Lior Pachter Profile picture
Dec 11 25 tweets 8 min read Twitter logo Read on Twitter
This speech by @FareedZakaria is a litany of misinformation. There is much to improve at US universities, but his claims are false and unhelpful.

A rebuttal: 1/🧵
The speech begins with the claim that the public has been losing faith in universities because universities are pushing political agendas instead of catering to excellence. But he provides no evidence of a link.

Hypothesis: the main factor is cost. 2/
foxbusiness.com/economy/colleg…
Image
He says that in 2016 70% headed for college vs 62% now. But provides no evidence that it's because of "American universities abandoning focus on excellence... to pursue... DEI".

America is an outlier among all advanced nations in cost of education. 3/
businessinsider.com/how-much-colle…
@FareedZakaria says that DEI started with the best of intensions. That universities wanted to ensure people felt comfortable on campus.

Actually, DEI started in in the 18th century. 4/washingtonpost.com/made-by-histor…
His framing of DEI as being about "safe spaces, trigger warnings, and microagressions" is also a gross misrepresentation. If we're going to talk about DEI in Ivy League schools let's talk about Yale first admitting women in 1968, Princeton 1969, Dartmouth 1972. 5/
Let's talk about rampant sexism in academia in the ensuing years, at every level, from undergraduate admissions to faculty hiring. A glimpse of what academia looked like in the 1980s: 6/washingtonpost.com/archive/opinio…
As for those "microaggressions" that @FareedZakaria dismisses out of hand... let me give one example: the first group meeting I attend was at @LBNLresearch when I was a postdoc in Berkeley. The professor yelled at a student presenting so loudly that he brought her to tears. 7/
Her sin: he didn't like the colors in one of her figures. He was screaming so loudly that you could hear him down the hall.

DEI at universities means many things, including normalizing behaviors that are conducive to study and research for all. That is a very good thing.
8/
@FareedZakaria scolds universities for issuing statements after the George Floyd murder. So are we to just accept this kind of terrorism?

Is this the "excellence in academia" he yearns for?
9/time.com/4568806/univer…
He asserts that the recent Supreme Court decision on that race based admissions shows they have gone too far. With such faith in the courts, and concern for Jewish students (he claims they don't "count" for DEI) does he support this call for genocide? 10/reuters.com/legal/governme…
The reality of universities is that ensuring students are "physically safe but intellectually unsafe" (@FareedZakaria quoting @VanJones68) is difficult. Universities try. Sometimes they get it right, sometimes they don't. 11/insidehighered.com/news/2016/08/0…
And that includes @Harvard, a university, like all others, trying to figure out DEI every day, as it should.

Certainly at times universities go too far. Sometimes not far enough. And leaders are not always up to the challenges at hand. 12/npr.org/sections/ed/20…
But @FareedZakaria also says that lack of political diversity is NEVER addressed, implying that a) universities are not politically diverse and b) they try to maintain that. Has he looked at the courses offered by @Stanford's Hoover Fellows recently? 13/hoover.org/stanford-cours…
Oh, and these are mostly taught by white men. Bringing me to another false claim of @FareedZakaria. He says a white man studying American presidency doesn’t have prayer of getting tenure. Is he worried about Adam McMahon? 14/rider.edu/about/faculty-…
Or Jon Rogowski? 15/


Or any of the other myriad white male professors recently hired to study the American presidency at US universities?iq.harvard.edu/people/jon-c-r…
Maybe he thinks tenured professors such as Charles Cameron didn't get tenure in the first place?

Or Stephen Skowronek? 16/politics.princeton.edu/people/charles…
politicalscience.yale.edu/people/stephen…
Speaking of Yale, @FareedZakaria claims grade inflation is rampant. Perhaps there is a problem, I haven't studied the issue carefully. But maybe also the students are just getting MUCH better.

Yale admissions rate in 2003: 13.8%. In 2022 it was 4.5%

17/yale.edu/about-yale/yal…
Which of course is also why SATs are mostly optional now. First, they are mostly *optional* (not ignored as @FareedZakaria claims). 87.5% have made them optional. And it's not because of DEI. It's because of the pandemic, which made it difficult to administer them. 18/
Yes, 64.7% of schools required SAT pre-pandemic. 34.3% now. But the fact that they are mostly optional means the students from poor background who do well can still use them. Of course, @FareedZakaria doesn't mention that rich students use them to feign qualifications. 19/
The cost of tutoring? In some cases several thousand dollars, and that was years ago.

And BTW, last year something like 30,000 students applying to @UCLA had a 4.0 GPA. This is not the 80s anymore (@FareedZakaria graduated from Yale '86).

20/foxbusiness.com/features/is-sa…
So are DEI initiatives the evil that @FareedZakaria makes them out ot be? I will say that I've seen failed policies in some schools, and mistakes made. But overall there have been many positive aspects to DEI efforts at universities, especially during the past few years. 21/
For example, the formalization of review policies, procedures and rubrics has helped to reduce the effects of sexism and racism in hiring. I was on a hiring committee a decade ago where male faculty would say "I like him, because he was my friend in grad school. He's smart".. 22/
... Now such ad-hoc assists by old boys for their buddies have a check via DEI procedures that require actually evaluating scientific competence. That is really what DEI means in universities right now. With all due respect to @FareedZakaria, I think he is wrong. 23/
I started by noting there is much to improve in universities. We have a huge gun problem that makes learning / teaching at a university terrifying. See
or @UNC just this year
24/cnn.com/2023/03/10/us/…
unc.edu/discover/lates…
Of course we are far from living in a country where every kid, regardless of background, family status, etc. has a fair shot at attending a good university. The moral arc of our universities is riddled with bullet holes. Literally. But it's bending in the right direction. 25/25

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More from @lpachter

Dec 12
🌌The virial theorem relates time-averaged kinetic energy of objects to their potential energy.

🧬The Price equation relates change in a trait over time in subpopulations to their fitness.

In we observe that the virial theorem is the Price equation. 1/🧵arxiv.org/abs/2312.06114
The virial theorem is a 150-year old tool in (astro)physics. First described by Rudolf Clausius in 1870 in connection with studies of heat transfer, it gained prominence after it was used by Fred Zwicky in 1933 to posit the existence of dark matter. 2/
The virial theorem is elementary calculus. For objects w/ mass m_1,..,m_n at positions z_1,..,z_n, velocities v_1,..,v_n, & acted on by forces F_1,...F_n, the virial "theorem" is the identity shown below. S = \sum_i p_iz_i (p_i is momentum), U is potential energy; T, kinetic.3/ Image
Read 15 tweets
Aug 23
A 🧵 on why Seurat and Scanpy's log fold change calculations are discordant. 1/

(based on the Supplementary Notes from ). biorxiv.org/content/10.110…

Image
I first became aware of the discrepancy in LFC reporting by Seurat and Scanpy from a preprint by @jeffreypullin and @davisjmcc:

The result seemed surprising because it didn't seem like calculating log(x/y) = log(x)-log(y) should be complicated. 2/
So what gives?

We have molecule counts X_{ig} where i ranges over cells & g over genes, and we consider two groups of cells G_1 and G_2 containing n_1 and n_2 cells respectively. Let's start with Seurat which calculates LFC according to the formula below. But what is Y_{ig}? 3/ Image
Read 27 tweets
May 2
Actually, not transforming the data outperforms log(y/s+1). 1/
The "performance" in this analysis boils down to checking consistency of the kNN graph after transformation. That's certainly a property one can optimize for, but it's by no means the only one. In fact, if it was the only property of interest, one could just not transform. 2/
Of course that is trivial and uninteresting. The purpose of normalization is to remove technical noise and stabilize variance. But then one should check how well that is done. And as it turns out, log(y/s+1) actually removes too much "noise". 3/
Read 6 tweets
May 2
In a recent preprint with @GorinGennady (biorxiv.org/content/10.110…) we provide a quantitative answer to to this question, namely what information about variance (among cells in a cell type, or more generally many cell types) does a UMAP provide? A short🧵1/
The variability in gene expression across cells can be attributed to biological stochasticity and technical noise. In practice it's hard to break down the variance into these constituent parts. How do we know what is biological vs. technical? 2/
Here's an idea: within a cell type, we can obtain an accurate estimate of gene expression by averaging across cells. Now we can get a lower bound for biological variability by computing the variance across very distinct cell types. 3/
Read 17 tweets
May 2
In 2019 "Single-cell multimodal omics" was deemed @naturemethods Method of the Year, and since then many new multimodal methods have been published. But are there tradeoffs w/ multimodal omics?

tl;dr yes! An analysis w/ @sinabooeshaghi & Fan Gao in biorxiv.org/content/10.110… 🧵1/
There are a lot of ways to look at this question and we have much to say (long 🧵ahead!). As a starting point let's begin with our Supplementary Figure 4. This is a comparison of (#snRNAseq+#snATACseq) multimodal technology with unimodal technology. Much to explain here: 2/ Image
(a) & (b) are showing the mean-variance relationship for data from an assay for measuring RNA and TAC (transposable accessible chromatin) in the same cells. The data is from ncbi.nlm.nih.gov/geo/query/acc.…
Cells from human HEK293T & mouse NIH3T3 were mixed. You're looking at the RNA. 3/
Read 21 tweets
Mar 23
To follow up on this comment by @nilshomer, I wanted to say a few things about why @sinabooeshaghi designed and developed seqspec (just pre-printed here biorxiv.org/content/10.110…), and our hopes for how it can be used for transparency and reproducibility in genomics. 🧵1/
Since the development of sequence census assays by Barbara Wold in her pair of transformative papers in 2007--2008 on Chip-seq and RNA-seq (science.org/doi/10.1126/sc… and nature.com/articles/nmeth…), the use of sequencing for molecular biology has exploded. 2/
Wold and Myers predicted this explosion in 2008, writing "an exciting frontier is just beginning to emerge" and recognizing the importance of "being able to assay the regulatory inputs and outputs of the genome routinely and comprehensively" nature.com/articles/nmeth… 3/
Read 16 tweets

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