Professor of Medicine at @UChicago. Decoding the human microbiome. BlekhmanLab.org

Chicago
What am I missing? Looks like a PhD rotation-level project with marketing hype.
Claude has discovered a previously unknown enzyme system hidden in the DNA of bacteriophages. Beside the enzyme’s gene sits a long array of repeating DNA—a structure that looks somewhat similar to CRISPR. We don’t yet understand what this system does, but only a handful of known systems share its features, and all of them are able to cut, copy, and paste DNA. Historically, the discovery of such programmable systems has helped revolutionize medicine. CRISPR, for instance, is now the foundation of genetic medicines. But it will take much more work to learn what this system does, and whether it can be put to similar use. Read more: anthropic.com/news/claude-di…
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This is exactly why I don't think AI will lead to biology breakthroughs anytime soon. Finding "potentially interesting" DNA sequences is easy -- the real bottlenecks are not computational blekhman.substack.com/p/why-…
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The computational methods are cool though
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The AI Discourse in Academia is Toxic. It Doesn’t have to be. My new post: blekhman.substack.com/p/the-…
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Cool list, but I wouldn't call it biology - very narrow to synbio/protein engineering A real biology Millennium list would include aging, development, immune prediction, host-microbe causality, disease (!). Fun thought exercise though
In light of the progress in mathematics, we at Edison Scientific and FutureHouse have assembled a set of Millennium Problems for Biology. They are chosen to be very hard to solve but very easy to validate in a simple laboratory environment. Any of these, if solved, would mark a major advance in biotechnology, and most of them would contribute materially towards curing disease. These are, in some sense, the “last reasonable eval” for AI in biology. This was work primarily by @MichaelaThinks and myself, with contributions from many others. Short descriptions below. The full descriptions of the problems with acceptance criteria are at the Bio Millennium Problems website, linked in the next post. Share more if you have ideas. If they meet our criteria, we’ll add them to our list (with attribution and permission).
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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: "what's the p-value cutoff in Fig 3B? Re-run at 0.01" nature.com/articles/s41586-0…
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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
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"Scientists spend years writing these proposals" Scientists spend years building expertise, infrastructure, recruiting collaborators, doing actual research, generating preliminary data, getting access to samples, etc. Then spend 2 weeks writing the proposal
I asked Astra to look through my published science, identify new directions, and draft five NIH R01 proposals -- the multiyear, $1M-$2M grants that support much of academic biomedical science. In about one hour, using roughly $20 in compute, it produced entirely reasonable proposals. They were well grounded in my work and structured to appeal to study section reviewers. They looked very similar to what I would write if my goal were to get another grant. Astra reproduced that logic well. It turned existing work into questions, hypotheses, and experiments that would look familiar and defensible to a study section. The output was immediately recognizable as the work of an experienced academic scientist. If AGI means being able to produce the work of highly trained professionals, this is a clear concrete example. It produced something academic scientists spend a great deal of time doing. Academic medical centers build careers, laboratories, and their finances around this process. Scientists spend years writing these proposals as the next fundable extension of their work.
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And the Specific Aims page is just one page in an R01 proposal with hundreds of pages of text. I mean, the writing here is good, but writing the specific aims page is not the hard part of putting together an R01
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Ran Blekhman retweeted
🚨🚨 THE MUCUS IS COMING TO AMERICA!! I'm excited to announce that I will be joining the wonderful @UWMadisonMMI to keep exploring the wonders of mucus! This would not have been possible without @VanessaSperand2 @markjmandel, Federico Rey, JD Sauer and many more at MMI.

ALT Slime Time Party GIF

Please help us welcome our new faculty member Dr. Shai Bel! The Bel lab uses state-of-the-art mouse models, combined with high resolution microscopy and molecular biology to understand how the intestine functions. mmi.wisc.edu/meet-our-resear…
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Ran Blekhman retweeted
"Universities are choosing to see AI as a slow-moving policy question rather than a fast-moving structural emergency. Instead of treating AI like a pandemic, they treat AI like a curriculum revision."
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: substack.com/home/post/p-213…
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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: substack.com/home/post/p-213…
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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 nature.com/articles/s41587-0…
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Weird list. Paris Hilton is included, but no Demis Hassabis, Jensen Huang, or Karpathy?
TIME’s new cover: Announcing the 2026 TIME100 AI, the world's most influential people in artificial intelligence time.com/collection/time100-…
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Ran Blekhman retweeted
Our work is featured on the cover!
New issue is out👉cell.com/cell/current Introducing DANDELION, a method to identify core genes of complex traits, the cover depicts a lung adorned with dandelions and background patterned with ATCG sequences representing application of the framework to reveal new asthma genes
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Good night from Chicago
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Ran Blekhman retweeted
No surprise at all. I try to review only work where I think I can contribute something meaningful, but the frequency of requests has become absurd. In a bit over a year I received 350 review requests. At 3h per review that is 1,050h of my life, or roughly $260k of expert time at $250/h. About six months of full-time work. Instead, what I get in return is a line in my CV saying I reviewed for journal X 😅
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
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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
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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/ckih9…
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