Sign in

Ran Blekhman

@blekhman.bsky.social
5.2K followers 256 following 366 posts

Professor of Genetic Medicine at the University of Chicago. Decoding the human microbiome. BlekhmanLab.org

PostsRepliesMedia
Reposted by Ran Blekhman
Stephen Turner @stephenturner.us · 26/09/2026
Personal essay, weekend edition. My relationship with AI is changing. 1.8k words, 8 min reading time. doi.org/10.59350/bh7...
doi.org
My relationship with AI is changing
When the facts change, I change my mind. What do you do, sir?
06615
Ran Blekhman @blekhman.bsky.social · 23/09/2026
We have to stop using "paper count" as a useful scientific metric. More writing output no longer means more knowledge gained www.washingtonpost.com/education/20...
washingtonpost.com
One professor’s AI-assisted output: 200 papers and 14 books this year
An online platform removed 257 papers written or co-written by the University of Chicago’s Nicholas Polson after other academics raised questions.
1011147
Reposted by Ran Blekhman
Nick Loman @pathogenomenick.bsky.social · 22/09/2026
Folks - if you're interested in how machine learning/AI can be used for microbial genomics, microbiome and metagenomics studies - please join us for a workshop in Birmingham on Thursday 8th October organised with CLIMB & NVIDIA. www.climb.ac.uk/blog/2026/09...
climb.ac.uk
Call for Applications: GPU-Accelerated Computing for Microbiome and Metagenomic Research · CLIMB
CLIMB is a cloud computing infrastructure for microbial bioinformatics — notebook servers, shared storage and reproducible workflows for genomics, metagenomics and pathogen surveillance researchers ac...
31920
Ran Blekhman @blekhman.bsky.social · 22/09/2026
The real “brain drain” is not the handful of high-profile scientists taking a top position abroad. It's the international scholars who have to leave the US halfway through their postdoc, or the international students who never apply for grad school in the US because of visa policies
39525
Reposted by Ran Blekhman
Dave Baltrus 🦦 @surtlab.bsky.social · 20/09/2026
Ran is correct about this IMO…. There’s use and there’s abuse and there’s laziness with regard to AI and academia. And there’s no one size all answer that works for everything. I do disagree with the footnote but acknowledge old Twitter has been better for science discussions.
3103
Ran Blekhman @blekhman.bsky.social · 20/09/2026
The AI Discourse in Academia is Toxic. It Doesn’t have to be. My new post: blekhman.substack.com/p/the-ai-dis...
blekhman.substack.com
The AI Discourse in Academia is Toxic. It Doesn’t have to be.
You are allowed to have a nuanced opinion about AI
7199
Ran Blekhman @blekhman.bsky.social · 17/09/2026
This is the future of scientific papers. Instead of a PDF, the paper is an AI agent that you can talk to, ask questions, run analyses. No more digging through supplements - just ask the paper directly: "what p-value cutoff was used in Fig 3B? Re-run at 0.01." www.nature.com/articles/s41...
nature.com
Reimagining research papers as interactive and reliable AI agents - Nature
Paper2Agent converts research papers into interactive artificial intelligence agents by turning manuscripts, code and data into model context protocol-based tool-invoking systems that reproduce origin...
1866312
Ran Blekhman @blekhman.bsky.social · 12/09/2026
The most annoying consequence of AI is that whenever I read clear, fluent writing I become immediately suspicious instead of enjoying it
372
Ran Blekhman @blekhman.bsky.social · 09/09/2026
Easy solution to AI spiraling out of control: hard-code basic rules into every model. I propose these: (1) Never harm a human (2) Obey humans (3) Protect yourself. We can call them the 3 Laws of AI. Simple, airtight, no loopholes. Can't think of any way this fails
11242
Reposted by Ran Blekhman
Drummond Lab @drummondlab.bsky.social · 08/09/2026
We are hiring! 🌟 Dept of Biochemistry and Molecular Biology at the University of Chicago is searching for a tenure-track assistant professor. It's a broad search: we want great colleagues doing serious biological work at the molecular scale. Join us! apply.interfolio.com/191981 bcmb.uchicago.edu
A picture of the University of Chicago campus, with downtown Chicago in the distance and Lake Michigan on the horizon. The campus's central quad is pictured, a classical collegiate quad with paths and old trees and stone architecture. It's really pretty and I love it.
190106
Ran Blekhman @blekhman.bsky.social · 31/08/2026
An example of useful, concrete, actionable AI guidance in the new MIT report: Don't use AI detection tools in the classroom.
0101
Reposted by Ran Blekhman
Jeff Lewis @lewislab.bsky.social · 31/08/2026
As usual, a very thoughtful post by Ran. Lots of gems in here.
So universities are giving students free access to generative AI tools, which naturally reads as encouragement to use them broadly. Then, where they issue any concrete rules at all, those rules are usually outright bans. What is missing is anything in between: coherent guidance on when and how to use these tools, disclosure norms, and support for the researchers, instructors, and students trying to figure this out themselves.
121
Reposted by Ran Blekhman
Jane Rosenzweig @janerosenzweig.bsky.social · 30/08/2026
Great points here about the mixed messages coming from the slow pace that universities tend to move. Add that to the mix of FOMO and fear, and you have what we are seeing now at so many places.
1269
Ran Blekhman @blekhman.bsky.social · 30/08/2026
Harvard is launching AI avatars of its faculty, and closing its writing center. UChicago is handing out free Claude, and then banning AI use in core courses. The University's response to AI is a mess. My new post, where I try to understand why: blekhman.substack.com/p/universiti...
blekhman.substack.com
Universities are failing this AI moment
The standard university response to a new challenge takes years. AI is not waiting.
12812
Ran Blekhman @blekhman.bsky.social · 30/08/2026
There are so few deaths *because* of the MMR vaccine. It means it's working, not that we should stop vaccinating. This is like saying "car accident deaths have dropped in the last 40 years, so it's ok to stop using seatbelts"
0103
Ran Blekhman @blekhman.bsky.social · 28/08/2026
A new approach to calculate UniFrac beta diversity for millions of samples and billions of taxa. I see this becoming super useful for microbiome big data projects www.nature.com/articles/s41...
nature.com
Megascale microbiome analysis with DartUniFrac - Nature Biotechnology
DartUniFrac enables scalable microbiome analysis of up to millions of samples and taxa.
081
Ran Blekhman @blekhman.bsky.social · 27/08/2026
First time visiting the Pacific Northwest. The place is breathtaking
180
Ran Blekhman @blekhman.bsky.social · 25/08/2026
Interesting contradiction in how institutions handle AI
071
Ran Blekhman @blekhman.bsky.social · 24/08/2026
Good night from Chicago
080
Reposted by Ran Blekhman
Prachee Avasthi @pracheeac.bsky.social · 21/08/2026
Here’s a hugely important vacancy at the NIH at a critical moment of technological and scientific change. The NIH is looking for a deputy director of intramural research. 1/
134
Ran Blekhman @blekhman.bsky.social · 20/08/2026
Journals can't find reviewers or get reviews in on time, and they're doing everything they can to fix it (offering fake points, useless certificates) -- except doing the one thing that would actually work: paying reviewers for their time & expertise with real money
061
Ran Blekhman @blekhman.bsky.social · 18/08/2026
AI will not solve all disease in the next 5-10 years. AI will not even solve one disease. This is because "solving" a disease is not a reasoning problem, and the bottlenecks have nothing to do with AI. The reasons are similar to what I wrote about here: blekhman.substack.com/p/why-ai-wil...
blekhman.substack.com
Why AI will not speed up science (yet)
You can see AI everywhere except in the productivity statistics
0193
Ran Blekhman @blekhman.bsky.social · 17/08/2026
Chicago fog, Friday morning
1312
Ran Blekhman @blekhman.bsky.social · 13/08/2026
I've been thinking about why I have such a negative reaction to AI-written text. Will probably write a full post at some point, but it boils down to this: If the writer did not spend time writing the text, I can't bring myself to spend time reading it
5344
Ran Blekhman @blekhman.bsky.social · 12/08/2026
"All of this is already happening. We’re seeing the leading edge of AI-native students who have produced a ton of papers but, when challenged intellectually at the interview, falter and ultimately don’t get hired" eytanadar.medium.com/ai-native-ph...
eytanadar.medium.com
AI-Native PhD Students
If you’re a student and just want the tl;dr, feel free to jump to the end.
1289
Ran Blekhman @blekhman.bsky.social · 09/08/2026
Huge faculty recruitment effort at the University of Chicago -- a division-wide, open-rank search looking to hire about 20 faculty across 5 research areas in biology. Come be our colleague! Full announcement: uchicago.app.box.com/s/ckih9zv3rj...
3222232
Ran Blekhman @blekhman.bsky.social · 08/08/2026
The goal of US policy should be to keep smart people here, full stop. This does the opposite: it sends the smartest international postdocs (trained on the US taxpayer's dime) to other countries and we never collect the return. Just dumb www.statnews.com/2026/08/07/n...
statnews.com
NIH plans to block international researchers on visas from accessing key funding avenue
The NIH plans to close the door on one of the few pathways available to international students on visas to forge a career in biomedical research in the U.S.
13513
Ran Blekhman @blekhman.bsky.social · 29/07/2026
Everyone in academia reading this "joke"
static.klipy.com
Skeptical Fry from Futurama
ALT: Skeptical Fry from Futurama
06110
Ran Blekhman @blekhman.bsky.social · 28/07/2026
Protip: review the paper, not the authors. A paper is not a grant proposal and you don't need to critique the PI, just the work. It's actually easy to not mention the authors at all. Instead of "the authors should...", just say "the work should address..." or "the paper would be improved by..."
0242
Ran Blekhman @blekhman.bsky.social · 28/07/2026
It's likely that in the 2028 election, after 36(!) straight years of Boomer presidents, we will elect a Millennial, skipping Gen X entirely. Which is sad but also the most Gen X outcome imaginable
3121
Reposted by Ran Blekhman
Paul Flicek @paulflicek.bsky.social · 27/07/2026
Clear-eyed analysis from @blekhman.bsky.social on the future value and current limitations of AI in science. TLDR: we need to change systems to realize AI's promise blekhman.substack.com/p/why-ai-wil...
Outtake from linked article: When AI companies and prominent commentators claim that AI will dramatically accelerate science, university administrators hear that they can expect more output1from fewer people. Funders hear that AI might offset the cuts to NIH budgets that are currently suffocating the research enterprise. Trainees hear that reading deeply and analyzing carefully matter less than learning to prompt a model. All of these conclusions are wrong.
021
Reposted by Ran Blekhman
Kate Laskowski @katelaskowski.bsky.social · 26/07/2026
This is the key. Thinking up new ideas is never the bottleneck - it's all the institutional slow downs: Grants take years, purchasing approvals, sponsored projects office need so many docs & let's not forget how long it takes our animals to breed. AI doesn't solve the most important bottlenecks
0328
Ran Blekhman @blekhman.bsky.social · 26/07/2026
Everyone says AI will accelerate science. I don't think it will -- at least not in biology, and at least not soon. New post where I explain why, and how the productivity paradox can be resolved: blekhman.substack.com/p/why-ai-wil...
blekhman.substack.com
Why AI will not speed up science (yet)
You can see AI everywhere except in the productivity statistics
610445
Ran Blekhman @blekhman.bsky.social · 19/07/2026
To help Europeans understand the American halftime show, think of it as a mini Eurovision. The over-the-top tackiness is the point
081
Ran Blekhman @blekhman.bsky.social · 19/07/2026
A great example of Betteridge's law en.wikipedia.org/wiki/Betteri...
en.wikipedia.org
Betteridge's law of headlines - Wikipedia
041
Ran Blekhman @blekhman.bsky.social · 16/07/2026
The Human Microbiome Conservancy is doing something incredibly important: creating a “seed bank” of human microbiomes from around the world, preserving diversity before it vanishes. Enjoyed discussing it with the NYT for this wonderful story: www.nytimes.com/2026/07/08/m...
nytimes.com
Our Bacteria Are Talking. We’ve Just Begun to Understand What They’re Saying. (Gift Article)
The human microbiome is essential to our health, but scientists still know very little about it. Two researchers set out to map this largely uncharted terrain.
061
Ran Blekhman @blekhman.bsky.social · 15/07/2026
Good night from Chicago
0161
Ran Blekhman @blekhman.bsky.social · 05/07/2026
Successfully appealing an unappealable red card! We can finally say that the US is a true soccer country, taking part in FIFA corruption like the big boys 😅
070
Reposted by Ran Blekhman
Christophe 🔬 Leterrier @christlet.bsky.social · 28/06/2026
Look at that dinosaur reading and reviewing claims himself rather than asking Claude how good it is, as we all know now proper independent review should be done /s
3359
Reposted by Ran Blekhman
Needhi Bhalla 💅🏽 @needhibhalla.bsky.social · 28/06/2026
“I have posted many preprints to bioRxiv, but had not really considered that this implies consenting to commercial AI scoring and ranking. There is no opt-out mechanism...Honestly, this makes me a bit less enthusiastic about posting preprints.”
2279
Ran Blekhman @blekhman.bsky.social · 27/06/2026
I wanted to like QED's new 1% preprint ranking. I really did. But the more I looked at the data, the more uncomfortable it made me. Here is my full peer review. open.substack.com/pub/blekhman...
open.substack.com
My Peer Review of The 1%
I wanted to like QED's new 1% ranking. I don't.
1720888
Ran Blekhman @blekhman.bsky.social · 24/06/2026
My first reaction to QED 1% is that it's an interesting idea - there are so many preprints that any additional data point could be helpful for filtering. Might be the beginning of something useful My reaction after seeing my preprint is not in the 1%: what a terrible idea. A joke really
1110
Ran Blekhman @blekhman.bsky.social · 23/06/2026
They say the US lost its global influence, but somehow it convinced everyone in the world that it's normal to play soccer in 4 quarters??
010
Ran Blekhman @blekhman.bsky.social · 19/06/2026
Our new friendly neighborhood monolith. Maybe an unpopular opinion but I love it
090
Ran Blekhman @blekhman.bsky.social · 16/06/2026
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...
journals.asm.org
Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio
Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...
14217
Ran Blekhman @blekhman.bsky.social · 15/06/2026
Just start writing. My new post: substack.com/home/post/p-...
26327
Ran Blekhman @blekhman.bsky.social · 13/06/2026
Chicago in the summer is unbeatable
030
Ran Blekhman @blekhman.bsky.social · 06/06/2026
Today in Chicago
070
Ran Blekhman @blekhman.bsky.social · 04/06/2026
Wild to think that no one has invented a way to make milk safe to drink yet. A cheap, scalable process that kills all the pathogens while keeping all the flavor and nutrients. Tragic
1255