We derive a working hypothesis for how the genetic code evolved, by assuming LUCA-depleted amino acids came early, using codons we infer via the 2-1-3 rule. We validate with independent data and a control ordering ecoevorxiv.org/repository/v... @seekingluca.bsky.social @hanonmcshea.bsky.social 1/13

We derive a working hypothesis for how the genetic code evolved, by assuming LUCA-depleted amino acids came early, using codons we infer via the 2-1-3 rule. We validate with independent data and a control ordering ecoevorxiv.org/repository/v... @seekingluca.bsky.social @hanonmcshea.bsky.social 1/13

This still has to go through the house, if not back and forth more times. CALL YOUR REPRESENTATIVES!

Princess Vimentin PhD | Cancer Biologist@princess-vimentin.bsky.social · 3d ago

Yaaas! Good news on a Sunday! The senate moves to temporarily ban the OMB proposal that would allow political appointees in charge of approving federal grants, especially #NIH grants. Recall that the OMB rule yielded 500k comments, 95% of them against it. 🧪 www.politico.com/news/2026/08...

In #GENETICS, @joannamasel.bsky.social and the team describe how we define fitness changes with context and propose a conceptual scheme where short-term and long-term fitness are best operationalized via organismal vital rates and genetic lineages, respectively. 🔗 buff.ly/S0UK9Mn

Zach Weinersmith@zachweinersmith.bsky.social · last wk.

Well that sucks. www.engadget.com/2225849/goog... Least bummer interpretation: AlphaFold served its purpose, DeepMind already spun off a drug lab, so it was time to reassign the time.

Our paper on how better amino acid substitution matrices trained on cleaned alignments improve gene tree inference, and on best practice for cleaning MSAs more broadly, is now out academic.oup.com/mbe/advance-.... New options in both IQTree and Muscle5. @phylowheeler.bsky.social

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models

Abstract. Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis and is prone to error. Unfortunately, algorithms that remove likely alig

academic.oup.com

Joanna Masel@joannamasel.bsky.social · 8mo ago

Sequence alignments are notoriously prone to error. Our latest preprint offers a new tool for filtering errors out, assesses it and other filtering tools, and recommends new best practice. www.biorxiv.org/content/10.6... @phylowheeler.bsky.social 1/10

The most anti-legal immigrant administration ever just made it illegal for international students to transfer schools or change majors or shift any "educational objective" in their 1st year and for graduate students **at any point** ever, at all. There is no legal basis for this

#SMBE #SMBE2026 Public Service announcement: If you want people to be able to find you in the app: (1) Click on the 'menu' lines (top right), (2) then click on "Privacy & Settings" and (3) *then* scroll to the bottom and click 'update'. This was not obvious to me.

Exclusive: The National Science Foundation is trimming this year’s budgets for hundreds of its traditional basic science programs by roughly 20% to 30%, even though its overall budget is down just 3%. https://scim.ag/4xY2KCm

Exclusive: NSF slashes research programs to support new tech initiative, insiders say

Unexpected shift in funds has meant sharp drop in grants this fiscal year

science.org

So the #SMBE2026 conference app seems pretty unusable. You can only star whole sessions not individual talks, and you can't see which talks are on at the same time. Before I burn CO2 feeding it to an AI agent to produce a usable spreadsheet, does anyone already have one?

1/ New paper with Elizabeth Borden, Karen Hastings, and Ryan Gutenkunst on immunoediting in human tumors. Ryan and I built the modeling side, so that's what I'll focus on here.

NIH T32 proposal with @joannamasel.bsky.social and @wheelerlab.org to renew the Computational and Mathematical Modeling in Biological Systems program for PhD students is funded, starting July 1! I look forward to supporting the next generation of quantitative biology researchers! cmmbs.arizona.edu

Our new paper doi.org/10.1098/rspb... on long-term genetic threats to small populations finds that "mutational meltdown" (bad mutations fixing) is less of a problem than "mutational drought" (too few good new mutations) @wmawass.bsky.social @uliseshmc.bsky.social @jeremyjberg.bsky.social 1/5

Extinction vortices are driven more by a shortage of beneficial mutations than by deleterious mutation accumulation

Abstract. Habitat loss contributes to extinction risk in multiple ways. Genetically, small populations can face an ‘extinction vortex’—a positive feedback

doi.org

Calling all Scientists! Research Administrators! Deans! Fans of Science! No one is coming to save us. Here is your assignment. I have written a step by step, easy to understand "how-to" document to help you comment on the proposed OMB rule. elizabethginexi.substack.com/p/what-we-ne...

What We Need to do NEXT: OMB’s Proposed Federal Financial Assistance Rule (OMB 2026-10817)

What OMB’s Proposed Federal Financial Assistance Rule Means in Practice

elizabethginexi.substack.com

1/ Our new paper in Systematic Biology "Modeling Site-and-Branch-Heterogeneity with GFmix" led by @cgpmcc.bsky.social describes improved ways to model compositional heterogeneity across both sites and branches—an important source of error in deep phylogenomics. doi.org/10.1093/sysb...

Modeling Site-and-Branch-Heterogeneity with GFmix

Abstract. Phylogenetic trees are often inferred from protein sequences sampled from diverse taxa across the tree of life. The compositions of these amino a

doi.org

One glimmer of hope in the Ebola response: Within hours of the outbreak in DRC being declared, researchers convened to prepare drug trials. A lot has changed on that front since the Ebola outbreak in West Africa a decade ago. But huge challenges remain 🧪 My story in @science.org (🧵 to come)

Can fast, nimble clinical trials deliver a drug to halt the new Ebola outbreak?

Past outbreaks spawned clever strategies for testing antivirals and antibodies, but researchers will still face major challenges on the ground

science.org

😀 Actually, what is a gain-of-function mutation? doi.org/10.1093/gene...

Actually, what is a gain-of-function mutation?

Abstract. For more than a century, scientists have worked to characterize, understand, and predict the consequences of mutations. For almost as long, scien

doi.org

Our paper unpacking "fitness" is out doi.org/10.1093/gene.... How to define fitness depends on what question you ask. Selection acts on organismal vital rates, longer-term outcomes make sense for genetic lineages, models link them. "Invasion fitness" = speed, but sometimes probability matters more.

Why there are so many definitions of fitness in models

Abstract. Evolutionary “fitness” is operationalized in many different ways in models. Its role is to quantify that which is favored by natural selection. G

doi.org

Joanna Masel@joannamasel.bsky.social · 2y ago

Our latest preprint doi.org/10.32942/X2V... explains why fitness can be defined in so many ways, and which version(s) you should use when. Fitness quantifies what natural selection favors. 1/

1/23 New preprint! Been thinking about the origin of cellular life. Specifically, how protocells (or *any* compartments) just aren't enough to support the evolution of increasingly complex cells. You gotta de-Darwinize the parts! The ribosome/genome do this. www.biorxiv.org/content/10.6...

We are failing the hantavirus drill. But even this great @dwallacewells.bsky.social article doesn't discuss frequent PCR tests for those quarantining at home. High viral load would trigger strict isolation before most transmission. Testing beats quarantining in a facility. Yes, it can be done.

Opinion | Hantavirus Isn’t Just a Threat. It’s a Test.

nytimes.com

We (with @dornhaus.bsky.social) finally wrote up our class on how to teach modeling to biologists, which ends up being a non-trivial exercise in understanding the roles that theory plays in the scientific method. We hope others will use our class, or simply enjoy the manuscript!

Anna Dornhaus@dornhaus.bsky.social · 4mo ago

Preprint: What good is modeling? Introducing biology students to theory - arxiv.org/abs/2604.13344 - how to teach and think about what modeling contributes to science. How does it fit into the scientific method? This is often misunderstood.

I hadn't realised that Bob Trivers had died. What a complicated legacy. jjffh.com/tribute/deta...

Robert Trivers Obituary | John J. Fox Funeral Home Inc | Larchmont, NY

View Robert Trivers's complete obituary, share memories, and explore 11 tribute posts from the community.

jjffh.com

With Eugene Koonin, we propose a concept of “the selfish ribosome”, under which evolution of life is viewed as a ribosomal takeover, where the ribosome evolved to consume most of the cell’s resources, while other cellular componentry ensures the propagation of the ribosome. arxiv.org/abs/2602.23268

New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects. www.nature.com/articles/s44...

Priority effects inhibit the repeated evolution of phototrophy - npj Complexity

npj Complexity - Priority effects inhibit the repeated evolution of phototrophy

nature.com

They're literally running out of lawyers in a state where the district judges are practically at war with the administration.

If we don’t create our dreams, who will?@newlife2024.bsky.social · 6mo ago

BREAKING: 8 more U.S. Attorneys in MN resign from Trump’s DOJ in protest as backlash grows. This isn’t normal; isn’t routine reshuffling. It’s a rebellion. Last month, 6 veteran prosecutors quit in protest. Normal staffing for the MN DOJ’s office is around 50 attorneys. They’re down to just 9.

New and Competitive renewals These are still be made VERY slowly. Only 75 awards have been made through 1/23/26. These are now from 7 institutes and centers (NIA (45), NINDS (16), NIDDK (5), NIDCR (4), NIDCD (2), NHLBI (1), and NCATS (1)). 3/3

🚨 New from me: Grant review at more than half of NIH's institutes could be frozen by the end of the year. That's because crucial NIH grant-review panels are slated to be empty at those institutes by Jan 2027. A wonky bureaucratic problem with big implications. A short 🧵

Exclusive: key NIH review panels due to lose all members by the end of 2026

Thirteen of the agency’s advisory councils, which must review grant applications before funding is awarded, are on track to have no voting members.

nature.com

A new preprint from the lab, with postdoc @deboraycb.bsky.social and collaborators @aidaandres.bsky.social and Tim Connallon: “Characterising the detectable and invisible fractions of genomic loci under balancing selection” www.biorxiv.org/content/10.6...

A recent scientific paper compared long-term mortality by vaccination status. I noticed that Table 2 drew a lot of attention, but was actually included in the paper as a static image. So I built a quick dataviz project to explore. 🧵