C. Brandon Ogbunu on Epistasis & The Primacy of Context in Complex Systems
COMPLEXITY
Evolutionism and Epistasis - What's the Connection?
i want to talk about John maynard smith and his idea of protein space. And how that can be used as an analogy for the concept of epistasis. Epistasis is this cunning edge concept in modern evolutionary genetics, right? i think it's a phenomeno because you stick things together and something surprising emerges. For example, e-mails sent by diginum could not have predicted phoenotype from individual individuals. But when you combine them, you get a phoenotype that would not have been predicted if they were alone.
Context is king: whether in language, ecology, culture, history, economics, or chemistry. One of the core teachings of complexity science is that nothing exists in isolation — especially when it comes to systems in which learning, memory, or emergent behaviors play a part. Even though this (paradoxically) limits the universality of scientific claims, it also lets us draw analogies between the context-dependency of one phenomenon and others: how protein folding shapes HIV evolution is meaningfully like the way that growing up in a specific neighborhood shapes educational and economic opportunity; the paths through a space of all possible four-letter words are constrained in ways very similar to how interactions between microbes impact gut health; how we make sense both depends on how we’ve learned and places bounds on what we’re capable of seeing.
Welcome to COMPLEXITY, the official podcast of the Santa Fe Institute. I’m your host, Michael Garfield, and every other week we’ll bring you with us for far-ranging conversations with our worldwide network of rigorous researchers developing new frameworks to explain the deepest mysteries of the universe.
This week on Complexity, we talk to Yale evolutionary biologist C. Brandon Ogbunu (Twitter, Google Scholar, GitHub) about the importance of environment to the activity and outcomes of complex systems — the value of surprise, the constraints of history, the virtue and challenge of great communication, and much more. Our conversation touches on everything from using word games to teach core concepts in evolutionary theory, to the ways that protein quality control co-determines the ability of pathogens to evade eradication, to the relationship between human artists, algorithms, and regulation in the 21st Century. Brandon works not just in multiple scientific domains but as the author of a number of high-profile blogs exploring the intersection of science and culture — and his boundaryless fluency shines through in a discussion that will not be contained, about some of the biggest questions and discoveries of our time.
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Discussed in this episode:
“I do my science biographically…I find a personal connection to the essence of the question.”
– C. Brandon Ogbunugafor on RadioLab
"Environment x everything interactions: From evolution to epidemics and beyond"
Brandon’s February 2022 SFI Seminar (YouTube Video + Live Twitter Coverage)
“A Reflection on 50 Years of John Maynard Smith’s ‘Protein Space’”
C. Brandon Ogbunugafor in GENETICS
“Collective Computing: Learning from Nature”
David Krakauer presenting at the Foresight Institute in 2021 (with reference to Rubik’s Cube research)
“Optimal Policies Tend to Seek Power”
Alexander Matt Turner, Logan Smith, Rohin Shah, Andrew Critch, Prasad Tadepalli in arXiv
“A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution”
C. Brandon Ogbunugafor, Daniel Hartl in PLOS Computational Biology
“The 300 Most Common Words”
by Bruce Sterling
“The Host Cell’s Endoplasmic Reticulum Proteostasis Network Profoundly Shapes the Protein Sequence Space Accessible to HIV Envelope”
Jimin Yoon, Emmanuel E. Nekongo, Jessica E. Patrick, Angela M. Phillips, Anna I. Ponomarenko, Samuel J. Hendel, Vincent L. Butty, C. Brandon Ogbunugafor, Yu-Shan Lin, Matthew D. Shoulders in bioRxiv
“Competition along trajectories governs adaptation rates towards antimicrobial resistance”
C. Brandon Ogbunugafor, Margaret J. Eppstein in Nature Ecology & Evolution
“Scientists Need to Admit What They Got Wrong About COVID”
C. Brandon Ogbunugafor in WIRED
“Deconstructing higher-order interactions in the microbiota: A theoretical examination”
Yitbarek Senay, Guittar John, Sarah A. Knutie, C. Brandon Ogbunugafor in bioRxiv
“What Makes an Artist in the Age of Algorithms?”
C. Brandon Ogbunugafor in WIRED
Not mentioned in this episode but still worth exploring:
“Part of what I was getting after with Blackness had to do with authoring ideas that are edgy or potentially threatening. That as a scientist, you can generate ideas in the name of research, in the name of breaking new ground, that may stigmatize you. That may kick you out of the club, so to speak, because you’re not necessarily following the herd.”
– Physicist Stephon Alexander in an interview with Brandon at Andscape
“How Afrofuturism Can Help The World Mend”
C. Brandon Ogbunugafor in WIRED
“The COVID-19 pandemic amplified long-standing racial disparities in the United States criminal justice system”
Brennan Klein, C. Brandon Ogbunugafor, Benjamin J. Schafer, Zarana Bhadricha, Preeti Kori, Jim Sheldon, Nitish Kaza, Emily A. Wang, Tina Eliassi-Rad, Samuel V. Scarpino, Elizabeth Hinton in medRxiv
Also mentioned:
Simon Conway Morris, Geoffrey West, Samuel Scarpino, Rick & Morty, Stuart Kauffman, Frank Salisbury, Stephen Jay Gould, Frances Arnold, John Vervaeke, Andreas Wagner, Jennifer Dunne, James Evans, Carl Bergstrom, Jevin West, Henry Gee, Eugene Shakhnovich, Rafael Guerrero, Gregory Bateson, Simon DeDeo, James Clerk Maxwell, Melanie Moses, Kathy Powers, Sara Walker, Michael Lachmann, and many others...
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