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Never underestimate MIT’s ability to oversell itself. (EDIT: see below, this is directed at the press release, which I perceive to be overstating the achieveme
by cauthon 4y ago
Never underestimate MIT’s ability to oversell itself.
(EDIT: see below, this is directed at the press release, which I perceive to be overstating the achievements presented in the paper, not the quality of the paper itself)
- warent 4y agoCare to elaborate? This just seems like an empty criticism without any value or substance
- cauthon 4y agoSure. A genome-wide perturb-seq experiment is a huge (and expensive) technical accomplishment, but the authors did not "map every human gene to its function". (Nor did they claim to, it's press release hyperbole.) One, there's ~20k protein-coding genes in the human genome, and they screened ~10k, analyzing about 2k (fig 2a). Two, all the functional annotation is based off transcription profiles. They essentially looked for clusters of genes with correlated expression, and assigned function based on genes with previous annotations (fig 2d, S4). It's a good resource, but there's a lot more molecular work to be done to validate the function of these genes.
- timy2shoes 4y ago> Two, all the functional annotation is based off transcription profiles. They essentially looked for clusters of genes with correlated expression, and assigned function based on genes with previous annotations This is an important point, because if you've ever worked with single cell data you'll know that the transcriptional profile is extremely noisy and your transcriptional profile to cell type map has many researcher degrees of freedom. I heard a story about a paper early in the single cell work that started with 53 cell types and after review ended up with 37 cell types. Are those true cell types? Did the experimenters validate that those cell types all performed different functions? Well, of course not. That's way too much work. Then add on technological biases, which make mapping between technologies difficult. I say this because they used a new sequencing technology that appears to have homopolymer bias (https://twitter.com/lpachter/status/1533875723995185153 https://twitter.com/lpachter/status/1533875723995185153), which will bias the gene quantification.
- cauthon 4y ago> I say this because they used a new sequencing technology that appears to have homopolymer bias (https://twitter.com/lpachter/status/1533875723995185153 https://twitter.com/lpachter/status/1533875723995185153), which will bias the gene quantification. I believe they used Illumina for the results presented in the main text and then re-sequenced with Ultima and replicated a subset of the analyses (fig s13). The Ultima proof-of-concept didn't appear to be relevant to the main study/conclusions
- dekhn 4y agoIs there a way to get the parent comment unflagged? The response from the commenter shows they have a lot to contribute, technically speaking.
- cauthon 4y agoThanks. I'll admit the first comment didn't contribute much and apologize for not including my thoughts from the follow-up. I just don't care for these sorts of hyperbolic press releases. It's part of the game, the big players are as good at sales as they are at science, but I've never been a fan of it.
- dekhn 4y agoUseful book that any starting professor should understand, even if they don't want to admit they are playing a game. science-by-press-release is a technique to master if you want to both maximize the impact of your work, and get tenure. https://www.amazon.com/Winning-Games-Scientists-Play-Sindermann/dp/0738204250 https://www.amazon.com/Winning-Games-Scientists-Play-Sinderm...
- Noumenon72 4y agoI have `showdead` turned on in my profile, and I saw this whole comment chain. Will people with it turned off still see the replies?
- wolverine876 4y agoYou can click 'vouch'.
- dekhn 4y agoThanks, I didn't realize you had to click through to the comment to see that.