AlphaFold: a solution to a 50-year-old grand challenge in biology • Hacker News Board

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

#671

Post by blinding-streak » Wed, Dec 02, 2020, 1:48 PM UTC

timr wrote: post #459

ramraj07 wrote: post #438

Earlier quoted context omitted.

We don't know too much about the exact model they made but it looks sufficiently generalizable to be able to give a candidate protein structure for any given sequence. It doesn't automatically cure cancer and inject the drug but that by itself is an amazing tool that if available to everyone will revolutionize biology experimentation. I will definitely blame the protein structure field in multiple levels though. It w…

"We don't know too much about the exact model they made but it looks sufficiently generalizable to be able to give a candidate protein structure for any given sequence. It doesn't automatically cure cancer and inject the drug but that by itself is an amazing tool that if available to everyone will revolutionize biology experimentation." They say on their own press-release page that side-chains are a future research p…

Are you always so dismissive of Nobel-level achievements?

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

#672

Post by blinding-streak » Wed, Dec 02, 2020, 2:05 PM UTC

woeirua wrote: post #106

aardvarkr wrote: post #92

Earlier quoted context omitted.

Every simulator is going to have error. In this case this biennial challenge represents the computational state of the art with scores of 30-40 over the last decade. The AlphaFold2 model sends that score up to 87 with errors about than the width of the atom. You can actually see the difference between their prediction and the actual result and it’s stunning. This is all on the blog site so I recommend reading before…

I read the blog. But there’s a big difference between a mind blowing tech demo and something that can be used in a commercially viable process.

Are you always so dismissive of Nobel-level achievements?

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

#673

Post by mensetmanusman » Wed, Dec 02, 2020, 2:19 PM UTC

pyhtel wrote: post #619

sockpuppet_12 wrote: post #616

Earlier quoted context omitted.

But if you unplug the machine its running on, its over.

Assuming the AI isn't a distributed system, sure

That is a plot of a novel. Humanity has to restart the entire global electrical grid to deal with an AI worm that accidentally causes epoch ending havoc :)

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

#674

Post by dnautics » Wed, Dec 02, 2020, 3:57 PM UTC

selestify wrote: post #651

dnautics wrote: post #581

Earlier quoted context omitted.

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?

Best is an orthogonal process (like NMR). Cryo-EM is getting better too so maybe that will start to be viable. Sometimes that's not possible, but you can use secondary evidence: "we know these three amino acids are important band hey look they touch in our model".

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

#675

Post by Octopodes » Wed, Dec 02, 2020, 4:58 PM UTC

mensetmanusman wrote: post #673

pyhtel wrote: post #619

Earlier quoted context omitted.

Assuming the AI isn't a distributed system, sure

That is a plot of a novel. Humanity has to restart the entire global electrical grid to deal with an AI worm that accidentally causes epoch ending havoc :)

Which novel?

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

#676

Post by dang » Wed, Dec 02, 2020, 6:41 PM UTC

kovek wrote: post #640

dang wrote: post #516

Earlier quoted context omitted.

I assume so, but haven't looked recently. I'll try to do that and report back here later. Feel free to ping me at hn@ycombinator.com if I forget. Edit: ok, for this thread so far, 95% of views are page 1, 4% are page 2, 1% are page 3. For https://news.ycombinator.com/item?id=25065026 , which had a "more pages" comment at the top: 93% of views were page 1, 5% page 2, 2% viewed page 3. For https://news.ycombinator.com/…

If you are fine serving more data, you could trigger a "More" automatically when the user minimizes a comment thread, and add the "More" comments to the bottom of the page? Also, to encourage people exploring "More" comments, maybe some comments inside the 2-3 megathreads showing in the first page can be minimized at first? I wonder what are the thoughts on these design. I really like how Hacker News is designed, tha…

My thoughts: the first suggestion is too complex for HN and would amount to a sort of infinite scroll, which users here would probably hate (many have said so pre-emptively!). The second suggestion is probably a good idea. I worked on it at one point but it turned out to be a little harder to get right than I expected. Will probably return to it.

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

#677

Post by alpple » Wed, Dec 02, 2020, 8:08 PM UTC

xphos wrote: post #346

Like this is awesome and a huge advancement but one thing that worries me with an AI solution is that it doesn't really draw us any closer to the why. Why do proteins fold the way they do? We can predict the resulting structure which is extremely significant, we have no clue why. While we get the insight of being able to predict some structures we don't get the insight of why things are happening the way they are. In…

It could be that more complex phenomenon don't have a simple explanation. It could be that they do. But, just because I would like a why, doesn't mean that there is one. (Personally I think there is a why.)

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

#678

Post by Ar-Curunir » Wed, Dec 02, 2020, 10:22 PM UTC

codingslave wrote: post #647

Ar-Curunir wrote: post #634

Earlier quoted context omitted.

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

There's a lot of fanciful stuff about "creative" and "absent-minded" people doing the best work, but what actually makes a good researcher is the same as in any other field: (a) curiosity (b) determination, and (c) hard work.

PhD programs don't take people who just have a good GPA; you have to have a research record before you're even in the consideration. I've been on an admissions committee, so this is not conjecture.

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

#679

Post by okarthik42 » Thu, Dec 03, 2020, 6:35 AM UTC

IMO, AlphaFold 2 is a great example of industrial research labs making huge breakthroughs. I'm not sure if AlphaFold 2 is over hyped or not (because I don't know anything about protein folding), but given how a lot of computational biologists reacted to the results (the co-founder of CASP seems very impressed :')), I suppose this a big deal. I hope DeepMind becomes the Bell Labs for AI. Bell Labs is the best example of industrial research labs making huge strides. Of course, AI doesn't exist yet, and deep "learning" is nothing but curve-fitting done in fancy ways, but I would not be surprised if DeepMind results in a few Turing and Nobel laureates.

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

#680

Post by codingslave » Thu, Dec 03, 2020, 12:42 PM UTC

Ar-Curunir wrote: post #678

codingslave wrote: post #647

Earlier quoted context omitted.

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

There's a lot of fanciful stuff about "creative" and "absent-minded" people doing the best work, but what actually makes a good researcher is the same as in any other field: (a) curiosity (b) determination, and (c) hard work. PhD programs don't take people who just have a good GPA; you have to have a research record before you're even in the consideration. I've been on an admissions committee, so this is not conjectu…

Right, but a modern research record is about incremental improvement. The argument being that low hanging fruit is often picked, and so the incremental is natural. My argument is that far too many people are gaming the academic system, using it as a form of status credentialing, which is hurting true academic research.