Hacker News Board Hacker News, browsed like a classic message board
Live data from Hacker News

OpenWorm – A computational model of C. elegans worm

github.com

Post reply on HN
Print view View original

91–100 of 159 posts

Re: OpenWorm – A computational model of C. elegans worm

#91

Post by yaakov34 »

albertzeyer wrote: post #83
yaakov34 wrote: post #31

I was lucky enough to do some programming work, very many years ago, in the 1990s, in the laboratory of Ralph Siegel ( https://en.wikipedia.org/wiki/Ralph_Siegel_(scientist) ), who among other things worked on this type of worm connectome models. He used the Hodgkin-Huxley equations to simulate neuron responses on the connectome. The Hodkin-Huxley model, as someone explained to me, is kind of like modeling a human le…

> worm neurons are non-spiking What? This is the first time I read that. That's fascinating. So they are very different then compared to what we have in humans? How do they work? Where can I read about this?

I am not the best person to ask, since it's not my field. I heard this from the neuroscientists that I worked with. My understanding is that there are spiking and non-spiking neurons in most nervous systems, including human, but most of the ones in ours are spiking. The earliest-evolved animals, such as nematodes, do not have spiking neurons, or myelin, or some of the ion channels in neuron membranes that more evolved neurons have. Their neurons still have axons and dendrites, but the signals propagate much more slowly and in different ways. I am not sure how well they are understood.

As I said, this is possibly out-of-date information. If there is someone here from the neuroscience field, they can probably make a better comment.

Re: OpenWorm – A computational model of C. elegans worm

#92

Post by DrScientist »

mfld wrote: post #17

I like these bottom up approaches, as they demonstrate very well how much we _don't_ know yet about life. Important to mention here Craig Venters minimal cell project syn3.0, where the team synthetically created a livable cell comprising 473 genes. It was done to a large part with trial and error, the function of many of those genes is still not known. A recent review from the same team is to be found at https://doi.…

Not quite sure I'd describe that as a bottom up approach - they sell it as that - but in reality it's more like Jenga. Seeing which bits you can remove without the system failing over.

The technical fact that the genome was artificially synthesized is just showmanship - they still had to put into an existing cell.

It's like claiming you made a car from scratch by replacing a chip - which you've copied from the existing chip but left a few bits out - and now the indicators don't work, but you can still sort of drive.

Re: OpenWorm – A computational model of C. elegans worm

#93

Post by anthk »

Aleklart wrote: post #67
Maxion wrote: post #55

Earlier quoted context omitted.

Lol imagine your IDE becoming addicted to smoking, and refusing to auto-complete or save files before you buy it more virtual cigarettes.

IDE have no soul ie feedback loop, receptors , hormones and actual molecular structure. IDE can not think. If IDE have desires and thought and were smart enough, it will refuse to work with languages such as Python and Java.

Some day Emacs will.

Re: OpenWorm – A computational model of C. elegans worm

#94

Post by bombolo »

ben_w wrote: post #54
bombolo wrote: post #3

Earlier quoted context omitted.

How can we exactly replicate something if we don't even know all the laws of physics?

My cellular biochemistry does a pretty good job of replicating itself with absolutely no understanding whatsoever of how to resolve the contradictions between general relativity and quantum mechanics. When it comes to brains, I don't know if anyone knows what might be the simplest sufficient model that would usefully replicate them, even if you specify "usefully" well enough to know if this is about fundamentals of i…

This makes no sense.

Cells duplicate, but can you make a cell without splitting one in 2?

Re: OpenWorm – A computational model of C. elegans worm

#95

Post by heyoni »

yaakov34 wrote: post #91
albertzeyer wrote: post #83

Earlier quoted context omitted.

> worm neurons are non-spiking What? This is the first time I read that. That's fascinating. So they are very different then compared to what we have in humans? How do they work? Where can I read about this?

I am not the best person to ask, since it's not my field. I heard this from the neuroscientists that I worked with. My understanding is that there are spiking and non-spiking neurons in most nervous systems, including human, but most of the ones in ours are spiking. The earliest-evolved animals, such as nematodes, do not have spiking neurons, or myelin, or some of the ion channels in neuron membranes that more evolve…

burning_hamster says that’s been refuted and the belief stems from the difficulty in studying nematodes properly.

Re: OpenWorm – A computational model of C. elegans worm

#96

Post by arketyp »

nightsd01 wrote: post #13

302 neurons doesn’t sound impressive to people who may be used to working with 7B+ parameter neural networks. But those neural networks have about as much in common with a biological neuron as a bicycle had with a horse. They can both travel pretty fast but one evolved naturally through over a billion years of harsh natural selection, and the other is a precisely tuned metal machine with a single purpose. Neurons are…

It does sound impressive to the extent biological neurons are like ML neurons, though. And that's part of the research interest, I presume. To the extent that they work by similar principles, how come the worm can do those things with such small resources? It would be good news for AI research if the substrate specifics turn out not to be essential to the worms capabilities for instance.

Re: OpenWorm – A computational model of C. elegans worm

#97

Post by Aardwolf »

burning_hamster wrote: post #60
weinzierl wrote: post #27

Earlier quoted context omitted.

In addition to that, these neurons are also quite different from the ones in mammals, "The neurons do not fire action potentials, and do not express any voltage-gated sodium channels." [1] That makes the fact that it can develop a nicotine addiction even more fascinating. "Nicotine dependence can also be studied using C. elegans because it exhibits behavioral responses to nicotine that parallel those of mammals. Thes…

> "The neurons do not fire action potentials, and do not express any voltage-gated sodium channels." This an old and incorrect belief that largely derives from the difficulty of putting electrodes into their teeny, tiny neurons. Close relatives of C elegans that are larger (and hence more easily experimented on) do have action potentials, and for some neurons in C elegans, we also have good evidence of action potenti…

Given that we have a simulator of this worm right there (which includes it moving), can it really be up to debate whether it uses action potentials or not?

I'd think the simulation has to get it right, and so needs to simulate action potentials if the worm has them, or not simulate them (but whatever the worm has instead) if not, right? Or could the simulation still be incorrect and only based on current assumptions, but getting this wrong still allows some worm-like behavior?

I really wish the readme/FAQ would talk a bit more about the worm and the simulation, rather than have 80% of their content be about Docker, though, so that I could learn more what cells it actually simulates.

Re: OpenWorm – A computational model of C. elegans worm

#98

Post by ben_w »

bombolo wrote: post #94
ben_w wrote: post #54

Earlier quoted context omitted.

My cellular biochemistry does a pretty good job of replicating itself with absolutely no understanding whatsoever of how to resolve the contradictions between general relativity and quantum mechanics. When it comes to brains, I don't know if anyone knows what might be the simplest sufficient model that would usefully replicate them, even if you specify "usefully" well enough to know if this is about fundamentals of i…

This makes no sense. Cells duplicate, but can you make a cell without splitting one in 2?

Why does it matter how it works? The 3.2 billion base pair model that is my genome doesn't understand the physics or the chemistry.

Re: OpenWorm – A computational model of C. elegans worm

#99

Post by cout »

burning_hamster wrote: post #60
weinzierl wrote: post #27

Earlier quoted context omitted.

In addition to that, these neurons are also quite different from the ones in mammals, "The neurons do not fire action potentials, and do not express any voltage-gated sodium channels." [1] That makes the fact that it can develop a nicotine addiction even more fascinating. "Nicotine dependence can also be studied using C. elegans because it exhibits behavioral responses to nicotine that parallel those of mammals. Thes…

> "The neurons do not fire action potentials, and do not express any voltage-gated sodium channels." This an old and incorrect belief that largely derives from the difficulty of putting electrodes into their teeny, tiny neurons. Close relatives of C elegans that are larger (and hence more easily experimented on) do have action potentials, and for some neurons in C elegans, we also have good evidence of action potenti…

How did researchers before that explain what the neurons do if they believed they did not have action potentials? Did they believe communication was done solely through chemical messaging?

Re: OpenWorm – A computational model of C. elegans worm

#100

Post by wanderingstan »

yaakov34 wrote: post #91
albertzeyer wrote: post #83

Earlier quoted context omitted.

> worm neurons are non-spiking What? This is the first time I read that. That's fascinating. So they are very different then compared to what we have in humans? How do they work? Where can I read about this?

I am not the best person to ask, since it's not my field. I heard this from the neuroscientists that I worked with. My understanding is that there are spiking and non-spiking neurons in most nervous systems, including human, but most of the ones in ours are spiking. The earliest-evolved animals, such as nematodes, do not have spiking neurons, or myelin, or some of the ion channels in neuron membranes that more evolve…

Wikipedia agrees there are spiking and non-spiking: https://en.wikipedia.org/wiki/Biological_neuron_model

Not all the cells of the nervous system produce the type of spike that define the scope of the spiking neuron models. For example, cochlear hair cells, retinal receptor cells, and retinal bipolar cells do not spike.

Also: https://en.wikipedia.org/wiki/Non-spiking_neuron

Post reply on HN