Big Biology

Can we study evolution in the wild? Are some species “super-evolvers”?On the episode, we talk with Alison Derry, a professor of biology at the University of Quebec in Montreal, and Andrew Hendry, a professor in the Department of Biology at McGill University, Canada. This episode is the second we’ve done on the team’s work, and Andrew was also a guest on our first episode in the series. This conversation was recorded live in front of an audience at Kenai Peninsula College, in Soldotna, Alaska. The college is just a few miles from the lakes where Alison, Andrew, and many of their colleagues and students carry out experiments on threespine sticklebacks. We ask Alison and Andrew about their research on the rapid evolution of these fish, which were recently reintroduced to the lakes, and how the introduction of two distinct stickleback ecotypes are affecting the evolution of zooplankton in the lakes. We also discuss the central position of sticklebacks in the food web and how the sticklebacks are impacting the ecosystems now as well as how they likely impacted the lakes in the evolutionary past. Art by Keating Shahmehri. Audio from Hunter Morrison at KDLL. Find a transcript of this episode on our website. This is a public episode. If you’d like to discuss this with other subscribers or get access to bonus episodes, visit bigbiology.substack.com/subscribe

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comWhat is mutation bias and how can scientists study it? How does changing a population’s mutation bias influence its evolutionary trajectory?In this episode, we talk with Deepa Agashe, an Associate Professor at the National Centre for Biological Sciences in Bangalore, India. We first talk with Deepa about mutation bias and how she uses  E. coli to understand it. We then focus on a 2023 PNAS paper about the fitness effects of experimentally changing the mutation bias in E. coli. In this research, Deepa and her team used a strain (MutY) of bacteria containing a mutation that knocks out an important DNA repair enzyme. They then isolated subsequent single mutations produced within both MutY and wildtype lines and studied the fitness effects of those mutations. Surprisingly, more than a third of mutations in the mutant lines were beneficial, and often across several different environments. Zooming out, the big picture is that shifts in mutation bias seem to generate new kinds of mutations that weren’t previously accessible to lineages, and a greater fraction of those may be beneficial in some circumstances.Art by Keating Shahmehri. Find a transcript of this episode on our website.

This week on Big Biology we're sharing an episode from The Naked Scientists Podcast about how humans lost their tails.Humans, chimpanzees, gorillas and orangutans do not have tails. It sets us apart from other primates, but suggests that our shared evolutionary ancestors had them. So why did we lose them, and how? Speaking with Chris Smith, from The Naked Scientists Podcast, NYU Grossman School of Medicine's Itai Yanai explains that the way this study began was literally a pain in the "tail" for one of his colleagues...Credit: The Naked Scientists Podcast This is a public episode. If you’d like to discuss this with other subscribers or get access to bonus episodes, visit bigbiology.substack.com/subscribe

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comAt what levels does causation happen in biology? Are metaphors useful for understanding biology?In this episode, we talk with Phil Ball, a science writer who was also an editor for the journal Nature for over 20 years. Phil has written over 25 books, but our conversation focuses on his most recent: “How Life Works: A User’s Guide to the New Biology.” In the book, Phil covers a wide-range of topics from cells to proteins to biological agency, and makes the argument that traditional ideas and simplified metaphors in biology often don’t hold up. We talk with Phil about the concept of the selfish gene and unpack what it actually means and when it’s useful. Then we dive into the paradox of how multicellular organisms are composed of multiple levels of agency, yet are complex agents themselves. Phil also discusses the biomedical implications of thinking about cancer as one in many possible states that cells can inhabit across a landscape.Art by Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow should biologists deal with the massive amounts of population genetic data that are now routinely available? Will AIs make biologists obsolete?In this episode, we talk with Andy Kern, an Associate Professor of Biology at the University of Oregon. Andy has spent much of his career applying machine learning methods in population genetics. We talk with him about the fundamental questions that population genetics aims to answer and about older theoretical and empirical approaches  We then turn to the promise of machine learning methods, which are increasingly being used to estimate population genetic structure, patterns of  migration, and the geographic origins of trafficked samples. These methods are powerful because they can leverage high dimensional genomic data. Andy also talks about the implications of AI and machine learning for the future of biology research. Cover Art by Keating Shahmehri. Find a transcript of this episode at our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow should we study complex biological networks? How do cells keep time and stay in sync? What does it mean for a network to be resilient?In this episode, we talk with Rosemary Braun, Associate Professor at Northwestern University in the Department of Molecular Biosciences and a member of the NSF-Simons Center for Quantitative Biology. Rosemary is broadly interested in learning whether “more is different” when it comes to complex molecular networks operating across different temporal and spatial scales. We talk with her about systems approaches to uncovering the “Rules of Life” and about circadian (daily) rhythms. She and her team use machine learning to understand emergent phenomena in networks, with the goal of helping medical professionals target treatments based on an individual patient’s circadian rhythm.Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow do biologists strike a productive balance between descriptive natural history and manipulative experiments in the lab or field? Should we bring back species to areas where they’ve gone extinct and what values do we use to make these decisions? What is wildness and how do we cultivate it?On this episode, we talk with Harry Greene, a herpetologist and adjunct professor of Integrative Biology at the University of Texas at Austin, whose distinguished career has spanned decades. Harry is an E.O. Wilson Award recipient and also received the PEN Literary award for his book, Snakes: The Evolution of Mystery in Nature. In the episode, we talk with Harry about the importance of natural history to biology. We also tackle the topic of rewilding, a type of biological restoration that involves translocating species where they still occur to regions where they no longer are found, in order to restore ecosystem function. Harry talks about how his views on rewilding have changed over time, including how rewilding ourselves could improve our health and happinessCover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comWhat is an agent, and does an organism have to be conscious to be one? How does organismal agency affect evolution?In this episode, we talk with Samir Okasha, a Professor of Philosophy of Science at the University of Bristol. Samir studies fundamental philosophical questions in evolutionary biology, most notably how selection acts on various levels of biological organization. Our discussion focuses on his book “Agents and Goals in Evolution,” in which he unpacks various definitions of agency and outlines their evolutionary implications. We talk about whether genes and groups of individuals can be agents, whether agency is heritable, where variation in agency comes from, and the relationship between agency and adaptation.Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comIf the tape of life were replayed, how recognizable would today’s species and ecosystems be? How and why does power increase over evolutionary time? How have humans unleashed so much power, and what are the consequences of that power for life on Earth? In this episode, we talk with Geerat Vermeij, a paleoecologist and evolutionary biologist in the Department of Earth and Planetary Sciences at UC Davis. He is a member of the National Academy of Sciences, and has published over 200 papers and five books. Our conversation focuses on his most recent book: “The Evolution of Power: A New Understanding of the History of Life.” In it, he asserts that power, the amount of energy an organism can take up or expend per unit time, has increased steadily during the history of life on Earth. On the episode, we discuss the idea of power, how species evolve more power, and how humans have unleashed more power than any other species (and whether we need to work on curbing this power). Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow are cephalopods like us, but also completely alien? How can they become so intelligent when they have such short lives? How do they coordinate a distributed set of brains?In this episode, we talk with Danna Staaf, a science communicator and marine biologist with a lifelong love of cephalopods. Danna earned a PhD from Stanford University studying baby squid, and she has written several cephalopod-themed books. Our conversation focuses on Danna’s most recent, The Lives of Octopuses and Their Relatives: A Natural History of Cephalopods, a beautiful exploration of the diversity of these wacky, wonderful creatures. We discuss cephalopod evolution, morphology, and reproduction, focusing on several fun facts that you can pull out at your next dinner party.Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comDoes biological plasticity have a cost? Are there evolutionary consequences of plasticity and of organisms acting on their environments?In this episode, we talk with Sonia Sultan, the Alan M. Dachs Professor of Science in the Department of Biology at Wesleyan University. Sonia has spent her career studying the interplay between organisms and their environment. Specifically, she studies how environmental conditions influence the development of organisms, and when and how these developmental trajectories can include niche construction. Sonia refers to this complexity as “entanglement,” genes and environments working together to alter phenotypic expression, but then variation in phenotypic expression feeds back on environments and genes to alter evolution. She put this perspective to the test in a recent paper she coauthored with Mike Wade in the Journal Evolution & Development. In it, Sonia and Mike took a new perspective on the Price equation, finding that niche construction and other forms of organismal agency can change evolutionary outcomes.Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow do small, founding populations establish and thrive in new places? What is biocontrol, and how is it carried out responsibly?In this episode, we talk with Ruth Hufbauer, a Professor of Applied Evolutionary Ecology at Colorado State University about the ways that organisms successfully establish new populations in new places. Ruth uses lab experiments on Tribolium flour beetles to understand how evolution facilitates or impedes the founding of populations. In our conversation with Ruth, we discuss range expansions, species invasions, and biocontrol among other topics. Biocontrol is of particular interest to Ruth, as it can be an effective way to control pests, but also comes with some risks that the control agents themselves get out of control. We also explore the genetic paradox of invasion, and talk about many potential mechanisms that could help populations to quickly spread to a new place.Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow do biologists categorize species? What’s the best and quickest way to describe millions of unknown species?On this episode, we talk with Michael Sharkey, an entomologist and taxonomist who spent much of his career at the University of Kentucky, and is now the director of the Hymenoptera Institute. Since its inception, taxonomy has relied on careful morphological analysis of specimens to delineate species. In the past few decades, the COI “barcode” region of the mitochondrial genome has become a key additional piece of genetic evidence used to characterize species. In a much-discussed 2021 paper, Michael and colleagues used barcoding to identify over 400 new species of braconid wasps. The backlash from scientists who adhere to traditional taxonomic methods was swift, and at times harsh, with critics claiming that relying primarily on COI to define species is simply unacceptable. Sharkey, however, remains convinced that taxonomy should embrace molecular tools, especially because millions of species are yet to be discovered and rates of extinction are ramping up. We talk with Michael about how many insect species there are, how barcoding can make taxonomy accessible to more scientists, and what the future of taxonomy might look like. Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow do living things exert agency in a world of strict physical and chemical laws? Do humans have free will? In this episode, we talk with Kevin Mitchell, an Associate Professor of Genetics and Neuroscience at Trinity College Dublin. The question of free will has been debated for decades by thinkers in physics, philosophy, psychology, and, more recently, biology. In his new book, Free Agents: How Evolution Gave Us Free Will, Kevin argues that agency is a fundamental characteristic of living systems and is essential for survival. In the episode, we discuss how agency emerges despite constraints imposed by basic physical and chemical principles, and how agency confers on organisms the power to shape both themselves and their environments. We also discuss practical approaches to studying agency by leveraging new technologies and by seeing through underlying assumptions and traditional reductionism. Cover Art: Keating Shahmehri. Find a transcript of this episode on our website.

This is a free preview of a paid episode. To hear more, visit bigbiology.substack.comHow can we reconcile the evolutionary problem of cooperation? What can social amoebae tell us about the origins of multicellularity?In this episode, we talk to Joan Strassmann and David Queller, professors at Washington University in St. Louis, about the evolution of cooperation and conflict. From social insects to humans, we can find instances of individuals seemingly sacrificing fitness for the good of the group. But, truly altruistic behavior poses a problem for evolutionary biologists because it challenges the assumption that natural selection favors individuals over groups. We talk with Joan and David about their work with the social amoeba, Dictyostelium discoideum. This species is known for its remarkable developmental cycle: when there is no more to eat, the starving amoebae aggregate into a slug-like organism, which then forms a fruiting body that releases spores in hopes of dispersing to a better place. The problem, evolutionarily, is that only a fraction of the cells in the fruiting body get to live on through offspring. This facultative lifestyle and the ability to combine genetically different cells makes D. discoideum a prime study species for understanding how relatedness impacts cooperation and conflict and the possible origins of multicellular organisms.Towards the end of the episode, we also talk about Joan’s new book Slow Birding: The Art and Science of Enjoying the Birds in Your Own Backyard.Cover art: Keating Shahmehri. Find a transcript of this episode on ⁠our website⁠.