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/
He came up to chat with me before the presentations. It was extremely awkward- how do you talk to someone who helped cause 300,000 deaths? 4/ theguardian.com/world/2008/nov…
I muttered something, gave my talk, and fled. I felt ashamed afterwards. I still do. This was not a time to be collegial, but to scream "go away!" and to warn the first-year students to get out. I did nothing of the sort. My politeness was cowardice. 5/
Another professor in the department wrote to me afterwards and said "too bad you were paired with Duesberg (but I heard that you fled before he began talking)". I still have the email dated 11/14/'08 and look at it from time to time to remind myself that silence is complicity. 6/
I was also a math professor at the time, and strangely, in that department I had been asked to *vouch* for Duesberg. Why, you might wonder, would someone in *math* care about me vouching for Duesberg? 7/
The reason was that one of Duesberg's strongest supporters, Serge Lang, was a regular visitor to the @UCBerkeley math department. 8/
Lang advocated for Duesberg, and some in the math department thought that as a computational biologist, I would be able to bolster Lang and Duesberg's claims. 😱 9/ link.springer.com/chapter/10.100…
In fact, when I found out what Lang was up to shortly after I joined the department in 1999, and protested, I was scolded and mocked for criticizing a "math genius".
Amazingly, the math department still hosts a "Serge Lange Undergraduate Lectures" series. I've always wondered whether the speakers realize that they are honoring a person who indirectly, but forcefully, helped in bringing about 300,000 deaths in South Africa. 11/
At @Yale Lang's obituary referred to him as an "ethicist" and his HIV/AIDS denialism wasn't mentioned at all. 13/ news.yale.edu/2005/09/26/mem…
Duesberg was active for a few more years after 2008, coming to campus regularly. He is 84 years old now, and still a professor @UCBerkeley. We (California taxpayers) still pay him a salary of 170,600 per year. I guess it is what it is? 14/14 berkeley.edu/directory/resu…
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but I propose an additional platinum standard for one click reproducibility.1/
By "one click", I mean that the entire analysis be reproducible in a (free) interactive online session of @colab (or other similar service). All steps of the analysis, from downloading data to generating figures are then not only automated but accessible for users. 2/
In response to questions & comments by @hippopedoid, @adamgayoso, @akshaykagrawal et al. on "The Specious Art of Single-Cell Genomics", Tara Chari & I have posted an update with some new results. Tl;dr: definitely time to stop making t-SNE & UMAP plots.🧵biorxiv.org/content/10.110…
In a previous thread I talked about the (von Neumann) elephant in the dimension reduction room: t-SNE & UMAP don't preserve local or global structure, they distort distances, and they are arbitrary. Almost everybody knows this but they are used anyway...
There were some interesting technical questions about our work. One question was the extent to which PCA pre-conditioning affects results. We examined this (Supp. Fig. 3). Tl;dr: it's time to stop making t-SNE & UMAP plots (with or without PCA pre-conditioning).
It's time to stop making t-SNE & UMAP plots. In a new preprint w/ Tara Chari we show that while they display some correlation with the underlying high-dimension data, they don't preserve local or global structure & are misleading. They're also arbitrary.🧵biorxiv.org/content/10.110…
On t-SNE & UMAP preserving structure: 1) we show massive distortion by examining what happens to equidistant cells and cell types. 2) neighbors aren't preserved. 3) Biologically meaningful metrics are distorted. E.g., see below:
These distortions are inevitable. Cells or cell types that are equidistant in high dimension must exhibit increasing distortion as they increase in number. Actually, UMAP and t-SNE distortions are even worse (much worse!) than the lower bounds from theory.
While it’s fun to banter about what constitutes a good lab, the part of this that is uncomfortable to discuss is that leaving a bad lab is in many cases near impossible. Few universities offer much support and PIs can and do retaliate, in some cases ending careers.
My first committee meeting of a biology student @UCBerkeley, when I was still a junior prof., resulted in a student breaking down in tears as he told us of abuse his advisor was inflicting on him. We brought this up with the advisor and department.
What happened? A few years later the professor was promoted to chair of the department.
If you're working on spatial transcriptomics, I think you'll find @LambdaMoses' "Museum of Spatial Transcriptomics", which analyzes the field via its metadata, to be an incredibly useful resource. biorxiv.org/content/10.110… 1/11
The museum is organized as a main paper that provides an overview of a book (i.e. the Supplementary Material) which is based on a database of papers in the field compiled by @LambdaMoses. First the database... docs.google.com/spreadsheets/d…
It contains several hundred papers. 2/11
To undertake a comprehensive study of the field, @LambdaMoses read all these papers carefully, starting with "prequel" literature to establish historical context. The database has detailed metadata including a summary of each paper. This timeline is just of the prequel. 3/11
Yesterday I posted a piece about @OrchidInc's polygenic embryo selection. I thought, based on a press release I read, that they were the first company to undertake polygenic embryo selection. 1/ liorpachter.wordpress.com/2021/04/12/the…
The press release started w/ "Orchid, the first preconception system to quantify how a couple's genetics impacts their future child's health, today announced a $4.5M seed round..". It went on to describe the company's polygenic embryo selection product. 2/ prnewswire.com/news-releases/…
I naïvely assumed that Orchid is the first company to embark on polygenic embryo selection, but TIL that is not the case. In fact, more than two years ago, an article in @TheEconomist discussed myome.