It models wiggling forward. It models wiggling backwards. And occasionally it models fucking itself. That’s it.
OpenWorm – A computational model of C. elegans worm
131–140 of 159 posts
Re: OpenWorm – A computational model of C. elegans worm
#132Earlier quoted context omitted.
> billions of DNA base pairs controlling their behavior Total genome size of C elegans is 100M.
Biologists should totally breed a subspecies of C elegans best suited for research purpose, call it C relevans.
...I hope you're happy. There's coffee everywhere now!
Re: OpenWorm – A computational model of C. elegans worm
#133Earlier 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…
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,…
Better information on what it actually simulates is here: https://docs.openworm.org/projects/
As of this year there are 3 known neuron classes in C. elegans that do exhibit action potentials. The rest exhibit graded potentials.
Re: OpenWorm – A computational model of C. elegans worm
#134Earlier 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?
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Re: OpenWorm – A computational model of C. elegans worm
#135I 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?
They aren't too different from human neurons. Non-spiking neurons also use nonlinear membrane dynamics to integrate inputs into a signal encoded by the voltage across the membrane. The cell then outputs a neurotransmitter in response to its voltage. In the case of a spiking cell and a spike dependent synapse, synaptic release is thought to be all or nothing. While in graded synapses, synaptic release is a more linear (modeled as a less steep sigmoid) function of voltage. Spiking cells can also have graded synapses (at least in crustaceans, I don't really know about vertebrates).
The idea is that spiking is one way to have a more robust signal over long distances: Crustaceans often have nonspiking local interneurons and spiking projection neurons and motor neurons. The problem of fast, reliable electrical signal transduction over long distances is also solved by having more insulation (particularly in vertebrates) or having thicker cables (particularly in invertebrates).
Humans also have non-spiking neurons with graded synapses in the retina.
Re: OpenWorm – A computational model of C. elegans worm
#136This project has existed for something like a decade. Does anyone know if there was any progress with it in the last few years?
Yes! News page here: https://openworm.org/news
Re: OpenWorm – A computational model of C. elegans worm
#137I would love to see a webassembly version of this engine so we can see these worms on a webbrowser. Wonder how hard it would be to do so. --- edit: Possibly baked already at http://wormsim.org/
Code for wormsim.org is here on Github btw: https://github.com/openworm/org.wormsim.frontend -- contributions welcome!
Re: OpenWorm – A computational model of C. elegans worm
#138Earlier quoted context omitted.
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?"
Would you mind explaining the unstated premise that basic research should in any way should be directly applied to solve real world problems?
Would you mind explaining why you think I said that?
Re: OpenWorm – A computational model of C. elegans worm
#139Earlier quoted context omitted.
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.
Sure, but if you can get some sort of understandable result, we might learn a bit more about what the worm's neurons are doing.
Re: OpenWorm – A computational model of C. elegans worm
#140Related:
OpenWorm - https://news.ycombinator.com/item?id=29045198 - Oct 2021 (110 comments)
OpenWorm – Create a virtual C. elegans nematode - https://news.ycombinator.com/item?id=8949408 - Jan 2015 (12 comments)
OpenWorm: A Digital Organism In Your Browser - https://news.ycombinator.com/item?id=7613732 - April 2014 (47 comments)
Openworm: c.elegans worm simulation - https://news.ycombinator.com/item?id=4208454 - July 2012 (14 comments)