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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

#441

Post by abecedarius »

DrScientist wrote: post #435
uptownfunk wrote: post #176

Very sad to see they did not make it open source. When you have a technology that has the potential to be a gateway for drug development, to the cures of new diseases, and instead you choose to make it closed, it is a very huge disservice to the community at large. Sure, release your own product alongside it, but making it closed source does not help the scientific community upon which all these innovations were buil…

I suspect https://www.isomorphiclabs.com/ is the reason. There are 3 basic ways to fund research. - Taxes - most academic research - begging - research charities - profits - companies like Google. Sometimes the lines get blurred - but I don't think you can expect Google to release as much of their work for free as people who are paid via central taxes.

Worth noting that they did release the AlphaFold 2 weights after a while. Milking an expensive discovery for a limited period should be considered laudable, unless you think tax funding of all research would be awesome and it's just a weird anomaly how the org producing these results was a tiny heterodox startup very recently.

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

#442

Post by consumer451 »

tsimionescu wrote: post #404
consumer451 wrote: post #347

Earlier quoted context omitted.

You raise an extremely important point. It appears to me that most people do not understand the implications of your point. Organized terrorism by groups is actually extremely rare. What is much less rare are mass shootings in the USA, by deranged individuals. What would a psychopathic mass shooter type choose as a weapon if he not only had access to semi-automatic weapons, but now we added bio-weapons to the menu? I…

> It seems very clear to me that when creating custom viruses becomes high school level knowledge That would be very bad indeed, but there is no path from AI to that. Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long t…

> Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long time, in a highly controlled environment. It's still biology lab work, even if you know exactly what you have to do.

You appear to be talking about today. I am referring to some point in the future.

If you extrapolate our technological progress out to the future, it certainly seems possible, at some point.

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

#443

Post by dekhn »

carlsborg wrote: post #439
dekhn wrote: post #23

Earlier quoted context omitted.

AlphaFold very explicitly (unless something has changed) removes NMR structures as references because they are not accurate enough. I have a PhD in NMR biomolecular structure and I wouldn't trust. the structures for anything.

Would you trust the CryoEM structures more?

yes, albeit with significant filtering.

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

#444

Post by dekhn »

hammock wrote: post #360
dekhn wrote: post #200

Earlier quoted context omitted.

That's the aspirational goal. And I would say that it's a bit of an inflexible one- for example, if we had an ML that could generate molecules that cure diseases that would pass FDA approval, I wouldn't really care if scientists couldn't explain the underlying principles. But I'm an ex-scientist who is now an engineer, because I care more about tools that produce useful predictions than understanding underlying princ…

> if we had an ML that could generate molecules that cure diseases that would pass FDA approval, I wouldn't really care if scientists couldn't explain the underlying principles It’s actually required as part of the submission for FDA approval that you posit a specific Mechanism of Action for why your drug works the way it does. You can’t get approval without it

How much do you believe that the MoA actually matches what is happening in the underlying reality of a disease and its treatment?

Vioxx is a nice example of a molecule that got all the way to large-scale deployment before being taken off the market for side effects that were known. Only a decade before that, I saw a very proud pharma scientist explaining their "mechanism of action" for vioxx, which was completely wrong.

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

#445

Post by dekhn »

lordnacho wrote: post #326
chasd00 wrote: post #270

Earlier quoted context omitted.

If all you can do is predict an outcome without being able to explain how then what have you really discovered? Asking someone to just believe you can predict outcomes without any reasoning as to how, even if you're always right, sounds like the concept of faith in religion.

The how is actually just further hypotheses. It's turtles all the way down: There is a car. We think it drives by burning petrol somehow. How do we test this? We take petrol away and it stops driving. Ok, so we know it has something to do with petrol. How does it burning the petrol make it drive? We think it is caused by the burned petrol pushing the cylinders, which are attached to the wheels through some gearing. H…

In the vein of "can a biologist fix a radio" and "can a neuroscientist understand a microprocessor", see https://review.ucsc.edu/spring04/bio-debate.html which is an absolutely wonderful explanation of how geneticists and biochemists would go about reverse-engineering cars.

The best part is where the geneticist ties the arms of all the suit-wearing employees and it has no functional effect on the car.

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

#446

Post by rolph »

DrScientist wrote: post #437
rolph wrote: post #39

Earlier quoted context omitted.

problem is biomolecules, are "chaperoned" to fold properly, only specific regions such as, alpha helix, or beta pleatedsheet will fold de novo. Chaperone (protein) https://en.wikipedia.org/wiki/Chaperone_(protein)

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

most protiens require chaperones, to fold properly.

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

#447

Post by tsimionescu »

consumer451 wrote: post #442
tsimionescu wrote: post #404

Earlier quoted context omitted.

> It seems very clear to me that when creating custom viruses becomes high school level knowledge That would be very bad indeed, but there is no path from AI to that. Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long t…

> Making custom viruses is never going to be an easy task even if you had a magic machine that could explain the effects of adding any chemical to the mix. You still need to procure the chemicals and work with them in very careful ways, often for a long time, in a highly controlled environment. It's still biology lab work, even if you know exactly what you have to do. You appear to be talking about today. I am referr…

Not based on AI biochemistry simulators, at the very least.

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

#448

Post by rolph »

staticautomatic wrote: post #380
rolph wrote: post #39

Earlier quoted context omitted.

problem is biomolecules, are "chaperoned" to fold properly, only specific regions such as, alpha helix, or beta pleatedsheet will fold de novo. Chaperone (protein) https://en.wikipedia.org/wiki/Chaperone_(protein)

In principle couldn’t we just incorporate knowledge about chaperones into the model?

the order of folding is crucial, this is a progression of folding events.

the difference is akin to origami vs a crumpled ball

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

#449

Post by DrScientist »

abecedarius wrote: post #441
DrScientist wrote: post #435

Earlier quoted context omitted.

I suspect https://www.isomorphiclabs.com/ is the reason. There are 3 basic ways to fund research. - Taxes - most academic research - begging - research charities - profits - companies like Google. Sometimes the lines get blurred - but I don't think you can expect Google to release as much of their work for free as people who are paid via central taxes.

Worth noting that they did release the AlphaFold 2 weights after a while. Milking an expensive discovery for a limited period should be considered laudable, unless you think tax funding of all research would be awesome and it's just a weird anomaly how the org producing these results was a tiny heterodox startup very recently.

> 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.

What's not fine is any benefiting company avoiding paying any tax back on resulting profits - that's just free riding - and many of the big tech companies are, in my view, guilty.

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

#450

Post by rolph »

DrScientist wrote: post #436
tsimionescu wrote: post #401

Earlier quoted context omitted.

The problem of producing bio weapons is not computational, it's physical in nature. Even if predictions from these tools become 100% accurate and encompassed 100% of the chemistry, you still need to actually do the manual steps to breed the bioagents. And, very importantly, you need to do so without getting you and your co-workers deadly ill long before finishing the thing. Which requires extremely sophisticated mach…

To be honest, apart from the containment systems you mentioned, much of biology basic research doesn't actually need that much sophisticated kit for basic cloning and genetic manipulation. A lot of the key reagents can just be bought - and BTW it's why code like Screepy exist ( https://edinburgh-genome-foundry.github.io/ ),. I think the real thing that stops it - it not that you can't make stuff that kills people, bu…

>>kit for basic cloning and genetic manipulation.

A lot of the key reagents can just be boughtalong with the cryo-fridges required to keep said reagents.

add about 10,000 usd to your purchase request.

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