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

news.ycombinator.com

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

#21

Post by yathern »

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).

I can write a program today that can simulate a worms "emergent behavior" without simulating the cells. Maybe a little 3D model that wriggles around. I can even do a human!

But I think what we're looking for here is something closer to emulation. In the same way that video game console emulators seek to reproduce the exact bugs that the original hardware produced - the value here does not come from abstracting away the lowest levels of behavior.

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

#22

Post by SketchySeaBeast »

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).

It seems to me that if you can fully simulate a worm you're probably only an order of magnitude of difficulty away from a person, but to get there you need to have crossed dozens across many domains.

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

#23

Post by salomon812 »

minihat wrote: post #9

Not close. This might be the best whole-animal sim available, and it is a for a worm: https://openworm.org/

And not just any worm, but a C. elegan, which always grows the exact same way every time. The whole reason those worms are so well understood was due to ease of analysis. Hell, it always has 302 neurons which always wire up in the same way. It couldn't be easier to simulate, and it's really hard to simulate!

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

#24

Post by [deleted] »

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…

[deleted]

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

#25

Post by salomon812 »

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…

> Anyway, drugs authorities have already approved drugs based on software simulations

The simulations you have linked aren't on the same scale. The paper uses the phrase "are powerful tools that COMPLEMENT traditional methods for gathering evidence"

And I'd argue this is more like detailed analysis rather than a simulation. It's like hoping you've found an immersive computer world like The Matrix, but it's a 2D side-scolling video game like Mario Bros.

I'd also question "approved drugs based on..." and instead argue they "didn't reject drugs based on..."

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

#26

Post by pton_xd »

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.

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

#27

Post by moralestapia »

On my research, I've done it with a plant (to a limited extent, obviously). The reason why I chose a plant is because they're less-complicated versions of animals, at least as far as my simulation was concerned.

We are "far" but it's that kind of thing that an unexpected breakthrough gets you 80% of the way. My bet would be, doable by 2040.

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

#28

Post by fakedang »

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.

There's an entire field called Biological Computing which studies precisely that (not AI, more around general purpose computing).

https://en.m.wikipedia.org/wiki/Biological_computing

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

#29

Post by tliltocatl »

Not going to happen. A model cannot be "valid" because by definition it's not ground truth (aka all models a wrong, some aren't too wrong). It can be good for some cases where it is known to match the reality good enough, but the cases any scientist care about are exactly those where existing models does not match the reality.
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