Tami Lieberman

The proportion of epistatic heritability that is estimated as additive by quantitative genetic models. Epistasis deviates more from additivity for lower frequency causal alleles, but on average >80% of biological GxG will just look like statistical G.

New Housing Slows Rent Growth Most for Older, More Affordable Units The nationwide housing shortage has driven rents up more in low-income neighborhoods than in the U.S. overall, but in areas that have recently added large amounts of housing, rents have fallen the mos...

"Allowing enough homes for everyone improves affordability overall, but the evidence shows it benefits low-income renters most."

Who knew?

Metagenomic selections reveal diverse antiphage defenses in human and environmental microbiomes Rodríguez-Rodríguez et al. use functional metagenomics to identify hundreds of sequences from diverse environmental bacteria that block phage infection when expressed in E. coli. Their discoveries inc...

The diversity of bacterial defence systems against phages (restriction endonuclease, #CRISPR, phage protein
sensing system (RexAB), cyclic oligonucleotide-based (CBASS), ADP ribosylation (DARTG)) is simply fascinating, and we continue to discover new ones !!!

www.cell.com/cell-host-mi...

Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization | mSystems In this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, ...

You can get an accurate estimate of total bacterial biomass from stool metagenomes by simply normalizing by host read count, without needing any additional measurements.

Excellent work by UW Master's student Gechlang Tang in @asm.org #mSystems Journal.

journals.asm.org/doi/10.1128/...
🧵

This surprisingly relaxing footage is from SIX MILES under the ocean – and it’s the deepest ecosystem yet discovered

Extra kudos and thanks to all the staff at NIH and NSF and other federal funding agencies for working extra hard in very small windows of opportunity to get grants reviewed and funds released before the attention-addled federal policies change again (on an hourly basis).

The History of the Panmictic Population Concept and Its Legacy in Contemporary Population Genetics ABSTRACT The panmictic population concept is at the heart of population, evolutionary and conservation genetics. However, in nature, true panmictic populations are vanishingly rare. As an idea conce...

🚨 New paper klaxon! 🚨

The History of the Panmictic Population Concept and Its Legacy in Contemporary Population Genetics

Quite niche admittedly, one for the historians of evolutionary thought, and population geneticists.

doi.org/10.1111/ahg....

Shout out to the WSJ journalists who reported on Vought’s impoundment by footnote, causing the White House to walk it back. Impact journalism!!

House is in recess. The Senate goes on recess at end of week.

This was heavily choreographed by Vought. Before the election he said the full Project 2025 was not public and would be handed to Trump directly. This was always part of Vought's plan.

We have run out of discretionary funding. I am not sure what we will do of this is really the policy til the end of the year. Can grants that didn't make it out the door in time even get funded with next year's budget?

I have an R01 that was supposed to start April 1, percentile of 2. Did some adjustments to JIT in early July...

Untangling phage immunity systems can be really challenging but @owentuck.bsky.social and team used phylogeny and biochemistry beautifully to show how a pair of genes got repurposed as a component in multiple defence systems.

In apprehension how like a god science is a process of holding fantasy accountable to fact

In this week's #substack post, I write about the intrinsic human capacity to fantasize about how the world works, and how the scientific process emerged when we started to hold our fantasies accountable to facts.

gibbological.substack.com/p/in-apprehe...

Hi! I made the science discussions feed. It’s a “trending” sort with more weight on replies than reposts/likes.

If you want something similar for your following feed that should be pretty easy with graze.social (which is what I used). You can choose if you want quote-posts and replies,

Preprint by @towalther.bsky.social at al! We design DNA hydrogel microparticles with sequence-controlled stiffness from 30 Pa to 6.5 kPa. They are remodelled in fibroblast spheroids www.biorxiv.org/content/10.1... Thanks @ibecbarcelona.eu @xaviertrepat.bsky.social @pcusachs.bsky.social

Thanks!

For a more twitter-like algorithm

I see. Is that the basic "science" feed or something else?

bsky.app/profile/did:...

So much engagement here!

It that an easy feed to reproduce with the list of people you're following, like papersky?

Biologist folk (especially in evolutionary biology and/or ecology, but it don’t matter):

Can you give me your favorite examples of trade offs in biology? Organism or system don’t matter. Primary literature or reviews preferred.

Amazing stuff. I'd like to point you to the incredible graphical abstract for this recent Cell manuscript.

doi.org/10.1016/j.ce...

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io

Please help spread the news.

Trash receptacle
Columbia, AL

"Our analysis identified 16 divergent and 165 convergent excludons in E. coli, as well as 10 divergent and 28 convergent excludons in S. aureus."

High-throughput single-cell isolation of Bifidobacterium strains from the gut microbiome https://www.biorxiv.org/content/10.1101/2025.07.23.666462v1

Microbial metal physiology: ions to ecosystems Nature Reviews Microbiology, Published online: 25 July 2025; doi:10.1038/s41579-025-01213-7Metal ions are required for all cells, and their homeostasis relies on ancient mechanisms that facilitate their import, distribution and storage. In this Review, Helmann discusses the key chemical concepts underlying microbial metal physiology and highlights several exemplary microbial systems.

New online! Microbial metal physiology: ions to ecosystems

Why didn't we perdue this story between 2020 and 2024?

A few comments - happy to explain in more detail When the paper was published, I was one of the people who publicly critiqued aspects of it. My biggest critique was of the press conference and the quotes and comments some of the authors made regarding the paper where they made claims about things that were not even in the paper. I also was deeply concerned that the authors refused to discuss critiques of their paper until those critiques were published in the peer reviewed literature. The paper certainly had multiple erroneous conclusions as well. But again, the biggest problem to me was the claims made at the press conference and in ongoing coverage that were even more misleading, wrong, and unwarranted than claims made in the paper. Despite my concerns about the paper and the discussions with the press, I do not agree with the decision to retract the paper now. This is for a few reasons including those below: First, it seems a bit strange to apply a new standard retroactively to papers from the past. There were standards for retraction at the time the paper was published and those were apparently applied, leading to them to not retract the paper. So - Science has new standards but it would make more sense to me to apply such standards moving forward. Second, there is no statement in the retraction notice that Science is going to retroactively go through other past publications to see if any also meet this new standard. So if they are going to retroactively apply this to the arsenic paper, what about the likely 100s to 1000s of other papers in Science and Science-associated journals with other major errors in conclusions? I personally know of many papers in science that have significant errors or wrong conclusions and would fit the COPE definitions likely. Third, I personally do not agree that the COPE guidelines Dr. Thorp is referencing are a useful tool in science publishing. Scientific articles may contain dozens to hundreds to thousands of different con…

It sort of conveys what I wrote to the author but I don't think strongly enough. So here is what I wrote to the author which she summarized in the section quoted above

This brings me back to such a specific place and time in my early PhD.