Lior Pachter
@lpachter.bsky.social
Bren Professor of Computational Biology @Caltech.edu. Blog at http://liorpachter.wordpress.com. Posts represent my views, not my employer's. #methodsmatter
Reposted by Lior Pachter
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.
November 8, 2025 at 11:57 PM
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.
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.
November 9, 2025 at 9:41 PM
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.
I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...
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…
liorpachter.wordpress.com
November 8, 2025 at 9:58 PM
I wrote a review of James Watson's obituary by CSHL: liorpachter.wordpress.com/2025/11/08/r...
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...
liorpachter.wordpress.com/2018/05/18/j...
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…
liorpachter.wordpress.com
November 8, 2025 at 4:29 AM
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...
liorpachter.wordpress.com/2018/05/18/j...
Reposted by Lior Pachter
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...
liorpachter.wordpress.com/2018/05/18/j...
November 7, 2025 at 11:44 PM
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.
Reposted by Lior Pachter
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...
liorpachter.wordpress.com/2018/05/18/j...
November 7, 2025 at 10:18 PM
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...
liorpachter.wordpress.com/2018/05/18/j...
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...
Hunting Yellow Pigs
YouTube video by Hunting Yellow Pigs
www.youtube.com
October 3, 2025 at 3:40 PM
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...
Reposted by Lior Pachter
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...
www.nature.com/articles/s41...
September 24, 2025 at 3:12 PM
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...
www.nature.com/articles/s41...
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...
liorpachter.wordpress.com/2025/09/22/z...
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…
liorpachter.wordpress.com
September 22, 2025 at 10:14 PM
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...
liorpachter.wordpress.com/2025/09/22/z...
Reposted by Lior Pachter
Reference-based variant detection with varseek https://www.biorxiv.org/content/10.1101/2025.09.03.674039v1
September 5, 2025 at 4:49 PM
Reference-based variant detection with varseek https://www.biorxiv.org/content/10.1101/2025.09.03.674039v1
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...
September 5, 2025 at 12:20 PM
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.
irma.nps.gov/DataStore/Do...
I took this photo on July 26, 2025.
August 3, 2025 at 10:49 PM
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.
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.
How can we reform science? I have some ideas. But I am not sure you’ll like them, because they don’t promise much. elevanth.org/blog/2025/07...
Which Kind of Science Reform
What hope is there for science reform, if we can't agree on what to reform? Right now, principles are more important than practices.
elevanth.org
July 21, 2025 at 10:58 PM
This is a good article and I completely agree with its argument for comprehensible research.
The confiscation of cell phones from children at schools & summer camps is largely the result of a national campaign by
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
July 6, 2025 at 3:22 PM
The confiscation of cell phones from children at schools & summer camps is largely the result of a national campaign by
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
@jonathanhaidt.bsky.social
But cell phones are safety devices used for notification & early warnings of active shooters, earthquakes, floods, tornados, tsunamis, wildfires, ..
Reposted by Lior Pachter
Many such cases - be on guard against DoPRA (science is complex, but let's not fool ourselves that pre-pub peer review functions in these situations; need a year of post-pub to read these things)
ah here's where I saw it! x.com/lpachter/sta...
June 23, 2025 at 9:00 AM
Many such cases - be on guard against DoPRA (science is complex, but let's not fool ourselves that pre-pub peer review functions in these situations; need a year of post-pub to read these things)
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Reply to: Reply to: False positives in the study of memory-related gene expression
In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…
liorpachter.wordpress.com
June 16, 2025 at 9:31 PM
I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...
Fly connectome, Willow, TOI-715 b, Alphafold3, R21/Matrix‑M, geometric Langlands, O4 run, lenacapavir... just to name a tiny sliver of science last year.. and some people think "science was not vibrant in 2024". 👀
June 12, 2025 at 9:44 PM
Fly connectome, Willow, TOI-715 b, Alphafold3, R21/Matrix‑M, geometric Langlands, O4 run, lenacapavir... just to name a tiny sliver of science last year.. and some people think "science was not vibrant in 2024". 👀
Call for nominations for the Trevisan prize: cs.unibocconi.eu/call-nominat...
Call for Nominations: Trevisan Prize 2025
cs.unibocconi.eu
June 7, 2025 at 7:32 PM
Call for nominations for the Trevisan prize: cs.unibocconi.eu/call-nominat...
Reposted by Lior Pachter
I developed accurate polygenic risk scores at 23andMe using its huge database and can attest to their limitations, I see this craze stemming from a deep ignorance about this topic.
@lpachter.bsky.social wrote an amazing piece on this back in 2021: liorpachter.wordpress.com/2021/04/12/t...
@lpachter.bsky.social wrote an amazing piece on this back in 2021: liorpachter.wordpress.com/2021/04/12/t...
The amoral nonsense of Orchid’s embryo selection
If you haven’t heard about Clubhouse yet… well, it’s the latest Silicon Valley unicorn, and the popular new chat hole for thought leaders. I heard about it for the first time a fe…
liorpachter.wordpress.com
June 4, 2025 at 11:47 PM
I developed accurate polygenic risk scores at 23andMe using its huge database and can attest to their limitations, I see this craze stemming from a deep ignorance about this topic.
@lpachter.bsky.social wrote an amazing piece on this back in 2021: liorpachter.wordpress.com/2021/04/12/t...
@lpachter.bsky.social wrote an amazing piece on this back in 2021: liorpachter.wordpress.com/2021/04/12/t...
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
False positives in study of memory-related gene expression - Nature
Nature - False positives in study of memory-related gene expression
www.nature.com
June 4, 2025 at 5:59 PM
As @neurome.bsky.social and Yu point out, #methodsmatter. They are spot on here: www.nature.com/articles/s41...
George Leitmann, Berkeley professor who authored an iconic textbook on optimal control in the 1960s passed away 2 weeks ago
www.berkeleyside.org/2025/06/03/g...
www.berkeleyside.org/2025/06/03/g...
Remembering George Leitmann, Nazi fighter, Nuremberg interrogator, Cal engineering professor
He was a decorated WWII veteran who helped liberate a concentration camp, a rocket scientist, a leading authority in game theory and the University of California's first ombudsman, in the 1960s.
www.berkeleyside.org
June 3, 2025 at 11:47 PM
George Leitmann, Berkeley professor who authored an iconic textbook on optimal control in the 1960s passed away 2 weeks ago
www.berkeleyside.org/2025/06/03/g...
www.berkeleyside.org/2025/06/03/g...
A win for Arakelov theory.
May 18, 2025 at 11:48 PM
A win for Arakelov theory.
Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social).
His thesis is on software, tools, and methods development for single-cell transcriptomics.
His thesis is on software, tools, and methods development for single-cell transcriptomics.
May 5, 2025 at 12:14 AM
Congratulations to @delaneyksull.bsky.social on successfully defending his PhD (photo below with his committee: Barbara Wold, @mitchguttman.bsky.social, and another of my former students @hjp.bsky.social).
His thesis is on software, tools, and methods development for single-cell transcriptomics.
His thesis is on software, tools, and methods development for single-cell transcriptomics.
Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...
May 4, 2025 at 11:56 PM
Congratulations to Anne Kil on successful defense of her PhD! Her thesis focused on engineering solutions for saliva as a biomedical diagnostic, from improved collection asmedigitalcollection.asme.org/medicaldevic... to assessing the potential of saliva multiomics www.biorxiv.org/content/10.1...