Big Biology

Rats, squirrels, coyotes, pigeons...often, we view animals like these as pests. We usually don't like them, even try to get rid of them…but what makes a species a pest? On this episode, we talk with Bethany Brookshire about her new book, Pests: How Humans Create Animal Villains. Bethany is a science journalist interested in human-animal conflict, and in the book, she tells the story of how both historical and cultural context explains why the same animal species can be viewed as a friend or foe. 

Bethany is also the host of the podcast Science for the People - check them out!

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On this episode, we talk with Stuart Newman, professor at New York Medical College. In his recent paper, “Inherency and agency in the origin and evolution of biological functions,” Stuart argues against the commonly held view that functions of traits necessarily arise from the process of natural selection. He instead advocates for an alternative called inherency, which suggests that groups of cells naturally possess traits that determine their potential morphology, which can then be modified further by natural selection. He supports this idea with examples of extant species - placozoans and sponges - that closely resemble the earliest animals. We discuss Stuart’s provocative paper, the concept of inherency, and its potential role in evolution.

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On this episode of Big Biology, we talk about the challenges of doing…big biology! The National Ecological Observatory Network, or NEON, is a US National Science Foundation-funded project that has started collecting massive amounts of data from terrestrial and freshwater habitats across a network of sites distributed across the United States. Scott Collins, a professor at the University of New Mexico, and Alan Knapp, a professor at Colorado State University, have been involved in developing, promoting, and sometimes criticizing NEON. We discussed with them the successes and potential of NEON and the major challenges and controversies that it has faced.  We also talked about how they believe NEON can have positive impacts in the future.

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On this episode, we take a break from the regular format to talk with Itai Yanai and Martin Lercher of The Night Science Podcast, a show that explores the creative side of science with guests from across the globe. Itai is a professor in the Department of Biochemistry and Molecular Pharmacology at the NYU School of Medicine, and Martin is a professor in both the Institute for Computer Science and the Department of Biology at Heinrich Heine University Düsseldorf. We had a great time chatting with them about our respective podcast experiences, trading tips and reflecting on our passion for science communication and the ways that it has impacted our own research.

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Donate to our spring fund drive! Or, become a patron! Or both! – hey, we’re not picky!

On this episode, we talk with Nick Barton, an evolutionary quantitative geneticist at the Institute of Science and Technology Austria. Quantitative genetics has changed a lot in the past 30 years, driven by massive advances in DNA sequencing power and by new statistical and computational approaches to harnessing the data flood. Nick works at the forefront of the field, developing and testing new theory, and we discuss both his research and his perspectives on these changes. We end by asking Nick about his advice for early career researchers who want to navigate the complex landscape composed of theory, computation, and data.

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Donate to our spring fund drive! Or, become a patron! Or both! – hey, we’re not picky!

In this episode, we talk with Arlin Stoltzfus, a research fellow at the University of Maryland’s Institute for Bioscience and Biotechnology Research. Arlin studies mutation bias – the idea that some types of mutations occur more often than others – and how these patterns can influence the evolutionary trajectories of populations. In the chat, we contrast this mutation-centric approach to evolution with more standard views in which selection does most of the creative heavy lifting. We center the talk around Arlin’s 2021 book - Mutation, Randomness, and Evolution, which offers a new conception of variation as a difference-maker in evolution. Looking forward, Arlin argues that a better understanding of mutation will make it easier to predict the origins and outcomes of different cancers and the evolution of infectious diseases and crop pests.

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On this episode, we talk with Uri Alon, systems biologist at the Weizmann Institute of Science, about biological networks. In the early 2000s, Uri discovered some of the fundamental characteristics of these networks and, since then, has worked to understand networks across different levels of biological organization. His work shows that, from genes to whole organisms, networks are filled with repeating patterns of connections known as network motifs, such as feedback and feedforward loops. We talk about how the motifs arise and what they mean for the performance and evolution of the systems in which they’re embedded. Moving farther afield, we also talk about how scientists can productively move into new areas, and how Uri teaches early-stage scientists to leap confidently into the unknown. And a bonus: Uri sings and plays guitar for us!

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On this episode, we talk with Tina Lasisi, incoming professor at the University of Michigan, about variation in human hair structure and skin color. We talk about why such variation may have evolved, and how biologists are studying it. We also discuss the implications of her work for the concept of race. Tina encourages scientists and the public to be curious about (rather than afraid of) human diversity, as it’s an obvious part of our world that should be understood from multiple perspectives, including biological.

Also be sure to check out the Preprints in Motion podcast here!

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Happy holidays from the Big Biology team! As a bonus episode this week, we are sharing Art's recent interview with James Fodor on The Science of Everything podcast. Art and James discuss various topics in evolution and genetics, covering material that spans years of Big Bio conversations.

Enjoy, and see you next year!

In this episode, we talk to John Glass, leader of the Synthetic Biology Group at the J. Craig Venter Institute. Over the past decade, Glass and colleagues developed techniques for manipulating and synthesizing entire bacterial genomes. Starting with Mycoplasma bacteria, which have very small genomes, they determined the minimal number of genes (473!) required to support life. They experimentally confirmed this number by synthesizing genomes from scratch, containing just the essential genes, and putting them into other bacteria whose genomes were removed. Cells in this lineage, called JCVI-syn3.0, grow and divide approximately like wildtype cells do.

We talk with John about how they pulled it off and what this minimal genome tells us about life more generally. We also chat about the functions of essential genes and what so-called non-essential genes may do in the wild. Finally, we touch on what if anything minimal genomes say about the origin of life and on the group’s ongoing efforts to synthesize entire cells – not just genomes! – from scratch.

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On today’s show, we talk with astrobiologist Sara Walker about this idea in relation to a new theory, called assembly theory, that she and colleagues are currently developing. Assembly theory characterizes the complexity of objects, including molecules, by how many steps are required to make them – the more steps, the higher the object’s complexity index. This perspective reorients our attention from the traits of objects that make them complex to the historical sequence of events that must have occurred to create them. Sara proposes that this idea provides natural ways to think about a large set of interesting processes, including how information is manifest and used in living systems, the creative roles of natural selection in evolution, and the ever present problem of understanding levels of selection.

This was Sara’s second appearance on the show, check out her first episode here.

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In this episode, we talk to Helen Scales, a marine biologist, writer, and broadcaster who has written the essential guidebook to the deep ocean titled “The Brilliant Abyss”. On our way to the bottom of the sea, Helen recounted her journey from academia to writing and shared some of the lessons for others looking to dive into science communication. She also introduced us to some of her favorite species and their unique adaptations for surviving at extreme depths as well as several threats that the deep ocean faces. Technology has not only opened up this ecosystem to exploration but also to exploitation. Helen lays out the current state of ocean conservation and offers some hope and advice to those looking to protect the planet's largest habitat.

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On this episode, we talk with Rajee Rajakumar, a professor at the University of Ottawa, who studies Pheidole ants to understand the interactions between their genes, their developmental environments, and their phenotypes. Rajee is also a HUGE ant fan! We talk with him about his 2018 paper in Nature about the mysterious organs that control these differences in development, and amazingly, how these organs could be socially regulated via pheromones.

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In this episode, we talk to Charles Piller, an investigative journalist who published a shocking story in Science magazine in July this year laying out compelling evidence for misconduct in multiple journal articles on Alzheimer’s disease. This misconduct appears to have occurred in recent papers involving the experimental drug, simulfilam, as well as older, foundational papers in Alzheimer’s research.

Charles’s story focuses on the sleuthing of Matthew Schrag, a neuroscientist and physician at Vanderbilt University who studies Alzheimer’s disease himself. In an extensive (even heroic) effort, Schrag identified over 100 potentially manipulated images in multiple major research papers. We talk with Charles about the consequences of those seemingly fraudulent images for the field and for public trust in science. We also talk about the potential consequences for whistleblowers like Schrag, and what journals and funding agencies are doing to support integrity in basic research.

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In this episode, we talk to Matt Barbour, a professor at the University of Sherbrooke, about “keystones” in biology. You’re probably familiar with the keystone species concept, but Matt’s research focuses on whether genes can play a similarly fundamental role in an ecosystem. In an incredible set of experiments, Matt and his colleagues used simple experimental food webs to find that the stability of these miniature complex systems was strongly associated to the genotype at one specific locus in the plant, Arabidopsis thaliana, called AOP2. The particular genetic variant led to complete breakdown of community stability, imbuing that gene with a keystone-like function.

We talk to Matt about his recent publication in the journal Science and discuss how results from his simple lab setup relates to keystone effects in natural communities.

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In this episode, we talk with author and University of Alberta professor Timothy Caulfield about decision making and misinformation in the modern world. A surprising number of “common sense” decisions that people make in their daily lives are not actually backed by strong scientific evidence, and Tim strives to debunk these in his recent book, “Relax, Dammit!: A User's Guide to the Age of Anxiety”.

Among other things, we discuss with Tim how often we should check email, and how risky it really is for kids to walk to school. We also talk about how science communication can be used to curb misinformation, and Tim shares his dos and don’ts for effective scicomm.

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Much of biological research over the past 50 years has relied on model organisms. These species – which include mice, rats, fruit flies, and others – have yielded many insights and led to the development of better molecular tools and a scientific culture centered on sharing. At the same time, the money and effort devoted to model organisms may have undermined work on a broader diversity of species, more representative of life as a whole. In this episode, we talk with Sabina Leonelli and Rachel Ankeny, two philosophers of biology, about the history of model organisms and the positives and negatives of studying them.

Sabina Leonelli is a professor and director of the Exeter Center for the Study of Life Sciences. Rachel Ankeny is a professor in the School of Humanities at the University of Adelaide. They are also authors of the book Model Organisms, a philosophical exploration of the concept of the 'model organism' in contemporary biology.

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Visit www.geneticsunzipped.com to learn more and see full episode transcripts, subscribe to Genetics Unzipped wherever you get podcasts, and say hello on Twitter @GeneticsUnzip

On this episode, Art and Marty talk with Joe Parker, an entomologist at Caltech. Joe has been collecting beetles since the age of 16, when he first became amazed by their incredible diversity. He now focuses on rove beetles and studies their evolutionary relationship with ants to understand how different species converge upon similar traits.

In this episode, Marty and Art talk with Joel Brown about how to contain cancer using basic ideas from ecology and evolution. To Joel, cells in tumors are like organisms in ecosystems, and fighting cancer means using what we know about species in nature to tilt the playing field against the worst kinds of cancer cells. He and his team at the Moffit Cancer Research Center in Tampa, Florida, are starting to have some remarkable success treating different kinds of cancer.

We interviewed Joel in front of a live audience at Circa 1949 in Tampa, FL—our first live event!

Tune into this podcast to hear Art and Marty talk to Sheila Patek about how mantis shrimp pack such a powerful punch and why we should care. For example, mantis shrimp hammers can be used hundreds of thousands of times to break open the tough shells of snails and clams, and this research may help inspire lightweight, heavy duty military armor.

Sheila studies the mechanics of ultrafast movements at Duke University. You may have seen her work featured by Science News (and numerous others) about the rules of animal fight clubs. But we can't talk about those.

On this episode of Big Biology, we talk with Michael Levin, a biologist at Tufts University who studies how electric fields inside animals guide cells during development and regeneration. His work shows that electric fields play fundamental roles in structuring body plans and, in some species, can even be inherited across generations.

On this episode, we talk to Graham Scott, a physiologist from McMaster University who studies the oxygen cascade in mice living on mountaintops, extreme environments for such small organisms. We discuss the concept of symmorphosis, the function and evolution of the oxygen cascade, and several clever experiments involving rat marathons and mighty mountain mice.

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On this episode of Big Biology, we talk with Steve Brusatte, professor of Paleontology and Evolution at the University of Edinburgh. Steve is the author of a new book: The Rise and Reign of the Mammals, which charts the evolution of our own mammalian ancestors, from those living in the time of the dinosaurs, through mass extinctions, to the diversity of mammals that dominate Earth today. We also talk to Steve about some of the remarkable people behind the discoveries that comprise what we know today.

In the last half of the show, we talk about Steve’s previous book: The Rise and Fall of the Dinosaurs, which caught the attention of Colin Trevorrow, director of Jurassic World.  Based on that book, Colin brought Steve on as the scientific advisor for the new film: Jurassic World Dominion. We chat with Steve about his role in the making of the film and what we can expect from the new dinos (spoiler: FEATHERS!)

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On this episode, Art and Marty talk to Fred Tauber, a professor emeritus of medicine and philosophy at Boston University, about how the immune system does more than just protect our bodies from pathogens. Fred has published a number of books on immunity and philosophy. In his most recent book, "Immunity: The Evolution of an Idea", he explores the ideas discussed in this episode in greater detail.

Our guest today, Van Savage, is a professor in the department of Ecology and Evolutionary Biology and the department of Biomathematics at UCLA. We chat with Van about universal features of branched networks. We discuss how these networks are space filling and how their evolved structures facilitate rapid and energy-efficient transport. We also discuss why networks are fractals – branching structures that are self-similar across scales. You’ve seen the fractal nature of networks if you’ve noticed similarities between branching patterns of rivulets on a muddy bank and river connections viewed from a jet at 20,000 feet. We also discuss how differences in networks among taxa arise from the materials they transport. At the end of the conversation, Van explains how network theory illuminates what we know about metabolic scaling and how understanding branching can improve everything from artificial hearts to urban planning.

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On this episode, we talk to Corrie Moreau, a professor of entomology at Cornell University, about the diversity and influence of microbes in ants. For Corrie, these microbes are a sort of internal rainforest, whose presence directly impacts the lives of the ants who carry them. Many ant-microbe relationships have evolved over millions of years, resulting in specialized interactions – from fungus-farming in leaf cutter ants, to insect mind control by the Ophiocordyceps fungus, to distortion of insect reproduction by Wolbachia bacteria. We also chat with Corrie about science communication, and how making biology a welcoming and diverse place will inspire the next generation of researchers and promote greater trust in science by the public.

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On this episode of Big Biology, we talk to Tim Lenton, Director of the Global Systems Institute (@GSI_Exeter) and a Professor of Climate Change and Earth System Science at the University of Exeter. In his 2021 Trends in Ecology & Evolution paper “Survival of the Systems,” Tim outlined his idea that large, complex systems--such as grasslands, coral reefs, and even human economies--are subject to a kind of natural selection based on their ability to persist. Tim argues that systems better able to extract and recycle resources will spread across landscapes and outcompete other such systems.

This episode is produced in collaboration with Trends in Ecology & Evolution (@Trends_Ecol_Evo). TREE, published by Cell Press, is a monthly review journal that contains polished, concise and readable Reviews and Opinions in all areas of ecology and evolutionary science. It aims to keep scientists informed of new developments and ideas across the full range of ecology and evolutionary biology--from the pure to the applied, and from the molecular to the global. Visit: http://www.cell.com/trends/ecology-evolution.

In this episode, we talk to Dan Nicholson, a philosopher and biologist from George Mason University about his new edited volume, "Everything Flows: Toward a Processual Philosophy of Biology". In it, he and colleagues argue that biological systems more resemble flames and tornadoes and other dynamically stable systems than clocks or other human-designed things. Dan thinks that life is better understood as flows of energy and matter, which means that trying to reduce biological things into smaller parts, a popular practice in biology known as reductionism, will ultimately fail because it misses the stream-like nature of life. In the show today, we discuss these ideas, what Dan calls a processual philosophy for biology, including what it means for evolution, medicine, and more.

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On this episode, we talk with Martha Muñoz, a professor in Yale’s Department of Ecology and Evolutionary Biology. We frame the chat in terms of two big ideas in thermal physiology – Janzen’s hypothesis and the Bogert Effect. Dan Janzen famously predicted that tropical ectotherms, with their relatively narrow thermal performance curves, would have a harder time moving up and over cold mountain passes. For organisms that rely on the environment to regulate their body temperatures, mountain passes appear higher in the tropics. These effectively higher mountains should lead to greater isolation of local populations and potentially greater rates of speciation because dispersal becomes more difficult. Charles Bogert focused on interactions between behavior and thermal evolution in ectotherms. He suggested that species with better capacity for behavioral thermoregulation would evolve more slowly – because thermoregulation shields thermal traits from the brunt of strong selection. We talk with Martha about these two ideas, and about how her work on Anolis lizards illustrates them.

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On this episode, we explore the interface of biology and resource management with Briana Abrahms, from the Department of Biology and the Center for Ecosystem Sentinels at the University of Washington. Climate change is increasingly forcing humans and animals into conflict, often with disastrous outcomes for all parties involved. Briana studies the causes of these conflicts and their links to serious human problems like forced labor, terrorism, piracy, and poaching.

We talk about collisions between whales and ships, conflict between ranchers and carnivores, and elephants running amok in India. We also talk about the illegal wildlife trade in Africa and about subsistence fishing, problems which in some places have been addressed by effective local governance. Finally, we talk about what governments, scientists, and regular people can do to help.

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On this episode of Big Biology, we talk with Kathryn Paige Harden, a professor in the Department of Psychology at the University of Texas at Austin where she leads the Developmental Behavior Genetics lab. Paige is the author of a new book, The Genetic Lottery: Why DNA Matters for Social Equality. In the book, Paige advocates for using genetic information to better understand variation in our life outcomes such as how many years of school we complete and other complex social, economic and educational conditions. She thinks that genetics can be a tool to help create a more equitable society, but her ideas have both ardent supporters and vociferous critics. We delve into why her book has been so controversial, how human genetic data might be used constructively and ethically, and whether the incorporation of more explicit evolutionary thinking about what genes actually do might prevent future misunderstanding and maybe even the misuse of genetic data.

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On this episode, we talk all things plasticity with David Pfennig, a professor at the University of North Carolina, and Nick Levis, a postdoc at Indiana University. Their research focuses on something they call plasticity-led evolution. Building on older ideas, David and Nick argue that novel environments release hidden, or cryptic, genetic variation in some individuals in a population, which in turn allow selection to act on trait variation that is only revealed as plasticity is induced.

We discuss these ideas using a fantastic real-world example: spadefoots. These burrowing amphibians have expanded into the American Southwest, and tadpoles of some species develop dramatically different morphologies depending on what’s available to eat in their early lives. If they eat pond scum, they tend to become placid omnivores, but if they eat meat, they become giant carnivores that devour other aquatic animals…and even each other.

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On this episode, we talk with paleontologist Henry Gee about his latest book, A (Very) Short History of Life on Earth. The book offers a kaleidoscopic tour through the roughly 4 billion year history of life on Earth in just 288 pages. Gee is a longtime editor at Nature, and a master writer and storyteller. He shares his approach to good writing and discusses why professional science writing is often so dull. We also touch on his favorite chapters in the short history of life on Earth, including why some species evolved such large body sizes.

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On this episode we talk with Henkjan Honing, professor of music cognition at the University of Amsterdam, about the biology of musicality. Among diverse species, he and his collaborators now study how and why some animals perceive elements of music but others do not.

We also discuss the earliest known examples of human musical instruments and the possible adaptive value of music. All of these topics and more are covered in his recent book, The Evolving Animal Orchestra: In Search of What Makes Us Musical.

Additional sound effects for this episode came from www.zapsplat.com

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On this episode, we talk to Toby Kiers, an evolutionary biologist at VU University Amsterdam, about the massive networks of arbuscular mycorrhizal fungi (AMF) that inhabit the soil beneath our feet. Toby studies the symbiotic relationship between AMF and 80-90% of plant species, through which the tube-shaped fungi cells trade nutrients with plant roots in exchange for carbon. We draw connections between these networks and human networks, and discuss whether economists should be taking notes from these systems.

We also talk about SPUN, a non-profit initiative Toby’s group recently launched with the goal of mapping these fungal networks and advocating for their protection worldwide.

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In this episode, we talk to Michael Purugganan, an evolutionary biologist at NYU, about some of our favorite foods, where they came from, and what to do to ensure we will still have them in the future.

We also talk about rice, an essential staple crop for the world. Michael describes his genomic work with rice to make it more robust and resilient, especially in the face of climate change and a growing human population. His research is part of a global effort to make a Green Super Rice, a rice variety suitable for the diverse challenges of the future.

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On this episode, we talk with Arvid Ågren, an evolutionary biologist and Wenner-Gren Fellow at Uppsala University, about his new book, “The Gene’s-Eye View of Evolution”. The book chronicles the history of gene-centric views of evolution, which burst onto the scene in 1976 with the publication of Richard Dawkins’s book, "The Selfish Gene". In the gene-centric worldview, genes and alleles take center stage as both key units of selection and drivers of the evolutionary process. Organisms and their phenotypes, by contrast, are viewed as transient vehicles – disposable somas constructed and controlled by genes whose purpose is simply to help those genes replicate.

Previous guests on Big Biology, including Denis Walsh, Denis Noble, Mike Levin and others, have argued strongly for an opposing point of view: that organisms, not genes, should be the focal level for understanding evolution. On this episode, we challenge Arvid to reconcile the gene’s-eye view with our more organism-centered views, and to account for important biological phenomena like the origin of life and adaptation. Our conflicting perspectives led to a stimulating conversation about the nature of evolution, whether the abstractions inherent to the gene’s-eye view are justifiable, and how alternative conceptions of adaptation might lead to unification in biology.

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On this episode, we talk with Tony Sinclair, professor emeritus of zoology at the University of British Columbia, about his new book “A Place Like No Other: Discovering the Secrets of Serengeti”. Since the 1960s, Tony has studied the bottom-up and top-down processes that regulate wildlife populations in the Serengeti. We talk about how he discovered the major rules of regulation, the unique geography and climate of the Serengeti, the major forces driving wildebeests on epic annual migrations, and the roles that elephants play in stabilizing ecosystems into alternative stable states. We also talk with Tony about the controversial topic of rewilding degraded ecosystems. Tony argues that effective strategies for rewilding emerge only from understanding the fundamental processes that shape ecosystems in the first place.

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How do diseases spread from animals to humans? Is it possible to forecast where disease outbreaks will occur and when they will blow up into major health crises? In one of the earliest episodes of Big Biology, Marty and Art talk to Barbara Han, a disease ecologist at the Cary Institute of Ecosystem Studies, about her research on zoonotic disease, how we track the spread of infectious diseases and whether we'll ever be able to predict outbreaks.

On this episode of Big Biology, we talk with Daniel Gibbs, a retired neurologist, about his new book: “A Tattoo on My Brain: A Neurologist’s Personal Battle Against Alzheimer’s Disease”. A few years back, Dan discovered his genetic predisposition to Alzheimer’s disease (AD), which motivated him to chronicle his journey from treating patients with dementia to his own experience with AD. Over 50 million people worldwide are diagnosed with AD, yet we still know surprisingly little about how this disease arises at the cellular and molecular levels, and much less about why such a devastating condition persists in spite of what should be strong natural selection against it.

In the episode, we discuss these enduring mysteries about Alzheimer’s, what it means to be an APOE4 homozygote, and what precautions individuals with AD can take to slow and best manage their symptoms.

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On this episode, we talk with Karl Friston, world-renowned neuroscientist at University College London, about his free energy principle. In order for the human brain or any other self-evidencing system (be it Earthly or alien) to exist, they must be able to make inferences about their environments, and adjust their internal models of the world to resist entropy. In the show, we discuss how Karl’s previous work as a psychiatrist led him to this theory, then take a deep dive into the free energy principle, discussing how it can help us understand stress, agency, DNA, and the possibility of life elsewhere in the universe.

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On this episode, we talk with UC Irvine evolutionary biologist Adriana Briscoe (@AdrianaBriscoe) about color vision in insects, particularly Heliconius butterflies. We discuss how their perception of the world has led to such massive diversification and how variation in the structure of the light-sensitive opsin proteins that detect light enable species to perceive the world differently. We also discuss how visual perception differences within species might shape behaviors such as pollination, and what ecological factors could drive visual system evolution across the tree of life.

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On this episode, we talk with Mark Denny, Stanford University professor of marine science and former director of the Hopkins Marine Station. In his 2019 paper, “Performance in a variable world,” Mark reviewed how organisms perform in highly variable environments -- a problem that has taken on new urgency as climates change. We also talk about extreme ecological events -- what they are, why they occur, and how they affect organisms. Often, extreme conditions arise from unusual combinations of otherwise normal patterns of variation in multiple underlying factors. Predicting the effects of climate extremes therefore requires holistic approaches to monitoring environments coupled with an integrative understanding of animal physiology and behavior.

This episode of Big Biology is sponsored by the Hopkins Marine Station of Stanford University. Founded in 1892, Hopkins Marine Station is the oldest marine laboratory on America’s west coast conducting research that addresses fundamental questions at every level of marine biology, from genes to ecosystems.

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On this episode of Big Biology, we talk with Avalon Owens (@avalonceleste), a PhD candidate at Tufts University whose research aims to better understand the effects of artificial light at night (or ALAN) on insects. We discuss what light at night is doing to insect populations, why some insects are attracted to light, and how lights might be compromising the pollination services and disease risks mediated by some insects. We also discuss the fascinating light-centered behavior of the fireflies, specifically how man-made light disrupts their ability to find mates. We close with ideas about what you can do to help reduce the effects of artificial light on wildlife broadly. Spoiler alert: turn ‘em off or buy some damn curtains!

This episode is sponsored by the Zoological Lighting Institute. Recognizing that natural light is a central aspect of animal health and ecological function, The Zoological Lighting Institute promotes scientific research to improve understanding of what artificial changes in light mean for animals and the human communities that depend on them. Through education on light pollution, ZLI hopes that proper and sustainable approaches to care and development of light sources can be taken by communities around the globe.

Photo: Lupines and Fireflies No. 3 by Mike Lewinski (CC BY 2.0)

On this episode, we talk to virologists Konstantin Chumakov and Robert Gallo about their recent paper entitled “Old vaccines for new infections”. They and their colleagues argue that we can fight novel pathogens, like SARS-COV2, by stimulating our innate immune systems with live-attenuated vaccines developed for other pathogens (e.g., measles, rubella, polio). Such an approach might buy us time, particularly for front-line health workers or the most vulnerable among us, while pathogen-specific vaccines are developed. Many LAVs are cheap, easy to distribute, and already available where SARS-COV2 is common but its vaccine is not. We talked with Chumakov and Gallo about the prospects of using the LAV approach for future pandemics, why we didn’t use them to control COVID, and the possible mechanisms by which these old vaccines wield their surprising power.

Image: Number of people fully vaccinated against COVID-19 as of June 16, 2021 (collated by Our World in Data https://ourworldindata.org/coronavirus). Total number of people who received all doses prescribed by the vaccination protocol. This data is only available for countries which report the breakdown of doses administered by first and second doses.

On this episode of Big Biology, we talk with Tufts University professor Michael Levin about his recent article in Aeon magazine called ‘Cognition all the way down’. In it, Mike and Dan Dennett discuss the phenomenon of agency and what it means for biology, basic to medical. We discuss with Mike what it means to be an agent - whether you’re a metabolite, a cell, or a human - and how agency affects and is affected by evolution. We discuss how agents at different levels of organization influence each other, how agency research could change our thinking about the ethics of artificial intelligence, and how the internet has expanded collective human agency by broadening our cognitive horizons.

If you missed our first chat with Mike on the role of bioelectric fields in development, tissue regeneration, and evolution, check that out here.

Photo: Douglas Blackiston and Sam Kriegman

In this episode of Big Biology, we talk with Jason Podrabsky, a professor of biology at Portland State University, about diapause – a remarkable physiological state in which organisms turn down their metabolic rates to a bare minimum. Diapause is a way of living through harsh conditions while spending as little energy as possible. We talk with Jason about how organisms enter diapause, what happens inside them during diapause (more than you would think!), and how they reboot their systems to emerge from diapause. We focus on Jason’s work with the amazing annual killifish. In some species in this group, embryos can go into diapause and survive for months in the dry mud of ephemeral ponds, waiting for the next rain to arrive.

Photo: Claire Riggs and Jason Podrabsky

On this episode of Big Biology, we talk to Tim Lenton, Director of the Global Systems Institute (@GSI_Exeter) and a Professor of Climate Change and Earth System Science at the University of Exeter. In his 2021 Trends in Ecology & Evolution paper “Survival of the Systems,” Tim outlined his idea that large, complex systems--such as grasslands, coral reefs, and even human economies--are subject to a kind of natural selection based on their ability to persist.  Tim argues that systems better able to extract and recycle resources will spread across landscapes and outcompete other such systems.

This episode is produced in collaboration with Trends in Ecology & Evolution (@Trends_Ecol_Evo). TREE, published by Cell Press, is a monthly review journal that contains polished, concise and readable Reviews and Opinions in all areas of ecology and evolutionary science. It aims to keep scientists informed of new developments and ideas across the full range of ecology and evolutionary biology--from the pure to the applied, and from the molecular to the global. Visit: http://www.cell.com/trends/ecology-evolution.

On this episode, we talk with Denis Walsh, a professor and philosopher of biology at the University of Toronto, about his book Organisms, Agency, and Evolution. The Modern Synthesis, which combines Darwin’s theory of natural selection and Mendel’s theory of genetic inheritance, was a giant leap forward in our understanding of the evolution of populations. Denis argues, however, that the extreme abstraction required by the synthesis derails our understanding of evolution. What’s needed instead, he suggests, is renewed focus on organisms. Because organisms have agency, they in effect construct the environments they experience, which in turn affects how selection acts on them. This view reestablishes organisms – not genes – as the central unit of evolution, just as Darwin’s ‘struggle for existence’ emphasized.

Photo credit: Blue Dragon nudibranch (Pteraeolidia ianthina) by Saspotato (CC BY-NC-SA 2.0)

On this episode of Big Biology, we talk to renowned author Walter Isaacson (@WalterIsaacson) about his new book, Code Breaker: Jennifer Doudna, Gene Editing, and the Future of the Human Race. We break down the rich history of the gene editing CRISPR-Cas9 system--from its initial discovery in bacteria to the current ethical considerations for using it in humans. We also talk about the life of Nobel Prize winning scientist Jennifer Doudna, who, along with Emmanuelle Charpentier, initially proposed CRISPR as a way to edit DNA and modify traits to fight disease. We then close with a discussion of what CRISPR-Cas9 means for the future of gene editing and just how far it could, or rather should, go.

Why are some corals more resilient to bleaching than others? How should we leverage genetic and epigenetic information to conserve coral diversity?
On this episode of Big Biology, we talk with Hollie Putnam (@HolliePutnam), a professor at the University of Rhode Island, about threats to coral reefs and the steps she and her colleagues are taking to preserve coral diversity. Warming oceans disrupt the relationships between corals and their symbiotic algae, which can lead to coral bleaching. Warming also alters the composition and function of the entire coral holobiont, the diverse community of other organisms that live together with corals and their algae. Hollie’s lab studies the causes of coral bleaching and the physiology of coral holobionts, both to understand the basic biology of corals and to selectively breed corals that can better tolerate future ocean conditions.     
This episode is sponsored by Journal of Experimental Biology. The journal is published by the Company of Biologists, a not-for-profit that has been supporting and inspiring the biological community since 1925. JEB is at the forefront of comparative physiology and biomechanics.

On this episode, we talk with Herman Pontzer (@HermanPontzer) of Duke University. We discuss his new book Burn, in which he examines -- and in some cases overturns -- received wisdom about human energy budgets and human metabolism. Much of the book is framed around Herman’s amazing long-term studies with the Hadza, a group of modern-day hunter-gatherers in Tanzania. That work reveals insights into human energy expenditure, helping reframe our Western dogmas about diet. He argues that because our metabolism evolved to cope with starvation, weight management is likely to be much more successful if we limit what we put into our bodies rather than how many calories we burn during exercise.  His evolutionary perspective also alters how we understand and treat metabolic disease, and the energetic limits to endurance among elite athletes. Those fitbits we love might not be as helpful as we’d like!

How did vocal learning evolve? What is special about human language? What brain structures are associated with speech and the many components of spoken language?

On this episode, we talk with Erich Jarvis (@erichjarvis), a professor at Rockefeller University, about the neurobiology of vocal communication. Erich’s ideas draw on the amazing breadth of auditory and vocal capacities among mammals and birds - from learning simple sounds to imitating sounds to producing complex, flexible vocalizations. We also discuss the unique “circuit within a circuit” neural networks of parrots that allow them to create such a rich repertoire of sounds. At the end, we talk about human speech and about what sign language, singing, and our “inner voice” tells us about its evolution.

In this episode of Big Biology, we talk with Rob Raguso, a professor at Cornell University, who studies insect-plant interactions. Rob discusses his work on diffuse coevolution between night blooming flowers and their long-tongued hawk moth pollinators, and how his and others’ ideas leading to geographic mosaic theory has helped us understand the evolution of novel traits. Rob says that plant-pollinator coevolution has had a huge and varied impact on human life and culture, well beyond its obvious effects on our agriculture. Coevolution between plants and their pollinators shaped our trade, our religious practices, and even the contents of our liquor cabinets.

Photo: Robert Raguso

In this episode, we talk with Dave Goulson (@DaveGoulson), a professor of biology at the University of Sussex. Dave studies the ecology and conservation of insects, particularly bumblebees, and he is the founder of the Bumblebee Conservation Trust. Bumblebees and wild bees provide pollination services for over 50% of the food we consume—so ensuring their long-term viability is critical to our food security. Dave says that bees and other insects face many challenges, especially from neonicotinoid insecticides and from protozoan diseases and ectoparasites. We talk with Dave about the effects of anthropogenic stressors and the rapid action needed from individuals, farmers, policymakers, and governments to help maintain healthy bee populations.

Photo: Pieter Haringsma

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On this episode of Big Biology we talk to Christine Cooper (@CECooperEcophys), a vertebrate ecophysiologist and professor at Curtin University, Australia. Christine’s research focuses on the thermal, metabolic, and water physiology of Australian mammals and birds. Her recent research, published in the Journal of Experimental Biology (a sponsor of this episode), details how one small and common bird, the zebra finch, responds to prolonged and intense Australian heat waves. We also discussed the evolution of vertebrate endothermy and how various other animals have evolved to cope with changes in temperature.

This episode is sponsored by Journal of Experimental Biology. The journal is published by the Company of Biologists, a not-for-profit that has been supporting and inspiring the biological community since 1925. JEB is at the forefront of comparative physiology and biomechanics.

Photo: Christine Cooper

Photo: Hannah Davis

On this episode of Big Biology we talk to Kevin Gaston (@KevinJGaston), a professor of Biodiversity & Conservation at the University of Exeter. Kevin is an expert on the ecological impacts of artificial light and in particular “sky glow”--the combined glow of all lights coming from cities and towns. In our chat, we discussed how light production has grown over the past several decades and the growing impacts that it's having on our planet. Further, we discuss some of the psychology behind the human desire for bright spaces and what we as individuals can do to reduce the impacts of light pollution on ourselves and the organisms around us.

This episode is sponsored by the Zoological Lighting Institute. Recognizing that natural light is a central aspect of animal health and ecological function, The Zoological Lighting Institute promotes scientific research to improve understanding of what artificial changes in light mean for animals and the human communities that depend on them. Through education on light pollution, ZLI hopes that proper and sustainable approaches to care and development of light sources can be taken by communities around the globe.

On this episode of Big Biology, a panel of experts discusses the virus’s trajectory and impact, and our options going forward. This conversation was recorded live at Busch Gardens in Tampa, Florida, in partnership with the University of South Florida College of Public Health and Morsani College of Medicine and the City of Tampa.

The panel consisted of Jane Castor, the mayor of Tampa, Kami Kim, a physician and professor who specializes in infectious diseases, Edwin Michael, an epidemiologist focused on the population ecology of disease transmission, and Michael Teng, an immunologist with expertise in vaccine development. We moderate as the experts look ahead, and discuss what we can expect long-term.

Photo: Allison Long

In this episode of BigBiology, we talk to Sean Caroll, an award-winning scientist, author, educator and, film-producer about his latest book, A Series of Fortunate Events, in which he writes about how chance has shaped life on Earth. In Sean’s view, chance is the creative process and contingency is the aftermath of chance. Consider the asteroid impact that killed off the dinosaurs and paved the way for the rise of mammals and ultimately humans. It could have missed our planet altogether. Or it could have hit 30 minutes earlier, or later, landing in the ocean and having effects that were much less severe.

Sean argues that chance is not limited to biology but plays a big role society including the entertainment industry. The common theme between thinkers and comedians is that they tell the truth, but in a very different way. How do comedians get away with bold statements while scientists run into a controversy for the same ideas? Do scientists have something to learn from comedians?

On this episode of Big Biology, we talk to Jeremy Goldbogen (@GoldbogenLab), a scientist at the Hopkins Marine Station at Stanford University. For the past few years he has been tracking blue whales, aiming to understand how their physiology sustains their massive size, and how food and environment play a role in whale gigantism. We talk about the evolution of extreme size, whether modern whales are bigger than the largest dinosaurs, how whale hearts are adapted for deep sea diving, and the fascinating innovations that both toothed and baleen whales have evolved to get the most out of a meal.

This episode of Big Biology is sponsored by Hopkins Marine Station of Stanford University. Founded in 1892, Hopkins Marine Station is the oldest marine laboratory on America’s west coast conducting research that addresses fundamental questions at every level of marine biology, from genes to ecosystems.

On this episode, we talk with Nick Lane, a biochemist and professor at University College London, about his 2015 book The Vital Question. Nick argues that protolife arose in alkaline hydrothermal vents deep in the early Earth’s oceans. The key early event was the evolution of metabolism powered by proton gradients. In other words, metabolism came first, and all of the rest of traits we think of as universal to life -- DNA, RNA, proteins, transcription, and translation -- came later. He also invokes an energetic perspective on the origin of eukaryotes, arguing that the acquisition of mitochondria distributed energy production through the cell volume, provided vastly more energy per gene, and allowed the dramatic expansion of eukaryotic genomes that in turn support the astonishing diversity of eukaryotic forms we see today.

Photo: Cryo-TEM shots of ‘protocells’ from Nick Lane

On this episode of Big Biology, we talk with spider venom expert Greta Binford (@gretabinford), a Biology Professor and Biology Department Chair at Lewis & Clark University. Her lab explores the vast chemical richness of spider venom and how those venoms have evolved. We talked with Greta about the function of venom, how it’s evolved throughout the tree of life, and the surprising role horizontal gene transfer--the idea that genes can jump sideways from one species into another--may have played in the origins of spider venom. Also, we get her candid thoughts on some cult spider horror flicks. We also cover her 2018 paper on venom protein evolution, which you can find here

Podcast art: Rosa Pineda

In this episode we talk with Kate Wong, a senior editor at Scientific American, about her latest article, The Origin of Us. Our understanding of hominin evolution over the past several million years has been transformed by exciting new fossil finds and new DNA sequence data. We talk with Kate about the biggest news, the luxuriant evolutionary bush from which our ancestors emerged in Africa, and her favorite fossil species.

Episode art: Comparison of Modern Human and Neanderthal skulls from the Cleveland Museum of Natural History via Wikimedia Commons. hairymuseummatt (original photo), DrMikeBaxter (derivative work) (CC BY-SA 2.0)"

You can listen to all of their episodes here: https://complexity.simplecast.com/

This episode, as well as show notes, are available here: https://complexity.simplecast.com/episodes/29

Complexity features wide-ranging conversations with the Santa Fe Institute’s scientists, mathematicians, philosophers and artists who are trying to understand the deepest mysteries of the universe.

The show covers a huge range of topics, delving into social science or economics as often as biology. We really encourage you to check it out

On this podcast, host Michael Garfield and SFI President David Krakauer discuss a series of essays by SFI scientists that try to makes sense of what the world will look like after the coronavirus pandemic. 

You can read those essays here: https://www.santafe.edu/research/projects/transmission-sfi-insights-covid-19

Today we’re replaying of our discussion with science writer David Quammen.

We talked with him in 2018 about his most recent book, the Tangled Tree, which explores the influence of horizontal gene transfer on the evolution of life on Earth.

But right now, it’s one of his previous books that is essential reading. In 2012, he published a book called Spillover that described the risk of new diseases jumping from wildlife to humans. Now, we’re seeing that scenario play out in a big way with the coronavirus pandemic.

In May, he wrote an article in the New Yorker arguing that the U.S. has one of the worse coronavirus outbreaks in the world because it failed to learn from previous pandemics. You should definitely check out both books, and his recent article. 

Photo: Ronan Donovan

What is life? How did life arise from non-life? What did life look like at its origin?

Tune into this podcast to hear Art and Marty talk with Sara Walker, an expert in astrobiology and theoretical physics at Arizona State University. They discuss how life might have arisen on Earth and why biologists and physicists should work together to find a theory of life.

Her ideas could help decide what to do about artificial intelligence (SPOILER: The robots will take over, but it’s going to be OK). They might also help us find life on other planets.

A significant portion of Doug’s work has been published in Journal of Experimental Biology, including this 2005 paper on the composition and structure of hagfish slime and this 2006 paper testing a key hypothesis about how hagfish use slime to defend themselves from predators. Fudge’s lab published recent papers on how slime glands refill after they eject their slimy contents and how they chemically stabilize coiled threads inside the glands before they are ejected. Papers in other journals explore how slime threads can be used to make bio-inspired fabrics and how slime threads are constructed and mature inside slime glands.

Cover photo by Brian Gratwicke.

Where did the new coronavirus come from? How can we be on the lookout for new diseases emerging from animals? Now that the coronavirus has infected humans, what’s the best path forward? In this episode of Big Biology, we talk with Andy Dobson, a disease ecologist at Princeton University who studies epidemics like the current COVID-19 outbreak. We talked with him about the possible animal origins of the virus, the best way to control its spread and strategies to avoid the next pandemic. Andy emphasizes that we shouldn’t blame wildlife for the coronavirus outbreak. It’s human behavior that led to this problem, and it’s human behavior that’s going to have to change to avoid the next ones. This episode is dedicated to Robert May,

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