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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

#161

Post by dekhn »

narrator wrote: post #140
dekhn wrote: post #93

Earlier quoted context omitted.

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

What if our understanding of the laws of the natural sciences are subtly flawed and AI just corrects perfectly for our flawed understanding without telling us what the error in our theory was? Forget trying to understand dark matter. Just use this model to correct for how the universe works. What is actually wrong with our current model and if dark matter exists or not or something else is causing things doesn't matt…

All models are wrong, but some models are useful.

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

#162

Post by lupire »

_just7_ wrote: post #145
HanClinto wrote: post #101

Earlier quoted context omitted.

Good question. Also makes me wonder -- where's the line? Is it reasonable to have "layperson" reviewers? Is it reasonable to think that regular citizens could review such content?

No, infact most journals have peer reviews cordoned off, not viewable to the general public.

That's pre-publication review, not scientific peer review. Special interests try to conflate the two, to bypass peer review and transform science into a religion.

Peer review properly refers to the general process of science advancing by scientists reviewing each other's published work.

Publishing a work is the middle, not the end of the research.

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

#164

Post by [deleted] »

dekhn wrote: post #93
moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

[deleted]

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

#165

Post by RandomLensman »

narrator wrote: post #140
dekhn wrote: post #93

Earlier quoted context omitted.

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

What if our understanding of the laws of the natural sciences are subtly flawed and AI just corrects perfectly for our flawed understanding without telling us what the error in our theory was? Forget trying to understand dark matter. Just use this model to correct for how the universe works. What is actually wrong with our current model and if dark matter exists or not or something else is causing things doesn't matt…

High accuracy could result from pretty incorrect models. When and where that woukd then go completely off the rails is difficult to say.

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

#166

Post by divbzero »

dekhn wrote: post #93
moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

There have been times in the past when usable technology surpassed our scientific understanding, and instead of being depressing it provided a map for scientific exploration. For example, the steam engine was developed by engineers in the 1600s/1700s (Savery, Newcomen, and others) but thermodynamics wasn’t developed by scientists until the 1800s (Carnot, Rankine, and others).

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

#167

Post by interroboink »

dekhn wrote: post #93
moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

> ... and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing

I don't quite understand this point — could you elaborate?

My understanding is that the ML model produces a hypothesis, which can then be tested via normal scientific method (perform experiment, observe results).

If we have a magic oracle that says "try this, it will work", and then we try it, and it works, we still got something falsifiable out of it.

Or is your point that we won't necessarily have a coherent/elegant explanation for why it works?

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

#168

Post by goggy_googy »

perihelions wrote: post #102
l33tman wrote: post #10

Earlier quoted context omitted.

That sucks a bit. I was just wondering why they are touting that 3rd party company in their own blog post, who commercialise research tools, as well. Maybe there are some corporate agreements with them that prevents them from opening the system... Imagine the goodwill for humanity for releasing these pure research systems for free. I just have a hard time understanding how you can motivate to keep it closed. Let's ho…

- "Imagine the goodwill for humanity for releasing these pure research systems for free." The entire point[0] is that they want to sell an API to drug-developer labs, at exclusive-monopoly pricing. Those labs in turn discover life-saving drugs, and recoup their costs from e.g. parents of otherwise-terminally-ill children—again, priced as an exclusive monopoly. [0] As signaled by "it is not possible to obtain structur…

What makes this such a "deeply broken situation"?

I agree that late-stage capitalism can create really tough situations for poor families trying to afford drugs. At the same time, I don't know any other incentive structure that would have brought us a breakthrough like AlphaFold this soon. For the first time in history, we have ML models that are beating out the scientific models by huge margins. The very fact that this comes out of the richest, most competitive country in the history of the world is not a coincidence.

The proximate cause of the suffering for terminally-ill children is really the drug company's pricing. If you want to regulate this, though, you'll almost certainly have fewer breakthroughs like AlphaFold. From a utilitarian perspective, by preserving the existing incentive structure (the "deeply broken situation" as you call it), you will be extending the lifespans of more people in the future (as opposed to extending lifespans of more people now by lowering drug prices).

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

#169

Post by RandomLensman »

xanderlewis wrote: post #43
moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

It depends whether the value of science is human understanding or pure prediction. In some realms (for drug discovery, and other situations where we just need an answer and know what works and what doesn’t), pure prediction is all we really need. But if we could build an uninterpretable machine learning model that beats any hand-built traditional ‘physics’ model, would it really be physics? Maybe there’ll be an inter…

Pure prediction is only all we need if the total end-to-end process is predicted correctly - otherwise there could be pretty nasty traps (e.g., drug works perfectly for the target disease but does something unexpected elsewhere etc.).

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

#170

Post by advisedwang »

moconnor wrote: post #32

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

In physics, we already deal with the fact that many of the core equations cannot be analytically solved for more than the most basic scenarios. We've had to adapt to using approximation methods and numerical methods. This will have to be another place where we adapt to a practical way of getting results.
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