Next step: uploaded lobsters in space
June 3, 2013 10:01 AM Subscribe
"OpenWorm is an attempt to build a complete cellular-level simulation of the nematode worm Caenorhabditis elegans. Of the 959 cells in the hermaphrodite, 302 are neurons and 95 are muscle cells. The simulation will model electrical activity in all the muscles and neurons. An integrated soft-body physics simulation will also model body movement and physical forces within the worm and from its environment." -- Bonus: explore the worm's cellular anatomy in 3D (WebGL required.)
More evidence that we're living inside a simulation
posted by crayz at 10:10 AM on June 3, 2013 [2 favorites]
posted by crayz at 10:10 AM on June 3, 2013 [2 favorites]
Nah. Next step: Nematode Fortress.
posted by Holy Zarquon's Singing Fish at 10:56 AM on June 3, 2013 [2 favorites]
posted by Holy Zarquon's Singing Fish at 10:56 AM on June 3, 2013 [2 favorites]
Gentlemen, we can rebuild it. We have the technology. We have the capability to build the world's first bionic worm. C.elegans will be that worm. Better than he was before. Better, stronger, faster.
posted by fredludd at 11:23 AM on June 3, 2013 [2 favorites]
posted by fredludd at 11:23 AM on June 3, 2013 [2 favorites]
Didn't Jorge Luis Borges write this story scientific paper already?
posted by IAmBroom at 12:40 PM on June 3, 2013 [1 favorite]
posted by IAmBroom at 12:40 PM on June 3, 2013 [1 favorite]
So awesome. Anyone know if anyone's actually ever accomplished this for any sort of multi-cellular organism?
posted by sp160n at 1:16 PM on June 3, 2013
posted by sp160n at 1:16 PM on June 3, 2013
That is really cool. I worked in bio simulations for a bit and they are doing some really impressive stuff. I'm also super impressed that this is a side project for some geeky folks, not a funded NIH project with a dozen grad students or anything.
posted by miyabo at 1:58 PM on June 3, 2013
posted by miyabo at 1:58 PM on June 3, 2013
Anyone know if anyone's actually ever accomplished this for any sort of multi-cellular organism?We will probably not have that any time soon, at least not at a reasonable level of detail.
Developing a detailed simulation of even the simplest whole organism is viciously hard because there is a mind-numbing amount of information involved and we also lack experimental data about so many of the details. The bad part is, a lot of the experiments are very hard to do.
The most comprehensive organism simulation currently known is this work by Karr et al. for an extremely simple bacterium, but that's a single-cell organism.
There are more examples of work on specific parts than there are whole-organism simulations. The largest neural simulation that I'm aware of is the Blue Brain Project (see also the Wikipedia entry), which, incidentally, recently was awarded a staggering amount of funding, so it is likely to grow in size and detail in the next few years. The Blue Brain Project is an effort to simulate the human brain based on known anatomical features and mathematical models of neural processing. However, unlike the OpenWorm project, they're not attempting to simulate mechanical properties, circulation, etc.
posted by StrawberryPie at 3:46 PM on June 3, 2013 [1 favorite]
StrawberryPie: "The bad part is, a lot of the experiments are very hard to do."
Wouldn't even a flawed simulation be of immense help with that though? I imagine you could run sims for whatever parameters and see if the model matches reality. Any discrepancies might actually be helpful in figuring out what's really going on even if direct experiments are hard/impossible to do.
posted by Hairy Lobster at 5:07 PM on June 3, 2013 [1 favorite]
Wouldn't even a flawed simulation be of immense help with that though? I imagine you could run sims for whatever parameters and see if the model matches reality. Any discrepancies might actually be helpful in figuring out what's really going on even if direct experiments are hard/impossible to do.
posted by Hairy Lobster at 5:07 PM on June 3, 2013 [1 favorite]
Hairy Lobster: " Wouldn't even a flawed simulation be of immense help with that though? I imagine you could run sims for whatever parameters and see if the model matches reality. Any discrepancies might actually be helpful in figuring out what's really going on even if direct experiments are hard/impossible to do.
"
Yup, broadly speaking, that's why people do simulations in the first place. All simulations are flawed simulations—a simulation is always an abstraction, a limited model of a hypothesized reality—but properly done, they can collect together what we think we understand into a concrete framework and then help identify where our understanding is wrong. To be useful in that way, a model has to be formal (i.e., not just written as words in paragraphs, but expressed in a mathematical framework) and mechanistic (i.e., be explicit about causal mechanisms involved in producing some phenomenon), not just phenomenological or statistical, which leads to the need to use computational models. (I particularly like this motivational diagram.)
The problem is the part about finding "any discrepancies": for that, you need data about the real thing.
posted by StrawberryPie at 7:56 AM on June 4, 2013
"
Yup, broadly speaking, that's why people do simulations in the first place. All simulations are flawed simulations—a simulation is always an abstraction, a limited model of a hypothesized reality—but properly done, they can collect together what we think we understand into a concrete framework and then help identify where our understanding is wrong. To be useful in that way, a model has to be formal (i.e., not just written as words in paragraphs, but expressed in a mathematical framework) and mechanistic (i.e., be explicit about causal mechanisms involved in producing some phenomenon), not just phenomenological or statistical, which leads to the need to use computational models. (I particularly like this motivational diagram.)
The problem is the part about finding "any discrepancies": for that, you need data about the real thing.
posted by StrawberryPie at 7:56 AM on June 4, 2013
StrawberryPie, would it be accurate to call the model of the worm an instantaneous model? I don't see any discussion of cellular generation or decay being factored into the model, thus the model demonstrates the electrical and physical activity of the worm at a specific point in time, with "perfect" anatomy, right?
posted by dobie at 10:03 AM on June 4, 2013
posted by dobie at 10:03 AM on June 4, 2013
Dobie: "... accurate to call the model of the worm an instantaneous model?"
In the sense that you mean, yes; however, I don't think people in biological modeling usually use the term "instantaneous" for that (though in other fields, people might). The reason is probably because "instantaneous" to a lot of people means "at an instant in time", or in a very short time interval, especially when numerical models are involved. In biological models that exclude things like growth, the characteristics that are modeled do still take place over possibly long periods of time. Even neural signal processing takes place over time.
Many models just assume that certain things take place over a much longer time scale than the ones they're interested in modeling, so in effect, they assume those things are constant over the time scale being modeled. The models that do include growth processes are quick to highlight that point—it's like everyone assumes there's no growth unless explicitly stated. (But that's changing pretty rapidly these days, because models are getting more detailed and because we have the computer horsepower to tackle models that weren't possible before. See, e.g., this paper from a group of colleagues, as just one example of many.)
posted by StrawberryPie at 8:22 PM on June 4, 2013 [1 favorite]
In the sense that you mean, yes; however, I don't think people in biological modeling usually use the term "instantaneous" for that (though in other fields, people might). The reason is probably because "instantaneous" to a lot of people means "at an instant in time", or in a very short time interval, especially when numerical models are involved. In biological models that exclude things like growth, the characteristics that are modeled do still take place over possibly long periods of time. Even neural signal processing takes place over time.
Many models just assume that certain things take place over a much longer time scale than the ones they're interested in modeling, so in effect, they assume those things are constant over the time scale being modeled. The models that do include growth processes are quick to highlight that point—it's like everyone assumes there's no growth unless explicitly stated. (But that's changing pretty rapidly these days, because models are getting more detailed and because we have the computer horsepower to tackle models that weren't possible before. See, e.g., this paper from a group of colleagues, as just one example of many.)
posted by StrawberryPie at 8:22 PM on June 4, 2013 [1 favorite]
Interesting, thanks! I was reading this article in last months Wired, and while it didn't go far into detail of what Markham was proposing, it seemed to me that it was missing discussion of how a model of the brain would need to include refactoring to accomodate the forming of new neural pathways. Sounds like that would be part of the model.
posted by dobie at 11:24 PM on June 4, 2013
posted by dobie at 11:24 PM on June 4, 2013
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posted by MartinWisse at 10:03 AM on June 3, 2013 [2 favorites]