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OpenWorm – A computational model of C. elegans worm

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

#121

Post by ummonk »

lukasday wrote: post #34

I love it when anything Caenorhabditis elegans (C. Elegans) related pops up because this little biological organism sits at this beautiful intersection between technology and biology and philosophy. The successful emulation of C. Elegans would represent a concrete step towards whole brain emulation and all the transhuman and ethical and moral quandaries that would bring. The general idea is that the human brain has b…

They wiggle forward, they wiggle backwards, and occasionally they f*** themselves. That's it.

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

#122

Post by anotheryou »

bee_rider wrote: post #110
anotheryou wrote: post #108

And to me this is just as sentient (or not) as the physical worm and deserves worm rights!

Does this actually become an interesting question at this point? I guess worms don’t have many rights anyway, but if they did, and this was a totally accurate simulation, why not give the digital worm rights?

not interesting for a worm but interesting for a first of its kind

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

#124

Post by jarrell_mark »

weinzierl wrote: post #27
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…

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…

Would like to see the openworm get addicted to virtual nicotine

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

#125

Post by omnicognate »

xvilka wrote: post #52

Connectome model of fruit fly brain was just recently published[1]. [1] https://hub.jhu.edu/2023/03/09/scientists-complete-first-map...

Which is awesome, but the C. Elegans connectome was published in 1989 and as you'll see if you investigate the linked project a bit we are absolutely nowhere near having C. Elegans' full set of behaviours emerge from a simulation of its neurons, or even to proving that it's feasible to do so.

This makes neurokernel [1] and the like seem just a tad ambitious. Good luck to them though.

[1] http://neurokernel.github.io/

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

#126

Post by tomjakubowski »

anthk wrote: post #93
Aleklart wrote: post #67

Earlier quoted context omitted.

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.

trained on everything you've been saying to M-x doctor

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

#127

Post by pests »

nycticorax wrote: post #114
burning_hamster wrote: post #60

Earlier quoted context omitted.

> "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…

Well, the 'canonical' action potential is mediated by sodium currents, so it's maybe not surprising that people concluded that C elegans don't have APs given that a) they don't have any genes for voltage-gated sodium channels, and b) when people had recorded from C elegans neurons (it's hard but not impossible), they had never seen action potentials. (So it's not like no one had looked, and then had concluded that th…

> are generated by calcium, not sodium currents, so one could even argue that they aren't action potentials in the strict sense

Does the underlying chemistry define if its an action potential or not? I thought an AP just needed a voltage differential regardless if its from calcium or sodium.

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

#128

Post by xkcd-sucks »

cout wrote: post #99
burning_hamster wrote: post #60

Earlier quoted context omitted.

> "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?

Classical action potentials are just one mechanism of INTRAcellular communication - You could think of it as a special case of signaling via chemical concentration, where the chemical is cations and the propagation is faster+more directed than diffusion. INTERcellular signaling is only rarely mediated directly by voltage. Also, action potentials are most "useful" for propagating a signal rapidly over a long distance - It kind of accelerates and error-corrects (= reverses diffusive broadening) voltage signals down a linear path. Action potentials are so well known mostly because they show up in stuff that's easy to observe (long motor neurons) and they're easy to quantify

Somewhat related, there is a roughly inverse correlation between neuron count and "computational power per neuron", "older and simpler" critters' neurons are more likely to be "less specialized" and more likely to use hundreds of different chemicals for transmitting intercellular signals, while "newer and more advanced" critters' neurons are more likely to be "specialized" and use just one chemical for transmitting intercellular signals

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

#129

Post by candrewlee14 »

It's always fun for me to see C. elegans meet software. This is amazing.

My undergrad degree capstone project was a flow-based visual C. elegans strain builder[1]. The team worked with two researchers who taught us a lot about genetics and basic C. elegans biology. They are a fascinating model organism, and it was a super fun project to work on. Even though it's got a very small potential userbase, it did have a potential userbase (which was more than you could say about most capstone projects). We used some interesting technology to build it (Tauri[2]: Rust + Web Frontend), learned some biology along the way, and ended up with a great prototype.

Since none of the software team had any background in genetics, modeling the data was pretty difficult. We'd meet with researchers, they'd teach us new genetics concept, we'd build our models, then the next week they'd say "OH we forgot to tell you about this caveat", then we'd go back to the drawing board, update the schema (thank heavens for migrations), rinse and repeat. It was a lot of fun though :) I couldn't have asked for much more out of a capstone project.

[1] https://worm-world.github.io/ [2] https://tauri.app/

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