These threads are always the same: lots of comments about protein folding, how amazing DeepMind is, how AlphaFold is a success story, how it has flipped an entire field on it's head, etc. The language from Google is so deceptive about what they've actually done, I think it's actually intentionally disingenuous.
At the end of the day, AlphaFold is amazing homology modeling. I love it, I think it's an awesome application of machine learning, and I use it frequently. But it's doing the same thing we've been doing for 2 decades: pattern matching sequences of proteins with unknown structure to sequences of proteins with known structure, and about 2x as well as we used to be able to.
That's extremely useful, but it's not knowledge of protein folding. It can't predict a fold de novo, it can't predict folds that haven't been seen (EDIT: this is maybe not strictly true, depending on how you slice it), it fails in a number of edge cases (remember, in biology, edge cases are everything) and again, I can't stress this enough, we have no new information on how proteins fold. We know all the information (most of at least) for a proteins final fold is in the sequence. But we don't know much about the in-between.
I like AlphaFold, it's convenient and I use it (although for anything serious or anything interacting with anything else, I still need a real structure), but I feel as though it has been intentionally and deceptively oversold. There are 3-4 other deep learning projects I think have had a much greater impact on my field.
EDIT: See below: https://news.ycombinator.com/item?id=32265662 for information on predicting new folds.
A lot of folks on HN end posts about a company with a sentence like “Disclaimer: I used to work for X”. This language (probably taken from contract law or something) is meant an admission of possible bias but in practice is also a signal that this person may know what they’re talking about more-so than the average person. After reading a lot of posts like this, it might feel reasonable for someone to flip the word around say something like “I need to disclaim…” when beginning a post, in order to signal their proximity to a topic or field as well as any sort of insider bias they may possess.
So sure, “I need to disclose” would’ve been the better word choice, but we all knew what GP was saying. It seems pedantic to imply otherwise.
That is synonymous with saying, “I will deny I am a professional structural biologist that works in this field every day.”
The person posting is actually a structural biologist. What they stated was cognitively dissonant with the intent of their post, and that’s what stopped me.
I don’t pay attention to typos or minor usage issues, but in this case, I read two more sentences and said, “What??”
EDIT: Two more things. First, I found the post interesting and useful. I didn’t say anything about breaking the argument.
Second, “I need to disclose…” is the exact opposite of what they said.