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Science Fare

High School Science Highlights

Season 1, Ep. 7

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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  • 10. Lisa Ammirati on Linking High School Science to the World Beyond the Classroom

    36:43
    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]
  • 9. Part 2 of Jill Herschleb on Discovery-Based Research with Single-Cell Genomics

    44:23
    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]
  • 8. Jill Herschleb on Discovery-Based Research with Single-Cell Genomics

    34:39
    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]
  • 6. Part 2 of Kelly Knudson on Using Archaeological Chemistry to Help Understand Feasting at a 2000-year-old Site in Peru

    28:29
    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]
  • 5. Kelly Knudson on Using Archaeological Chemistry to Help Understand Feasting at a 2000-year-old Site in Peru -- Part 1

    31:40
    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]
  • 4. Part 2 of Jamie Morton on Finding Associations Between the Microbiome and Autism

    26:40
    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]
  • 3. Jamie Morton on Finding Associations Between the Microbiome and Autism -- Part 1

    30:01
    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]
  • 2. Part 2 of Hashim Al-Hashimi on Why We Should See Biological Molecules as Computing Machines

    37:31
    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]