[HN Gopher] OpenWorm - A computational model of C. elegans worm
___________________________________________________________________
OpenWorm - A computational model of C. elegans worm
Author : dvrp
Score : 417 points
Date : 2023-07-07 07:08 UTC (15 hours ago)
(HTM) web link (github.com)
(TXT) w3m dump (github.com)
| umutisik wrote:
| "Congratulations! You can now join the Devs project."
| krzat wrote:
| 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?
| xvilka wrote:
| Connectome model of fruit fly brain was just recently
| published[1].
|
| [1] https://hub.jhu.edu/2023/03/09/scientists-complete-first-
| map...
| omnicognate wrote:
| Which 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/
| c7DJTLrn wrote:
| So is this an exact digital replica of a worm?
| bombolo wrote:
| How can we exactly replicate something if we don't even know
| all the laws of physics?
| Leo_Germond wrote:
| 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...
| bombolo wrote:
| 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.
| Leo_Germond wrote:
| You're welcome, but your point was not very clear.
| ben_w wrote:
| My 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 wrote:
| This makes no sense.
|
| Cells duplicate, but can you make a cell without splitting
| one in 2?
| ben_w wrote:
| Why 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 wrote:
| That'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 wrote:
| I'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 wrote:
| Abstraction. 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.
| highduc wrote:
| clearly 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.
| dekhn wrote:
| If 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_Effectivene
| ss...
| nightsd01 wrote:
| The 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 wrote:
| Well the question asked if it was exact. I pointed out why
| it can't be.
| chromanoid wrote:
| This 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-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 wrote:
| Replicating 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 wrote:
| 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 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 wrote:
| And for some reason it is because somehow life is not
| able the produce rotating axles?
| dekhn wrote:
| You mean like this?
| https://en.wikipedia.org/wiki/Flagellum
| cnlevy wrote:
| Rotating molecular motors exist (a proton powered turbine
| in the video)
|
| http://biovisions.mcb.harvard.edu/anim_mitochondria.html
| PeterisP wrote:
| Not only, it's also because of the square/cube law making
| it impossible to have a 50 ton flyer that flies in the
| same manner as a 5 kg flyer, you can't simply scale
| things up.
| chromanoid wrote:
| 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 how intelligence works
| in biological creatures, it is still curious how we
| struggle even with a "simple" organism like C.elegans.
| XorNot wrote:
| 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.
| chromanoid wrote:
| 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.
| XorNot wrote:
| No but we observably do know that that the connections
| between cells are important, to the point that by
| mimicking that we've derived significant benefit.
|
| The Wright flyer didn't flap, and the wings only
| superficially look like anything a bird has.
| chromanoid wrote:
| > No but we observably do know that that the connections
| between cells are important, to the point that by
| mimicking that we've derived significant benefit.
|
| That is true and it shows even more how important
| observabilty is for science and engineering. That's also
| why a simulation that actually provides an accurate
| enough model of reality might help us so much. The
| problem with AI right now is, that we try or even claim
| to understand Unix by mimicking the functionality of
| transistors.
|
| > The Wright flyer didn't flap, and the wings only
| superficially look like anything a bird has.
|
| They tried to mimick bird wings when coming up with
| flight control mechanisms.
| nightsd01 wrote:
| The bird and the airplane is such an excellent analogy!
| circuit10 wrote:
| I got it from a video I saw so I didn't make it myself
|
| https://youtube.com/watch?v=eaYIU6YXr3w?t=106
|
| I'm not sure the timestamp works but it's at 1:46
| chromanoid wrote:
| It's not only about exact simulation. And we actually do
| understand how birds can fly on a mechanical basis. This is
| not true for C.elegans' inner workings.
| [deleted]
| comfypotato wrote:
| In defense of the project: they've been working a lot over
| the last 10 years. They recently published what they call a
| "liquid neural network" where they've isolated the neuron
| structure doing the work. It outperforms CNNs for some niche
| tasks, and it uses a fraction of the resources.
| chromanoid wrote:
| Just to make this clear, I think this project is actually
| one of the few sane engineering approaches for starting to
| understand how our brain works. Sure, claims of simulating
| a cat brain or even a human brain in some manner are much
| more catchy, but it seems to be pretty arrogant if we
| struggle even with C.elegans.
| comfypotato wrote:
| Nematode specifically, which is a very little worm.
| [deleted]
| dang wrote:
| Related:
|
| _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)
| eterevsky wrote:
| This project has existed for something like a decade. Does anyone
| know if there was any progress with it in the last few years?
| slars0n wrote:
| Yes! News page here: https://openworm.org/news
| luc4sdreyer wrote:
| I used to follow their progress but I unsubscribed from the
| mailing list due to donation request spam. There have been very
| few public updates in the past year. There is still some
| movement but it seems to be happening at a geologic pace from
| my perspective.
| dilawar wrote:
| 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, "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
| FrustratedMonky wrote:
| 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'.
| Gordonjcp wrote:
| > 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 wrote:
| Plot twist; he's got an "Ask Me about Neal Stephenson"
| t-shirt.
| TruthWillHurt wrote:
| Wow it's amazing how much progress was made on this! a full
| simulation!!!!
| sledgehammers wrote:
| 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 :)
| Pannoniae wrote:
| I think this is excitement, not sarcasm :)
| MrTrvp wrote:
| brother you are a sledgehammer but you need to be just a
| hammer for now
| ranguna wrote:
| Even of the OP was being sarcastic, this type of language is
| unnecessary.
| boredumb wrote:
| 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
| mofosyne wrote:
| I 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/
| slars0n wrote:
| Code for wormsim.org is here on Github btw:
| https://github.com/openworm/org.wormsim.frontend --
| contributions welcome!
| quickthrower2 wrote:
| Is it simulating cells? atoms? or treating the neurons as black
| boxes?
| miltondts wrote:
| From 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 (linked in the original
| github page)
| max_ wrote:
| Noam 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
| jcims wrote:
| Watching the little worm writhe on the screen made me realize
| that you could just sit there and torture it with impunity. Kinda
| creepy.
| Rarebox wrote:
| Would that be morally close to torturing an equally intelligent
| real worm?
| lclarkmichalek wrote:
| It models wiggling forward. It models wiggling backwards. And
| occasionally it models fucking itself. That's it.
| drakonka wrote:
| 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.
| akokanka wrote:
| Work seems to have stopped last year.
| JPLeRouzic wrote:
| As 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_ wrote:
| Have a look to Neuron / Core neuron
| (https://www.neuron.yale.edu/neuron/ /
| https://github.com/BlueBrain/CoreNeuron), Nest
| (https://www.nest-simulator.org/) and for the ultra low level
| STEPS (https://github.com/CNS-OIST/STEPS). For most
| computational neuroscientist, they are the bread and butter.
| JPLeRouzic wrote:
| Thanks!
| lz400 wrote:
| 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.
| hwillis wrote:
| > 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.
| candrewlee14 wrote:
| It'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/ [2] https://tauri.app/
| yaakov34 wrote:
| 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 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 wrote:
| Out of curiosity - were there any commercial applications this
| was being developed towards?
| yaakov34 wrote:
| Ralph'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 wrote:
| > 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?
| hacker934 wrote:
| 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.
| yaakov34 wrote:
| I am not the best person to ask, since it's not my field. I
| heard this from the neuroscientists that I worked with. My
| understanding is that there are spiking and non-spiking
| neurons in most nervous systems, including human, but most of
| the ones in ours are spiking. The earliest-evolved animals,
| such as nematodes, do not have spiking neurons, or myelin, or
| some of the ion channels in neuron membranes that more
| evolved neurons have. Their neurons still have axons and
| dendrites, but the signals propagate much more slowly and in
| different ways. I am not sure how well they are understood.
|
| As I said, this is possibly out-of-date information. If there
| is someone here from the neuroscience field, they can
| probably make a better comment.
| heyoni wrote:
| burning_hamster says that's been refuted and the belief
| stems from the difficulty in studying nematodes properly.
| wanderingstan wrote:
| Wikipedia agrees there are spiking and non-spiking:
| https://en.wikipedia.org/wiki/Biological_neuron_model
|
| _Not all the cells of the nervous system produce the type
| of spike that define the scope of the spiking neuron
| models. For example, cochlear hair cells, retinal receptor
| cells, and retinal bipolar cells do not spike._
|
| Also: https://en.wikipedia.org/wiki/Non-spiking_neuron
| lukasday wrote:
| 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 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.uo...
|
| [1] https://github.com/nemaload
|
| [2] https://www.jefftk.com/p/we-havent-uploaded-worms
|
| [3] https://www.quora.com/Is-Larry-Page-funding-any-
| neuroscience...
|
| [4] https://arxiv.org/pdf/2109.10474.pdf
|
| [5] https://onlinelibrary.wiley.com/doi/10.1002/cyto.a.24483
|
| [6]
| https://www.sciencedirect.com/science/article/pii/S095943882...
|
| [7] https://www.cnn.com/2015/01/21/tech/mci-lego-worm/
|
| [8] https://ccneuro.org/2018/proceedings/1149.pdf
|
| [9] https://www.lesswrong.com/posts/mHqQxwKuzZS69CXX5/whole-
| brai...
| Gordonjcp wrote:
| 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?"
| luc4sdreyer wrote:
| Would you mind explaining the unstated premise that basic
| research should in any way should be directly applied to
| solve real world problems?
| Gordonjcp wrote:
| Would you mind explaining why you think I said that?
| chromanoid wrote:
| The real world application would be to understand how more
| complex nerve systems might work. Understanding enables
| progress.
| Gordonjcp wrote:
| 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.
| FrustratedMonky wrote:
| I actually take this as a positive, they have uploaded a shell
| of a 'brain', and have identified the next problem, 'weights'.
| Why isn't what they have done so far be amazing enough to start
| tackling the next thing. I am surprised that with Neural Nets
| being such a hot bed, the amount of money pouring into AI, and
| NeuralLink type research, that they would have a hard time with
| funding.
|
| Watching that lego worm really zapped my brain, seemed like we
| were on the cusp of something. Maybe we still are, and just
| misjudged the time-scale on progress.
| ramraj07 wrote:
| There are a bunch of labs that are making progress in reading
| the full nervous system (so to speak) realtime in live worms. I
| like especially the outputs from Andrew Leifer lab in
| Princeton. I anticipate some very interesting results to come
| from these labs in the next decade.
|
| I briefly considered doing a postdoc in one of these labs,
| because I love working worms and agree with your proposition
| that next logical step in neuroscience is modeling and fully
| understanding an entire organism. The late Sydney Brenner asked
| for the same in 2011 [1].
|
| But most academic labs doing well won't even consider a postdoc
| application from a student who didn't work in the exact same
| field. Solidified my decision to never be part of the Ponzi
| scheme that is academic research.
|
| The beauty of C. Elegans is that you actually need very little
| to start working with them. All the strains are available for
| 10 bucks a pop, you can do most work at room temperature. I
| only need to invest on a very custom (but not necessarily
| outrageously expensive) microscope to start working on this
| topic in my garage. Which I absolutely plan to start in the
| next few years. I've done the math and it'll cost me less than
| owning a cheap boat lol. If anyone wants to fund me I'll be
| open to it too :)
|
| 1. Sydney, B. & Sejnowski, T. J. Understanding the human brain.
| Science 334, 567 (2011).
| ummonk wrote:
| They wiggle forward, they wiggle backwards, and occasionally
| they f*** themselves. That's it.
| Geee wrote:
| Waiting for the day when we can observe an actual worm and
| predict its movements exactly by simulating them ahead of time.
| lionkor wrote:
| That'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.
| nightsd01 wrote:
| 302 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
| weinzierl wrote:
| 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. These responses include acute
| response, tolerance, withdrawal, and sensitization."_ [1]
|
| [1] https://en.m.wikipedia.org/wiki/Caenorhabditis_elegans
| burning_hamster wrote:
| > "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 potentials [1, 2]. Absence of evidence is not
| evidence of absence.
|
| [1] Lockery SR, Goodman MB. The quest for action potentials
| in C. elegans neurons hits a plateau. Nat Neurosci. 2009
| Apr;12(4):377-8. doi: 10.1038/nn0409-377. PMID: 19322241;
| PMCID: PMC3951993.
|
| [2] Jiang, J., Su, Y., Zhang, R. et al. C. elegans enteric
| motor neurons fire synchronized action potentials underlying
| the defecation motor program. Nat Commun 13, 2783 (2022).
| https://doi.org/10.1038/s41467-022-30452-y
| nycticorax wrote:
| Well, the 'canonical' action potential is mediated by
| sodium currents, so it's maybe not surprising that people
| concluded that C elegans don't have APs given that a) they
| don't have any genes for voltage-gated sodium channels, and
| b) when people had recorded from C elegans neurons (it's
| hard but not impossible), they had never seen action
| potentials. (So it's not like no one had looked, and then
| had concluded that they don't exist. They looked and didn't
| see them.) In the paper that originally reported APs in C
| elegans (Liu et al 2018), they were looking in a specific
| neuron (AWA), and they had to elicit a 'plateau potential'
| by depolarizing the cell for a while before the spikes were
| revealed, riding on top of the plateau.
|
| The APs discovered by Liu et al (2018) are generated by
| calcium, not sodium currents, so one could even argue that
| they aren't action potentials in the strict sense. Also,
| they seem to be rather difficult to elicit, and it's still
| not clear whether neural computation in C elegans is mostly
| AP-mediated, or if APs are the exception rather than the
| rule.
|
| Liu, Q., Kidd, P. B., Dobosiewicz, M. & Bargmann, C. I. C.
| elegans AWA olfactory neurons fire calcium-mediated all-or-
| none action potentials. Cell 175, 57-70 e17 (2018)
| https://doi.org/10.1016/j.cell.2018.08.018
| pests wrote:
| > are generated by calcium, not sodium currents, so one
| could even argue that they aren't action potentials in
| the strict sense
|
| Does the underlying chemistry define if its an action
| potential or not? I thought an AP just needed a voltage
| differential regardless if its from calcium or sodium.
| Aardwolf wrote:
| 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, but getting this wrong still
| allows some worm-like behavior?
|
| I really wish the readme/FAQ would talk a bit more about
| the worm and the simulation, rather than have 80% of their
| content be about Docker, though, so that I could learn more
| what cells it actually simulates.
| jacquesm wrote:
| Not necessarily, because you could also simulate the worm
| without neurons at all. It's the closeness of the
| simulation to the real thing that demands that it is done
| right and the question effectively is: is this simulation
| close enough that if such a detail would be wrong that it
| would fail?
|
| One way to answer that would be to add and remove such
| mechanisms to see if it would lead to different behavior.
| _aavaa_ wrote:
| That isn't immediately true, with enough fitting
| parameters you can capture the effect underlying
| behaviour without explicitly capturing it, or even
| without knowing it exists.
|
| "With four parameters I can fit an elephant, and with
| five I can make him wiggle his trunk." - John von Neumann
| [0]
|
| [0]: https://doi.org/10.1119%2F1.3254017
| slars0n wrote:
| 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.
| KMag wrote:
| I suspect slarsOn is the founder of the project (also my
| old roommate). (Stephen, maybe post a top-level
| comment/introduction? Also, hi!)
| cout wrote:
| 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?
| nycticorax wrote:
| You don't need spikes to have computation. Deep networks
| don't have spikes.
| xkcd-sucks wrote:
| Classical action potentials are just one mechanism of
| INTRAcellular communication - You could think of it as a
| special case of signaling via chemical concentration,
| where the chemical is cations and the propagation is
| faster+more directed than diffusion. INTERcellular
| signaling is only rarely mediated directly by voltage.
| Also, action potentials are most "useful" for propagating
| a signal rapidly over a long distance - It kind of
| accelerates and error-corrects (= reverses diffusive
| broadening) voltage signals down a linear path. Action
| potentials are so well known mostly because they show up
| in stuff that's easy to observe (long motor neurons) and
| they're easy to quantify
|
| Somewhat related, there is a roughly inverse correlation
| between neuron count and "computational power per
| neuron", "older and simpler" critters' neurons are more
| likely to be "less specialized" and more likely to use
| hundreds of different chemicals for transmitting
| intercellular signals, while "newer and more advanced"
| critters' neurons are more likely to be "specialized" and
| use just one chemical for transmitting intercellular
| signals
| [deleted]
| robwwilliams wrote:
| Neural computing without action potents is commonplace.
| Computational interactions among cells and neurons in
| retina are almost all graded potentials that modulate
| transmitter release or conductances through gap
| junctions. Retinal ganglion cells of course do generate
| conventional spikes--to pass a data summary to midbrain.
| hypothalamus, and dorsal thalamus.
|
| Action potential are almost strictly INTRAcellular events
| (minor exception being ephaptic effects) that are
| converted in a surprisingly noisy way into presynaptic
| transmitter release and variable postsynaptic changes in
| conductances.
|
| Action potential are a clever kludge necessitated by
| being big and having long axons and needing to act
| quickly.
| jarrell_mark wrote:
| Would like to see the openworm get addicted to virtual
| nicotine
| miohtama wrote:
| Next: OpenSmoker.py
| Maxion wrote:
| Lol imagine your IDE becoming addicted to smoking, and
| refusing to auto-complete or save files before you buy it
| more virtual cigarettes.
| airstrike wrote:
| It's like when the xbox 360 would request users to drink
| Mountain Dew verification cans to validate
| badrequest wrote:
| shhhhh, you're giving them ideas!
| Aleklart wrote:
| 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.
| miohtama wrote:
| My IDE does only LSD and PHP
| anthk wrote:
| Some day Emacs will.
| tomjakubowski wrote:
| trained on everything you've been saying to M-x doctor
| Blackthorn wrote:
| It's not a real doctor, but it is a real worm.
| moffkalast wrote:
| Sounds like it needs an OpenNicotine patch.
| [deleted]
| arketyp wrote:
| It does sound impressive to the extent biological neurons are
| like ML neurons, though. And that's part of the research
| interest, I presume. To the extent that they work by similar
| principles, how come the worm can do those things with such
| small resources? It would be good news for AI research if the
| substrate specifics turn out not to be essential to the worms
| capabilities for instance.
| petters wrote:
| > billions of DNA base pairs controlling their behavior
|
| Total genome size of C elegans is 100M.
| thriftwy wrote:
| Biologists should totally breed a subspecies of C elegans
| best suited for research purpose, call it C relevans.
| [deleted]
| razodactyl wrote:
| ...I hope you're happy. There's coffee everywhere now!
| bee_rider wrote:
| 100Mdna, and they call it elegant? Biologists must be VSCode
| users.
| api wrote:
| The best way of looking at it is that a single biological
| neuron is itself a complex machine full of genetic control
| circuits that sort of resemble neural networks and most
| importantly have memory/state that persists over both short and
| long periods of time. Each neuron is a full-ass living organism
| that itself is capable of learning and behavior, not a
| parameter is a model.
|
| A virtual "neuron" by contrast is a very simple mathematical
| abstraction. It's vastly less computational complexity than a
| biological neuron. A connectome is only a very coarse grained
| map of how neurons relate, not a complete "neural network"
| layout. Not even close.
|
| It might be possible to model a biological neuron using a sub-
| neural-network with state within a larger neural network, but
| assuming that can be computationally equivalent we don't really
| know how many equivalent computational "neurons" would be
| required to model the full breadth of computationally relevant
| biological neuron behavior.
|
| So a worm with 302 biological neurons could be computationally
| equivalent to billions of virtual neurons. We really don't
| know.
|
| Given that neurons have memory it may look a little like LSTM
| networks, and biological neural networks are not just feed
| forward so they're definitely closer to an RNN.
|
| The above is why I laugh at the mind uploading people and would
| only stop laughing if we could both understand and model the
| relevant behavior of biological neurons and somehow extract
| usable state from living neurons. That's all 100% science
| fiction at the moment. The people who think we are about to
| upload minds are ignorant of biology.
| pouulet wrote:
| Reminds me of the first episode of Devs (
| 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 wrote:
| A 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 wrote:
| Creepy stuff with creepy implications, pretty fun show!
| anotheryou wrote:
| And to me this is just as sentient (or not) as the physical worm
| and deserves worm rights!
| bee_rider wrote:
| Does 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 wrote:
| not interesting for a worm but interesting for a first of its
| kind
| seydor wrote:
| 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
| Sharlin wrote:
| Certainly 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 wrote:
| They're computer programs, not living beings. Biology is
| still light-years ahead of the complexity of our computer
| systems.
| chromanoid wrote:
| 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.
| mfld wrote:
| I 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
| .
| DrScientist wrote:
| Not 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.
| flobosg wrote:
| 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
| teucris wrote:
| That 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.
| comfypotato wrote:
| Would love to see this applied to the fruit fly connectome that
| was on the front page the other day.
| nethdeco wrote:
| I 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 wrote:
| So... if you exit the simulation, did you kill a worm?
| voz_ wrote:
| Yes
| ajuc wrote:
| If you saved the state somewhere - nope.
| dullcrisp wrote:
| Only on Unix
| goldenkey wrote:
| Where's the windows in this place? I see /dev/null but I'm
| afraid to venture into it.
| xena wrote:
| Have some wine and you'll be fine
| goldenkey wrote:
| Very good bottler! :-)
___________________________________________________________________
(page generated 2023-07-07 23:02 UTC)