AlphaFold 3 predicts the structure and interactions of life's molecules • Hacker News Board

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

#501

Post by nybsjytm » Sat, May 11, 2024, 9:21 PM UTC

moomin wrote: post #492

nybsjytm wrote: post #430

Earlier quoted context omitted.

No, how?

Massively overpromising unachievable things. From wikipedia: https://en.wikipedia.org/wiki/Republic:_The_Revolution Initial previews of Republic in 2000 focused upon the purported level of detail behind the game's engine, the "Totality Engine". Described as "the most advanced graphics engine ever seen, (with) no upper bound of on the number of polygons and objects", it was claimed the game could "render scenes with a…

Thanks, I'd never heard about this before. I definitely think it helps in understanding his commentary. It's really a shame that DeepMind picked up his communication style.

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

#502

Post by DrScientist » Mon, May 13, 2024, 7:21 PM UTC

rolph wrote: post #446

DrScientist wrote: post #437

Earlier quoted context omitted.

Chaperones exist - however many proteins will quite happily fold in isolation without any external help.

most protiens require chaperones, to fold properly.

Most? Evidence?

Almost all the 3D structures that Alphafold was trained on were generated from crystals of pure protein.

ie made without chaperones.

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

#503

Post by DrScientist » Mon, May 13, 2024, 7:33 PM UTC

abecedarius wrote: post #462

DrScientist wrote: post #449

Earlier quoted context omitted.

> 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.

Yep not knocking alphafold - Alphafold showed it could be done[1], and others have subsequently followed.

However if all the tech companies hoover up all the profits and simultaneously avoid paying the appropriate level of taxes - then the cycle of innovation isn't sustainable. As well taxes paying for that pre-competitive data, they train the next generation of PhDs.

[1] There were other groups making progress with DL based structure prediction before Alphafold, but alphafold was a leap forward.

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

#504

Post by mistermann » Fri, May 17, 2024, 4:08 PM UTC

ajuc wrote: post #493

mistermann wrote: post #491

Earlier quoted context omitted.

AI arguably accomplishes this using some form of abstraction though does it not? Or, consider the art word broadly, artists routinely engage in various forms of unusual abstraction.

> AI arguably accomplishes this using some form of abstraction though does it not? It's unabstractable for people, because the most abstract model that works still has far too many variables for our puny brains. > artists routinely engage in various forms of unusual abstraction Abstraction in art is just another, unrelated meaning of the word. Like execution of a program vs execution of a person. You could argue exec…

> It's unabstractable for people, because the most abstract model that works still has far too many variables for our puny brains.

Abstraction doesn't have to be perfect, just as "logic" doesn't have to be.

> Abstraction in art is just another, unrelated meaning of the word.

Speaking of art: have you seen the movie The Matrix? It's rather relevant here.