Kaitlin

Why does the naked mole rat have the longest lifespan of any rodent, nearly 40 years?
A 30-year long mystery unraveled @ScienceMagazine today!
Its cGAS enzyme in cells has 4 missense mutations that upends its function, promoting DNA repair and suppressing inflammation
www.science.org/doi/10.1126/...

Don’t forget the biophysics!

1. pubmed.ncbi.nlm.nih.gov/35957822/
2. www.frontiersin.org/journals/end...

AI-Generated “Workslop” Is Destroying Productivity Despite a surge in generative AI use across workplaces, most companies are seeing little measurable ROI. One possible reason is because AI tools are being used to produce “workslop”—content that appea...

hbr.org/2025/09/ai-g...

10 Rules for a Structural Bioinformatic Analysis The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

This was a great read! If it were up to me, this specific part of rule #4 would be expanded into a full Opinion piece, because proteins for structural characterization are definitely not sampled IID from uniprot/wherever

YouTube video by ProteinDesignStudio Screen binders using ipSAE

pip install ipsae
from www.linkedin.com/in/ullah-sam...

www.youtube.com/watch?v=A5ph...
PyPI pypi.org/project/ipsae/
His github fork github.com/ullahsamee/I...
My github github.com/DunbrackLab/...
Paper www.biorxiv.org/content/10.1...
For designed protein binders www.biorxiv.org/content/10.1...

The final version of our multispectral microscopy manuscript is now online at Nature Photonics: www.nature.com/articles/s41...

The main additions are some further comparisons to yet more unmixing algorithms, in which we find that our algorithm is still the most accurate.

If you place a camera in the lion habitat …

They’re going to turn it into a giant cat toy

RCSB PDB - 1DVS: CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH RESVERATROL CRYSTAL STRUCTURE OF HUMAN TRANSTHYRETIN IN COMPLEX WITH RESVERATROL

another one to watch out for imo (even if resveratrol is keeping him in check here)

www.rcsb.org/structure/1DVS

www.nytimes.com/2025/09/07/s...

This bit:

I don’t trust him

It is Spring 2

Congrats to our current postdoc Amir on his latest publication with the Shakhnovich and Rodnina labs! Check out this thread about their really interesting study, combining all-atom simulation with experiment to reveal a protein's co-translational folding pathway at an atomistic level of detail

👇👇👇

also prevents one from getting pointlessly hung up about if things are objective or could be. a key component of being regular imo

Recently tested some de-novo minibinders against two targets (thanks Adaptyv!) designed using our open-source design library, `mosaic`; our best method got hit rates of 7/10 and 8/10 and affinities as low as single-digit nanomolar. Wrote up some thoughts here: blog.escalante.bio/minibinder-d...

Continuum mechanics is hard to learn because there are so many moving parts.

i think the thing about predicating philosophy of science on "falsifiable predictions" is that it licenses the sale of predictions as a kind of science

I also did this

a comic with four panels. First one, top left: a dinosaur says "Indohyus, my brother, I've decided to search for more food in the waters." Second: first dinosaur with a new dino. The new dino says, "You will regret this, Pakicetus. The enviornment [SIC] will force you to adapt." "I just need some shrimps lol I will be perfectly fine." Third panel: "35 million years later..." it shows a whale underwater saying "aaaaooooooooaaaaah" and "mruuuuuuuuh" fourth panel: whale, says "bwooooooeeeeee" and a deer says "wtf"

didn't make this and if you did i am happy to credit you

Moooom can you come pick me up the Niskanen Center people are trying to make me play board games again

@atwilliams.bsky.social blog posts on Keynes’s view of probability are fun

Is it really interesting to find a neuron correlated with some feature you already knew existed? This limits the scope of discovery imo

Also puzzled by this thing everyone does now where they try to interpret latent spaces of neural networks. You already have one system that’s hard to interpret. What is gained by adding a second one and trying to interpret that instead?

To be sure, there’s still a lot of great deep learning stuff happening, but I wish I saw more careful thinking about what signals are in what data and whether we’re going to find any more quick wins from what public data are out there. The quality of the PDB is unmatched among public data

Basically every day I see a preprint or paper showing that deep learning fails to outperform simple baseline models on protein tasks that aren’t structure prediction, yet the hype persists!

Brad Mehldau Trio

Having the drawing helps to clarify what we are talking about, but seems to me if you’re trying to optimize a binding affinity that you probably don’t need to know anything about the transition state at all, and possibly not even about the second free energy well