zlacker

> The distinction I'm trying to make is that there's a difference between looking at pre-existing data and modeling (ultimately homology modeling, but maybe slightly different) and understanding how protein folding works, being able to predict de novo how an amino acid sequence will become a 3D structure.

Your objection is that alphafold is a chinese room?

What does that matter? Either it generates useful results or it doesn't. That is the metric we should evaluate it on.

>>bawolf+(OP)
Because it's being presented as something that it isn't. It's a better way to analyze data that we got experimentally, and to predict how new data will fit into what we know. It's not de novo understanding, which is the holy grail and what the field is ultimately trying to accomplish. It's Tesla's adaptive cruise control being sold as full self driving. Yes, they are close things - one is an approximation of the other, but being really really good at adaptive cruise control has basically zero carryover to full self driving. FSD isn't a linear progression from adaptive cruise control, and understanding how proteins fold isn't a linear progression from AlphaFold sequence homology/homology modeling. It's not even close to the same thing, AlphaFold doesn't even move the needle for our understanding of how proteins fold, and yet it's sucking all the air out of the conversation by presenting itself like it solved this problem.

It's a really good, fancy model completely reliant on data we already have empirically (and therefore subject to all the same biases as well).

>>COGlor+Of
I'm assuming "de novo" means from first principles?

i really don't think anyone is presenting alphafold as if its a physics simulator operating from first principles.

Like obviously alphafold does not "understand". Maybe i have blinders on for being in the computer field, but i would assume that it goes without saying that a statistical deep learning AI model does not tell us how to solve the problem from first principles.

Like yes, alphafold isn't the final chapter in protein folding and that is obvious. But it seems a stretch to dismiss it on those grounds. If that's the metric we're going with then we can dismiss pretty much everything that has happened in science for the past thousand years.

> re self driving car metaphor

I think this is a bad metaphor for your purposes, because self-driving cars aren't de novo understanding, and arguably do have some carry over from things like adaptive cruise control.