Neat. I'm wondering how much of inner cell biology can be abstracted away.
How accurate can neuron simulation be without underlying chemistry and physics?
OpenWorm – A computational model of C. elegans worm
41–50 of 159 posts
Re: OpenWorm – A computational model of C. elegans worm
#42So... if you exit the simulation, did you kill a worm?
Yes
Re: OpenWorm – A computational model of C. elegans worm
#43Earlier quoted context omitted.
This is a fundamentally flawed way of questionning, "knowing all the laws of physics" is probably impossible to achieve, but we still produce accurate predictions for a lot of phenomena. You can see that we do in fact "replicate" (predict would be a more proper term) things despite not knowing all the laws of physics: weather, movement of the stars, cooking time for a browned piece of bread...
I was replying to someone asking if it was "exact"… and no it isn't… You listing a bunch of simulations, that are notoriously not 100% correct proves my point, thanks.
You're welcome, but your point was not very clear.
Re: OpenWorm – A computational model of C. elegans worm
#44Wow it's amazing how much progress was made on this! a full simulation!!!!
Are you shitting on peoples work just for the sake of shitting on it? edit. this comment seems unpopular, my intent was to defend the worm against trolls :)
brother you are a sledgehammer but you need to be just a hammer for now
Re: OpenWorm – A computational model of C. elegans worm
#45Waiting for the day when we can observe an actual worm and predict its movements exactly by simulating them ahead of time.
Re: OpenWorm – A computational model of C. elegans worm
#46302 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…
Next: OpenSmoker.py
Re: OpenWorm – A computational model of C. elegans worm
#47Earlier quoted context omitted.
This. Submarines don't swim like fish, airplanes don't fly like birds and cars don't run like gepards. Edit: I am surprised at the downvotes. In general, we learn from the nature, but aping it usually proved too difficult and often unpractical at the same time. Do we really want to replicate worm intelligence for practical purposes, or do we want something different? I would say that a machine which can, say, analyze…
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.
Re: OpenWorm – A computational model of C. elegans worm
#48I 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.…
A paper tracking the evolution of this minimal cell over two thousand generations has just been published: https://www.nature.com/articles/s41586-023-06288-x
Re: OpenWorm – A computational model of C. elegans worm
#49This 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…
> Connectomics used to be a big word when I started my Ph.D.
On a scale of one to ten, how sick are you of people asking you about Neal Stephenson - "The Fall, or Dodge in Hell"?
Re: OpenWorm – A computational model of C. elegans worm
#50So... if you exit the simulation, did you kill a worm?
Only on Unix