Joanna Masel

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

Priority effects inhibit the repeated evolution of phototrophy - npj Complexity npj Complexity - Priority effects inhibit the repeated evolution of phototrophy

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...

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

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

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.

🚨 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 🧵

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.
🧵

Oh no!

Allele Frequencies at Recessive Disease Genes are Mainly Determined by Pleiotropic Effects in Heterozygotes The classic theory of mutation-selection balance predicts the equilibrium frequency of genetic variation under negative selection. The model predicts a simple relationship between the total frequency ...

Our latest preprint revisits the classic model of mutation-selection balance.

Do human recessive genes fit Haldane's 100-year old model?

This work is by the wonderful @jonj-udd.bsky.social, and co-mentored by @jeffspence.github.io

www.biorxiv.org/content/10.6...

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...

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis, and is prone to error. Unfortunately, algorithms that remove likely alignment errors from MSAs sometimes also remove informati...

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

Take-home: substitution matrix quality matters. Instead of using ModelFinder, use IQ-Tree’s QMaker to build your own for your taxon of interest, trained on strictly filtered alignments. And use CLOAK before inferring trees. 10/10

For the sequence whose gene tree you are inferring, strict filters hurt, and our new gentle filter CLOAK performs best. Propagating uncertainty from our 16 variant alignments into a consensus among 16 variant trees was worse, showing the presence of systematic not just random alignment error. 9/10

Using a substitution model trained on strictly filtered alignment data leads to better inference on gene trees, bringing them closer to the known species tree according to Lin-Rajan-Moret distance (an improved extension of Robinson-Foulds distance). 8/10

Stricter filters have stronger effects in reducing exchangeabilities associated with less plausible amino acid substitutions, i.e. those that require more than one mutation, according to the genetic code. 7/10

Phylogenetics relies on substitution models (rates of evolution between amino acids or nucleotides), which are normally decomposed into a symmetric exchangeability matrix and equilibrium frequencies. Filtering reduces exchangeabilities between amino acids not linked by single mutations 6/10

In a trade-off between precision and recall, CLOAK is the best gentle filter, the “partial filtering” option within Divvier doi.org/10.1093/molb... is the best strict filter, and TAPER and the Divvier’s divvying option are in between. GUIDANCE2 and HmmCleaner perform less well. 5/10

Our new program CLOAK (CLeaning On Alignment C[K]onsensus) uses 16 variant alignments generated by Muscle5 (3 perturbations of HMM × 3 perturbations of guide tree), and retains only the pairs for which all 16 agree. You can call it within Muscle5 with the option “-cloak”. 4/10

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference Abstract. Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to erro

Unfortunately, when building a gene tree, every bit of information can be important enough such that filtering alignments (at least with older tools) can make tree inference worse doi.org/10.1093/sysb... 3/10

Trigger warning: the attached images of real multiple sequence alignments may cause feelings of distress among biologists: 2/10

Improved gene tree inference from removing alignment errors both from focal genes and when training substitution models Multiple Sequence Alignment (MSA) is a key step in phylogenetic analysis, and is prone to error. Unfortunately, algorithms that remove likely alignment errors from MSAs sometimes also remove informati...

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

Twins Are So Much More Interesting Than Heritability Estimates On starting places, "missing environmentality," and the Waddington landscape of life

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

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

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!

I have no idea about whether he is religious. I was responding to what you wrote about how the Nazis would have classified him, which has a clear factual answer.

From Hebrew school to halls of power: Stephen Miller’s unlikely journey When Stephen Miller began to crop up in headlines last spring as a member of then-candidate Donald Trump’s inner circle, those who knew him as the scion

I don't think what you say fits the facts: jewishjournal.com/news/united-...

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...

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.

Headless bodies hint at why Europe’s first farmers vanished Wave of mass brutality accompanied the collapse of the first pan-European culture

Well there's your problem.

www.science.org/content/arti...

Part 1: My Life Is a Lie How a Broken Benchmark Quietly Broke America

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-...

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...