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OpenWorm – A computational model of C. elegans worm
- jcims 3y agoWatching the little worm writhe on the screen made me realize that you could just sit there and torture it with impunity. Kinda creepy.
- c7DJTLrn 3y agoSo is this an exact digital replica of a worm?
- bombolo 3y agoHow can we exactly replicate something if we don't even know all the laws of physics?
- nightsd01 3y agoThe same way we can simulate the movements of the planets - it will never be exact, but the better we understand it, the more precisely we can simulate it
- bombolo 3y agoWell the question asked if it was exact. I pointed out why it can't be.
- highduc 3y agoclearly depends on needed resolution and our ability to recreate the material structure. you don't have to understand much about wood to build a chair.
- Leo_Germond 3y agoThis 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...
- bombolo 3y agoI 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.
- Leo_Germond 3y agoYou're welcome, but your point was not very clear.
- ben_w 3y agoMy cellular biochemistry does a pretty good job of replicating itself with absolutely no understanding whatsoever of how to resolve the contradictions between general relativity and quantum mechanics. When it comes to brains, I don't know if anyone knows what might be the simplest sufficient model that would usefully replicate them, even if you specify "usefully" well enough to know if this is about fundamentals of intelligence or about the impact of drugs on cognition, which are two completely different standards. For example, perceptrons are a toy model, but modern AI can do more in (breadth XOR single-skill performance in various domains) than any single human, even with much smaller parameter counts than we have synapses; but the broad-skilled ones also mess up in inhuman ways, like being equally good at advanced calculus as basic arithmetic, or being a poet at the level of stereotypical teenager but in every language simultaneously. If anyone's made a neutral network that can get high on simulated caffeine — and I'm not saying it hasn't been done — it's not reached any of the places I follow discussions on this kind of thing. (Google didn't help, results were about software named Caffeine and non-artificial neurones).
- bombolo 3y agoThis makes no sense. Cells duplicate, but can you make a cell without splitting one in 2?
- ben_w 3y agoWhy does it matter how it works? The 3.2 billion base pair model that is my genome doesn't understand the physics or the chemistry.
- mrguyorama 3y agoThat's entirely wrong. The interactions of proteins and amino acids and ions IS, at a fundamental level, the evaluation of physics over time.
- ben_w 3y agoI'm not saying it isn't physics, I'm saying it doesn't know what the physics is. We're physics too, but we don't know how it all fits together. If a sub-part of us that knows less than we do can make a copy of us, despite not knowing how it all works, that's an existence proof that we don't need to understand how it all works to make a copy of us.
- Legend2440 3y agoAbstraction. You don't need to know what's going on at the quantum level because higher-level simulations can capture all the properties you care about.
- dekhn 3y agoIf the "something" never exploits a particular law, then in principle you could simulate it if you knew all the laws that actually applied (imagine a hypothetical biological organism that never exploited or experienced quantum entanglement). But strictly speaking, as we understand it, it's not possible to replicate something exactly without recapitulating the exact laws and running a deterministic simulation, which is not practical. I don't think anybody is really attempting to exactly replicate things, but rather to create a physical model which can be calcualted and contains enough similarity or transferrability to be able to make accurate generalized predictions about the behavior of the simulated system. How and why that works with modern math methods is still somewhat mysterious. The most useful thing written about that so far is https://en.wikipedia.org/wiki/The_Unreasonable_Effectiveness_of_Mathematics_in_the_Natural_Sciences https://en.wikipedia.org/wiki/The_Unreasonable_Effectiveness...
- chromanoid 3y agoThis is the goal. > Our main goal is to build the world's first virtual organism - an in-silico implementation of a living creature - for the purpose of achieving an understanding of the events and mechanisms of living cells. This blog post is interesting: "Whole Brain Emulation: No Progress on C. elegans After 10 Years" https://www.lesswrong.com/posts/mHqQxwKuzZS69CXX5/whole-brain-emulation-no-progress-on-c-elegans-after-10 https://www.lesswrong.com/posts/mHqQxwKuzZS69CXX5/whole-brai... As other mentioned in the comments of the post, it is certainly also a matter of funding, but still I think it is very interesting how we still struggle to simulate a 302 cell worm, while some people expect an artificial superintelligence in the next ten years.
- circuit10 3y agoReplicating something exactly is a lot harder than making something that does the same thing in a different way. We can build planes that travel far faster than a bird could but that doesn’t mean it’s easy for us to exactly replicate how a bird flies, so I don’t think this says anything about how far away we are from a superintelligence
- inglor_cz 3y agoThis. 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 chemical compounds for their potential biological functions, is a very practical form of "intelligence" and yet very far from any biological intelligence that was ever produced in vivo. Worms cannot do that and even humans struggle with such tasks.
- szundi 3y agoAnd for some reason it is because somehow life is not able the produce rotating axles?
- comfypotato 3y agoNematode specifically, which is a very little worm.
- TruthWillHurt 3y agoWow it's amazing how much progress was made on this! a full simulation!!!!
- sledgehammers 3y agoAre 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 :)
- JPLeRouzic 3y agoAs an amateur scientist with an interest in neurodegenerative diseases, I am interested in neurons simulations. As a model with neurons and muscles, Openworm looks very interesting for application in ALS (Lou Gherig's disease).
- adev_ 3y agoHave a look to Neuron / Core neuron (https://www.neuron.yale.edu/neuron/ https://www.neuron.yale.edu/neuron/ / https://github.com/BlueBrain/CoreNeuron https://github.com/BlueBrain/CoreNeuron), Nest (https://www.nest-simulator.org/ https://www.nest-simulator.org/) and for the ultra low level STEPS (https://github.com/CNS-OIST/STEPS https://github.com/CNS-OIST/STEPS). For most computational neuroscientist, they are the bread and butter.
- JPLeRouzic 3y agoThanks!
- nightsd01 3y ago302 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 similar, they are incredibly sophisticated biological machines, with billions of DNA base pairs controlling their behavior. The emergent behavior of neurons in both biological and AI systems are pretty fascinating
- petters 3y ago> billions of DNA base pairs controlling their behavior Total genome size of C elegans is 100M.
- thriftwy 3y agoBiologists should totally breed a subspecies of C elegans best suited for research purpose, call it C relevans.
- deleted 3y ago[deleted]
- razodactyl 3y ago...I hope you're happy. There's coffee everywhere now!
- bee_rider 3y ago100Mdna, and they call it elegant? Biologists must be VSCode users.
- ssr2020 3y ago100M. Did you look at the programs's size in your phone? This tiny animal code contain all the systems and members of this creature. Birth,creation,death, feeding,growth, movement, sensation.. etc inside the universe. There is no difference this animal and bee or human beings. "In order to be the author of the action directed towards the creation of the bee in question, a power and will are necessary that are vast enough to know and secure the conditions for the life of the bee, and its members, and its relationship with the universe. Therefore, the one who performs the particular action can only perform it thus perfectly by having authority over most of the universe." from Quran's light
- mfld 3y agoI 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.org/10.1016/j.cell.2022.06.046 https://doi.org/10.1016/j.cell.2022.06.046 .
- flobosg 3y agoA 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 https://www.nature.com/articles/s41586-023-06288-x
- DrScientist 3y agoNot quite sure I'd describe that as a bottom up approach - they sell it as that - but in reality it's more like Jenga. Seeing which bits you can remove without the system failing over. The technical fact that the genome was artificially synthesized is just showmanship - they still had to put into an existing cell. It's like claiming you made a car from scratch by replacing a chip - which you've copied from the existing chip but left a few bits out - and now the indicators don't work, but you can still sort of drive.
- comfypotato 3y agoWould love to see this applied to the fruit fly connectome that was on the front page the other day.
- deleted 3y ago[deleted]
- eterevsky 3y agoThis project has existed for something like a decade. Does anyone know if there was any progress with it in the last few years?
- dilawar 3y agoI 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, "real neuron is way too complicated!". IMHO, chemical computations are often over-looked in neural "computation" communities which are extremely hard to model. Forgetting modelling, we don't know reaction parameters of most proteins and other molecules involved. Electrical side of computation is easy to measure and one can understand why we started with it. There are a thousands types of proteins even in a small structure such as synapse, and individual protein can implement interesting non-linear computation. E.g. CaMKII can implement and bistable switch (flip-flop) and thus store 1-bit of memory using just a few molecules (the real story is a much more complicated). https://youtu.be/vJBUaS0r9IU https://youtu.be/vJBUaS0r9IU
- Gordonjcp 3y ago> 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"?
- PTOB 3y agoPlot twist; he's got an "Ask Me about Neal Stephenson" t-shirt.
- FrustratedMonky 3y agoYeah, 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'.
- quickthrower2 3y agoIs it simulating cells? atoms? or treating the neurons as black boxes?
- miltondts 3y agoFrom a quick read of the model used [0], it seems to simulate neurons and muscles at a functional level (not atoms or cell internals). [0] - https://github.com/openworm/c302 https://github.com/openworm/c302 (linked in the original github page)
- yaakov34 3y agoI 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) 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 leg as three rigid blocks connected by hinges - it's enough to be useful in many models, but of course it's not a full description. Also, it may not the right model for worm neurons, because worm neurons are non-spiking, and the HH equations describe neurons that produce trains of spikes; they exist in more complicated nervous systems. The HH equations are used in simulations because it's the mathematical model we have, and it seems that they're still used by the OpenWorm project. (I am not very sure about properties of worm neurons, I heard about this a long time ago and the information may be out of date). I think it's great that this work is still going on, it may produce insights about functioning of nervous systems. But the difficulties are fierce, and we're making very slow and difficult progress in an immense unknown area.
- boredumb 3y agoOut of curiosity - were there any commercial applications this was being developed towards?
- yaakov34 3y agoRalph's main work was on neural impulses in the visual cortex, and on measurements of various potentials in the living brain. He published a memoir called "Another Day in the Monkey's Brain". I believe he had potential medical applications in mind, but I don't think anything that was close by. Unfortunately, he died of an illness in 2011.
- albertzeyer 3y ago> 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?
- lukasday 3y agoI 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 billions of neurons, Elegans has hundreds (and we've had them mapped since 1986). If one can successfully "upload" Elegans, then humans are just a matter of scale. However, it should be noted that the field, and specifically this line of research, hasn't produced much in the way of results in 10+ years. University of Oregon planned (though I can't tell if they ever developed) NemaSys[0] ~1997. OpenWorm has been exploring this since 2011. Project Nemaload explored it a bit from 2011-2013.[1] But each project ran into three problems: - Knowing the connections isn't enough. We also need to know the weights and thresholds. We don't know how to read them from a living worm.[2] - C. elegans is able to learn by changing the weights. We don't know how weights and thresholds are changed in a living worm.[2] - Funding [3] The best we can do is modeling a generic worm - pretraining and running the neural network with fixed weights. Thus, no worm is "uploaded" because we can't read the weights, and these simulations are far from realistic because they are not capable of learning. Hence, it's merely a boring artificial neural network, not a brain emulation. Relevant neural recording technologies are needed to collect data from living worms, but they remain undeveloped (but in progress?[4][5][6]), and the funding simply isn't there. OpenWorm got the idea to plug their connectome into a Lego robot[7] and got it to exhibit the tap-withdrawal behavior of the nematode, but it had technical limitations preventing easy modification of the connectome or introduction of new models of neural dynamics. JHU Applied Physics Lab extended the work by using a basic integrate and fire model to simulate the neurons and assigned weights by determining the proportion to the total number of synapses the two neurons on either side of the synapses shared and in the end got the simulated worm to reverse direction when bumping into walls.[8] At this point, humanity seems to have abandoned emulated worm driven mechanisms which is honestly kind of a loss. There's no real ending to this comment. Love this project, loves what it stands for, looking forward to seeing progress in this field. And a lot of this information was pulled from this blog post[9] which was also mentioned in the comments somewhere. [0] https://web.archive.org/web/20030115124331/http://www.csi.uoregon.edu/projects/celegans/ https://web.archive.org/web/20030115124331/http://www.csi.uo... [1] https://github.com/nemaload https://github.com/nemaload [2] https://www.jefftk.com/p/we-havent-uploaded-worms https://www.jefftk.com/p/we-havent-uploaded-worms [3] https://www.quora.com/Is-Larry-Page-funding-any-neuroscience-mind-uploading-projects-besides-the-NEMALOAD-project https://www.quora.com/Is-Larry-Page-funding-any-neuroscience... [4] https://arxiv.org/pdf/2109.10474.pdf https://arxiv.org/pdf/2109.10474.pdf [5] https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24483 https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24483 [6] https://www.sciencedirect.com/science/article/pii/S0959438820301689 https://www.sciencedirect.com/science/article/pii/S095943882... [7] https://www.cnn.com/2015/01/21/tech/mci-lego-worm/ https://www.cnn.com/2015/01/21/tech/mci-lego-worm/ [8] https://ccneuro.org/2018/proceedings/1149.pdf https://ccneuro.org/2018/proceedings/1149.pdf [9] https://www.lesswrong.com/posts/mHqQxwKuzZS69CXX5/whole-brain-emulation-no-progress-on-c-elgans-after-10-years https://www.lesswrong.com/posts/mHqQxwKuzZS69CXX5/whole-brai...
- nethdeco 3y agoI think in 2018 they ported the same model into a lego robot, and pretty much had a POC on how the worm would function in the real world.
- plasticeagle 3y agoSo... if you exit the simulation, did you kill a worm?
- krzat 3y agoNeat. I'm wondering how much of inner cell biology can be abstracted away. How accurate can neuron simulation be without underlying chemistry and physics?
- Geee 3y agoWaiting for the day when we can observe an actual worm and predict its movements exactly by simulating them ahead of time.
- lionkor 3y agoThat's part of the scientific process, and probably the most valuable part (that sets it apart from e.g. religion). It's very exciting to me when a theory makes predictions, and those predictions turn out to be true - it's beautiful.
- xvilka 3y agoConnectome model of fruit fly brain was just recently published[1]. [1] https://hub.jhu.edu/2023/03/09/scientists-complete-first-map-of-an-insect-brain/ https://hub.jhu.edu/2023/03/09/scientists-complete-first-map...
- omnicognate 3y agoWhich 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/ http://neurokernel.github.io/
- mofosyne 3y agoI 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/ http://wormsim.org/
- slars0n 3y agoCode for wormsim.org is here on Github btw: https://github.com/openworm/org.wormsim.frontend https://github.com/openworm/org.wormsim.frontend -- contributions welcome!
- seydor 3y agomany 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
- Sharlin 3y agoCertainly it is worth it to study how exactly biology and biochemistry gives rise to complex behavior! Basic research like this doesn’t have to justify itself with potential applications. Besides, there’s really no evidence that deep networks are any kind of an analogy to animal nervous systems. They might just as well be aliens as far as cognition goes.
- sfn42 3y agoThey're computer programs, not living beings. Biology is still light-years ahead of the complexity of our computer systems.
- chromanoid 3y agoWe 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.
- boredumb 3y agoFascinating 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
- drakonka 3y agoI 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.
- tleilaxu 3y agoThat sounds absolutely amazing! In a similar position to you regarding an amateur interest. I’d have loved to have been there too.
- lz400 3y agoI 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.
- hwillis 3y ago> the connectome is there, we know all the neurons and their connections No- each synapse has its particular neurotransmitters, and the distance, size, shape, number of receptors, and associated glial cells have very large impacts on transmission. The distance and thickness of axons also impacts the strength of signal delivered. That's all very hard to measure. Neurons are also very sensitive to signal strength and timing. Eg inhibitory synapses work by opening holes in the cell wall, causing them to leak charge over time. You get that rate slightly wrong and it can hugely change the behavior of the cell. The connectome is a bit like an untrained model of insane complexity, and each neuron has several weights that describe behavior over time as well as in direct response to signals. Without the weights it can't be emulated.
- pouulet 3y agoReminds me of the first episode of Devs ( https://www.imdb.com/title/tt8134186/ https://www.imdb.com/title/tt8134186/ ) where an artificial intelligence engineer does a demo about syncing, and then predicting the future movements of a nematode worm. Great show by the way!
- 3cats-in-a-coat 3y agoA great show only made greater by the fact it came before LLMs entered the public consciousness, but this concept of having information you extrapolate from with great accuracy is central to the show (all I'll say).
- edwinksl 3y agoCreepy stuff with creepy implications, pretty fun show!
- max_ 3y agoNoam Chomsky says there are two kinds of AI. 1. The first kind of AI research is more like engineering for example creating self driving cars, language translation & object recognition. 2. The second kind of AI research is trying to replicate the intelligence of living organisms (humans, worms) with models that are consistent with what cognitive scientist have. An example for such a system is one that would pick up any human language with very little supervision. Like children for example. Open worm seems like no. 2. Any one have any interesting resources for no. 2 type AI? I would love to explore it some more. [0]: https://youtu.be/TAP0xk-c4mk https://youtu.be/TAP0xk-c4mk
- anotheryou 3y agoAnd to me this is just as sentient (or not) as the physical worm and deserves worm rights!
- bee_rider 3y agoDoes 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?
- anotheryou 3y agonot interesting for a worm but interesting for a first of its kind
- bee_rider 3y agoI actually don’t know, are there any ethical guidelines for working with very limited animals like this? I know they are pretty limited intelligence wise, but I would hope the researchers at least kill them in a quick, painless manner when the experiments are done. I guess if the computer mode really is true on a physical level it is owed the same (minimal) level of decency somehow.
- anotheryou 3y agoMy point is: let's discuss this before we simulate more complex life and let's not draw some arbitrary line in the sand or call it all "artificial = not worthy anything".
- bee_rider 3y agoYeah, I agree, definitely at least that it is an insufficiently explored ethical issue. I suspect people are just leaning on the intuitive answer (that it is just a computer program), and the fact that we just don’t have the ability to simulate anything that has, like, obvious rights yet. I don’t think the first will really stand up to scrutiny, and the second is clearly a temporary solution (to the extent that it even is a solution).
- akokanka 3y agoWork seems to have stopped last year.
- candrewlee14 3y agoIt'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/ https://worm-world.github.io/ [2] https://tauri.app/ https://tauri.app/
- tleilaxu 3y ago>"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. Doesn’t sound that different from standard business software development! Fascinating project. Really enjoyed reading about it - well done!
- teucris 3y agoThat we can run a simulation of an organism that looks and acts like the real thing evokes a rare sense of wonder I thought I could never again experience from technology.
- lclarkmichalek 3y agoIt models wiggling forward. It models wiggling backwards. And occasionally it models fucking itself. That’s it.
- dang 3y agoRelated: OpenWorm - https://news.ycombinator.com/item?id=29045198 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 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 https://news.ycombinator.com/item?id=7613732 - April 2014 (47 comments) Openworm: c.elegans worm simulation - https://news.ycombinator.com/item?id=4208454 https://news.ycombinator.com/item?id=4208454 - July 2012 (14 comments)
- umutisik 3y ago"Congratulations! You can now join the Devs project."
- tgbusbice 3y agoAs a founding member of OpenWorm, I emulated the connectome and applied it to robotics almost 10 years ago (https://youtu.be/YWQnzylhgHc https://youtu.be/YWQnzylhgHc). In this experiment, each neuron is represented as a single program and uses UDP messaging to communicate between the individual neurons (programs). There was a number of issues I ran into and probably #1 is the fact that connectomes are highly recurrent which in my experiment lead to what I called UDP stacking; i.e. the activations (UDP messages) come in faster than the program can process them. I have downloaded the complete (so far) Drosphilia connectome and working to create an emulation. I am exploring Hypervectors to emulate neurons or neuropils but still working on the concept. I have tried many other ideas including Adjacency Matrices and Function programming where each Function is some part of the animal nervous system (e.g. with C elegans think Sensory, Interneuron and Motor as 3 distinct functions and programs). The C elegans emulation was also done in a single Python app, translated to several other programming languages, that also showed clear emulation in many different robots. Ablation tests demonstrated how the emulated nervous system is congruent to the biological nervous system through observable behaviors of both. There are two extremes on the evolutionary continuum of nervous systems with the worm's brain on one end and the human brain on the other. However, even with the Worm's nervous system, we can clearly see general intelligence and a gateway to AGI.