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Simulating 1 second of real brain activity takes 40 minutes and 83K processors

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Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#21

Post by lvs »

deletes wrote: post #15
foobarbazqux wrote: post #10

To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. This matters, for example, if we want to simulate neuronal plasticity or the effect of antidepressants. We're an incredibly long way from a full simulation, which wou…

To correctly model a cell you would need to simulate every atom and there are about 10^11 to 10^14 (!) of them in a single cell. I think an interesting number would be how many atoms does it take to simulate one atom reasonably well. Then you could get correct results for some ( really ) small biological functions.

Your point is valid, but many people are trying to "correctly model a cell" without making a total atomistic simulation (which is clearly not going to happen any time soon). It's all about what questions you're looking to ask of a model.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#22

Post by foobarbazqux »

gwern wrote: post #13
foobarbazqux wrote: post #10

To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. This matters, for example, if we want to simulate neuronal plasticity or the effect of antidepressants. We're an incredibly long way from a full simulation, which wou…

> To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. To me, this mostly shows that naive beliefs about difficulty aren't really accurate ('but it should it harder to simulate a brain than a cell, because it's bigger r…

Sure, but that's also for a bacterial cell. We have 50 times as many genes and you can't easily culture humans on a Petri dish for experimentation. A single gene can take years of work to understand.

Yes, you can simulate anything if you abstract away enough. But if the goal is a convincing replication, you'll need to include lots of intracellular effects.

In the end, I believe that practical simulation of a whole brain that you can have a conversation about its existence with is more difficult than the development of quantum computing powerful enough to break all existing crypto.

The work is still interesting, if only because it pushes the limits of what we can do. But I might want to start with an ant brain.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#23

Post by foobarbazqux »

deletes wrote: post #15
foobarbazqux wrote: post #10

To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. This matters, for example, if we want to simulate neuronal plasticity or the effect of antidepressants. We're an incredibly long way from a full simulation, which wou…

To correctly model a cell you would need to simulate every atom and there are about 10^11 to 10^14 (!) of them in a single cell. I think an interesting number would be how many atoms does it take to simulate one atom reasonably well. Then you could get correct results for some ( really ) small biological functions.

Usually people modeling cells don't consider molecular dynamics, they consider concentrations of proteins, ions, and metabolites. A full MD simulation would obviously be superior, but useful predictions could be made without it.

It's hard to say which is the better approach. On the one hand you have MD from which you could technically build an accurate model "from scratch", folding all of your own proteins as part of the simulation, but it is exceedingly expensive to do that. On the other hand, you have a model built at the level of biochemical reactions and molecular biology, which is computationally feasible, but then you don't have enough information from bench work to flesh it out.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#24

Post by Dylan16807 »

gwern wrote: post #13
foobarbazqux wrote: post #10

To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. This matters, for example, if we want to simulate neuronal plasticity or the effect of antidepressants. We're an incredibly long way from a full simulation, which wou…

> To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. To me, this mostly shows that naive beliefs about difficulty aren't really accurate ('but it should it harder to simulate a brain than a cell, because it's bigger r…

Why does it show that the belief isn't accurate? This isn't simulating a brain, it's simulating the connections in a brain and pretending the neurons are about as complex as wires. That is a model that is possibly correct, but there's certainly no evidence it's correct.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#25

Post by oh_teh_meows »

anigbrowl wrote: post #2

Unfortunately, that's only for a number of cells equivalent to 1% of a human brain. A full brain's worth of simulation would take 2.5 days....although that much is probably not necessary. It will fall soon enough, though.

I'm not certain if that extrapolation you made of the time it takes to simulate a brain at the same abstraction level is valid. You're assuming the computation cycles needed will scale linearly, which might not be true considering that the brain is a network of neurons, where each neuron has a high number of in/out links to many other neurons. Consider the case where you take n seconds to simulate n neurons. Now add another neuron with connections to perhaps n/2 existing neurons. You'll have to iterate over each in/out edge of that neuron. Since adding just one neuron increases the time by a non-constant factor, the resources needed would increase more than just linearly. All this of course depends on the abstraction model, and I admit I know nothing about it.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#26

Post by cabalamat »

pervycreeper wrote: post #4
anigbrowl wrote: post #2

Unfortunately, that's only for a number of cells equivalent to 1% of a human brain. A full brain's worth of simulation would take 2.5 days....although that much is probably not necessary. It will fall soon enough, though.

The thought that we are maybe two decades away from having the computing power to simulate a human brain in realtime (and much more than that subsequently) is astounding, even in this age of technological wonder.

Assuming (1) it's parallelisable (2) this is an accurate enough similation, and (3) a whole human brain is 100 times bigger, we'd need 406083k*100 processors which is about 20 billion.

We could do it now (hardware-wise), if we really wanted to.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#27

Post by dnautics »

gwern wrote: post #13
foobarbazqux wrote: post #10

To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. This matters, for example, if we want to simulate neuronal plasticity or the effect of antidepressants. We're an incredibly long way from a full simulation, which wou…

> To put this claim in perspective, we are still unable to simulate a single cell by modeling everything we know from biochemistry, even if we ignore molecular dynamics. Mostly this is because we don't know what many genes and the proteins they encode do. To me, this mostly shows that naive beliefs about difficulty aren't really accurate ('but it should it harder to simulate a brain than a cell, because it's bigger r…

I happen to work in the synthetic biology lab at the venter institute, although not on this project - two of our researchers are coauthors on this paper - and my personal opinion is that this paper is a joke. Note that the guys who made the simulation didn't even pick the correct organism. The cell that we have synthetic control over is M. mycoides, not M. genitalium. Lest this seem like a nit-pickey detail, until they rewrite their software for mycoides, in broad strokes the model is essentially untestable, since we don't have broad-scale control over the genitalium genome like we do mycoides.

Also note that: "The model accounts for previously observed gene essentiality with 79% accuracy." This is REALLY bad. Considering they are 'seeding' the model using a biased structure that automatically "knows" that certain genes are essential (for example, they have a 'module' for replication that probably zeroes out if you are missing an important replication component, as opposed to simulating how those genes work at a low level) this is probably somewhere close to as good as flipping a coin.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#28

Post by pervycreeper »

cabalamat wrote: post #26
pervycreeper wrote: post #4

Earlier quoted context omitted.

The thought that we are maybe two decades away from having the computing power to simulate a human brain in realtime (and much more than that subsequently) is astounding, even in this age of technological wonder.

Assuming (1) it's parallelisable (2) this is an accurate enough similation, and (3) a whole human brain is 100 times bigger, we'd need 40 60 83k*100 processors which is about 20 billion. We could do it now (hardware-wise), if we really wanted to.

Admittedly, I was just spitballing from the parent poster's numbers. But the idea that brain simulation is not that far off still seems plausible given those extra considerations.

Re: Simulating 1 second of real brain activity takes 40 minutes and 83K processors

#29

Post by frozenport »

jevinskie wrote: post #17
deletes wrote: post #15

Earlier quoted context omitted.

To correctly model a cell you would need to simulate every atom and there are about 10^11 to 10^14 (!) of them in a single cell. I think an interesting number would be how many atoms does it take to simulate one atom reasonably well. Then you could get correct results for some ( really ) small biological functions.

Aren't you modeling a subset of the universe at that level? Isn't a model supposed to provide a higher level understanding/abstraction?

In cases where qualitative meaning is nontrivial, you don't know 100% what is going on, it is nevertheless possible to implement parametric studies for some target parameter.
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