Joshua B. Plotkin

Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback - Nature Ecology & Evolution A model of intrahost poliovirus replication shows that, after several rounds of replication, pocapavir, a poliovirus capsid inhibitor, collapses viral density, preventing intracellular interactions th...

Very cool work.

Intracellular interactions shape antiviral resistance outcomes in poliovirus via eco-evolutionary feedback

www.nature.com/articles/s41...

Strong endorse.

Hi everyone! I'm co-organizing this retreat/workshop June 15-19 for those looking to get started in mathematical/computational modeling of biological processes. Location is a beautiful farm in NC. Please share with students and others who want to build modeling skills. Interdisciplinarity welcome!

#gobirds

As a former physics undergraduate, giving a colloquium in a physics department feels like a very full-circle moment ☺️

Steve Bannon casually texting with Jeffrey Epstein about meetups in Paris, oh and about Jared, Ivanka and so much more.

Grep game very strong tonight.

6 points of fuckno to Trump across all counties

Language Models are Injective and Hence Invertible Transformer components such as non-linear activations and normalization are inherently non-injective, suggesting that different inputs could map to the same output and prevent exact recovery of the in...

I did not expect that: Large Language Models are invertible:

arxiv.org/abs/2510.15511

Philly Halloween

Agent-based models move into the economic mainstream In the 1980s and ’90s, SFI played laboratory to a promising new method known as agent-based modeling. In ensuing decades, agent-based models (ABMs) proliferated across many fields, including economics...

What if one model could realistically predict the economy of an entire country? The entire world? A month-long working group, co-organized by SFI External Professor @doynefarmer.bsky.social, made the case that agent-based models may bring this vision to life:

456: Kaleda Denton | Following the Majority - How Conformity Shapes Culture and AI In this episode of the Armen Show, Armen Shirvanian interviews Dr. Kaleda Denton, a post-doctoral fellow at the Santa Fe Institute. They discuss the interdisciplinary nature of the Institute, the concept of niche construction in biology, and the dynamics of decision-making, particularly the differences between following the mean versus the majority. The conversation also explores the limitations of game theory, the role of cultural evolution in cooperation, and the impact of AI on accessibility and learning. They delve into the importance of reducing polarization while maintaining diversity in viewpoints, emphasizing the need for mixing and collaboration across different fields and perspectives. In this engaging conversation, Dr. Kaleda Denton and Armen Shirvanian explore a variety of topics including the distinction between majority and mean opinions, the challenges of reading in the digital age, and the implications of large language models (LLMs) on culture. They discuss the importance of communication in society, the influence of close circles versus wider communities in learning, and the role of influential figures in personal development. The conversation also delves into the concept of memes and cultural transmission, the impact of role models on cumulative culture, and the question of human uniqueness in the context of cultural evolution. Check out Kaleda's website at https://www.kaledadenton.com/ 00:00 Introduction to the Podcast and Guest 03:01 The Santa Fe Institute: A Unique Interdisciplinary Environment 05:56 Niche Construction and Extended Evolutionary Synthesis 08:56 Mean vs. Majority: Insights from Research 12:08 Game Theory and Its Limitations 15:03 Cultural Evolution and Cooperation 17:59 The Role of AI in Learning and Accessibility 20:54 Conformity Across Species and LLMs 23:59 The Importance of Current Information 27:03 Final Thoughts on AI and Human Interaction 36:57 The Quirks of AI Hallucinations 38:53 The Evolution of Language Models 39:35 Agency and Individuality in AI Interactions 41:41 The Flattening of Ideas and Language 43:42 Cognitive Offloading and Its Consequences 45:04 Reducing Polarization Through Interaction 48:39 The Importance of Mixing Perspectives 50:02 The Dangers of Majority Influence 53:51 Understanding Mean vs. Majority Opinions 01:04:32 Risks and Opportunities in Cultural Evolution 01:10:02 The Impact of Headlines on News Consumption 01:11:46 The Need for Positive News 01:15:04 Learning from Close Circles vs. Wider Communities 01:17:23 Influential Figures in Personal Development 01:18:44 The Evolution of Human Uniqueness 01:22:38 Understanding Memes and Cultural Transmission 01:23:10 The Multiplicative Costs of Altruism 01:36:09 The Role of Role Models in Cumulative Culture

Honoured to have done my first ever podcast on The Armen Show! Besides science, math, & academia, we talked about:

-LLMs hyping up bad ideas
-My 5 foster cats, but whether I'm secretly a dog person
-How it would be nice to "skip" & "mute" people in real life 😛

Check it out! 😄

tinyurl.com/yc4hjz2x

Natural evolution of intermale sexual behavior by multiple pheromone switches among Drosophila species https://www.biorxiv.org/content/10.1101/2025.10.14.682417v1

Now hiring a computational postdoc (evolutionary genomics, molecular evolution) in my lab at Emory University.
If you’re interested in population genetics, fitness landscapes, and viral evolution — get in touch.
faculty-emory.icims.com/jobs/151181/...

Morning dirty #bearpondespresso

Longshan Temple #infrared

Fiat 600

Firenze

#brigantine

Trastevere, Rome

#michelangelo #academia

#michelangelo #academia

#bernini #borghese

Some nice trains.

Evolutionary Games: Mathematical Theory and Biological Insights

I am really happy to share that there will be a @nitmb.bsky.social workshop next year on mathematical and biological features of evolutionary game theory.

It was really fun to co-organize this workshop with Olivia Chu, Alex McAvoy, and @jplotkin.bsky.social.

www.nitmb.org/evolutionary...

Yamato-sugi, a 4000 year old Yakusugi

Here’s a nice mushroom. #yakushima

Trainspotting trifecta (Sobu, Chuo, Marunouchi)

Hijiribashi