What 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

At 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.

How 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.

How 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.

How 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 happiness

Cover art: Keating Shahmehri. Find a transcript of this episode on our website.

What 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.

On this episode, we talk with Alina Chan, postdoc at the Broad Institute of MIT and Harvard and co-author with Matt Ridley of Viral: The Search for the Origin of COVID-19. SARS-CoV-2 could have plausibly jumped into humans in Wuhan via one of two paths. The first is zoonotic transfer from wild bats to humans, possibly via an intermediate animal host. The second is some kind of lab accident: researchers working on a SARS-CoV-2-like virus accidentally became infected with it and then transmitted it to others in Wuhan. Although early discussions among virologists reached the consensus that the origin was almost surely zoonotic, more recent discussions have started to take the lab-leak theory seriously. Unfortunately, we still lack conclusive evidence in support of either hypothesis. And, as public leaders have co-opted the investigation for nonscientific reasons, the subject of COVID’s origin has become practically taboo.

Alina’s approach is to “follow the data,” leaving no stone unturned, and we believe that it is our responsibility as scientists to do the same. We talk to Alina about her book, as well as the many new things that have been revealed about COVID’s origins since its 2021 publication. Towards the end of the chat, we discuss the implications of what we’ve learned about SARS-CoV-2 for how we should prepare for and deal with future pandemics.

We hope that this episode inspires you to seek the best possible explanation of COVID origins. Please write to [email protected] and tell us what you think, and share with friends and family. 

Cover art: Keating Shahmehri

How 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.

If 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.

How 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.