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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

#341

Earlier quoted context omitted.

Consider that humans also learn from other humans, and sometimes surpass their teachers. A bit more comfortable?

Ahh, but the new young master is able to explain their work and processes to the satisfaction of the old masters. In the 'Science' of our modern times it's a requirement to show your work (yes, yes, I know about the replication crisis and all that terrible jazz). Not being able to ascertain how and why the ML/AI is achieving results is not quite the same and more akin to the alchemists and sorcerers with their cypher…

I’ll add that specially when it comes to playing go, professionals who are at the peak of their ability can often find the best move at a given point but be unable to explain why beyond “it feels right” or “it looks right”.

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

#342
post #44

> Thrilled to announce AlphaFold 3 which can predict the structures and interactions of nearly all of life’s molecules with state-of-the-art accuracy including proteins, DNA and RNA. [1] There's a slight mismatch between the blog's title and Demis Hassabis' tweet, where he uses "nearly all". The blog's title suggests that it's a 100% solved problem. [1] https://twitter.com/demishassabis/status/1788229162563420560

How to make the share price go up…surprised?

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

#343
post #93

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

For some, this conversation started when the machine derived four colour map proof was announced which is almost 5 decades ago in 1976

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

#344
post #239

This tool reminds me that the human body functions much like a black box. While physics can be modeled with equations and constraints, biology is inherently probabilistic and unpredictable. We verify the efficacy of a medicine by observing its outcomes: the medicine is the input, and the changes in symptoms are the output. However, we cannot model what happens in between, as we cannot definitively prove that the medi…

I’d say it’s always been the case for medicine, when people first used medicines, the intention was never to fully understand what happens, just save a life, eliminate or reduce symptoms.

Now we’ve built explainable systems like computers and software, we try to overlay that onto everything and it might not work.

To quote Alan Watts, humans like to try square out wiggly systems because we’re not great and understanding wiggles.

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

#345
post #61

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

> What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? A better analogy is "weather forecasting".

interesting choice considering the role chaos theory plays in forever rendering long term weather predictions impossible, by humans or LLMs.

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

#346
post #194

Earlier quoted context omitted.

The goal of science has always been to discover underlying principles and not merely to predict the outcome of experiments. I don't see any way to classify an opaque ML model as a scientific artifact since by definition it can't reveal the underlying principles. Maybe one could claim the ML model itself is the scientist and everyone else is just feeding it data. I doubt human scientists would be comfortable with that…

That ship sailed with Quantum physics. Nearly perfect at prediction, very poor at giving us a concrete understanding of what it all means. This has happened before. Newtonian mechanics was incomprehensible spooky action at a distance, but Einstein clarified gravity as the bending of spacetime.

I think this relies on either the word “concrete” or a particular choice of sense for “concrete understanding”.

Like, quantum mechanics doesn’t seem, to me, to just be a way of describing how to predict things. I view it as saying substantial things about how things are.

Sure, there are different interpretations of it, which make the same predictions, but, these different interpretations have a lot in common in terms of what they say about “how the world really is” - specifically, they have in common the parts that are just part of quantum mechanics.

The qau that can be spoken in plain language without getting into the mathematics, is not the eternal qau, or whatever.

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

#347

Earlier quoted context omitted.

Any organization/country that has the ability to use a tool like this to create a bio weapon is already sophisticated enough to do bioterrorism today.

Alright, but now picture this: it's now open to the masses, meaning an individual could probably even do it.

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?

It seems very clear to me that when creating custom viruses becomes high school level knowledge, and the tools can be charged on a credit card, nuclear weapons will be relegated to the second most likely way that our human civilization will end.

I believe the two concepts being brought together here are the Law of Large Numbers, and the sudden ability for one single human to kill at least millions.

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

#348
post #93

Earlier quoted context omitted.

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

What if our understanding of the laws of the natural sciences are subtly flawed and AI just corrects perfectly for our flawed understanding without telling us what the error in our theory was? Forget trying to understand dark matter. Just use this model to correct for how the universe works. What is actually wrong with our current model and if dark matter exists or not or something else is causing things doesn't matt…

Wouldn’t learning new data and results give us more hints to the true meaning of the thing? I fail to see how this is a bad thing in anyone’s eye.

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

#349

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

Physicists like to retroactively believe that our understanding of physical phenomena preceded the implementation of uses of those phenomena, when the reality is that physics has always come in to clean up after the engineers. There are some rare exceptions, but usually the reason that scientific progress can be made in an area is that the equipment to perform experiments has been commoditized sufficiently by engineering demand for it.

We had semiconductors and superconductors before we understood how they worked -- on both cases arguably we still don't completely understand the phenomena. Things like the dynamo and the electric motor were invented by practice and later explained by scientists, not derived from first principles. Steam engines and pumps were invented before we had the physics to describe how they worked.

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

#350
post #93

Stepping back, the high-order bit here is an ML method is beating physically-based methods for accurately predicting the world. What happens when the best methods for computational fluid dynamics, molecular dynamics, nuclear physics are all uninterpretable ML models? Does this decouple progress from our current understanding of the scientific process - moving to better and better models of the world without human-int…

If you're a scientist who works in protein folding (or one of those other areas) and strongly believe that science's goal is to produce falsifiable hypotheses, these new approaches will be extremely depressing, especially if you aren't proficient enough with ML to reproduce this work in your own hands. If you're a scientist who accepts that probabilist models beat interpretable ones (articulated well here: https://no…

What always struck me about Chomskyists is that they chose a notion of interpretable model that required unrealistic amounts of working interpretation. So Chomsky grammars have significant polynomial memory and computational costs for grammars as they approach something resembling human grammar. And you say, ok, the human brain can handle much more computation than that, and that's fine. But (for example) context-free grammars aren't just O(n^3) in computational cost; for a realistic description of human language they're O(n^3) in human-interpretable rules.

Other Chomsky-like models of human grammars have different asymptotic behavior and different choices of n, but the same fundamental problem; the big-O constant factor isn't neurons firing but rather human connections between the n inputs. How can you conceive of human minds being able to track O(n^3) (or whatever) cost where that n is everything being communicated -- words, concepts, symbols, representations, all that jazz and the polynomial relationships between them?

But I feel an apology is in order: I've had quite a few beers before coming home, and it's probably a mistake to try to express academically charged and difficult views on the Internet while in an inebriated state. Probably the alcohol has substantially decreased my mental computational power. However, it has only mildly impaired my ability to string together words and sentences in a grammatically complex fashion. In fact, I often feel that the more sober and clear-minded I am, the simpler my language is. Maybe human grammar is actually sub-polynomial. I have observed the same in ChatGPT; the more flowery and wordy it has become over time, the dumber its output.

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