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AlphaFold: a solution to a 50-year-old grand challenge in biology

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Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#651

Post by selestify »

dnautics wrote: post #581
rsfern wrote: post #565

Earlier quoted context omitted.

I’m not a protein crystallographer, but here’s my generalist take. We understand the physics of e.g. X-ray diffraction pretty well, so we can fit pretty decent forward models for the x-ray data given a proposed structure. The hardest task here is getting a good enough guess at the structure to optimize the physical model, and it’s my impression that people use an iterative model refinement workflow. At least that’s h…

X-ray diffraction is pretty nutty, too. You're taking the diffraction pattern, which is the fourier transform of the electron density. Fourier transform results are complex-valued data. Unfortunately, we don't really have X-Ray lasers, so you can only get the intensities and not the phases of those diffraction spots. Since mother science hates us, it of course the case that, in a fourier transform "more information"…

> Yes, it's entirely possible to converge on a wrong structure

I guess my question is, how do you know if you’ve converged on the right structure or not? Is there a different experiment you could do?

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#652

Post by gwicks56 »

softwaredoug wrote: post #648
jboggan wrote: post #645

Earlier quoted context omitted.

I used to work in one of the top labs doing protein folding, in fact I recognize some lab mates who survived to have their own labs in this year's CASP top ten ranking. Something is a bit rotten though because I'd guess about half of us burned out of academia entirely, and the state of the art at the time was regrettable. I remember one model doing rather well except the weights of the various physical forces were wr…

This is exactly my point. There is something rotten in the research labs where society is not getting return on investment for basic research. If the goal is to just produce researchers that can work at corporate research labs, then I feel we could get more bang for the buck. If the goal is to do move research in the public good, something needs to change. Maybe it’s the fact there’s too little money out there, and i…

From my experience working as an engineer in Academia, there is a big problem in anything AI related, in that anyone decent can instantly increase their pay by 200 -1000% just by leaving for one of the big tech companies. Half the phD students don't even bother finishing, before being given an offer they can't refuse. How can academia compete with that, given sky high student debt, an extremely uncertain path to tenure etc etc

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#653

Post by MarkMc »

Ono-Sendai wrote: post #618

Can some explain why you can't just run a simulation simulating the forces between the amino acids, and let the protein curl up based on those forces?

Jason Crawford answers your question here: https://twitter.com/jasoncrawford/status/1333576261877125121...

Short answer: it's extremely computationally expensive

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#654

Post by drdeca »

_0w8t wrote: post #650
drdeca wrote: post #639

Earlier quoted context omitted.

Huh? How is it necessary to speak of time when discussing whether there exists e.g. a solution to a set of equations? Or whether there is a finite simple group with given number of elements, or the like?

Does the solution to an equation exist before one stated the equation? Does a particular phrase exist before one has written it? Does it continue to exist after all its copies were erased? And even if one answers positively to such questions based on a belief (it is not provable), like "yes, they always exist", one has to define what "always" means.

Their existence is not at all dependent on such things. (Note that I didn’t use the word “always”.)

If the answer to a question of “Why [...]_1?” would be “Because there is a [...]_2 such that [...]_3 .”, then there is such a [...]_2 such that [...]_3 . (Possible exception : if “because you asked that question” would be part of the answer.)

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#655

Post by qqqwerty »

Jach wrote: post #579
mnky9800n wrote: post #530

Earlier quoted context omitted.

People seem to forget that you need a system like academia that's allowed to fail. Most companies aren't allowed to fail when they need to have quarterly returns. Of course academia has become more and more competitive. But tbh I think the answer is that the funding hasn't increased equally with the number of quality people who could stay in academia. But who knows.

Stability "like academia" is rich, given all we've heard about "publish or perish". Modern academia is a poor fit for increasingly any case you can think of besides maintaining the status of academia. But sure, there needs to be some stability and ability to "fail"/i.e. produce something worthless. Corporate research departments provide this -- if they didn't, they wouldn't have a research department and indeed many…

We are in a period of historically low interest rates. If and when interest rates rise, these moonshot research startups will get dropped like a hot potato.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#656

Post by krick »

This is great and I feel weirdly relieved (considering I don't actually really gain anything from that).

That, on the other hand, makes me feel sad and almost depressed every time:

> It uses approximately 16 TPUv3s (which is 128 TPUv3 cores or roughly equivalent to ~100-200 GPUs) run over a few weeks, a relatively modest amount of compute in the context of most large state-of-the-art models used in machine learning today

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#657

Post by PaulDavisThe1st »

softwaredoug wrote: post #648
jboggan wrote: post #645

Earlier quoted context omitted.

I used to work in one of the top labs doing protein folding, in fact I recognize some lab mates who survived to have their own labs in this year's CASP top ten ranking. Something is a bit rotten though because I'd guess about half of us burned out of academia entirely, and the state of the art at the time was regrettable. I remember one model doing rather well except the weights of the various physical forces were wr…

This is exactly my point. There is something rotten in the research labs where society is not getting return on investment for basic research. If the goal is to just produce researchers that can work at corporate research labs, then I feel we could get more bang for the buck. If the goal is to do move research in the public good, something needs to change. Maybe it’s the fact there’s too little money out there, and i…

The problem is that people in academia and outside of it were saying the same thing in the 70s, 80s, 90s, 00's ... so if you really want to make the claim that "society is not getting return on investment for basic research", you need to claim with a straight face that this also applies to the last 50 years of academic basic research (at least). Alternatively, explain what has changed and when.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#658

Post by peacefulhat »

qqqwerty wrote: post #655
Jach wrote: post #579

Earlier quoted context omitted.

Stability "like academia" is rich, given all we've heard about "publish or perish". Modern academia is a poor fit for increasingly any case you can think of besides maintaining the status of academia. But sure, there needs to be some stability and ability to "fail"/i.e. produce something worthless. Corporate research departments provide this -- if they didn't, they wouldn't have a research department and indeed many…

We are in a period of historically low interest rates. If and when interest rates rise, these moonshot research startups will get dropped like a hot potato.

Why should they rise? Maybe they should stay low if it is so productive.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#659

Post by vkou »

peacefulhat wrote: post #658
qqqwerty wrote: post #655

Earlier quoted context omitted.

We are in a period of historically low interest rates. If and when interest rates rise, these moonshot research startups will get dropped like a hot potato.

Why should they rise? Maybe they should stay low if it is so productive.

Because in addition to funding moonshot project plays, low interest rates also fund a lot of really stupid investments that should never have been funded, and that go belly-up at the first sign of a tightening fiscal market.

When too many of those really stupid investments go belly up at once, it's called a bubble popping, and it is catastrophic to the economy.

Re: AlphaFold: a solution to a 50-year-old grand challenge in biology

#660

Post by Jach »

calf wrote: post #584
Jach wrote: post #579

Earlier quoted context omitted.

Stability "like academia" is rich, given all we've heard about "publish or perish". Modern academia is a poor fit for increasingly any case you can think of besides maintaining the status of academia. But sure, there needs to be some stability and ability to "fail"/i.e. produce something worthless. Corporate research departments provide this -- if they didn't, they wouldn't have a research department and indeed many…

That's all nice in theory, but what's the compelling empirical evidence for corporate science vs academic research? A professor might conversely argue the open nature of scholarship and freedom of inquiry as being essential to basic science, and capitalist businesses fundamentally cannot provide that. So it goes back to empirical support. And last I checked, companies still need a pool of trained PhDs to choose from,…

Elsewhere in the thread makes plenty of cases for corporate advances, even (or perhaps especially?) in the 20th century with e.g. Bell Labs et al. I think the empirical results are pretty good for corporate science.

As for 'needing' PhDs, I'm not sure. Having some can be convenient, yes, but in many cases not necessary. In some fields the only way to get caught up (i.e. no corporation will train you directly) may be with academic foundations but is a PhD necessary or just some relevant graduate work?

As an example N=1 to show a PhD is not needed always, Jeff Jonas formerly held the title of IBM Chief Scientist where he did some state of the art work in entity resolution. He didn't even finish high school.

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