Reposting this old thread on the "Pervasive findings of directional selection" from ancient DNA. While the authors extended their results in various ways, I think many of these points still stand.

I thought it was an Onion article

It's looking increasingly likely that I'll be hiring a 3-year computational pop-gen postdoc/PhD-level scientific programmer to start this Fall (2026). If you or someone you know is defending soon, and looking for a position, please DM/write to me! Thanks!

Join us in Montreal for the Canada/US Northeast hub! I will give a talk and @gmdouglas.bsky.social @nagissa.bsky.social & Tim Blower will surely give *great talks* Opportunities for student talks and posters and a good time guaranteed!

Our paper is out m in BioEssays! We explore how a process-based view of biology, focusing on dynamic interactions rather than individual molecules, can reshape how we think about cell polarity, opening up new questions and ways of doing cell biology. onlinelibrary.wiley.com/doi/10.1002/...

It looks like there will be an open postdoc position in my lab soon. I'll be looking for someone with substantial wet-lab experience in microbiology / microbial ecology / evolution / physiology. If everything goes well, an ad will be coming. But if you know someone, ask them to reach out already.

I’ve been warned that by engaging in politics, I might undermine myself as a scientist. Or worse, reduce the trust that people have in me or scientists as a whole. This latter point is the thesis of a recent article by Byron Hyde: link.springer.com/article/10.1... I disagree for multiple reasons.

1/25 New paper out in PNAS! We show that the fitness costs of reproductive specialization, where somatic cells give up reproduction, scale inversely with organism size. Larger organisms can afford far more soma, removing a key barrier to multicellular complexity.

So, thing that is apparently better understood inside academia than outside of it: International students pay sticker price. Most domestic students do not. International students are subsidizing the education costs for domestic students, as per student governmental funding drops.

We posted a new theory preprint. I am very interested to hear what the community thinks about it. We looked at the dynamics of evolution on several (simple) models of modular genotype-phenotype-fitness maps and found that populations approach a quasi-steady state we call "module-selection balance".

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

If preparing figures please consider "colorblind friendly" approaches (www.nature.com/articles/d41...). I am missing the long-wave opsin, which manifests in strange ways: I can't discern red vs. black. This dichromacy is rare and severe, but ~300 million have more common forms addressed in link.

Share as widely as possible. www.simonsfoundation.org/grant/center...

Yeah, it's real. My proposal has been sitting at NSF for over a year now!

tl;dr: NIH is running at about 60% of pre-Trump levels and NSF is running at about 20% of pre-Trump levels of funding-outlays (some directorates far below even that). Utterly catastrophic. An unforced disaster for U.S. society, and the world

For #NSF and #NIH watchers, Grant Witness now has interactive data on numbers of grants and total funding obligations, broken down by institute and directorate, new awards and non-competitive renewals. The stranglehold on new awards is still a disaster. grant-witness.us/funding_curv...

"AI scientists are building ever-larger models, and then claiming that each model can solve even more than the previous one. Then, model in hand, they go around looking around for problems to solve" stevensalzberg.substack.com/p/ai-is-star...

Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez

Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social

The conference is quickly filling up! Don't wait to sign up. We also received some funding and can offer fellowships to graduate students and postdocs. Won't cover the whole cost but will certainly make it much easier!

We're hiring a *post doc*! Are you a global change ecologist (broadly defined) and want to work with Jenny McGuire, @benjaminfreeman.bsky.social, me & many others?!🦎🐦🦴⛰️ Come join an amazing, hungry, and very exciting eco-evo group here at GT! careers.hprod.onehcm.usg.edu/psc/careers/...

If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk

NIH/NSF funding is, for all intents and purposes, frozen again. This somehow almost feels worse than last year. They are running out the clock on biomedical science and all PIs can do is scramble to finish projects before our resources dry up. www.science.org/content/arti...

NSF Update through March 13, 2026 1/2

#ggtree has a relatively steep learning curve. But after looking at a few Python alternatives eg., toytree, ETE, Bio.Phylo it's hard to match its layout versatility. 21 tree variants with just a few lines of code. #rstats #phylogenetics #bioinformatics

Anyone who is interest in NIH science funding should look through this thread. It's very informative (and disheartening, of course).

Experimental Evolution of Yeast Reveals Trade-offs Between Early and Late Stationary Phase https://www.biorxiv.org/content/10.64898/2026.03.12.711341v1

From genes to collective modes: biological constraints shape metabolic evolution https://www.biorxiv.org/content/10.64898/2026.03.11.711104v1

Nice to see this published at @PLoS Comp Bio. Big improvements after peer review and important input from @gsherloc.bsky.social! Hopefully, this tool will be helpful for those interested in using barcodes for detecting new beneficial mutations. journals.plos.org/ploscompbiol...

The 2026 National Science Foundation budget is $8.75 Billion.

I'm thankful to MBE for publishing this paper. I wan't sure anybody would. The handling editor (I now know was Jeff Townsend) was great, as were the 2 reviewers. It is not an outcome/product/discovery, it is my way of thinking about HGT & pangenomes 1/3 academic.oup.com/mbe/article/...

Looks like a very important check on LLMs in protein structure/function prediction.

Curious about the origin of development during the transition to multicellularity? A very belated preprint alert: bit.ly/4rr2mHU Reproduction emerges from ecological interactions at the onset of multicellularity. A short 🧵 with lots of videos...

🌿 Postdoc opportunity in plant evolutionary ecology/genetics! My lab in the Dept. of Ecology & Evolutionary Biology at the University of Michigan is recruiting a postdoctoral researcher to start Fall 2026. We study plant adaptation, using weeds as model systems. #Postdoc #EcoEvo Pls RT!

It’s not even the top 1% of labs, because it’s entirely stochastic at the 1st percentile. They’re all good, but likely no better than anything else in the top 10%.

This is very depressing. It basically means that only the absolute top labs could get funding in 2025. If this continues for the next 1-2 years, many labs will stop doing research...

Here is the "effective payline" for each institute, estimated (by Claude) as the percentile where one can expect 80% probability of funding from a logistic regression fit. The effective payline has gone from a historic ~12% to 6% in 2025.

Our story on the evolution of colistin resistance is just out on @plosbiology.org (journals.plos.org/plosbiology/... Evolution doesn’t happen in isolation. We show that competing fungi can rewire the evolutionary trajectory of colistin resistance in P. aeruginosa. Great teamwork with the Ernst lab

Curious about why polymicrobial interaction matters? Check out more future work from my lab (www.labofpie.org)

Researchers in the US might be having feelings about writing grants atm-I know I am! We still need to write them. In this Evolution Exchange, I again chat with Sam Scheiner, who summarizes how to write a competitive proposal. His advice is gold, and helpful regardless of funder. Pls RT!

We are deeply saddened to share the news of the passing of David Botstein, a towering figure in modern #genetics and a foundational force behind SGD. www.yeastgenome.org/blog/in-memo... #yeast #modelOrganism

Preposterous! Saying that Russell Vought is a leech would be an insult to leeches.

Very sad news. David Botstein made enormous contributions to molecular biology & genetics. I first met him in a grad school interview. I learned something from him each of the few times I saw him since. Indelible personality. Here he is giving a keynote at the 2015 UCSD Genetics Retreat.

I was sad to learn that my postdoctoral mentor, David Botstein, died yesterday. I started with David as a postdoc in 1998, and he had a profound effect on both my life and scientific career. He was a giant in the field of genetics, making seminal contributions in both yeast and human genetics. 1/

I have to say, I am quite impressed with Claude-Opus-4.6. I had very interesting conversation with it trying to explain a puzzling phenomenon that we observed in our experiments. The internal monologue is fascinating and reveals solid reasoning characteristic of a very good 1st year PhD student.

Federal funding for US biomedical research is moribund. Since October 1 2025, NIH is -80% in new grants and -70% in values (total dollars). Labs are closing down and researchers are leaving science. To what end?

OK I don't have access to the whole article but the overall point / summary is very very troubling www.statnews.com/2026/02/24/e... #epstein

How to avoid getting an education while paying for one:

#Genomics methodologies can often introduce bias, resulting in inaccurate predictions. In #GENETICS, Michael Overton and @skryazhi.bsky.social present an improved genotyping pipeline for analyzing mutation accumulation in #yeast with a more reliable statistical estimations. buff.ly/1rcGasy

Country's budget is the clearest quantification of society's values.