Lior Pachter Profile picture
Feb 13 14 tweets 4 min read
This essay by @HeidiRehm is thoughtful and I appreciate that it was difficult to write. But there are several statements in it that are problematic, some are harmful, and since it's being widely circulated I have a few counterpoints. Let's start with the discussion about crying:
@HeidiRehm writes that in her office "no single male has been in tears, they have all been female" and she explains that by suggesting that women are not "in control of [their] emotions", yet men "get angry, raise [their] voices, and become argumentative" in "these situations".
I honestly don't know what she is talking about. I've been a professor for 20+ years. In that role, the first time I saw anyone cry was a woman in a group meeting of a famous PI (I was invited as a guest). She was a postdoc, and presented work she had been doing for >2 months.
The PI started screaming at her at the end of her talk, insulting her results, telling her that she was lazy, and that her work would never land her a Cell, Science or Nature paper. He literally screamed at her to leave the room and get out of his sight.
Yes, she cried, but she had good reason to. I would have cried too if I'd been yelled at like that but that hasn't happened to me, because like most men in academia, I've given hundreds of talks and haven't been yelled at a single time.
But I've seen men cry in front of profs. Once in a qualifying exam on which I was a member, a student did very poorly and failed. He then cried and explained that the father of his fiancee would not allow him to marry her unless he got a Ph.D. He begged us to pass him, in tears.
You know why so many women are crying in academia? Because women are being sexually harassed, verbally harassed, yelled at in groups meetings, told they are stupid, told they are not fit to be scientist, and all this by men in positions of power of them.
They cry because they see their dreams of being scientists fade in moments of abuse that shatter idyllic beliefs science as a search for the beauty and truths of nature.
Not all women experience abuses during their training. Some are lucky- maybe they worked with a good mentor. Maybe they just got lucky. But just look up how many men have been sexually harassed vs. women in the academic sexual misconduct database: …ademic-sexual-misconduct-database.org
Separately, the Broad is an amazing place, but while it may "offer an environment to work together with colleagues on the most challenging issues in science, technology and medicine" I'm not sure it "breaks down the many barriers of individual competition" in the field.
The Broad is *fiercely* competitive; I'm not talking about researchers there, but about the Institute. When the director "reviews" a field writing two founders of it out of history in a case where the Broad has a major COI that's not breaking down barriers liorpachter.wordpress.com/2016/01/18/the…
And frankly, it's not just this aspect of the Broad culture has led to negative competitive issues in several fields. This is not the thread or place to air grievances, but many Broad initiatives are antithetical to collaboration.
Maybe I will, actually, write something soon about Terra. Have you tried downloading data from there recently?
I do agree that Eric's departure is sad.

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More from @lpachter

Feb 14
If you work w/ single-cell RNA-seq & are performing RNA velocity analyses, you might find this @GorinGennady et al. preprint w/ Meichen Fang & Tara Chari of interest. It's a deep dive into the method, and navigation of the 67 pages may be aided w/ this🧵1/
biorxiv.org/content/10.110…
As a starting point, it's worth noting that the two popular packages right now, scVelo (@VolkerBergen et al. from @fabian_theis' lab) and velocyto (@GioeleLaManno et al. from the @slinnarsson and @KharchenkoLab labs), yield discordant results on a simple example (see below). 2/ Image
The inferred directions should recapitulate a known differentiation trajectory from radial glia to mature neurons. However, scVelo reverss the trajectory, despite "generalizing" velocyto & relying on a better model. Also sometimes it's scVelo that works well. So what gives? 3/ Image
Read 27 tweets
Jan 26
Yeah, well, it turns out grandma figured out all of the analysis methods for single-cell RNA-seq. 1/
Grandma figured out pseudotime. 2/ academic.oup.com/bioinformatics…
Grandma figured out that there is interesting geometry underlying gene expression. 3/
academic.oup.com/bioinformatics…
Read 9 tweets
Jan 22
Is a single-cell RNA-seq atlas really an atlas? A short thread about #scRNAseq, maps, and atlantes (yes, the plural of atlas is atlantes! h/t @NeuroLuebbert). 🧵1/
Atlantes must be accurate to be useful, and the vexing question for centuries, namely how to best represent the spherical earth in 2D, is nontrivial. There have been many proposals with pros & cons for each (because the sphere and the plane have different Gaussian curvatures). 2/
In #scRNAseq, atlases of cells have become synonyms with UMAP figures of gene expression matrices (used to be t-SNE but UMAP seems more popular now). Map making from gene expression matrices is more challenging than map making of our 3D world; #scRNAseq is in ~10⁴ dimensions. 3/
Read 26 tweets
Jan 22
Grigory Pereleman was making less than $100/month while working on the solution of the Poincaré conjecture at the Steklov Institute. He won't live forever, but his ideas will.
newyorker.com/magazine/2006/…
His critiques of mathematicians hold true for scientists more generally: "...there are many mathematicians who are more or less honest. But almost all of them are conformists. They are more or less honest, but they tolerate those who are not honest."
The @NewYorker piece is filled with good quotes and anecdotes that many could learn from.

"Speed means nothing. Math doesn’t depend on speed. It is about deep." - Yuri Burago. This is so so true, and not just for math.
Read 7 tweets
Oct 7, 2021
The 17 #BICCN @nature papers on the primary motor cortex in mouse (+some human & marmoset) that were published yesterday are a major step forward in terms of open science for an @NIH consortium. For reference, links to the open access papers are here: nature.com/collections/ci… 1/🧵
First, the #BICCN required preprints of all the papers to be posted on @biorxivpreprint, and as a result the papers were already online 1-1.5 years ago. Of course the final versions now published have been revised in response to peer review. 2/
Speaking of peer review, almost all the papers were published along with the reviews. In combination with the preprints, this provides an unprecedented view of how consortium work is reviewed and how authors respond. Real data for this perennial debate: 3/
Read 17 tweets
Sep 29, 2021
In 2008, as a new professor of molecular and cell biology @UCBerkeley I presented at a seminar series intended to introduce 1st year students to research in the department. Two profs. presented each time, with food beforehand. I was paired with Thai food and Peter Duesberg. 2/
I knew of Peter Duesberg and his HIV/AIDS denialism, but I hadn't realized that he worked @UCBerkeley. We were now colleagues in the same department. 😱 3/
Read 14 tweets

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