[DrierCycle]

AlphaFold is optimization, not thinking. Propaganda 'r us.

[fredoliveira]

Did you watch the documentary? Would probably fare better if you did, because it'd give you the context for the film title.

[DrierCycle]

I'm an hour into it, unconvinced.

The illusion that agency 'emerges' from rules like games, is fundamentally absurd.

This is the foundational illusion of mechanics. It's UFOlogy not science.

[Rochus]

Not sure why this is downvoted. The comment cuts to the core of the "Intelligence vs. Curve-Fitting" debate. From my humble perspective as a PhD in the molecular biology /biophysics field you are fundamentally correct: AlphaFold is optimization (curve-fitting), not thinking. But calling it "propaganda" might be a slight oversimplification of why that optimization is useful. If you ask AlphaFold to predict a protein that violates the laws of physics (e.g. a designed sequence with impossible steric clashes), it will sometimes still confidently predict a folded structure because it is optimizing for "looking like a protein", not for "obeying physics". The "Propaganda" label likely comes from DeepMind's marketing, which uses words like "Solved"; instead, DeepMind found a way to bypass the protein folding problem.

[dekhn]

If there's one thing I wish DeepMind did less of, it's conflating the protein folding problem with static structure prediction. The former is a grand challenge problem that remains 'unsolved' while the latter is an impressive achievment that really is optimization using a huge collection of prior knowledge. I've told John Moult, the organizer of CASP this (I used to "compete" in these things), and I think most people know he's overstating the significance of static structure prediction.

Also, solving the protein folding problem (or getting to 100% accuracy on structure prediction) would not really move the needle in terms of curing diseases. These sorts of simplifications are great if you're trying to inspire students into a field of science, but get in the way when you are actually trying to rationally allocate a research budget for drug discovery.

[HarHarVeryFunny]

It seems that to solve the protein folding problem in a fundamental way would require solving chemistry, yet the big lie (or false hope) of reductionism is that discovering the fundamental laws of the universe such as quantum theory doesn't in fact help that much with figuring out the laws/dynamics at higher levels of abstraction such as chemistry.

So, in the meantime (or perhaps for ever), we look for patterns rather than laws, with neural nets being one of the best tools we have available to do this.

Of course ANNs need massive amounts of data to "generalize" well, while protein folding only had a small amount available due to the months of effort needed to experimentally discover how any protein is folded, so DeepMind threw the kitchen sink at the problem, apparently using a diffusion like process in AlphaFold 3 to first determine large scale structure then refine it, and using co-evolution of proteins as another source of data to address the paucity.

So, OK, they found a way around our lack of knowledge of chemistry and managed to get an extremely useful result all the same. The movie, propaganda or not, never suggested anything different, and "at least 90% correct" was always the level at which it was understood the result would be useful, even if 100% based on having solved chemistry / molecular geometry would be better.

[DrierCycle]

I'm concerned that coders and the general public will confuse optimization with intelligence. That's the nature of propaganda, substituting sleight of hand to create a false narrative.

btw an excellent explanation, thank you.

[tim333]

I think if you watch the actual film you'd find they don't claim AlphaFold is thinking.

[aschla]

https://news.ycombinator.com/newsguidelines.html

[DrierCycle]

https://news.ycombinator.com/item?id=44203562

[HarHarVeryFunny]

Sure, but AlphaFold is still probably the most impactful and positive thing to have come out of "Deep Learning" so far.

[theturtletalks]

Didn’t the transformer model come from AlphaFold? I feel like we wouldn’t have had the LLMs we use today if it wasn’t for AlphaFold.

[dwa3592]

what is thinking?

[DrierCycle]

Sharp wave ripples, nested oscillations, cohering at action-syntax. The brain is "about actions" and lacks representations.

[__patchbit__]

Creatively peeling the hyper dimensional space in the scope of simplectic geometry, markhov blanket and helmholtz invariance????