William DeWitt

Coding After Coders: The End of Computer Programming as We Know It

A very good article on AI and coding from the NYT

by @clivethompson.bsky.social

Here's a gift link: www.nytimes.com/2026/03/12/m...

NEE Focus issue on "Evolution in medicine", including a comment article from @alisonfeder.bsky.social and me.

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...

Call Me by Your Names | Ian Tattersall The quest to fathom the riotous diversity of nature is absorbingly told in a virtual double biography of the great taxonomist Carl Linnaeus and his contemporary, the count of Buffon.

Long before Darwin, the French polymath comte de Buffon “accepted both that species could become extinct and that they could change, and he even entertained the idea that humans and apes…might have had a common ancestry.” —Ian Tattersall

We have posted data providing real-time measurement of human neutralizing antibody landscape to seasonal influenza.

Data explain spread of subclades K (H3N2) & D.3.1.1 (H1N1), identify subclade K subvariants w reduced neutralization, & can inform choice of strains for next vaccine.

Learning the Principles of T Cell Antigen Discernment T cells are central to the adaptive immune response, capable of detecting pathogenic antigens while ignoring healthy tissues with remarkable specificity and sensitivity. Quantitatively understanding h...

Happy to share our latest review article, “Learning the Principles of T Cell Antigen Discernment.” www.annualreviews.org/content/jour...
with @fxpbourassa.bsky.social , Sooraj Achar and Grégoire Altan-Bonnet ! 1/4

From Pankaj’s Mehta group www.biorxiv.org/content/10.6... “Our findings highlight the need for rigorous benchmarking and suggest that the biology of cell identity can be captured by simple linear representations of single cell gene expression data.” 🔥🔥🔥

xkcd.com/1217/

Registration is open for the inaugural GRC conference in the Function of Evolving Systems. Aug 9-14, 2026, Waterville Valley. Truly stellar speaker lineup. Student/postdoc fellowships are available! Please come join us! www.grc.org/function-of-... @joybergelson.bsky.social

"Fascism works by making the extreme normal. Habit, as Samuel Beckett has it, is a great deadener. It has been obvious since the start of Trump’s second term that he is trying to make the sight of armed and masked men with virtually unlimited powers one to which Americans are accustomed."

One of my neighbors was murdered in the streets today by ICE agents motivated by this sort of race science propaganda.

What does fighting look like? Different for everyone, without a doubt. But whatever form it takes, it's more than just conviction or advocacy or solidarity. (1/n)

Agent Psychosis: Are We Going Insane? What’s going on with the AI builder community right now?

Weekend thoughts on Gas Town, Beads, slop AI browsers, and AI-generated PRs flooding overwhelmed maintainers. I don't think we're ready for our new powers we're wielding. lucumr.pocoo.org/2026/1/18/ag...

The lab is looking to hire 2 new undergraduate researchers! You'll get to work on yeast experimental evolution & genomics. UW students only (and this link won't work for others, sorry). Work study students very welcome to apply! Pays the prevailing minimum wage. app.joinhandshake.com/emp/jobs/106...

I am hiring a staff bioinformatician for my new lab at the University of Utah! Please consider applying if you are on the hunt:
employment.utah.edu/salt-lake-ci...

Opinion: Remembering Renee Good Renee Good won a national prize six years ago for her poem "On Learning to Dissect Fetal Pigs," which muses on science and faith. Good was shot to death by an ICE agent this week in Minneapolis.

Renee Good won a national prize six years ago for her poem "On Learning to Dissect Fetal Pigs," which muses on science and faith. Good was shot to death by an ICE agent this week in Minneapolis.

Trump Can’t Cap Overhead Rate on NIH Grants to Research Universities, Appeals Court Rules The ruling is a victory for higher-education associations who challenged the proposed 15-percent cap, calling it illegal and claiming it would devastate the research enterprise.

a huge victory for universities, worth billions of dollars: Trump can’t cap indirect-cost rates on NIH grants, appeals court rules
www.chronicle.com/blogs/the-tr... via @andyandy.bsky.social

Trump’s War | David Cole “It was a brilliant operation, actually.” So claimed Donald Trump early this morning in a phone call with The New York Times about the US military’s

The invasion of Venezuela is being defended as a law enforcement operation and ”self-defense.” It is neither.

It is imperialism, pure and simple.

And illegal seven ways to Sunday.

www.nybooks.com/online/2026/...

The Restless Clock, Jessica Riskin How Life Works, Philip Ball The MANIAC, Benjamín Labatut Any Person is the Only Self, Elisa Gabbert

Favorite reads, 2025

Now accepting applications for SFI’s 2026 CSSS program, a 3-week experience for graduate students, postdoctoral fellows, and professionals to explore foundational theory, engage in collaborative projects, and connect with a global research community.

Apply by Feb 4, 2026
www.santafe.edu/csss

The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31

probgen2026.github.io

I've slowly been reformatting notes from my population and conservation genetics course at Montana State University into a web book—a rough draft is now live here: elinck.org/popgen_conge...

How much better is an ancestral recombination graph (ARG) than a site frequency spectrum (SFS)? For recovering mutation rate history, we can answer fairly precisely because both ARG and SFS are linear transforms of mutation rate history. This blog post uses spectral analysis to clarify the picture.

What sets the mutation rate of a cell type in an animal species? Germline mutation rates per generation are strikingly similar across animals, despite vast differences in life histories. Analogously, in at least one somatic cell type, mutation rates at the end of l...

Happy to highlight an essay I wrote together with @marcdemanuel.bsky.social,
@natanaels.bsky.social and Anastasia Stolyarova, trying to think through what sets the mutation rate of a cell type in an animal species: www.biorxiv.org/content/10.6... 1/n

More than half of researchers now use AI for peer review — often against guidance A survey of 1,600 academics found that more than 50% have used artificial-intelligence tools while peer reviewing manuscripts.

Just decline the peer review invitation.

What are you people even doing?

What a journey it has been! Thanks for writing the story behind the paper. A lot of what I know about how-to-science I learned by working with you all on this over multiple career stages.

The point is much broader than poliovirus and pocapavir: if we're trying to design therapeutics that exploit social interactions between viruses, we need to account for the effects of therapeutic success in diminishing those interactions.

bsky.app/profile/alex...