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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

#461

Post by TeMPOraL »

tsimionescu wrote: post #456
TeMPOraL wrote: post #455

Earlier quoted context omitted.

> 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?

> Do you see any chemistry-as-a-service products that sell to the general public?

Sort of? Depends on how general you insist the general public to be. Never used one myself, but I used to lurk on nootropic and cognitive enhancement groups, and I recall some people claiming they managed to get experimental nootropics synthesized and sent from abroad, without any special license or access. And then there's all the lab supply companies - again, I never tried, but talking with people I never got the impression it's in any way restricted, other than being niche; I never heard them e.g. requiring a verified association with an university lab or something. Hell, back in high school, my classmate managed to get his hand on some uranium salts (half for chemistry nerdom, half for pure bragging rights), with zero problems.

> 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?

Given that I know for a fact that making several kinds of explosives and propellants is a bored middle-schooler level problem, I imagine sarin is also synthesizeable by a smart amateur. Fortunately, the intersection of being able to make it, and having a malicious reason for it, is vanishingly small. But I don't doubt that, should a terrorist group decide to use some of either, there's approximately nothing that can stop from cooking some up.

What makes me more nervous about potential biosafety issues in the future is that, well, sarin is only effective as far as the air circulation will carry it; pathogens have indefinite range.

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

#462

Post by abecedarius »

DrScientist wrote: post #449
abecedarius wrote: post #441

Earlier quoted context omitted.

Worth noting that they did release the AlphaFold 2 weights after a while. Milking an expensive discovery for a limited period should be considered laudable, unless you think tax funding of all research would be awesome and it's just a weird anomaly how the org producing these results was a tiny heterodox startup very recently.

> Worth noting that they did release the AlphaFold 2 weights after a while. Yes - though I don't think Isomorphic labs existed at that point. Obviously the real reason AlphaFold was possible was the huge tax payer funded effort running over decades to generate a diverse, high quality 3D structure dataset. However that's why we put taxes into research - to spur innovation in a pre-competitive way - so that's fine. Wha…

The data is a treasure. It was just as available to others, before and after.

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

#463

Post by [deleted] »

falcor84 wrote: post #277
uptownfunk wrote: post #176

Very sad to see they did not make it open source. When you have a technology that has the potential to be a gateway for drug development, to the cures of new diseases, and instead you choose to make it closed, it is a very huge disservice to the community at large. Sure, release your own product alongside it, but making it closed source does not help the scientific community upon which all these innovations were buil…

The closer it gets to enabling full drug discovery, the closer it also gets to enabling bioterrorism. Taking it to the extreme, if they had the theory of everything, I don't think I'd want it to be made available to the whole world as it is today. On a related note, I highly recommend The Talos Principle 2, which really made me think about these questions.

[deleted]

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

#464

Post by flobosg »

rolph wrote: post #450
DrScientist wrote: post #436

Earlier quoted context omitted.

To be honest, apart from the containment systems you mentioned, much of biology basic research doesn't actually need that much sophisticated kit for basic cloning and genetic manipulation. A lot of the key reagents can just be bought - and BTW it's why code like Screepy exist ( https://edinburgh-genome-foundry.github.io/ ),. I think the real thing that stops it - it not that you can't make stuff that kills people, bu…

>>kit for basic cloning and genetic manipulation. A lot of the key reagents can just be bought along with the cryo-fridges required to keep said reagents. add about 10,000 usd to your purchase request.

Most reagents and kits for molecular cloning will be fine at -20°C.

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

#465

Post by akira2501 »

bluerooibos wrote: post #433
akira2501 wrote: post #229

Earlier quoted context omitted.

> it'll be nearing 100% in the next couple of years. What are you basing this on? There is no established "moores law" for computational models.

Computational models have been shown to improve with computing power though, right? It's a tongue in cheek comment about how fast models have been improving over the last few years, but I forgot HN scrutinizes every comment like it's a scientific paper.

The ROI exponentially decreases with language models. At this point, each percentage point of accuracy costs you tens of billions, and the projections show a solid wall approaching with the current implementation tricks.

It's an off the cuff comment, at this point though, HN apparently needs to bully everyone who refuses to go along with the zeitgeist, as if being negative near a thing would destroy it.

I guess the 'h' no longer stands for 'hacker.'

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

#466

Post by thom »

abecedarius wrote: post #438
RUnconcerned wrote: post #420

Earlier quoted context omitted.

Stockfish has not incorporated ideas from AlphaZero. Stockfish's NN eval technology, NNUE, comes from Shogi and it predates Alphazero there. The 2nd strongest engine, Leela Chess Zero, is indeed directly inspired by AlphaZero, though, and did surpass Stockfish until NNUE was introduced.

Hmm: NNUE was introduced in 2018, the AlphaZero preprint 2017, AlphaGo 2015-2016. I checked this because my memory claimed that it was AlphaGo's success that sparked the new level of interest in NN evaluation. Wouldn't surprise me if AlphaZero's improvements had no influence in that timeline, but for AlphaGo it would.

The original NNUE paper cites AlphaZero[0]. The architectures are different because NNUE is optimized for CPUs and uses integer quantization and a much smaller network. I don't think one could credibly claim that it would have come about if not for Google making so much noise about their neural network efforts in Go, Chess and Shogi.

0: https://github.com/asdfjkl/nnue/blob/main/nnue_en.pdf

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

#467

Post by MaxikCZ »

bongodongobob wrote: post #355
uptownfunk wrote: post #323

Earlier quoted context omitted.

The risks don't exceed what is already out there. If someone wants to do damage, especially in America, there are more than enough ways they can do it already. The technology should be made free. I also wonder how much the claims are being exaggerated and are marketing-speak vs. real results. Is there any benchmark for this that they have published?

No. I love to be egalitarian as well but this AI thing really feels different. We didn't just invent a better plow or a more durable sword. We're working on making a better brain. I think social media shows us a pretty good slice of the average person and it's not great. Now imagine they can manipulate the smartest person in the world to do dangerous, dumb shit.

>we didnt just invent a better plow

But we invented metalworking. And if metal were for kings chairs only, we would still have no plows.

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

#468

Post by boxed »

j7ake wrote: post #135
boxed wrote: post #91

Earlier quoted context omitted.

Are you an editor or reviewer?

If you read the standards it applies broadly beyond reviewers or editors. > A condition of publication in a Nature Portfolio journal is that authors are required to make materials, data, code, and associated protocols promptly available to readers without undue qualifications.

That's a much better rule!

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

#469

Post by thom »

RUnconcerned wrote: post #420
kriro wrote: post #419

Earlier quoted context omitted.

I think Alphazero is a lot more interesting than Stockfish though. Most notably it lead me to reevaluate positional play. Iirc A0 at around 2-3 ply is still above SuperGM Level which is pretty mind-blowing. Based on this I have increased my strategy to tactics ratio quite a bit. FWIW Stockfish is always evolving and adapting and has incorporated ideas from A0.

Stockfish has not incorporated ideas from AlphaZero. Stockfish's NN eval technology, NNUE, comes from Shogi and it predates Alphazero there. The 2nd strongest engine, Leela Chess Zero, is indeed directly inspired by AlphaZero, though, and did surpass Stockfish until NNUE was introduced.

For whatever it's worth, the NNUE training dataset contains positions from Leela games and several generations of self-play. Stockfish wouldn't be where it is if not for Google's impact. AlphaFold will likely have a similar impact on our understanding of protein structure. I don't know why everyone is so offended by them puffing their chests out a little bit here, the paper's linked in the article.

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

#470

Post by BriggyDwiggs42 »

FeepingCreature wrote: post #434
BriggyDwiggs42 wrote: post #411

Earlier quoted context omitted.

It’s very frustrating when people consider the possession of information equivalent to malice. It suggests that the right way to run society is to keep people stupid and harmless.

Okay, I'll live in the harmless society, you go live in the harmful society.

Remember, I also said stupid. Ima go live in the non-dummy society and you can do whatever.
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