iiinova — where your digital self keeps evolving

Joanna Masel @joannamasel.bsky.social · 11/09/2026

Novavax/Nuvaxovid is available today. I got it at cvs after checking www.nuvaxovid.com/vaccine-loca... and just showing up to cvs - it's not on their booking system, but they have it.

nuvaxovid.com

NUVAXOVID™ Vaccine Locator | Patient Site

Find NUVAXOVID by entering a zip code in the vaccine locator.

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Mike Wiser @drmikewiser.bsky.social · 05/09/2026

Anyway, if you’re not already aware, new boosters are out, and rah’s antihistamine protocol reduces side effects in a substantial fraction of cases. bsky.app/profile/raha...

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Nigel Goldenfeld @nigelgoldenfeld.bsky.social · 07/08/2026

What do the earliest organisms tell us about where life began on earth? This fantastic paper addresses this issue through analyses that expose early metabolism, & what the environment contributed to kick start it. Even if wrong it is worth reading for the clear introduction to metabolism.

science.org

Intermediate stages in the origin of metabolism at a phosphorylating hydrothermal vent

Enzymatic metabolism emerged from metal-catalyzed, aqueous reactions of H2, CO2, NH3 and phosphite at a hydrothermal vent.

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Joanna Masel @joannamasel.bsky.social · 04/08/2026

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

ecoevorxiv.org

The series of genetic codes that preceded our own

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Susana Wadgymar🌿🔬 @smwadgymar.bsky.social · 02/08/2026

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

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Genetics Society of America @genetics-gsa.bsky.social · 01/08/2026

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

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Joanna Masel @joannamasel.bsky.social · 27/07/2026

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

academic.oup.com

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

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David J. Bier @davidjbier.bsky.social · 16/07/2026

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

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Darren Obbard @darrenobbard.bsky.social · 27/06/2026

#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.

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Science Magazine @science.org · 22/06/2026

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%. scim.ag/4xY2KCm

science.org

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

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Joanna Masel @joannamasel.bsky.social · 21/06/2026

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?

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David Castellano @castellanoed.bsky.social · 11/06/2026

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.

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Ryan Gutenkunst @ryangutenkunst.bsky.social · 09/06/2026

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

cmmbs.arizona.edu

Home | Computational and Mathematical Modeling of Biomedical Systems

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elizabethginexi.bsky.social @elizabethginexi.bsky.social · 29/05/2026

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...

elizabethginexi.substack.com

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

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Andrew Roger @andrewjroger.bsky.social · 28/05/2026

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...

doi.org

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

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Kai Kupferschmidt @kakape.bsky.social · 27/05/2026

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)

science.org

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

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Joanna Masel @joannamasel.bsky.social · 16/05/2026

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.

doi.org

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

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Will Ratcliff @wcratcliff.bsky.social · 13/05/2026

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...

biorxiv.org

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Joanna Masel @joannamasel.bsky.social · 13/05/2026

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.

nytimes.com

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

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Joanna Masel @joannamasel.bsky.social · 16/04/2026

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!

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Mart Krupovic @mkrupovic.bsky.social · 03/03/2026

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

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Will Ratcliff @wcratcliff.bsky.social · 03/02/2026

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...

nature.com

Priority effects inhibit the repeated evolution of phototrophy - npj Complexity

npj Complexity - Priority effects inhibit the repeated evolution of phototrophy

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Andy Craig @andycraig.bsky.social · 03/02/2026

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

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Jeremy Berg @jeremymberg.bsky.social · 29/01/2026

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

A line graph of the number of NIH awards for new and competitive renewal grants made in fiscal year 2026 compared to fiscal years 2021 through 2025. The curve for fiscal year 2026 appears to be essentially at zero on this scale.

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Max Kozlov @maxkozlov.bsky.social · 22/01/2026

🚨 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 🧵

nature.com

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.

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Max Reuter @maxreuter.bsky.social · 21/01/2026

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...

biorxiv.org

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Mike Honey @mikehoney.bsky.social · 20/12/2025

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. 🧵

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Carl Zimmer @carlzimmer.com · 06/12/2025

A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...

doi.org

Redirecting

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Kathryn Paige Harden @kph3k.bsky.social · 04/12/2025

I wrote about missing heritability, "missing environmentality," and why I still think twin studies are interesting and valuable: kathrynpaigeharden.substack.com/p/twins-are-...

kathrynpaigeharden.substack.com

Twins Are So Much More Interesting Than Heritability Estimates

On starting places, "missing environmentality," and the Waddington landscape of life

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Snowden St. @snowden.st · 02/12/2025

Currently dorking out over this graph about child mortality with my brother. Just mind boggling to take in.

chart of child mortality in history, roughly 48% for all societies across the globe…until the 20th century, where it plummets to 4%

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Ben Allen @evodynamics.bsky.social · 02/12/2025

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!

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Elizabeth Jacobs, PhD @elizabethjacobs.bsky.social · 28/11/2025

This article provides more data showing how easy it is to manipulate humans on social media. These researchers rerouted the algorithm on Twitter to push some users toward “antidemocratic attitudes and partisan animosity”. It only took 1 week to elicit changes that used to take 3 years.

science.org

Reranking partisan animosity in algorithmic social media feeds alters affective polarization

Today, social media platforms hold the sole power to study the effects of feed-ranking algorithms. We developed a platform-independent method that reranks participants’ feeds in real time and used thi...

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TKarney @pecunium.bsky.social · 26/11/2025

We have a “poverty trap” and it’s driving the destruction of social cohesion. The “poverty line” is’t 35,000, it’s $150,000, and making more than one, and less than the other is worse than being “poor”. Which is why the rage. www.yesigiveafig.com/p/part-1-my-...

yesigiveafig.com

Part 1: My Life Is a Lie

How a Broken Benchmark Quietly Broke America

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John Holbein @johnholbein1.bsky.social · 26/11/2025

Does blinding--i.e., concealing applicants' identities--reduce gender gaps in academic conference paper acceptances? Nope! Does blinding do anything? It does! Blinding reduces gaps in acceptances by institution rank. haruka-uchida.github.io/websitefiles...

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Mike Barker @barkerms.bsky.social · 26/11/2025

Please pass along - We've extended the CAMBIUM fellowship deadline to December 15! Our NSF NRT supports new grad students to harness biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, ecology & more. cambium.arizona.edu 🧬🌐🌎

Sonoran Desert landscape looking west across Avra Valley from Tucson Mountain Park. In the foreground, a desert trail winds through cholla cacti, saguaros, ocotillo, and native shrubs. The valley stretches to distant mountain ranges on the horizon under a dramatic sky of blue patches and white cumulus clouds with rays of light breaking through.

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Svetlana Dodonova @dodonova-sveta.bsky.social · 28/10/2025

Lab’s first paper is out!! We show the first structures of #Asgard #chromatin by #cryo-EM 🧬❄️ Asgard histones form closed and open hypernucleosomes. Closed are conserved across #Archaea, while open resemble eukaryotic H3–H4 octasomes and are Asgard-specific. More here: www.cell.com/molecular-ce...

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Ruben C. Arslan @ruben.the100.ci · 23/11/2025

Rares: Contrast his summary with the abstract of Wainschtein et al. Focusing on ultra-rare to the exclusion of rare/de novo/structural variants seems like cherry picking a threshold in this context.

Amazingly, with three different method and datasets, the estimated “narrow-sense” heritability comes in at ~30% (shown above in blue). What about rare variants? In the two studies where common variant / GWAS heritability was estimated (Young et al. and Wainschtein et al.), it accounted for ~85% of the total narrow-sense heritability estimate, indicating that rare variants make a relatively small contribution on average and GWAS provides an only slightly lower bound on total narrow-sense heritability. As tentative support, Wainschtein et al. conducted an exploratory analysis of the heritability from 760 million “ultra-rare” variants and found that they added essentially nothing (~0.12%) to the total heritability estimate on average.

Low minor allele frequency variants in low linkage disequilibrium (LD) with neighboring variants were enriched for heritability, to a greater extent for protein-altering variants, consistent with negative selection. Our results imply that rare variants, in particular those in regions of low linkage disequilibrium, are a major source of the still missing heritability of complex traits and disease.

Graph from Wainschtein et al. showing rarer alleles have bigger individual effects.

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Sasha Gusev @sashagusevposts.bsky.social · 21/11/2025

I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵

theinfinitesimal.substack.com

The missing heritability question is now (mostly) answered

Not with a bang but with a whimper

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Michael Baym @baym.lol · 20/11/2025

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...

science.org

Intracellular competition shapes plasmid population dynamics

From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

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