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Ask HN: How close are we to replace animal models with software?

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Re: Ask HN: How close are we to replace animal models with software?

#41

Post by romwell »

pton_xd wrote: post #26
wildermuthn wrote: post #19

Biology is an organic computation that runs at the speed of existence. There may be no way to simulate this computation in silicon at the same scale, insofar as biology is already massively parallel and may very well involve quantum computation. Put another way, if we accept for a moment that the universe is a simulation, it may be fundamentally impossible for an in-simulation simulator to ever reach the computationa…

So what you're saying is, the most efficient AI is not a data center of GPUs, it's... a giant tank of lab-grown brains.

>So what you're saying is, the most efficient AI is not a data center of GPUs, it's... a giant tank of lab-grown brains.

That's literally what a think tank is.

Or a research university, for that matter. The labs are where our brains grow.

Re: Ask HN: How close are we to replace animal models with software?

#42

Post by Palomides »

typon wrote: post #10
snek_case wrote: post #4

We can't even simulate a single cell. At least not accurately. You'd need to be able to simulate ribosomes, gene expression, epigenetic factors. Still a lot we don't understand because even single cells are incredibly complex electrochemical machines.

I can imagine a world where you can simulate a simple organism like a worm without knowing how to simulate the cells that make it. This is because emergent behaviour of complex systems can be much simpler than the constituent parts of that system (temperature vs. knowing particle velocities).

there's https://openworm.org/ for simulating a c. elegans, but think you're underestimating the complexities

Re: Ask HN: How close are we to replace animal models with software?

#43

Post by JPLeRouzic »

salomon812 wrote: post #20

Hi! My professional job is to write emulators, my wife is a molecular biologist, and as a kid I had dreams of writing the exact software you are referencing, so I think I have a decent handle on this question. We are no where close. We are ludicrously far away. Let's define the exact scenario: we want to replace clinical trials with a software simulation of the human body. If the simulation shows ill side-effects, we…

Thanks for your answer, but pharmaceutical companies have used software for decades to describe how a drug behaves in a body and to do toxicology studies.

And there are software approaches for humans like this one:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7285886/

Re: Ask HN: How close are we to replace animal models with software?

#44

Post by jryb »

JPLeRouzic wrote: post #17
snek_case wrote: post #4

We can't even simulate a single cell. At least not accurately. You'd need to be able to simulate ribosomes, gene expression, epigenetic factors. Still a lot we don't understand because even single cells are incredibly complex electrochemical machines.

Thanks for your answer, but we either don't understand the biology of the animal models that we use. I think that medicine and drug regulations do not use the same conceptual framework as biology. Medicine and drug regulations are pragmatic, hence the concept of clinical trial: They test if something works while minimizing the confounding factors. They do not try to understand the biology down to cellular force field…

Yes, but while animals are a black box to some extent, the outcomes of the experiments are not. And you don't have to worry about whether your results are an artifact of your simulation.

Your instincts are good - if we could simulate people in silico we could basically understand and cure every disease - but the scale of such a simulation is literally (not figuratively!) astronomical. Biological systems are way, way, way more complex than they appear and our computers are (currently) hopelessly inadequate.

Re: Ask HN: How close are we to replace animal models with software?

#45

Post by the_real_cher »

ewjt wrote: post #40
the_real_cher wrote: post #6

Biology is a borderline infinite system depending on how deep you go. We need to be able to model molecular forcefields to be able to model DNA expression to be able to model protein expression to be able to model, layers and layers of higher order molecules just to represent a cell. Then...you have combining cells to make an organism and the interaction of the organism with its environment which affects all of the a…

Do you actually need to simulate at that minuscule level of detail? Or is it possible for a system to be built that can approximate biology similar to how LLMs approximate cognition without true understanding and reasoning?

I don't know.

I guess it depends on how accurate you want to get and when testing therapies for humans you probably want to be pretty accurate.

There may be some abstraction layer that provides 'good enough' accuracy though that I'm not aware of.

Re: Ask HN: How close are we to replace animal models with software?

#46

Post by jcfrei »

wildermuthn wrote: post #19

Biology is an organic computation that runs at the speed of existence. There may be no way to simulate this computation in silicon at the same scale, insofar as biology is already massively parallel and may very well involve quantum computation. Put another way, if we accept for a moment that the universe is a simulation, it may be fundamentally impossible for an in-simulation simulator to ever reach the computationa…

Lots of biological processes are indeed parallel but that doesn't mean they are all different. Once the most important ones are understood we can reasonably simulate how biology works. Just like you can simulate a much more complex CPU on a lower end CPU - just at a reduced clock speed.

Re: Ask HN: How close are we to replace animal models with software?

#47

Post by vogu66 »

For additional insight, we are not actually able to fully model a single bacterial culture, gene expression is random and we are barely getting to know one gene at a time when considering dynamics and not just steady state (we also have some idea how to represent an average bacterium's gene expression at steady state, if they were all doing the same thing, but they aren't)

As far as I know, we are actually closer to (less far from) in vitro models where you culture human cells into organs very close to real ones and apply drugs to those organs. I think they already do that with skin for cosmetics but everything else is far away (key word: I think, not sure).

Re: Ask HN: How close are we to replace animal models with software?

#48

Post by JPLeRouzic »

poidos wrote: post #13

Not even close. We don't yet have a computational model that accurately reproduces all the properties of water , the solvent where most life of interest occurs. And, if and when we have one, and are able to develop accurate models for the myriad proteins involved (an even worse problem,) and we're able to develop accurate models for all their interactions (O(huge)), and so forth, the computational cost to simulate sy…

Thanks for your answer, but reproducing an organism down to the cell force fields is not my point.

My point is that animal models are extremely imperfect, otherwise we would not spend billions on clinical trials.

On the other hand, now there are many software that are used in medicine to predict the behavior of an organ in some circumstances. Whole-body simulations of pharmacokinetics and toxicology have existed for two decades and are now quite accurate.

I feel that we are now on the verge of integrating those many approaches. For instance:

https://pubmed.ncbi.nlm.nih.gov/38480804/

So I ask, if it's possible to use soon, the integration of these software components to replace the pre-clinical usage of animal models.

Re: Ask HN: How close are we to replace animal models with software?

#49

Post by shwaj »

pton_xd wrote: post #26
wildermuthn wrote: post #19

Biology is an organic computation that runs at the speed of existence. There may be no way to simulate this computation in silicon at the same scale, insofar as biology is already massively parallel and may very well involve quantum computation. Put another way, if we accept for a moment that the universe is a simulation, it may be fundamentally impossible for an in-simulation simulator to ever reach the computationa…

So what you're saying is, the most efficient AI is not a data center of GPUs, it's... a giant tank of lab-grown brains.

They didn’t say that at all. It seems like you wanted to say it.

Re: Ask HN: How close are we to replace animal models with software?

#50

Post by max_ »

The body of animal is computationally irreducible.

It is impossible to create a shortcut using software that can "skip ahead" and accurately predict what the body will do given arbitrary initial conditions.

This is possible only for stuff like eclipses because they are reducible.

To simulate an animal model, you will have to replicate it's environment, all it's proteins all it's, all it's hormones, all it's cellular structures and all it's physical & psychological behaviour.

Not only that, we also have know know 100% how they all work.

An animal is a complex system and complex systems often can't be reduced in to simple constituents used to make accurate predictions.

Link — https://en.wikipedia.org/wiki/Computational_irreducibility

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