I want to point out that there has been some very small amounts of progress in the last 10 years on the problem of moving from connectome to simulation rather than no progress.
First, there has been interesting work at the JHU Applied Physics Lab which extends what Busbice was trying to do when he tried to run as simulation of c elegans in a Lego Mindstorms robot (by the way, that work by Busbice was very much overhyped by Busbice and in the media, so it’s fitting that you didn’t mention it). They use a basic integrate and fire model to simulate the neurons (which is probably actually not very accurate here because c elegans neurons don’t actually seem to spike much and seem to rely on subthreshold activity more so than in other organisms). To assign weights to the different synapses they used what appears to be a very crude metric—the weight was determined in proportion to the total number of synapses the two neurons on either side of the synapse share. Despite the crudeness of their approach, the simulated worm did manage to reverse it’s direction when bumping into walls. I believe this work was a project that summer interns did and didn’t have a lot of funding, which makes it more impressive in my mind than it might seem at first glance.
Another line of work that seems worth pointing out is this 2018 work simulating “hexagonal cells” in the drosophilia which has been done at Janelia: “A Connectome Based Hexagonal Lattice Convolutional Network Model of the Drosophila Visual System”. They claim “Our work is the first demonstration, that knowledge of the connectome can enable in silico predictions of the functional properties of individual neurons in a circuit”. I skimmed this paper and found it a bit underwhelming since it appears the validation of the model was mostly in terms of summary statistics.
Finally, for anyone who wants to learn what happened with the OpenWorm project, the CarbonCopies Foundation did a workshop in June 2021 with Steven Larson. A recording of the 4 hour event is online. I was present for a bit of it at the time it aired, but my recollection is dim. I believe part of the issue they ran into was figuring out how to simulate the physiology of the neuron (ie all the non-neuronal cells). Some people in the OpenWorm open source community managed to build a 3D model (you can view it here). If I recall correctly, he mentioned there was some work to embed that model in a fluid dynamics simulation and “wire it” with a crude simulation of the nervous system, and they got it to wiggle in some way that looked plausible.
I want to point out that there has been some very small amounts of progress in the last 10 years on the problem of moving from connectome to simulation rather than no progress.
First, there has been interesting work at the JHU Applied Physics Lab which extends what Busbice was trying to do when he tried to run as simulation of c elegans in a Lego Mindstorms robot (by the way, that work by Busbice was very much overhyped by Busbice and in the media, so it’s fitting that you didn’t mention it). They use a basic integrate and fire model to simulate the neurons (which is probably actually not very accurate here because c elegans neurons don’t actually seem to spike much and seem to rely on subthreshold activity more so than in other organisms). To assign weights to the different synapses they used what appears to be a very crude metric—the weight was determined in proportion to the total number of synapses the two neurons on either side of the synapse share. Despite the crudeness of their approach, the simulated worm did manage to reverse it’s direction when bumping into walls. I believe this work was a project that summer interns did and didn’t have a lot of funding, which makes it more impressive in my mind than it might seem at first glance.
Another line of work that seems worth pointing out is this 2018 work simulating “hexagonal cells” in the drosophilia which has been done at Janelia: “A Connectome Based Hexagonal Lattice Convolutional Network Model of the Drosophila Visual System”. They claim “Our work is the first demonstration, that knowledge of the connectome can enable in silico predictions of the functional properties of individual neurons in a circuit”. I skimmed this paper and found it a bit underwhelming since it appears the validation of the model was mostly in terms of summary statistics.
Finally, for anyone who wants to learn what happened with the OpenWorm project, the CarbonCopies Foundation did a workshop in June 2021 with Steven Larson. A recording of the 4 hour event is online. I was present for a bit of it at the time it aired, but my recollection is dim. I believe part of the issue they ran into was figuring out how to simulate the physiology of the neuron (ie all the non-neuronal cells). Some people in the OpenWorm open source community managed to build a 3D model (you can view it here). If I recall correctly, he mentioned there was some work to embed that model in a fluid dynamics simulation and “wire it” with a crude simulation of the nervous system, and they got it to wiggle in some way that looked plausible.
Thanks for the info. Your comment is the reason why I’m on LessWrong.