Rudolfo Karl, Elvira Mass, Dagmar Wachten @wachtenlab.bsky.social and colleagues discover that renal tissue-resident macrophages promote cystogenesis in early polycystic kidney disease. #JCSciliaSI journals.biologists.com/jcs/article/...

"Solving a Million-Step LLM Task with Zero Errors", from the inimitable Elliot Meyerson (et al.)

Nature research paper: iPEX enables micrometre-resolution deep spatial proteomics via tissue expansion go.nature.com/4qRtP6F

NEWS: Oxford scientists capture genome’s structure in unprecedented detail @rdm.ox.ac.uk scientists have achieved the most detailed view yet of how DNA folds and functions inside living cells, using a new technique called MCC ultra .

Profits from scientific publishing are eye-watering, costing us billions. In ‘The Drain of Scientific Publishing’ (arxiv.org/abs/2511.04820), (building on ‘The Strain of Scientific Publishing’ doi.org/10.1162/qss_a_00327) we show how it is harmful – and unnecessary.

What a thrill to be part of @talkingpointsmemo.com's series about the past 25 years of digital media! I wrote about why private equity goons destroyed Deadspin and why it matters.

Back on track: Funders hold all the cards. There's this flawed view that authors are consumers and journals are producers. Wrong. Funders and institutes are consumers. They contract authors to produce research, and they pay for journals to QC the work. Funders are the consumers. 8/n

Fundamentally, what we need is leadership. But we break with the chorus of most #OpenScience initiatives here and emphasize very strongly that this leadership must come from funders and institutions. We researchers can support the battle, but we cannot lead the charge. Funders hold the cards. 6/n

More fundamentally, every active scientist has been brought up in a system where The Drain was already normalized. This system hasn't always existed. For-profit publishers are a recent invention. Their value proposition has always been awful, and now they are actively eroding trust in science. 5/n

For-profit journals are supposed to improve research quality, yet they're perversely incentivized to churn out whatever they can monetize. This was happening before AI (see Strain: bit.ly/43gJPUM), and AI will make it worse. It's insane that we volunteer our time to help them do so. 4/n

We wrote the Strain on scientific publishing to highlight the problems of time & trust. With a fantastic group of co-authors, we present The Drain of Scientific Publishing: a 🧵 1/n Drain: arxiv.org/abs/2511.04820 Strain: direct.mit.edu/qss/article/... Oligopoly: direct.mit.edu/qss/article/...

The protein concentration in the cytoplasm is so high that the average protein has a water hydration shell with a thickness of only ≈ 10 water molecules separating it from the adjacent protein hydration shell. 1/2

Bullies gain power when their misconduct succeeds in causing righteous people to yield in the face of wrongdoing. That’s why voting for Trump's continuing resolution - without any protection against his health care cuts or his growing illegality - is a mistake. I voted NO.

Meanwhile, CEOs make 280 times the typical worker today. The system is rigged.

The advances we've made in statistics, experimental study design, and causal inference over the past century are remarkably useful for understanding our world. But there is never been a push to make people use them like we are seeing with generative AI. Perhaps take a moment to consider why.

Proteoforms encoded by the same gene have different interactomes. This challenges: 1⃣ The interpretation of data from affinity reagents directed towards shared epitopes. 2⃣ The assignment of functions to genes. When will biological research focus on such functional differences?

Excited to embark on this scientific journey with Ewa Paluch and Daniel StJohnston to understand fundamentals of epithelial tissue and cell shapes! Thank you to @erc.europa.eu for the support!

🚀 Exciting news! ERC Synergy Grant of €8.5 million to Sara Wickström @sarawickstrom.bsky.social, Daniel St Jonston @gurdoninstitute.bsky.social and Ewa Paluch @universitypress.cambridge.org! This highly interdisciplinary project will boost our understanding of tissue biology. #ERCSyG @erc.europa.eu

📣 Read the full news here: www.mpi-muenster.mpg.de/press-releas...

A probabilistic histological atlas of the human brain for MRI segmentation @nature.com www.nature.com/articles/s41...

Spatial dynamics of brain development and neuroinflammation @rongfan8.bsky.social @yalepress.bsky.social @gocastelobranco.bsky.social @ki.se www.nature.com/articles/s41...

A framework for the computational design, screening and characterization of fully de novo antibodies with atomic-level precision in both structure and epitope targeting @nature.com @uwproteindesign.bsky.social @bakerlabpodcast.bsky.social www.nature.com/articles/s41...

Our study, just published in #ScienceAdvances and funded by @hfspo.bsky.social, explores the post metamorphic cell composition of the sea urchin juvenile, revealing that its body is head-like. Long considered brainless creatures, they’re all brain instead! www.science.org/doi/10.1126/...

Development that lasts a life time. Check out the 2025 special issue of @dev-journal.bsky.social on Lifelong Development: the Maintenance, Regeneration and Plasticity of Tissues journals.biologists.com/dev/issue/15...

The {sf} package continues to blow my mind with how easy it is to make maps with #rstats and ggplot (code for that map here gist.github.com/andrewheiss/...)

Our #JCSciliaSI is complete Explore our ToC: journals.biologists.com/jcs/issue/13... Our cover image shows tracheal epithelial cells from an air-liquid interface culture imaged using U-ExM from Oliver Mercey and Marine Brunet @centriolelab.bsky.social. journals.biologists.com/jcs/article/...

Oocyte-like mouse cells made from stem cells even without the guiding signals from ovarian cells. Another step towards in vitro gametes. www.cell.com/developmenta...

extraordinarily deep investigation of the human fetal heart with spatial and single cell approaches. With a comment by postdoc Lisa Iwamoto-Stohl and I. www.nature.com/articles/s41... www.nature.com/articles/s41...

chatomics! new blog post: Understanding prcomp() center and scale Arguments for Single-Cell RNA-seq PCA divingintogeneticsandgenomics.com/post/unders...

«Silicon Valley isn’t building apps anymore. It’s building empires.» The Authoritarian Stack: A mapping of firms, funds, and political actors turning core state functions into private platforms, by @francescabria.bsky.social et. al. for @fesonline.bsky.social www.authoritarian-stack.info

For the eternally curious (me!), Wikipedia is like a road map to human knowledge, a modern extension of the ethos of the public library. And thanks to donations & the work of volunteers, it's available to everyone without regard to ability to pay.

Been reading "What is Innateness?" by Paul Griffiths (2002) philpapers.org/rec/EGRWII in which he offers this very sound advice:

I had a long conversation with MIT Tech Review’s @willdouglasheaven.bsky.social about AGI; it fed into this very good read on the rise of AGI orthodoxy

Good (long) Sunday read about how the “AGI narrative” works — spoiler: “It’s not utopia or hell—it’s OpenAI and its peers making a whole lot more money.” Here are a few more quotes/important points I likes to read:

Which features of tissue flows are most robust and how do they emerge from #EpithelialMechanics? I’m @alex-plum.bsky.social (@mattiaserra.bsky.social group) and I’ll be sharing some papers on characterizing and controlling avian gastrulation flows.

There were 26,802 submissions to arXiv in Oct 2025 alone (CSV: arxiv.org/stats/get_mo...). It's a shame that a preprint server can no longer serve preprints, but I don't see how quality can be sustained at this volume of submissions.

Another casualty of the LLM revolution. In "arXiv’s CS category, review articles and position papers must now be accepted at a journal or a conference and complete successful peer review."

One of my favorite effects. They sense the environment with electricity and if both use the same frequency, signals collide. So they have to detune. But who goes up and who goes down on a matter of social dominance!! Oscillation as a social construct!!

Obama: "They never miss a chance to scapegoat minorities and blame DEI for every problem under the sun. You got a flat tire? Must be DEI. Your wife kicked you out? DEI. Who knew?"

Yesterday I was discussing the intractibility of glioblastoma with a neuroscience colleague--this could be transformative 🧪

An extraordinary result for ipilimumab immunotherapy given as a first line therapy for glioblastoma share.google/485XFZxmBm26...

Natty is my old boss. His team is reporting that the reported 1200 killed by the RSF in Sudan yesterday was off, by about an order of magnitude. Any massacre is horrific, but I expect this to get far far worse.

JNK integrates immune and stress signals to balance apoptosis and proliferation in airway progenitors https://www.biorxiv.org/content/10.1101/2025.10.30.685523v1

Great Blueprint from @arnaghosh.bsky.social on our newest paper on representational geometry! tl;dr: we find that during pretraining LLMs undergo consistent cycles of expansion/recuction in the dimensionality of their representations & these cycles correlate with the emergence of new capabilities.

Talking about spooky stuff…try to do awake mouse fMRI. Oh, you want it spookier? Try to add simultaneous Ca2+ imaging. Now, do it all again, longitudinally…. So proud to finally have this out!!! 🐭 🧠 🧲 Go read…if you dare!! 👻 www.biorxiv.org/content/10.1...

Take a look at our paper! Led by @francimandi.bsky.social in the Lake lab: "Longitudinal, simultaneous wide-field fluorescent Ca2+ imaging and fMRI in awake mice" !!!! www.biorxiv.org/content/10.1...

Excited to share my latest postdoc work on systemic metabolic homeostasis! We show that nutrient consumption fluxes compete, and this competitive catabolism helps explain why obesity drives diabetes. Explore the model with our interactive web app: compcat.princeton.edu doi.org/10.1101/2025...

Ten years ago, I saw a paper with some data that has bothered me ever since: B cells in a 0-100 ng/mL gradient of CCL19 are attracted to CCL19, but B cells in 0-500 ng/mL are repelled (see movie, ignoring the big clusters for now!). Why? Here's our model! doi.org/10.1101/2025...

#RNAsky #SpatialGeneExpression share.google/OuxQ2j5N1phh...