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...

Good night from Chicago

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 😅

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

“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.”

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...

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

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??

Our new friendly neighborhood monolith. Maybe an unpopular opinion but I love it

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/...

Just start writing. My new post: substack.com/home/post/p-...

Chicago in the summer is unbeatable

Today in Chicago

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

Visited the grand canyon last year and a rainbow appeared *inside* the canyon

Reminder: giving an AI the prompt "You are a world expert in X" doesn't make it a world expert. It doesn't give the model additional knowledge or improve its reasoning. All it does is change the *style* of the output, so it sounds like an expert, even when it's wrong.

Chicago riverwalk, memorial day weekend

Wabash Avenue bridge, Chicago, today

Five Things (May 23, 2026): AI in life sciences. doi.org/10.59350/810...

What you see in the Sun, is the Chicago skyline from the Indiana Dunes beach, across Lake Michigan. You can see it from 50 miles of distance due to a form of superior mirage, because the skyline is seen above where it's actually located. [📷 wesskywalker]

"This is why LLM AI will not solve cancer or climate change. Those problems require long time horizons, willingness to fail publicly, cooperations across competitors, and subordination of short-term returns to outcomes that may take decades to materialize." www.tomorrowsmess.com/p/the-fox-an...

me checking eRA Commons:

Some thoughts on where AI in genomics stands right now, building on a symposium we recently hosted at UChicago. Seven points, ranging from why scaling DNA models hasn't delivered, to why metadata is the real bottleneck, to the weird backlash against AI in academia open.substack.com/pub/blekhman...

good morning

reading about people taking ivermectin for hantavirus and the stories are really heartworming

Happening today!!

🔬How do clinical exposures shape the gut microbiome, and how do longitudinal clinical–microbiome signatures predict patient outcomes? Come find out at my poster #194 today at 7:30 pm at @cshlmeetings.bsky.social Biology of Genomes 2026! #bog26 @blekhman.bsky.social

Fabulous day in Chicago. Feels like summer 🌞

🧬 AI in Genomics Symposium next week! We're bringing together leading scientists from across academia and industry pushing the boundaries of AI in genomics research Join us May 8 at the University of Chicago - KCBD Auditorium, 9:30–5:00, reception to follow. No registration needed!

My take is that "Competitive but not discussed" is essentially not competitive. Meaning, these will not be funded. Program Officers are struggling to fund even highest scoring proposals right now. I don't see a world where C-NDs are even considered.

This is totally reasonable and normal and not a bubble www.cnbc.com/2026/04/15/a...

Cool new study -- they used historical water and well water fluoride levels across Wisconsin counties, and linked these to IQ and cognition from age 16 all the way to age 80. Guess what they found? No association between fluoride levels and cognition - at any age www.pnas.org/doi/full/10....

I'm moving to Purdue University as a tenured professor this summer! Excited to hire postdocs there and get a lab up and running with @runxishen.bsky.social as co-lead. More details: www.linkedin.com/posts/anneca...

Visited Zion National Park for the first time - impossible to convey how beautiful it is

Sean Davis & I are hiring a postdoc to work on turning massive public biological data collections into reusable engines for discovery. #ML / #AI + large-scale omics + open software Details + apply: cu.taleo.net/careersectio... seandavi.github.io | thekrishnanlab.org @cubiomedinfo.bsky.social

I'm generally a fan of AI, but I just don't see how this is going to improve polling. Will just make an already messy data even more biased and problematic

“first drafts of Results, Discussion, and Introduction should be the trainee’s own work. AI can help with grammar…tightening prose…critiquing the logic of an argument you’ve already made. But the hard part of forming the argument needs to be yours.’ blekhman.substack.com/p/you-need-t...

A lab using my recent articles on AI use during PhD training doi.org/10.5281/zeno... & doi.org/10.5281/zeno... to kickstart a discussion and draft guidelines for their group is exactly the kind of use I hoped these articles would inspire! Highly recommend reading Ran's post.

I wrote about why every lab should have AI use guidelines, and how to do it. open.substack.com/pub/blekhman...

After 13 years, the Blekhman Lab has a new website: blekhmanlab.org The old one was hand-coded HTML from my first week as a faculty member. It... showed its age. This one was built with Claude Code. Progress on multiple fronts.

Southern Utah countryside

"AI scientists are building ever-larger models, and then claiming that each model can solve even more than the previous one. Then, model in hand, they go around looking around for problems to solve" stevensalzberg.substack.com/p/ai-is-star...

Layers. Today in Chicago

Predicting host sex from metagenomic data Cool approach that uses the "host contamination" reads in shotgun metagenomic data, and (using as few as 450 reads) can accurately predict host sex. Works well across different host species and body sites www.biorxiv.org/content/10.6...

Project Hail Mary is one of my favorite books of the last few years, but it was hard to suspend disbelief with some of the story lines. Like that the main character is a PhD microbiologist who is also an expert in physics. Impossible

We're searching for the next Director of the Duchossois Family Institute at UChicago The most exciting leadership role in microbiome science right now: lead faculty, cutting-edge cores, and an FDA-approved facility for microbiome therapeutics Email/DM me if interested apply.interfolio.com/182203

Something that keeps happening recently: I open an email (or essay, cover letter, whatever), within 0.5 seconds recognize it's AI-written, then I delete it immediately. Anyone else's brain developed this new pattern recognition skill?

Leipzig U and the MPI for Evolutionary Anthropology (MPI-EVA) have an open faculty position (W2) in evolutionary population genetics! This position is tenured and comes with generous core funding. We are eager to welcome a new colleague! Deadline March 11. www.uni-leipzig.de/en/newsdetai...

Got 5 NIH study section invitations in one week. For 5 different panels in May. Never happened before. Not sure what's going on but feels like there is a serious strain on the system.