Executive Editor at Life Science Alliance: https://nitter.cf/t.co/RCS3L4PRC9 Now with even less Musk: https://nitter.cf/t.co/C7i7rnBOT0
New York, NY
Joined June 2008
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Writing about negative data was fun because I read a bunch of Stephen Jay Gould, plus a related commentary by Howard Bowerman.
Both provided fantastic examples outside cell biology and biomedicine that perfectly highlight the universality of this issue:
timisstuck retweeted
Scientific Reports on hold in PubMed while NLM reevaluates journal
Scientific Reports, published by Springer Nature, has around 50 full-time deputy, senior and associate editors, and more than 11,000 editorial board members. Its article processing charge is $2850.
retractionwatch.com/2026/10/…
timisstuck retweeted
A very interesting, and IMO mechanistically plausible, argument. It the sort of argument scholars of AI in science *could* be measuring/testing but currently aren't
Important result on ~one~ of the multiple functions of peer review.
A lot of studies on AI in peer review don't consider time spent vs human review. I think it is a huge feature so its inclusion here is really valuable, even if it is generally expected.
Lots of debate this week on whether journals should ban AI in peer review.
We actually tested this in our new preprint, and the results were pretty clear to me.
For context, I've reviewed for most of the big journals and evaluated 1,000 human reviews as an editor. I love to read and evaluate science.
TLDR: From now on I won't do any peer review without AI. For clinical trials, I'd even call human-only review dangerous 🧵
It seems non-controversial that if a reviewer *fully* abdicates their peer review to AI, that is a no-no.
If the journal is asking a human to review, they presumably want the human's judgement.
As @anshulkundaje agrees, the best use case may be augmenting your review with AI.
This aligns w my experience as an editor:
“AI certainly surfaces useful / good comments, particularly on methods, but many of the comments can be pedantic. Many models also still have terrible judgment about the other aspects that determine a study's value”
Seeing this study being widely re-shared with the take away that now AI >= human in peer review, in every dimension. People need to tone it down a little... This is primarily GPT evaluating Claude's comments. To me, the more useful signal is the 3 past editors of unnamed journals rating human vs Claude reviews, but this is only related to just 10 papers, it's not clear the editors have specific expertise in the paper topics or methods, and it reads as though the editors looked at the reviews but not the actual papers. I know we will need AI in the loop in some fashion to manage the paper deluge. I also realize that AI is already widely used in peer review and it's better to step in to manage / govern that process than let people do whatever they want. In my experience, AI certainly surfaces useful / good comments, particularly on methods, but many of the comments can be pedantic. Many models also still have terrible judgment about the other aspects that determine a study's value, e.g., whether the question is important. We're not yet at the point of ditching the human. Note: I'm pushing back here on the interpretations people are sharing when circulating this work, not the discussion in the paper itself.
timisstuck retweeted
I'm obsessed with these empty clathrin cages people are seeing in neurons, and don't understand why others are not. So I put everything together and wrote a brief review (Current Opinion in Neurobiology, free access for 50 days):
sciencedirect.com/science/ar…
"Wisdom is a slow process; it requires deliberately boiling knowledge over time”
Out now @LSAjournal, a deep meditation on how we get from data collection to a richer understanding of biology. Really grateful for this beautifully written piece by @dokhlab !
Read the whole thing here: life-science-alliance.org/co…
Honestly impressed with how tone-deaf this marketing from @qedScience is!
"Judge the science before you commit to a full read"
Their calm assurance that you should turn off your brain and go with their little number ... insane.
timisstuck retweeted
Congratulations to Karl, Peter, and Georg! Another great example of how basic research - in this case, understanding how an algal cell responds to light - can have an enormous impact on our understanding of something as complex as the brain.
BREAKING NEWS
The 2026 #NobelPrize in Physiology or Medicine has been awarded to Karl Deisseroth, Peter Hegemann and Georg Nagel “for their discoveries concerning light-gated ion channels and optogenetics.”
timisstuck retweeted
In our October issue: Combining two spatial transcriptomics probe sets on the same sample, how epithelial cells remember prior physical constraints, and a novel single-cell translation profiling technique!
hubs.la/Q04z0HPY0
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Haha. Wow glam journals stepping it up a notch. "Open peer review" with redactions. They should charge another 16K for access to the redactions 😆
Human vs murine IL-2?? If you are a mouse T cell, prevailing wisdom says it doesn't matter. But papers on IL-2 species specificity are ~30 years old. Brian Sheridan and colleagues found a modest but persistent survival advantage for murine IL-2 👇
life-science-alliance.org/co…
How the heck do super broad acting antimicrobials actually work?? these authors have some answers.
Drug-induced metabolic remodeling promotes antimicrobial activity in macrophages and extends longevity in vivo
@RSUinfo @RutgersU @RutgersNB @Waksman_Inst
hubs.la/Q04xQYgF0
timisstuck retweeted
I wish we didn’t need these again, but here is the honest version of Anthropic’s biology announcement 🥳🥳🥳
(Caveat: I haven’t worked in bioinformatics for many years.)
The good: Anthropic ran ~950 Claude agents over a large biological sequence database. Claude searched, wrote code, compared sequences and genomic neighborhoods, and found an interesting pattern that apparently had not been noticed before: a known reverse transcriptase associated with another gene and a repetitive DNA array.
That is cool. Automating this kind of open-ended bioinformatics search at scale is useful, and Claude may have found a lead a human would have missed.
But: Claude did not do a biological experiment. It searched databases and analyzed data.
Humans then took the candidate into the wet lab. And the wet-lab result so far is modest: they showed that the repeat array produces short RNAs.
We still don’t know what the system does. No function, mechanism, phenotype, targeting, defense activity, or programmability has been demonstrated.
This is also where the CRISPR framing gets ahead of the result. Right now, “it has some features reminiscent of known programmable systems” is a hypothesis for what to investigate next, not a discovery that it behaves like CRISPR.
And there is a missing baseline: bioinformatics has had tools for finding unusual gene neighborhoods and candidate systems for years. The interesting comparison is 950 Claude agents vs. an expert using the best existing computational pipelines - not Claude vs. someone manually looking through 200,000 sequences.
So my honest announcement would be:
Claude autonomously found an interesting candidate for a previously uncharacterized biological system. A small human wet-lab experiment confirmed that part of the candidate is expressed. We don’t yet know what it does.
That is a good result.
But in a regular biology lab, this isn’t the finished paper. It is the result you show at lab meeting and say: “This looks interesting. Now we need to figure out what the hell it does.”
Maybe that next step leads to a major discovery. But that discovery hasn’t happened yet.
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…
timisstuck retweeted
Every so often I look at who is publishing what, and how often.
When I was looking at the the last three years, I saw that Scientific Reports has more documents indexed on Scopus that any other outlet.
The infographic shows how many documenst have been indexed by Scopus in the last three years, how many documents Scientific Reports has had indexed and how this translates to how many articles they publish each day.
I have also calcuated what this would translate to in revenue if we take the current article processing charge (APC) of $2,850.
These figures should be taken with caution and treated as an upper bound as the APC could have been less a couple of years ago, there may be waivers, individual arrangeements etc.
.. but if this is information is not shared by the publsiher then we can only make our own estimimates.
