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David Crotty

@dacrotty.bsky.social
1.5K followers 254 following 896 posts

Executive Director, Cold Spring Harbor Laboratory Press. Head Chef at The Scholarly Kitchen. Ex-Publishing Consultant, Ex-Editor-in-Chief, Ex-Scientist, Ex-etc. All opinions my own.

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Reposted by David Crotty
Alejandro Montenegro @aemonten.bsky.social · 6h
A new issue of CSH Protocols is out! @cshlpress.bsky.social The cover image highlights the work by Zimina et al., who summarize various approaches for examining meiosis & meiotic recombination in maize, & introduce a set of accompanying protocols to study meiosis in this species🌽 ⬇️Links below
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Jennifer Ouellette @jenlucpiquant.bsky.social · 7h
Tiny image sparks big backlash in Nikon photo contest. Dr Ning Xu denies he broke the rules of Nikon's annual Small World In Motion contest. www.bbc.co.uk/news/article...
bbc.co.uk
Tiny image sparks big backlash in Nikon photo contest
Dr Ning Xu denies he broke the rules of Nikon's annual Small World In Motion contest.
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Damon K @dadadrummer.bsky.social · 30/09/2026
I thought this weirdness about copyright needed to be pointed out dadadrummer.substack.com/p/rough-music
dadadrummer.substack.com
Rough Music
Chalking the line between music that uses machine learning, and GenAI
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Lisa Janicke Hinchliffe @lisalibrarian.bsky.social · 28/09/2026
They do. But they also say authors should submit their own work, declare funding and COIs, etc. So, you know. 🤷🏼‍♀️ As long as we look to journals to catch bad behavior rather than the field to deal with it (shame, censure, expulsion, etc), well, 🤷🏼‍♀️.
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Carl Zimmer @carlzimmer.com · 27/09/2026
Four days ago, a scientist was surprised by the news that Anthropic discovered new virus genes for making DNA. He says he’s been studying them for years—and feeding his data to Anthropic’s AI as part of his own research. Coincidence? Here’s my story. nyti.ms/3VSWayc
nyti.ms
Did Anthropic’s A.I. Really Make a Scientific Discovery on Its Own? (Gift Article)
An expert at the University of Copenhagen said his team had been sharing its research with the company’s A.I. model, Claude, and that its new finding matched their work.
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Josh Marshall @joshtpm.bsky.social · 28/09/2026
These sound like non-trivial problems.
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Chris Lintott @chrislintott.bsky.social · 27/09/2026
On similar lines, if we’re not careful: A. Scientific journals will only accept submissions from established researchers working within institutions. B. Data we’ve spent ages making open will be hidden to avoid the expense of continued download by bots.
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McSweeney's @mcsweeneys.net · 27/09/2026
"I don’t know about you, but I can’t wait to get my hands on some fucking gourds and arrange them in a horn-shaped basket on my dining room table. That shit is going to look so seasonal." buff.ly/pykYN6f
buff.ly
It’s Decorative Gourd Season, Motherfuckers
For the seventeenth year: Welcome to autumn, fuckheads.
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David Crotty @dacrotty.bsky.social · 27/09/2026
On craft, AI, and what gets lost when we skip the slow part (gift link) www.nytimes.com/interactive/...
nytimes.com
Opinion | A.I. Shortcuts Are Ruining How We Think (Gift Article)
Anything worth remembering came from a person who did not know where she or he was going until arriving.
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Alejandro Montenegro @aemonten.bsky.social · 24/09/2026
I'm shocked, SHOCKED! www.nature.com/articles/d41...
nature.com
Hundreds of ‘free’ academic journals have started charging fees
A study tracking diamond open-access journals has found an increase in titles switching to other publishing models — especially over the past few years.
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David Crotty @dacrotty.bsky.social · 24/09/2026
For those who attended Silverchair's #strategies26, the articles I mentioned during the panel I was on are as follows: AI and reading and Foxes and Hedgehogs here: scholarlykitchen.sspnet.org/2026/09/23/a...
scholarlykitchen.sspnet.org
AI and Scholarly Reading: Foxes versus Hedgehogs - The Scholarly Kitchen
Some readers are foxes, and some are hedgehogs. What kind of reader is AI, and how will that impact both the practice of science and the business of journal publishing?
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Leah McElrath @leahmcelrath.bsky.social · 24/09/2026
AP Stylebook warns against anthropomorphizing AI systems: “Avoid language that gives them human characteristics… Instead, explain what a system does, how well it performs, who built it and who could be affected by it.”
APStylebook @APStylebook
X.com
Artificial intelligence systems do not think, feel, want or understand. Avoid language that gives them human characteristics. This is called anthropomorphizing, when we ascribe human traits, emotions or behaviors to non-human things, such as animals or inanimate objects.
Instead, explain what a system does, how well it performs, who built it and who could be affected by it.
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Richard Sever @richardsever.bsky.social · 23/09/2026
"one can’t help but think there’s perhaps an unsubtle critique of the academic career and funding system inherent in a prolific researcher publicly stating that their own publications are both too abundant and not worth reading even for their own students" scholarlykitchen.sspnet.org/2026/09/23/a...
scholarlykitchen.sspnet.org
AI and Scholarly Reading: Foxes versus Hedgehogs - The Scholarly Kitchen
Some readers are foxes, and some are hedgehogs. What kind of reader is AI, and how will that impact both the practice of science and the business of journal publishing?
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aj-boston.neocities.org @aj-boston.bsky.social · 23/09/2026
"The author would like it to be made clear that this is not an AI-generated image, rather it is a poorly photoshopped collage of separate stock photos." Hell yeah, brother.
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Society for Scholarly Publishing @scholarlypub.bsky.social · 23/09/2026
AI and Scholarly Reading: Foxes versus Hedgehogs - The Scholarly Kitchen
scholarlykitchen.sspnet.org
AI and Scholarly Reading: Foxes versus Hedgehogs - The Scholarly Kitchen
Some readers are foxes, and some are hedgehogs. What kind of reader is AI, and how will that impact both the practice of science and the business of journal publishing?
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Sabina Pagotto @spagotto.bsky.social · 23/09/2026
A little bit about reading, a lot about how in scholarship the process should be as important as the output. Unfortunately, we were already in a world where output was king way before the AI wave came along and exacerbated all these problems. (500 papers not worth reading!!)
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David Crotty @dacrotty.bsky.social · 23/09/2026
New from me today @scholarlykitchen.bsky.social -- some thoughts on scholarly reading, and what happens if we outsource our information gathering and learning to AI. Also, foxes and hedgehogs. scholarlykitchen.sspnet.org/2026/09/23/a...
scholarlykitchen.sspnet.org
AI and Scholarly Reading: Foxes versus Hedgehogs - The Scholarly Kitchen
Some readers are foxes, and some are hedgehogs. What kind of reader is AI, and how will that impact both the practice of science and the business of journal publishing?
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Sarah Andersen @sarahseeandersen.bsky.social · 22/09/2026
The image is of a four panel comic.
In the first panel we see Sarah, the protagonist, next to a stick figure labeled “AI”. The stick figure says, “my outputs look just like yours now.”
The second panel zooms in on Sarah’s face. Above her we see text reading “I think”.
The third panel zooms in closer on Sarah’s face. Text above her reads “you missed”.
The fourth panel shows Sarah drawing happily in a sunlit room. The text above her reads “the point”.
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Drew Magary @drewmagary.bsky.social · 21/09/2026
“Like everything else online, cooking-recipe searches have been rendered unreliable thanks to SEO-gaming, AI fuckery, and all other manner of digital nonsense.” defector.com/i-fought-a-p...
defector.com
I Fought A Pie And I Won | Defector
Sometimes a recipe leads you astray. It happens to the best of us, myself included. Sometimes a bad recipe will leave you with no recourse. You simply have to accept that you wasted all of your time a...
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@LaBonneLaB @labonnelab.bsky.social · 20/09/2026
Another assault on science. It is relentless... www.nytimes.com/2026/09/20/s...
nytimes.com
White House Moves to Take Control of N.I.H. Grants (Gift Article)
Federal officials are drafting an executive order that would place grants under review by an outside panel, the latest effort to redirect billions of dollars in research spending.
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Richard Sever @richardsever.bsky.social · 20/09/2026
"All corners of academia will soon be flooded with AI-generated research....Maths and CS go first because their entire output is symbol manipulation...Biology comes later not because biologists are cleverer but because the rate-limiting step is physical" giorgio.gilest.ro/the-weimar-o...
giorgio.gilest.ro
The Weimar of knowledge – la bottega
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Hetan Shah @hetanshah.bsky.social · 17/09/2026
AI is screwing up journal papers: Journal editor asks authors of 10 submitted papers to meet and discuss their paper. Of the 7 that showed up, 3 were unable to answer basic questions about the paper and 3 had difficulty when asked further questions on technical details… medium.com/@TmlrOrg/ask...
medium.com
Asking Authors About Their Own Papers
By Nihar B. Shah
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Genes & Development @genesdev.bsky.social · 18/09/2026
We are saddened by the loss of G&D's long-time Editor, Terri Grodzicker. When Terri stepped down as Editor in 2022, friends and colleagues wrote about her contributions to the research community. We are re-visiting these pieces, and thinking of her. ➡️ genesdev.cshlp.org/content/37/1-2.t…
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#BruceSterling @bruces.bsky.social · 17/09/2026
*Before we get all purist about it, how much of "human" DNA is viralized junk-DNA that isn't even people. Quite a lot of, eight percent, maybe even 40 percent *What if I haul out my 40 percent and replace it with USDA-grade rat or fruit-fly, would I be better off www.cshl.edu/the-non-huma...
cshl.edu
The non-human living inside of you | Cold Spring Harbor Laboratory
« Previous Story Next Story » Half of your genome started out as an infection; if left unchecked, some parts of it can turn deadly all over again. The human genome contains billions of pieces of infor...
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Jennifer Regala @jenniferaregala.bsky.social · 18/09/2026
The #sspND2026 meeting never disappoints 💕✨
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Richard Sever @richardsever.bsky.social · 17/09/2026
fascinating. Seems premised on the idea that all papers have code and usable data though. That may come to pass but certainly isn't true now. most do not have code, and outside genomics, etc. the data landscape is highly fragmented, many wet labs still wedded to paper notebooks, etc.
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Leah @leah.myatproto.social · 17/09/2026
nope, nope, no, no and absolutely not
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jamelle @jamellebouie.net · 16/09/2026
"I wrote the piece and Claude found the links relevant to my claims" is, even without the AI, such an admission of poor thinking and argumentation. your claims should emerge from the evidence!
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Richard Sever @richardsever.bsky.social · 15/09/2026
After Terri stepped down as G&D Editor, friends and former colleagues contributed a series of wonderful essays about her for a special issue. I encourage anyone who'd like to know more about her to read them 3/n genesdev.cshlp.org/content/37/1...
genesdev.cshlp.org
Table of Contents — January 1, 2023, 37 (1-2)
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Richard Sever @richardsever.bsky.social · 15/09/2026
Deeply saddened to learn of the death of my colleague Terri Grodzicker. She was an amazing molecular biologist who did fundamental work on adenovirus. Many will know her as the charismatic long-time editor of Genes & Development and organizer of CSHL meetings 1/2 en.wikipedia.org/wiki/Terri_G...
en.wikipedia.org
Terri Grodzicker - Wikipedia
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Kevin Gannon (now a Moo Deng fan account) @thetattooedprof.bsky.social · 14/09/2026
The whole thread, but especially this 👇. Teaching is not simply content delivery, and almost none of the "let's put AI in education" discourse acknowledges that fundamental reality. Probably because it's emanating from everyone except actual teachers.
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@LaBonneLaB @labonnelab.bsky.social · 14/09/2026
Some Rare good news: Judge postpones the DHS rule . restricting international students to 4 years the day before it would have taken effect. International students add so much to our scholarship and economy. storage.courtlistener.com/recap/gov.us...
storage.courtlistener.com
Memorandum & Order – #50 in Presidents' Alliance on Higher Education and Immigration v. United States Department of Homeland Security (D. Mass., 1:26-cv-13799) – CourtListener.com
District Judge F. Dennis Saylor, IV: MEMORANDUM AND ORDER ON MOTION FOR PRELIMINARY INJUNCTION. Plaintiffs' motion for APA § 705 relief, a preliminary injunction, or, in the alternative, summary judgm...
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Laura Helmuth @laurahelmuth.bsky.social · 09/09/2026
FOIAed records show the DOJ accused prominent journals of being “partisans in various scientific debates” & demanded explanations of their editorial processes. www.aip.org/fyi/doj-offi... by @danvergano.bsky.social
aip.org
DOJ Official Queried a Dozen Journals on 'Partisan' Views in 2025
The Justice Department fulfilled the public records request for the letters just as their author departed the agency.
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Alejandro Montenegro @aemonten.bsky.social · 27/08/2026
And not only "magic hands": this also highlights the importance of proper documentation and carefully prepared protocols. We are glad to contribute to this via CSH Protocols.
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Richard Van Noorden @richvn.bsky.social · 25/08/2026
Everyone's talking about Pangram and other AI-detection software like GPTZero. They promise impressive accuracy at spotting AI-written text. Science journals are starting to use them. How good are they? @miryamnaddaf.bsky.social and I take a look for @nature.com 🧵 www.nature.com/articles/d41...
nature.com
AI-detection tools have made huge leaps forward — how good are they?
Scientists and publishers are testing a new breed of software that promises impressive accuracy at spotting AI-written text.
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Greg Pak @gregpak.net · 18/08/2026
Time and time again, generative "A.i." advocates reveal themselves to be focused on product over process. The PROCESS of creative and intellectual work is where everything happens. Writing is thinking. If you're not actually writing, you're cheating yourself of the real value of the process.
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Jennifer Ouellette @jenlucpiquant.bsky.social · 19/08/2026
"Sabotage": Experts, lawmakers blast RFK Jr. for destroying healthcare research arstechnica.com/health/2026/...
arstechnica.com
"Sabotage": Experts, lawmakers blast RFK Jr. for destroying healthcare research
US healthcare is broken. Under RFK Jr., the research agency working to fix it is, too.
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Gavin Schmidt @climateofgavin.bsky.social · 18/08/2026
The difference in utility between the use of ML to tackle big data problems that would otherwise be intractable & the use of LLMs to produce pointless slop is so large they cannot both be usefully described as “AI“. The first is making real progress, the second is dragging us towards the abyss.
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Dan Silverman @dmsilverman.bsky.social · 18/08/2026
I‘m far from an AI doomer, but it is amazing how many serious voices — on LinkedIn, no less! — are sharing stories about how AI slop is quickly becoming one of the top problems they see in academic writing and research “AI will 10x our research!” doesn’t seem to be surviving encounters with reality
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David Crotty @dacrotty.bsky.social · 18/08/2026
Silicon Valley Executives Are Tech Fans. Just Not for Their Own Kids. (Gift link) www.nytimes.com/2026/08/18/t...
nytimes.com
Silicon Valley Executives Are Tech Fans. Just Not For Their Own Kids. (Gift Article)
At home, moderation and restraint are the rule for tech parents. Boredom is exalted. Maybe they’re onto something.
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John Scalzi @scalzi.com · 17/08/2026
"AI" has existed in its current form for barely four years and the fact that it's jammed up the cognitive development of an entire generation that fast (and that there's a specific overclass of techofascists who are deeply thrilled about this) is a big damn red flag. www.nytimes.com/2026/08/17/u...
nytimes.com
What Do Students Lose When They Stop Writing? (Gift Article)
Educators are worried that many students can no longer write essays without A.I. And it’s costing more than just grammar skills.
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Inside Higher Ed @insidehighered.com · 17/08/2026
NIH Proposes Removing Peer Review Scores From Grant Applications bit.ly/4cIBYVi
National Institutes of Health building
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Cold Spring Harbor Laboratory @cshlnews.bsky.social · 17/08/2026
National Nonprofit Day is a perfect time to recognize the invaluable contributions of nonprofits. At CSHL, we have one goal: advancing the scientific community to make lives better tomorrow. Let's take a look at what CSHL has achieved in 2026 so far! #NationalNonprofitDay #ScienceMakesLifeBetter
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David Crotty @dacrotty.bsky.social · 17/08/2026
“there is no part of the writing process that can be handed over to A.I. without some cost” (gift link) www.nytimes.com/2026/08/17/u...
nytimes.com
What Do Students Lose When They Stop Writing? (Gift Article)
Educators are worried that many students can no longer write essays without A.I. And it’s costing more than just grammar skills.
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Julie Novkov @jnovkov.bsky.social · 16/08/2026
Another rule proposal that would undermine competitive peer review in science. If you are in the health sciences or an aligned field, consider submitting a comment.
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Zach Hazard Vaupen @emo-sludge.com · 15/08/2026
"There's nothing ethically wrong with what I'm doing, but for some uh, other reason, I cannot allow anyone to know I'm doing it"
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Richard Sever @richardsever.bsky.social · 13/08/2026
bioRxiv/medRxiv have been dealing with endless bot attacks recently (plus usual DDOS stuff, etc). Tricky to address without impacting genuine users - many of you affected. Apologies. We're working with our hosting service on solutions & think we're getting there [he shouts in his Red Queen costume].
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Simon Davies @simonfd.bsky.social · 12/08/2026
Obviously this is mostly to do with the commercial publisher's enormous marketing budget. But it's also evidence to me that academics, generally, are happy to prop up the extractive publishers, & simply do not care about changing the system. If they wanted to, they have the option to do so.
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Aaron Clauset @aaronclauset.bsky.social · 11/08/2026
Very much agree with Pieris's argument: investing public funds exclusively in research 'applications' (believing that they have greater and more immediate economic value) will destroy the real driver of economic growth: basic science is the *only* economic engine arxiv.org/abs/2608.00172
Money quote from the preprint's conclusion : "The choice being presented to the scientific community — discovery or appli-cation, curiosity or impact — is a zero-sum illusion. The researchers who pursue fundamental questions are the same ones who end up transforming medicine, defence and industry — not because they planned to, but because transformative discoveries do not respect funding categories. Fundamental research is the foundation of the building. No one sees it while the skyscraper is standing, but remove it and everything above comes down."
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David Crotty @dacrotty.bsky.social · 10/08/2026
"Using generative AI inherently exposes you to the risk of career-ending accusations of plagiarism." www.carlsonlab.bio/thoughts/the...
carlsonlab.bio
The only reason you’ll ever need not to write with AI — The Carlson Lab
Over the last year, our lab has been developing a policy on AI use. To do this, we did three main things: We read a lot of academic publications and tech news. We set up an #ai channel on our la...
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