Big Biology

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.

In this podcast, Rosemary Braun discusses studying complex biological networks, circadian rhythms, and using machine learning to target treatments based on individual circadian rhythm. The episode explores the search for undiscovered rules in biology, dynamics of gene expression networks, resilience in circadian clockkeeping, and the impact of genetic variations on gene regulation.

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.

Samir Okasha, Professor of Philosophy of Science at the University of Bristol, discusses the concept of agency in evolution, exploring definitions of agency, genes as agents, agency in group dynamics, and the relationship between agency and adaptation.

Geerat Vermeij, a paleoecologist and evolutionary biologist, talks about power as a driving force in the history of life. He discusses how power has evolved in different organisms, the role of power in human history, and the need to curb our power. The podcast explores topics such as power dynamics, agency in evolution, and the perils of human power monopoly.

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.