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AlphaFold 3 predicts the structure and interactions of life's molecules

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Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#451

Post by staticautomatic »

flobosg wrote: post #422
staticautomatic wrote: post #380

Earlier quoted context omitted.

In principle couldn’t we just incorporate knowledge about chaperones into the model?

In a way it is already incorporated. Broadly speaking, chaperones function by restricting the available conformational sampling space for the protein to fold. Some researchers even consider the ribosome as a chaperone of sorts for the nascent protein chain it synthetizes. Protein structure prediction methods do the same: they find ways of restricting the conformational space to explore, in hopes of finding the global…

Then it’s not clear to me exactly why should chaperones be a problem, though I get the gist intuitively

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#452

Post by drdeca »

d0mine wrote: post #432
drdeca wrote: post #400

Earlier quoted context omitted.

... because people understand things about what is described when dealing with such systems in physics, and people don't understand how the weights in ML learned NNs produce the overall behavior? (For one thing, the number of parameters is much greater with the NNs)

Looking at Navier-Stokes equations tells you very little about the weather tomorrow.

Sure. It does tell you things about fluids though.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#453

Post by rolph »

staticautomatic wrote: post #451
flobosg wrote: post #422

Earlier quoted context omitted.

In a way it is already incorporated. Broadly speaking, chaperones function by restricting the available conformational sampling space for the protein to fold. Some researchers even consider the ribosome as a chaperone of sorts for the nascent protein chain it synthetizes. Protein structure prediction methods do the same: they find ways of restricting the conformational space to explore, in hopes of finding the global…

Then it’s not clear to me exactly why should chaperones be a problem, though I get the gist intuitively

if you want a protien or any other bio molecule to fold properly, a chaperone system must be either designed or elucidated.

the primary sequence is not the only consideration for proper folding.

chaperones allow higher energy folding events to occur and be maintained until subsequent modification stabilizes high energy structural motif.

chaperones also enforce an A before B before C regime of folding so that the sequence doesnt just crumple up according to energy of hydrostatic interactions

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#454

Post by thealig »

thom wrote: post #408
porphyra wrote: post #381

Earlier quoted context omitted.

They also had a headline for Alphazero that convinced everyone that they crushed Stockfish and that classical chess engines were stuff of the past, when in fact it was about 50 elo better than the Stockfish version they were testing against, or roughly the same as how much Stockfish improves each year.

And then what happened is AlphaZero changed the professional game in various interesting ways, and all its ideas were absorbed into Stockfish. A little bombast is forgivable for technology that goes on to have a big impact, and I don’t doubt it’s the same story here.

> all its ideas were absorbed into Stockfish

don't think that is true, Stockfish incorporated NNUE techniques through a fork https://www.chess.com/news/view/stockfishnnue-strongest-ches...

being transparent with the setup of your invention is always a good thing.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#455

Post by TeMPOraL »

tsimionescu wrote: post #404
consumer451 wrote: post #347

Earlier quoted context omitted.

You raise an extremely important point. It appears to me that most people do not understand the implications of your point. Organized terrorism by groups is actually extremely rare. What is much less rare are mass shootings in the USA, by deranged individuals. What would a psychopathic mass shooter type choose as a weapon if he not only had access to semi-automatic weapons, but now we added bio-weapons to the menu? I…

> It seems very clear to me that when creating custom viruses becomes high school level knowledge That would be very bad indeed, but there is no path from AI to that. Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long t…

> You still need to procure the chemicals and work with them in very careful ways, often for a long time, in a highly controlled environment. It's still biology lab work, even if you know exactly what you have to do.

You can get that as-a-Service, and I imagine that successes in computational biology will make mail-order protein synthesis broadly available. At that point, making a bioweapon or creating a grey goo (green goo) scenario will be a divide-and-conquer issue: how many pieces you need to procure independently from different facilities, so that no one suspects what you're doing until you mix them together and the world goes poof.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#456

Post by tsimionescu »

TeMPOraL wrote: post #455
tsimionescu wrote: post #404

Earlier quoted context omitted.

> It seems very clear to me that when creating custom viruses becomes high school level knowledge That would be very bad indeed, but there is no path from AI to that. Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long t…

> You still need to procure the chemicals and work with them in very careful ways, often for a long time, in a highly controlled environment. It's still biology lab work, even if you know exactly what you have to do. You can get that as-a-Service, and I imagine that successes in computational biology will make mail-order protein synthesis broadly available. At that point, making a bioweapon or creating a grey goo (gr…

We know the principles of how to make very powerful and dangerous anorganic compounds today, with extreme precision. Do you see any chemistry-as-a-service products that sell to the general public? Is it easy to obtain the components and expertise to make sarin gas, a clearly existing and much simpler to synthesize substance than some hypothetical green goo bioweapon?

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#457

Post by TeMPOraL »

ramon156 wrote: post #318
pythonguython wrote: post #301

Earlier quoted context omitted.

Any organization/country that has the ability to use a tool like this to create a bio weapon is already sophisticated enough to do bioterrorism today.

Alright, but now picture this: it's now open to the masses, meaning an individual could probably even do it.

Honestly, I wouldn't worry about bioterrorism as much as handling mishap. Stick new proteins into a bacteria the wrong way, don't wash hands thoroughly enough, and suddenly something is eating all the trees in the region, or whatnot.

Designing an effective, lethal pathogen - fast enough to do damage, but slow enough to not burn itself out - is hard. Accidentally making something ecologically damaging is probably much simpler, and I imagine the future holds plenty such localized minor ecophagy[0] event.

--

[0] - Yes, I totally just learned that term from https://en.wikipedia.org/wiki/Gray_goo a minute ago.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#458

Post by hibikir »

mda wrote: post #425
porphyra wrote: post #381

Earlier quoted context omitted.

They also had a headline for Alphazero that convinced everyone that they crushed Stockfish and that classical chess engines were stuff of the past, when in fact it was about 50 elo better than the Stockfish version they were testing against, or roughly the same as how much Stockfish improves each year.

Alphazero indeed crushed stockfish with a novel technique, I think it deserved all the praise.

It definitely deserved a lot of praise, but the testing situation wasn't really against a fully fledged stockfish running on similar hardware, but one that, among other things, had no opening library.

The issue is not whether alphazero was impressive, but that we should be careful about the specific claims of the press releases, as they are known to oversell. The whole thing would have been impressive enough if the games had been against the last release of stockfish with good hardware, just for the way it played.

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#459

Post by staticautomatic »

rolph wrote: post #453
staticautomatic wrote: post #451

Earlier quoted context omitted.

Then it’s not clear to me exactly why should chaperones be a problem, though I get the gist intuitively

if you want a protien or any other bio molecule to fold properly, a chaperone system must be either designed or elucidated. the primary sequence is not the only consideration for proper folding. chaperones allow higher energy folding events to occur and be maintained until subsequent modification stabilizes high energy structural motif. chaperones also enforce an A before B before C regime of folding so that the sequ…

Sure, I get the mechanics. My question is, if we can incorporate knowledge about chaperones into the models as explicit or latent variables, so to speak, then why can’t the models predict something like “probability of molecule a given the presence of chaperone b”?

Re: AlphaFold 3 predicts the structure and interactions of life's molecules

#460

Post by rolph »

staticautomatic wrote: post #459
rolph wrote: post #453

Earlier quoted context omitted.

if you want a protien or any other bio molecule to fold properly, a chaperone system must be either designed or elucidated. the primary sequence is not the only consideration for proper folding. chaperones allow higher energy folding events to occur and be maintained until subsequent modification stabilizes high energy structural motif. chaperones also enforce an A before B before C regime of folding so that the sequ…

Sure, I get the mechanics. My question is, if we can incorporate knowledge about chaperones into the models as explicit or latent variables, so to speak, then why can’t the models predict something like “probability of molecule a given the presence of chaperone b ”?

it sure can, given enough computation, chaperones are often protiens themselves but can be otherwise; they are subject to the same forces so twist and turn fold and conform.

they often interact with each other, and must exert influence at proper stage of modification.

other effects beyond foldingoccur, such as addition or elimination of prosthetic groups.

the take home message is fallacy of oversimplifying the process of many molecules plus ionic enironment, interacting to influence a single molecule

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