I was truly heartbroken to hear about Richard's passing.
He was a great mentor and the one who introduced me to the amazing world of proteins. Richard would see the beauty in science, and science in daily life objects, and his vision really shaped my own approach of biomolecular modeling.
Thanks, it's on my reading list now!
That's what I see happening with AI. It's force-fed to everyone at a rate that society cannot deal with. Pretty much all the issues that critics point out look solvable, but not rapidly.
I am pretty sure this is only one mechanism out of many, but I haven't seen anyone try to untangle them.
Another mechanism I see is society adapting to new tech more slowly than the rate of the incoming change. The initial impact *is* negative, as critics point out, but initial problems get solved.
Formation "Construction et animation d'une communauté autour du développement d'un logiciel libre"
30 juin - 2 juillet à Autrans
La formation est ouverte et gratuite à tous les membres des laboratoires de recherche académique en France.
animeopensource.sciencesconf.org
You can now sign up for the next session of the MOOC
"Reproducible Research II: Practices and tools for managing computations and data"
which opens on May 5th.
www.fun-mooc.fr/en/courses/r...
🧪
"Humans reading AI-generated code doesn’t scale."
Actually, humans reading code never scaled. We just pretended it did.
We need a science of how to reason about systems without reading code (AI summaries are not the solution). You can start at: moldabledevelopment.com
LLM answers only look like answers.
They are actually possible hypotheses in disguise.
New blog posts: "Preparing for scientific deepfakes"
blog.khinsen.net/posts/2026/0...
"What I haven't seen yet, but expect to see soon, is the scientific equivalent of deepfakes: made-up results that come with made-up code that reproduces them."
🧪 #metascience
@khinsen.scholar.social.ap.brid.gy Talking to myself across the bridge...
A week ago, we had an open conversation amongst senior academics in leadership roles and their use of LLMs (in both their leadership capacities and individually). Small group, not representative, but it already taught me a great deal about the diversity of perspectives (& their consequences). 1/
An interesting experiment in reproducibility: the NanoBubbles project is looking for researchers/labs in nanotechnology who can help with understanding the discrepancy between an widely cited work and its mostly failed replication
I am looking for papers that report on quantum chemistry computations performed on quantum computers.
NOT theory
NOT running on simulators
NOT benchmarks
(all those are easy find)
but computations of real chemical interest on real quantum devices.
No, DeepMind has not solved the protein folding problem.
#Alphafold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination.
RE: https://spore.social/@yoginho/115918117109281530
Recommended!
We've got ISSUES. Literally.
We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?
arxiv.org/abs/2601.07563
A 🧵 1/n
My wish for 2026 for academia specifically, is to push back against fascist framings, reasoning, and industry capture in our universities. My suggestions are below. But please do anything you can if you're an academic. 🌿 Even if it's tiny. 🐁 Every pebble helps build a damn against fascist forces. 🪨
RE: https://mastodon.social/@Viss/115841064419194751
Hello Readers on #Bluesky: there really is no excuse anymore, *not* to migrate to the #Fediverse and escape your corporate overlords.
Empire or rebellion? This is the question.
Which one do you support?
Your actions shout louder than your […]
2020s: AI "System Prompts" are lengthy, carefully constructed sets of expert rules about a particular domain, created by "prompt engineers".
1980s: AI "Expert Systems" were lengthy, carefully constructed sets of expert rules about a particular domain, created by "knowledge engineers".
Many toots, but nothing long-form I can think of. Open Source is ultimately a means that can be applied towards many ends. There's full corporate Open Source (e.g. Chromium and Firefox). There's also corporate takeover of Open Source with academic origins (e.g. Scientific Python).
Rate your score on Factor Fexcectorn.
Well done, Scientific Reports. pubpeer.com/publications...
Proteins are dynamic structures, but structural biology often shows them as static snapshots. Inspired by long-exposure photography and generative art, I built ProteinCHAOS, an artistic tool inspired by molecular dynamics to capture protein flexibility over time, much like long-exposure images.
Call for contributions/demos for programming 2026 in Munich, March. Ooh I'll have some serious shit cooking by then.
2026.programming-conference.org/home/substra...
Very happy to share our collaborative project on FAM118 proteins - noncanonical sirtuins that form filaments and process NAD in human and other vertebrate cells.
However, for the blog, I'll keep the static site as well. It's archivable and usable without JavaScript. Plus the posts get DOIs.
We have a long way to go before we can put together all the desirable features for scientific publishing!
Turning my blog into a HyperDoc is one of my projects!
As for network/server dependency, I am betting on having Common Lisp on WASM in the near future, and then I can run everything in the browser, while retaining the server option for heavier computations or larger datasets.
Thanks for reporting! I had forgotten install the SBCL source package on the server. That should be fixed now.
New blog post: "Explorable explorable explanations"
Building on Bret Victor's concept of "explorable explanations" for scientific publishing.
blog.khinsen.net/posts/2025/1...
🧪 #MetaSci
