Lior Pachter Profile picture
Sep 24, 2020 18 tweets 8 min read Read on X
In response to criticism of the lack of any women on the recent @numpy_team paper, the authors have floated a narrative that this is the result of "societal constraints", and meager origins of the project. The truth does not abide. 1/
Let's start with a bit of history. NumPy has its origins in code developed in the 1990s, with the first official version released by Travis Oliphant (@teoliphant) in 2006. Kudos to him for an important effort; NumPy has had a huge impact on scientific software. 2/
However the idea that all the developers were men because of "societal constraints", that there just weren’t any interested women, and that they’ve always wanted to work with women but just couldn’t because they were not funded... that's just baloney. 3/
In 2006, when he released v1.0 of NumPy, Travis Oliphant was an assistant professor of Electrical and Computer Engineering at @BYU. His research was on applied math / numerical analysis / scientific computing for engineering and biomedical problems. 4/
Taking a look at his publications (scholar.google.com/citations?hl=e…), we see that he has authored 54 papers. In total he has had dozens of coauthors on numerous articles in a variety of areas. Out of his 54 he co-authored with a woman exactly twice 😱. 5/
The SciPy paper has 1 woman out of 33 authors. I leave it as an exercise for the reader to find the other paper that has a single woman author. 6/
Misogyny is not created in a vacuum. @teoliphant was a faculty member in a misogynist department. His department at @BYU had zero women out of 25 faculty when he worked there. 7/ web.archive.org/web/2005102700…
Even today, in 2020, with 24 tenure track or tenured faculty in the department, there is only 1 woman. There is one more woman who is the one and only adjunct professor in the department. ece.byu.edu/faculty 8/
One is reminded of this poster from the math department @byu a few years ago: 9/
Turning to funding, shortly after releasing the first version of NumPy, Oliphant became president of Enthought, which was specifically devoted to supporting and developing NumPy for Scientific Computing. Enthought was not NumPy, but NumPy work supported Enthought’s mission. 10/
There is no doubt that many programmers contributed their time, uncompensated, to NumPy. But NumPy has not been without funding. In 2013, DARPA dished out $3 million for Python “Big Data” development informationweek.com/software/infor… including funding for @teoliphant and Blaze. 11/
This work was done at a company, Continuum, that Oliphant founded for the purpose of developing NumPy, and where he employed key developers of NumPy. Continuum is now called Anaconda.anaconda.com 12/
Meanwhile Oliphant moved on, founding Quansight, where he again employs several key developers of @numpy_team. The leadership team at Quansight is 12 men and 1 woman. quansight.com/about-us 13/
Ralf Gommers (@ralfgommers), who blocked me for talking about the lack of women on the NumPy paper, works for @teoliphant at Quansight. He is the director of Quansight Labs. 14/
All of this is **before* NumPy receives @cziscience funding. And the funding goes to… Ralf Gommers at *Quansight*. Remember “societal constraints” and “volunteers”… give me a break. 15/ chanzuckerberg.com/eoss/proposals…
Is NumPy great software? Absolutely.
Do I use it? Yes (I also listen enjoy listening to Wagner).

Is the lack of women on the NumPy paper just an unfortunate result of societal constraints, a leaky pipeline, and lack of resources of some guys in a garage? I don't think so. 16/
A constructive path forward can taking many forms, but it has to begin with an honest accounting of the past. 17/
The OSS community has done many great things, and it is an amalgamation of many teams and projects so one cannot generalize about it. But the idea that all of it is ethical and equitable is nonsense. 18/

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More from @lpachter

Sep 10
So this plagiarism thing has happened to our lab.. again. This time it's plagiarism of our poseidon syringe pump paper @booeshaghi et al., 2019 in @SciReports:
Text has been plagiarized, as well as figures copied directly here: 1/🧵nature.com/articles/s4159…
ijirset.com/upload/2024/ma…
Here is figure 1 from our paper (LHS) and figure 1 in the plagiarized paper (RHS) published in the "International Journal of Innovative Research" 2/ ijirset.com/upload/2024/ma…

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The text seems to have been rewritten with an LLM. Our introduction (LHS) vs. the plagiarized version (RHS): 3/
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Read 11 tweets
Aug 16
I've checked this paper out, as instructed. I was also interested in the main result for personal reasons: I'm 51 years old. Is it true that I've just gone through a major change? And that another one awaits me in just a few years?

Some comments on the paper in this thread 1/🧵
The main result about major changes in the mid 40s and 60s is shown in this plot (Fig. 4a). First, I redrew it with axes that start at 0, so the scale of change here was clearer. Not as impressive, but maybe it's a thing? 2/
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The authors say that this finding is even corroborated in another study (ref 14). But that's not true. I looked it up, and it shows something totally different (see RHS Fig 3c from ref 14). No change in mid 40s, but a change in the mid 30s, and the real change in the 80s 😕 3/
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Read 17 tweets
Aug 10
I recently posted on @bound_to_love's work quantifying long-read RNA-seq. In response, a scientist acting in bad faith (Rob Patro @nomad421) trashed our work. This kind of mold in science's bathroom is extremely damaging so here's a bit of bleach. 1/🧵
At issue are benchmarking results we performed comparing our tool, lr-kallisto, to other programs including Patro's Oarfish. Shortly after we posted our preprint Patro started subtweeting our work, claiming we'd run an "appallingly wrong benchmark" and that we're "bullies". 2/
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This was followed, within days, by Patro posting a hastily written preprint disguised as research work on benchmarking, but really just misusing @biorxivpreprint to broadcast the lie that our work "... may be repeatable, but it appears neither replicable nor reproducible." 3/ Image
Read 25 tweets
Aug 1
This recently published figure by @Sarah_E_Ancheta et al. is very disturbing and should lead to some deep introspection in the single-cell genomics community (I doubt it will).

It demonstrates complete disagreement among 5 widely used "RNA velocity" methods 1/ Image
This is of course no surprise. In "RNA velocity unraveled" by @GorinGennady et al. in @PLOSCompBiol we wrote 55 page paper explaining the many ways in which RNA velocity makes no sense. 2/ journals.plos.org/ploscompbiol/a…
We're not the only ones to understand how flawed RNA velocity is. The paper from the groups of @KasperDHansen and @loyalgoff is titled "pumping the brakes on RNA velocity". The whole notion of putting arrows on UMAPs is ridiculous. 3/genomebiology.biomedcentral.com/articles/10.11…
Read 6 tweets
Jul 29
I was recently schooled on some Gen Z and Gen Alpha brainrot. Here's a yap about it:

1/🧵
Delulu:

"I just submitted my R01. I'm sure this one is going to finally get funded!"

You're delulu.

2/
Cap:

"Reviewer #3 accepted our paper without revisions no cap!!"

You're capping be for real! 3/
Read 13 tweets
Jul 25
Challenge accepted. Here are a few comments on the paper after starting to wade through its massive content. The paper in question is 1/🧵 nature.com/articles/s4158…
First, the claim that "lower OPC fraction across regions and, in particular, in non-neocortex regions was significantly associated with impaired cognition (Supplementary Fig. 37d)" is not true. Supp. Fig. 37d is below. I've boxed in red the panel the claim is based on. 2/ Image
The R^2 value, i.e. proportion of variance explained is 0.0256. The "significance" claim is based on the reported p-value of 0.0071 which is less than 0.05. However significance vanishes once one corrects for the number of tests performed. 3/
Read 22 tweets

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