Lior Pachter

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...

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...

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...

YouTube video by Hunting Yellow Pigs Hunting Yellow Pigs

The @HCSSiM program has been an educational gem for decades, leading "to a world where people value the truth and the project of finding the truth". www.youtube.com/watch?v=lnL2...

Happy to share the Biodiversity Cell Atlas white paper, out today in @nature.com. We look at the possibilities, challenges, and potential impacts of molecularly mapping cells across the tree of life.
www.nature.com/articles/s41...

Zbąszyń The mathematician Carl Friedrich Gauss invented the heliotrope for long-distance surveying in 1821. Just a year later, he proved that least squares regression provided the BLUE estimator for data w…

I recently visited the town of Zbąszyń in Poland. I took some time there to reflect on the plight of refugees and to bear witness for the dead and the living. This led me to write something up about its history.
liorpachter.wordpress.com/2025/09/22/z...

Reference-based variant detection with varseek https://www.biorxiv.org/content/10.1101/2025.09.03.674039v1

Brilliant work by Joseph Rich and Conrad Oakes working out the math and implementing wompwomp. It has been submitted to @bioconductor.bsky.social and in the future we may also implement it in Python to facilitate usage with single-cell genomics packages. Any feedback will be appreciated. Thx!

he underlying optimization problems are NP-hard, but for many visualization tasks can probably be solved optimally. It was fun returning to Bryant and Huson's NeighborNet as a good heuristic, but there is certainly room for improvement.

The advantage of organizing with wompwomp is evident in the clarity one sees when tracing, say, the Lannisters vs. Westeros

The improvements produced by wompwomp are evident in the Game of Thrones dataset displayed at the opening of this thread. To the left is the alluvial plot without wompwomp, to the right with wompwomp.

Optimizing alluvial plots Alluvial plots can be effective for visualization of multivariate data, but rely on ordering of alluvia that can be non-trivial to arrange. We formulate two optimization problems that formalize the ch...

The underlying optimization questions turned out to be really interesting. The methods underlying wompwomp are described in the accompanying preprint on @cscg-bot.bsky.social. arxiv.org/abs/2509.03761

Work on wompwomp was motivated by plots made for this paper, where we first implemented a naïve approach to optimizing an alluvial plot (Fig. 1 panel D)
bsky.app/profile/alii...

wompwomp sorts columns and blocks within columns to best reveal structure in data. For instance, this is a comparison of clustering algorithms viewed in a randomly organized alluvial plot, fixed columns (only blocks sorted), and fully optimized with wompwomp.

In a new work with Joseph Rich and Conrad Oakes we tackle the problem of how to best organize alluvial plots. We formalize two optimization problems and develop a solution for them based on the neighbornet algorithm, implemented in the program wompwomp: github.com/pachterlab/w...

Glacial area reduced by 41.6% from 1896 to 1921. Between 2015 and 2021, the rate at which Mount Rainier glaciers were losing area was more than two times faster than the rate estimated for the period of 2009 to 2015.

irma.nps.gov/DataStore/Do...

I took this photo on July 26, 2025.

This is a good article and I completely agree with its argument for comprehensible research.

Is there such a device?