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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

#71

Post by boredumb »

Fascinating to see this again it's been at least a decade since I first found it. Projects like this always make make me glad to see because it's almost "useless" work that I imagine will be a foot note to some seriously impressive future technology. Very cool work in the mean time. As an aside - this brings back a weird feeling of nosatlgia, but this repository also brought me back to a time where I was stuck in an over-engineered .NET shop and i'm now debating if we start the day off with whiskey after having a flashback to being asked to implement "Ninject" into a massive spaghetti banquet of a code base (collective hope that dep injection fixes bad code).

In case anyone is worried I write software in Rust and Golang now and my life has improved significantly since the origins of this worm and people taking dep injection frame works seriously. :D

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

#72

Post by boredumb »

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…

Out of curiosity - were there any commercial applications this was being developed towards?

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

#73

Post by chromanoid »

XorNot wrote: post #47
chromanoid wrote: post #21

Earlier quoted context omitted.

Yeah, but we understand why birds can fly and why fish can swim and how gepards can run, at least on a mechanical basis. This is not true for how this 302 cell organism works. We don't know and struggle to understand. That's actually the reason why the project exists. To find out how everything works with an bottom-up approach. While we may find shortcuts or even superior forms of intelligence without understanding h…

Except understanding how a bird can fly had little bearing on building the Wright brothers flyer. And most of the details of bird flight were not exactly discovered till well after commercial air travel was commonplace.

While the exact details were not understood, the mechanics were visible and explainable to some extent. The Wright brothers were at least inspired by birds. https://www.wright-brothers.org/History_Wing/Wright_Story/In...

We still don't know how cells in C. elegans work together. It's neither visible nor explainable on a satisfying level.

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

#74

Post by drakonka »

I went to an OpenWorm mini-conference of some kind in London a few years back - a couple of days talking about worm locomotion. Knowing nothing about worms or animal locomotion in general, I was a complete layman with an amateur interest in life simulation and understood next to nothing. But it was still fascinating, and was so cool to meet people passionate about this.

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

#75

Post by lz400 »

I looked at this a few years back. I've always kept some hope that the Kurzwellian eschatology had some validity. You know, first we simulate a C.elegans and once that's done, it's only a matter of scale up before we can simulate a human and then boom singularity sky. And, really, how difficult is it to simulate a silly worm? after all the connectome is there, we know all the neurons and their connections, should be easy.

Well, when I looked at it I was shocked: it doesn't work! sure it could replicate some basic movements but many things that the stupid worm actually does where still a mystery. The docs didn't seem like people were close to figure it out either. And sure enough, a few years later seems like they gave up. And afaik that hyped European brain emulation project also folded in the midst of corruption allegations no less.

I think we don't understand any of this and we seem very far from it too. I think it's back to science fiction novels for a while.

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

#76

Post by miohtama »

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.

My IDE does only LSD and PHP

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

#77

Post by FrustratedMonky »

dilawar wrote: post #33
eterevsky wrote: post #29

This project has existed for something like a decade. Does anyone know if there was any progress with it in the last few years?

I did my Ph.D. in computational neuroscience (2020 grad). This project is often used to joke about the limitation of computational modelling of nervous system. If you can't compute the behavious of an effing worm with mere ~300 neurons, whats the point of all hot-air around connectomics (mapping connections of the brain). Connectomics used to be a big word when I started my Ph.D.. The apologists are always like, "rea…

Yeah, like hormones, (I'm assuming what you are calling chemical computations). Maybe this isn't forgotten, just not figured out yet. Maybe future GPTs will have some other layer of weights, or different level of feedback, that could be called 'hormones'.

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

#78

Post by chromanoid »

seydor wrote: post #64

many years ago this was interesting. Nowadays, with the progress in deep models i m not sure if there is much to learn from c.elegans. What is this useful for? For high level cognition, it's much more fruitful to study how deep models do it. For low level brain diseases, c.elegans is too simplistic to tell us anything we dont already know

We don't know anything substantial about C.elegans in this regard. That is actually the point. This is even more true for more complex nerve systems.

The whole deep learning stuff is basically roughly inspired by a tiny part of the visual cortex (see also Neocognitron). I am not sure how brain diseases can be understood by looking at such simplistic (yet powerful) machines.

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

#79

Post by chromanoid »

Gordonjcp wrote: post #51
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…

What would a "real world" application of this be? Could I for example chuck a bunch of simulated worms onto a map and have it solve a route? "Given enough worms, all Travelling Salesman problems are shallow?"

The real world application would be to understand how more complex nerve systems might work. Understanding enables progress.

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

#80

Post by moffkalast »

Maxion wrote: post #55
miohtama wrote: post #46

Earlier quoted context omitted.

Next: OpenSmoker.py

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

Sounds like it needs an OpenNicotine patch.
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