann reveals his ideas at the Hixon Symposium at Caltech in 1948 [7:30];
*Von Neumann’s question: how can you build a machine that can build a machine more complex than itself, similar to how living organisms evolve into more complex organisms? [9:20];
*Von Neumann’s solution [10:50]; with copying error providing the basis for the evolution of complexity [12:20];
*Five years before the discovery that DNA had the double helix structure, von Neumann used principles of math, theorizing and thinking, to work out how complexity can and must evolve [15:00];
*All living organisms carry a copy of the instructions to build the organism [17:00];
*Turing and the general purpose programmable computer [18:00];
*The idea of states as fundamental components of computation in Turing’s machine [20:30];
*What it means that there is no solution to the decision problem [25:50];
*Hashim’s quest to understand Turing’s 1936 paper and the connection to biomolecules [27:30]
Hosted on Acast. See acast.com/privacy for more information.
Welcome to the Science Fare podcast!
On the Science Fare podcast, I aim to bring you conversations with scientists doing fascinating, cutting-edge work on all kinds of interesting phenomena, ranging from physics to chemistry to biology, and even the nature of science itself. Each conversation is split into two parts, and at the end of part two, we'lll draw connections between the scientist's research, and one or two high school science learning standards from that scientist's state.
Tune in for some Science Fare!
Hosted on Acast. See acast.com/privacy for more information.
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