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

deepmind.com

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

#641

Post by [deleted] »

mensetmanusman wrote: post #526
softwaredoug wrote: post #487

Earlier quoted context omitted.

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

Academia is for generating problem solvers. Teams are small and made of people who will be there for around 5 years. A better comparison would be to national labs, but they are tasked with projects that make no sense for industry to tackle. The system is working as intended, all players are needed. The team at Alphafold busted their chops in academia and went on to working on problems they could spend decades on.

[deleted]

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

#642

Post by softwaredoug »

C4stor wrote: post #629
softwaredoug wrote: post #487

Earlier quoted context omitted.

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

The deepmind research team is essentially all PhD though, so it seems academia isn't doing such a bad job.

Specifically the linked article wonders about the research environment of academia compared to industry. Why teams of hundreds in academia with their own super computing resources couldn’t make the same advances. He posits there’s something not great going on about how academic research environments make advances, the poor incentive structures, the abuse and burnout of PhDs, the lack of open sharing of findings, the obsession with publication quantity over quality...

There’s a reason these PhDs at Google mind aren’t in academia after all doing the same work

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

#643

Post by sudosysgen »

complexmango wrote: post #631
sudosysgen wrote: post #586

Earlier quoted context omitted.

The conclusion we came to is that such a being would have to have it's own, metaphysically superior, time and space, and our time would be a subtime of it as well as our space would be a subspace of it. The concept of a being subject to causality presupposes something akin to time.

No. The concept is that there is an infinite, indescribable void from which emerges consciousness manifested in matter. And conscious matter creates universes constantly, that appear out of the void, hence creating time and space. This would also imply that its possible not only to change the future, but also the past. The masters advise, however, that these are distractions and that the journey inevitably leads to e…

I was referring specifically to Abrahamic religion, though of course what you say can be right in other spiritualities.

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

#644

Post by sudosysgen »

ben_w wrote: post #623
FeepingCreature wrote: post #600

Earlier quoted context omitted.

That's a distinction without a difference though.

There is a potential difference, I think. Consider if this universe exists only as a simulation (I’ve met some theists making this category of comparison but with different language). The laws of physics are identical in both directions for the arrow of time, so the starting point of the simulation from the point one view of the outside universe can be any point in time from the perspective of the inhabitants. In thi…

Well yes, from our point of view. But I'd understand that there still must be something like time from the point of view of those that wrote the simulation.

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

#645

Post by jboggan »

softwaredoug wrote: post #487
cs702 wrote: post #118

Two years ago, after DeepMind submitted its first set of predictions to CASP (Critical Assessment of protein Structure Prediction), Mohammed AlQuraishi, an expert in the field, asked, "What just happened?" https://moalquraishi.wordpress.com/2018/12/09/alphafold-casp... Now that the problem of static protein structure prediction has been solved (prediction errors are below the threshold that is considered acceptable i…

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

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 wrong, so much that some signs were negative and what should have been electrostatic repulsion was actually electrostatic attraction between similar charges. This was 10 years ago of course, but all of the field improvements were relatively incremental and small until AlphaFold came along.

Modern academia exists to further modern academia, no more and no less. I became disillusioned of any search for truth and progress during my time there, it was really just about showing up the Baker lab at the next CASP and getting the next round of grants secured.

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

#647

Post by codingslave »

Ar-Curunir wrote: post #634
codingslave wrote: post #497

Earlier quoted context omitted.

Academia keeps employing people who have done well in classes and within fine bounds. Its a careerist track. Industry cares about results, its more meritocratic

I wish people would stop making reductive and false statements. Life isn't this simple.

This is actually something I feel strongly about. The absent minded creative professor is the one who traditionally has made the breakthroughs. Recent years has instead seen the straight A student with no curiosity making it into programs, when they really have no business doing novel research and are better suited as orderly wage slaves

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

#648

Post by softwaredoug »

jboggan wrote: post #645
softwaredoug wrote: post #487

Earlier quoted context omitted.

> I don’t think we would do ourselves a service by not recognizing that what just happened presents a serious indictment of academic science. Much like other fields, I do begin to question the academic structure to making advances. It appears something is rotten in the state of academia. Oddly it's academia doing incremental improvements to existing methods but industry making novel leaps and bounds... The other majo…

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 it causes everyone to chase meager grant money. Or that there’s too much competition between groups. Or a million other reasons.

But I’d love to see it fixed and have more faith in public investment in basic science.

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

#650

Post by _0w8t »

drdeca wrote: post #639
_0w8t wrote: post #613

Earlier quoted context omitted.

One cannot define the notion of “exist” without explicitly or implicitly referring to time. So the question of existence without time reduces to absurdity like can one exist without existing?

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.
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