Lior Pachter

Yes- in our setup (trying to identify related claims / results via neighbors in a kNN in a latent space) it's similar words / terminology. There are undoubtedly many other causes in other settings right now.

There is a reason for a different word when machines do it. Machines are definitely making an error, and it is a type of error that maybe can be fixed.

At least one can hope.

4/4

We're using the term "paracite" to describe such an error by a machine. Certainly it's happening now. E.g. in the case of UMAPs and my paper with Tara Chari, see this rubbish: www.oreateai.com/blog/navigat... 3/

Yet this paper that cites us makes it sound like we approve of UMAP for certain tasks (just not others). That's not true. academic.oup.com/bioinformati...

This is obviously bad practice, but it can be hard to know if it's accidental error, sloppiness, or deliberate misrepresentation. 2/

The specious art of single-cell genomics Dimensionality reduction is standard practice for filtering noise and identifying relevant features in large-scale data analyses. In biology, single-cell genomics studies typically begin with reductio...

The use of a citation in a way that misrepresents what the authors of the cited paper are saying is not a new AI phenomenon- humans have done it for a long time (and frequently). E.g. in journals.plos.org/ploscompbiol... we were critical of UMAPs arguing they should not be used, period. 1/

Yes. That's exactly right and is exactly what we wrote.

FWIW I agree with @merz.bsky.social on the importance of custom, bespoke, hypothesis driven science. I personally much prefer it to large-scale stamp collecting.

AI hallucinations in science manuscripts are a nuisance. Paranormal citations, or paracites, will be a nightmare.

www.biorxiv.org/content/10.6... (w/ @sina.bio & @lauraluebbert.com).

Peer review is often opaque and confusing. @elife.bsky.social worked to change that.

In a new preprint, we show how eLife’s Publish, Review, Curate model makes it possible to evaluate AI-generated reviews (with OpenEval) against human peer review. w/ @lauraluebbert.com and @lpachter.bsky.social

Watson. Of course.

Join us tomorrow at the #SystemsVirologyJournalClub. @lauraluebbert.com will present her work with @lpachter.bsky.social on detecting viruses at single-cell resolution and uncovering associated changes in host gene expression.

Paper: pubmed.ncbi.nlm.nih.gov/40263451/

The January issue is live nature.com/nbt/volumes/44
/issues/1

On the cover, Luebbert et al. present a method to detect viral sequences in bulk and single-cell transcriptomic data using conserved amino acid domains instead of annotated reference genomes go.nature.com/4lGrSY3

First I'm hearing of DOPRA, love it! "Denial of peer review attack" concept by @lpachter.bsky.social

ChatGPT and the Meaning of Life: Guest Post by Harvey Lederman Scott Aaronson’s Brief Foreword: Harvey Lederman is a distinguished analytic philosopher who moved from Princeton to UT Austin a few years ago. Since his arrival, he’s become one of my …

I highly recommend reading @harveylederman.bsky.social's essay on the meaning of life, the universe, and everything as you ponder the end of 2025, and other things that may soon end as well...

scottaaronson.blog?p=9030

That is what a Denial of Peer-Review Attack looks like (DOPRA: credit to @lpachter.bsky.social for the term) x.com/lpachter/sta...

Time for MM...

Multi-Modal (single-cell genomics)... flip it around... Wicked Witch! 😈

My student Catherine Felce will be defending her thesis @caltech.edu next week. If you're in the area consider attending; it will be a treat!

Cat's recent work:

journals.aps.org/pre/abstract...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...

Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances Evolutionary changes to gene expression are understood to be a major driver of phenotypic divergence between species. Researchers have investigated the drivers of this divergence by fitting evolutiona...

We've got a really cool preprint out in collaboration with @lpachter.bsky.social's awesome student Cat Felce. Using biophysical models and RNA-seq data, we explore the mechanisms of selective constraint on mRNA abundance, finding constraint on decay rate www.biorxiv.org/content/10.1...

When I was 17, I attended a seminar Watson gave about the RNA tie club and their 1954 summer in Woods Hole. During the seminar, the 76 year old shared headshots of young women he took on beach dates. He also showed lab group photos and took the time to point out the women he had harangued for dates.

Separately, I don't understand your final comment: " Exactly what form [genetic determinism] takes in any one case depends on culture, family, temperament — even, a little, your genes."

Can you provide evidence for your (part) genetic basis claim?

Nobel Laureate James Watson, Co-Discoverer of DNA Says "Some Anti-Semitism Is Justified" In January Esquire Magazine Scientist James D. Watson, co-discoverer of the structure of DNA and a Nobel Prize winner, says anti-Semitism is justified, in a recent magazine interview. The ADL called Dr. Watson's remarks about Je...

I read your NYT piece. Is there a reason you didn't address Watson's comment that "some anti-semitism is justified"? I've always wondered what he meant by that, i.e., how much anti-semitism is justified and in what form? And whether it's relevant that Franklin was Jewish?

spme.org/spme-researc...

In 1982, I was in the Jackson Laboratory Research Training Program. As part of the program, we got to attend the Short Course lectures. At the end of one lecture by a young researcher, this old guy very viciously and aggressively lit into him. Turned out that the nasty old guy was Jim Watson.

Report from 1992 in Nature on the cDNA controversy:
www.nature.com/articles/356...

Worth reading Baltimore's report at the time: genome.gov/sites/defaul...

"Consideration should be given to... cDNA maps. The Committee recognizes the many challenges... it is not yet known to what extent eukaryotic cells rely on control at the transcriptional level."

Watson's objection to cDNA sequencing was that the function of the genes was not yet known 👀

A strange take considering he did not have that objection to working on the structure of DNA when the function of DNA was not known.

Venter's paper on ESTs: www.science.org/doi/10.1126/...

One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.

Review of Cold Spring Harbor Laboratory’s Obituary for Dr. James Watson James Watson, who described himself as “not a racist in a conventional way”, has died at the age of 97. Below is a review of an obituary for Dr. James Watson published by Cold Spring Ha…

I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...

James Watson in his own words “Some anti-Semitism is justified” “Whenever you interview fat people, you feel bad, because you know you’re not going to hire them” “Japan should be bombed for d…

Scientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted.
liorpachter.wordpress.com/2018/05/18/j...

No, James Watson was not a "complicated" person. He was a bad person, and also a bad scientist. These racist, sexist statements, his sincere beliefs, are both morally indefensible and scientifically absurd. With every year that passes, let his name fade and Rosalind Franklin's shine the brighter.

In case anyone is wondering if Watson was really THAT bad, @lpachter.bsky.social compiled a list of quotes that are absolutely not for the faint of heart.
liorpachter.wordpress.com/2018/05/18/j...

A plea for academic truth - Journal of Comparative Physiology A In her book Why trust Science?, Naomi Oreskes examines the question of what it means to say that “science corrects itself”, highlighting the importance of the social process of science and specificall...

link.springer.com/article/10.1...