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C. Elegans: The worm that no computer scientist can crack
- ddtaylor 2y agoI was reading the article and it disappeared entirely. Is there website functional? Is this intentional?
- 0manrho 2y agoWhat do you mean by "disappeared"? Did the page just go white/black or something? I didn't experience that while reading the article (waterfox browser), and can't recall that ever happening on Wired, and I somewhat frequently read wired articles (few times a week, not a registered/paying member). I tried it in chromium (no extensions) and if you scroll there is a fullpage ad where the article seems to "disappear" but it's essentially an ad fold, and if you keep scrolling the rest of the article is there. Otherwise not sure what you mean? What browser you using?
- mitchbob 2y agohttps://archive.ph/2025.03.27-055757/https://www.wired.com/story/openworm-worm-simulator-biology-code/ https://archive.ph/2025.03.27-055757/https://www.wired.com/s...
- ninetyninenine 2y agoWhich is the more advanced life form? C. Elegans or LLM? I vote LLM.
- someothherguyy 2y agoc. elegans can reproduce autonomously, can source its own energy inputs, etc. also, last i checked, an llm doesn't meet the definition of life form.
- sambeau 2y agoC. Elegant can suffer from depression, exhibiting some behaviours similar to humans with depression.
- isaacfrond 2y agoWell, by definition we are simulation LLMs just fine, but per the article we are utterly failing on Elagans, so it seems the smart money is on the latter.
- idiotsecant 2y agoMore complex and more advanced are not the same thing. Evolution produces a lot of twisty little passages that are only that way because it happened to work.
- 0x000xca0xfe 2y agoLLM research has a much bigger budget than C. Elegans research.
- fossgeller 2y agoThat says more about the industrializaton of scientific research than anything. LLMs is the new hype product of tech companies. Wait a couple years and the interest will die out. Maybe we’ll live the day when true neuroscience (none of that Andrew Huberman stuff) will be trending.
- ninetyninenine 2y agoDoesn’t mean it’s more complex though. It just means the complexity is harder to capture and copy. LLMs are built via algorithm. Given enough data and a large enough neural network the complexity of an LLM is boundless. I guess my question is are existing LLMs more complex?
- jxkdbdndbeb 2y agoI would please advise you to study biology ... The amount of cool shit that goes on at a microscopic level will amaze you
- jxkdbdndbeb 2y agoAlso c. Elegans hands down
- piyuv 2y agoThis is the content i come here for
- smj-edison 2y agoIt's pretty crazy just how computationally intense biological simulations are. The timesteps are just so tiny and the number of nodes involved is insane...
- 3np 2y agoThat's life.
- FerretFred 2y agoYeah, I found this when I was Boinc protein folding for Covid. The work units ran for hours, my towercPC nearly melted, and then I found that this produced mere milliseconds of simulation!
- xattt 2y ago> nearly melted I’ll be that guy, but a computationally complex problem won’t push your computer to a temperature beyond design limits.
- FerretFred 2y agoYou're welcome to come to my attic office in summer, as they ambient temperature reaches 200F m a sunny day and my obsolete-but-powerful tower PC consumes 350W power and adds to the tropical heat :)
- LoganDark 2y ago> a computationally complex problem won’t push your computer to a temperature beyond design limits. Allegedly. It allegedly won't do that. Practically, running your CPU at design limits for a very long period of time tends to cause the temperature of the rest of the chassis to want to equalize to that temperature, which can be above comfort limits.
- inglisilihsh 2y agohttps://en.wikipedia.org/wiki/Hyperbole#:~:text=Hyperbole%20is%20often%20used%20for,or%20ironic%20or%20comic%20effects. https://en.wikipedia.org/wiki/Hyperbole#:~:text=Hyperbole%20...
- Animats 2y agoIt's good that they are still trying. It would be really nice to know how biological neurons really work. That it's so hard, even with the connectome available indicates something important. I used to think Open Worm was going to be a big deal. Top-down AI seemed to be stuck during the AI Winter. But machine learning got unstuck and Open Worm is still stuck.
- melagonster 2y agoWhen last time I hear about the neuron simulation project, they can not get new budget.
- cb321 2y agoDue to its technical content, some may be unaware that the author of TFA, Claire L. Evans, is a bona fide rock star: https://en.wikipedia.org/wiki/Claire_L._Evans https://en.wikipedia.org/wiki/Claire_L._Evans with a grammy nomination and everything: https://www.grammy.com/artists/claire-l-evans/280302 https://www.grammy.com/artists/claire-l-evans/280302 . There are not many out there recognized for both music and science writing.. :-)
- mateus1 2y agoInteresting, thanks for sharing. I’m going to read her book “Broad band” on women that made the internet.
- 4gotunameagain 2y ago[flagged]
- frozenseven 2y ago[flagged]
- FrustratedMonky 2y agoAll that was mentioned was that the author was a singer. So singer and a writer. That was only point made.
- 4gotunameagain 2y ago[flagged]
- sitkack 2y agoNeat book, https://en.wikipedia.org/wiki/Broad_Band https://en.wikipedia.org/wiki/Broad_Band For a copy near you, https://search.worldcat.org/title/1077130914 https://search.worldcat.org/title/1077130914 1hr long lecture by Claire Evans https://www.youtube.com/watch?v=wLQKp8mHHJ0 https://www.youtube.com/watch?v=wLQKp8mHHJ0
- metalman 2y agoI have a law to describe human's and our technology: if it can be done, it is bieng done if it cant't be done yet, a bunch of people are trying now,if it's impossible, and multiply proven so, some people are trying anyway, and all of it in complete disregard for any concievable utility or benifit but I cant help but wonder, if and when , someone playing with worm neurons, or myclium networks will get a hello world, and post instructions on how to get it to run doom, which presumably would involve some sort of transaction, involving energy nutritional, and reproductive advantages.
- the__alchemist 2y ago> His goal is nothing less than a digital twin of the real worm, accurate down to the molecule. I am nitpicking this: The state of computational chemistry is not at a level to support this. I'm optimistic we'll get there eventually; need to find novel approaches, and current ones are too imprecise, or too slow. I think the connectome aspect is more interesting, as it may be feasible to get there 100% without a computational chem breakthrough.
- firtoz 2y agoWhat's the latest and the best so far? Are they using GPGPU? Is quantum computing there yet, or would it help? Heuristics and sampling?
- rsfern 2y agoGPGPU is definitely mainstream for large scale quantum and molecular simulation. Quantum computing might help speed up electronic structure calculations, but my impression is that it’s still in its infancy To give a sense of the scale of this problem, the largest frontier simulations I’m aware of are around the trillion atom scale. (On tens of thousands of GPUs [0]) Based on a quick web search, a c elegans cell is between 3 microns and 30 microns in diameter, so if we assume we can count atoms using the density of water then an all-atom simulation of a single neuron would need between 5e11 to 5e14 atoms. c. Elegans has 302 neurons so simulating the full neural network will be 2-5 orders of magnitude larger than current frontier simulations. Honestly more doable than I thought it would be, though all-atom simulation of a full organism still seems quite out of reach This is all with classical force fields. Doing this simulation at the electronic structure level is much much harder with our current modeling capabilities 0: https://www.mrs.org/meetings-events/annual-meetings/archive/meeting/presentations/view/2024-fall-meeting/2024-fall-meeting-4151737 https://www.mrs.org/meetings-events/annual-meetings/archive/...
- kaferoni 2y agoThere's also interesting custom-made machines for molecular simulations that don't rely on GPGPUs and are significantly faster, e.g.: - https://arxiv.org/abs/2405.07898 https://arxiv.org/abs/2405.07898 - https://www.psc.edu/resources/anton/ https://www.psc.edu/resources/anton/
- qrios 2y agoInteresting article, but no reference to "DEVS"? Prediction of the worms behaviour is a key scene[1] in the opening episode. [1] https://www.youtube.com/watch?v=xEfyT3vLD2c https://www.youtube.com/watch?v=xEfyT3vLD2c
- resource0x 2y agoThis podcast will be a shocking experience for anyone who still holds reductionist views on life. https://www.youtube.com/watch?v=c8iFtaltX-s https://www.youtube.com/watch?v=c8iFtaltX-s Michael Levin's channel: https://www.youtube.com/results?search_query=michael+levin+academic+content https://www.youtube.com/results?search_query=michael+levin+a... His blog: https://thoughtforms.life/ https://thoughtforms.life/
- didericis 2y ago"The Matter with Things" by Iain McGilchrist has the same effect. Highly recommend it.
- resource0x 2y agoBy any chance, have you watched the videos from the recent conference? https://ctr4process.org/conference/metaphysics-and-the-matter-with-things-thinking-with-iain-mcgilchrist/ https://ctr4process.org/conference/metaphysics-and-the-matte...
- didericis 2y agoNo, but I will. Thanks. (link isn’t loading for me on mobile, will try again later)
- red75prime 2y ago> a shocking experience for anyone who still holds reductionist views on life. As far as I understood he doesn't state that life cannot be explained by physics. But that it might be more productive to choose a more high level view. Makes sense. If a set of physical laws allows life at all, life will maintain its own set of rules (related to reproduction, goal-directed behavior and so on) regardless of low level "implementation details" that are dependent on particulars of the physical laws.
- resource0x 2y agoPlease read this essay and make your own conclusions. (He rejects physicalism in no uncertain terms). https://thoughtforms.life/platonic-space-where-cognitive-and-morphological-patterns-come-from-besides-genetics-and-environment/ https://thoughtforms.life/platonic-space-where-cognitive-and...
- 6d6b73 2y agoOpenWorm is dead afaik. Larson took some of the code and started his own company Metacell. It's not that we can't crack it, it's simply that nobody really dedicated enough time and resources to do it.
- moffkalast 2y ago> But there’s a difference between schematics and an operating manual. “We know the wiring; we don’t know the dynamics,” Cohen said. They have the architecture, but can't read the weights and biases as it were? I was under the impression that they somehow mapped the activations, but if not then they're really just flying blind.
- Willingham 2y agoThis project seems a bit funny to me. Cell level simulation is the current bottleneck of the project, why would we not start at the cellular level, and then move up to multicellular organisms? Of course this ultimately leads to the question, can we truly simulate anything if we can’t simulate at the quantum level?(at scale) It would be quite profound to find out that we can fully simulate complex life while abstracting the lower levels, if that were the case, maybe we don’t need them either! Good riddance to all those quantum conundrums (;
- VirusNewbie 2y agoI think the assumption is some abstractions aren't leaky.
- acchow 2y agoThe abstractions are fictional. The system wasn’t “designed” with separation. We just pretend they are there for tractability.
- VirusNewbie 2y agoCertainly this isn't true at every level of granularity unless you're making some Penrosian claim about QM affecting say, one's decision tree? Which is a valid though quite disputed claim, say more about that if you believe it though.
- acchow 2y agoWhy not? “~= 0” just means we likely will be unable to measure any effect. Not that there literally is no effect. Us being unable to do science on something means we cannot scientifically state that it does not exist. Not that we can categorically state that it does not exist.
- JR1427 2y agoOne interesting fact about C. elegans is that the way the grow from 1 cell to adult (~1000 cells) is almost completely reproducible between different worms. I.e. the pattern of cell division and the positions and identities of the cells is very fixed, with known timing etc. Compare this to mammalian development, where even at the early stages, development becomes less rigid and operates by "course correction", rather than by following strict sequences. (I studied the early development of C. elegans for my PhD)
- fastaguy88 2y agoLet's see: C elegans -- the worm no computer scientist can crack S. cerevisiae -- the yeast no computer scientist can crack E. coli -- the bacterium no computer scientist can crack HIV -- the virus no computer scientist can crack Has a computer scientist cracked any complex system that was not engineered?