7 ms·

Simulating C. elegans brain, body and environment interactions

68 points by lamename 2y ago

memtet 2y ago
[dead]
ruthmarx 2y ago
I have this simulation on my computer, it's really interesting to see. Limited inputs, and the same neurons light up every time for the same input. These animals are 'conscious' yet not capable of any kind of higher thought, basically just a early type of organic robot. Fascinating.
dsjoerg 2y ago
Openworm looks interesting but also looks dead so.
- Palomides 2y ago
  my bystander understanding: the problem is that openworm knows how the neurons are connected, but not how they're weighted and trigger each other, or how it adjusts them, and it seems like there hasn't been enough funding to take it to the next level in the past, like, 15 years it's unclear to me how much of the result from this paper is algorithmic rather than directly founded in measured data, but it's very cool to see more work in this area.
  - verteu 2y ago
    They claim their simulation moves in a "zigzag" pattern that's qualitatively similar to the real animal: > During locomotion, the input of sensory neurons exhibited fluctuations due to the zigzag movement of the body’s head (Fig. 5c). The membrane potentials of each individual motor neuron also oscillated in response to the sensory input, especially the head motor neurons (Fig. 5d). The activation of muscle cells revealed traveling waves from the head to the tail (Supplementary Fig. 4), accompanied by alternating contractions and relaxations of dorsal and ventral muscle cells (Fig. 5e). These findings resemble observations in biological experiments
    - RaftPeople 2y ago
      > They claim their simulation moves in a "zigzag" pattern that's qualitatively similar to the real animal: It seems like they need to show it following chemical gradients the way c elegans does, I don't think any of these simulations has been successful at that.
- cyberax 2y ago
  I remember reading a blog post saying that C. elegans is not a good example of neural networks, for the same reason demoscene is not a good example of computer programming. C. elegans connectome was tweaked and optimized by evolution to be as compact as possible. So just like with demoscene, untangling and simulating it will require deep knowledge of the underlying "physical" platform. More complex organisms might actually be _easier_ to simulate.
  - ruthmarx 2y ago
    > C. elegans connectome was tweaked and optimized by evolution to be as compact as possible. It's not like it's compressed or optimized or anything, it's just incredibly simple.
    - cyberax 2y ago
      It's not that simple. A third of the body of C.elegans consists of neural tissue, it's incredibly energy-expensive. So it was optimized a lot, and there are some hidden interactions between neurons that are not directly connected.
      - ruthmarx 2y ago
        > there are some hidden interactions between neurons that are not directly connected. How is that possible? What is the link, the method of communication? If that isn't known how is it known the interaction is taking place? Do you still have the link to the blog post?
        RaftPeople 2y ago
        > How is that possible? The neuron state is impacted by: neurotransmitters, electromagnetic fields, the chemical soup that it sits in, etc. An interesting example of how non-simple this stuff is: a new study (https://www.nature.com/articles/s42003-024-06778-2 https://www.nature.com/articles/s42003-024-06778-2) where both the intracellular calcium level and the membrane potential were measured at the same time. The result: The membrane potential encoded the presence of an odor The intracellular calcium level encoded the magnitude of the odor
- pests 2y ago
  The open worm can die too!? /s
fnordpiglet 2y ago
https://github.com/Jessie940611/BAAIWorm https://github.com/Jessie940611/BAAIWorm
xt00 2y ago
Reminds me of "Devs": https://www.youtube.com/watch?v=xEfyT3vLD2c https://www.youtube.com/watch?v=xEfyT3vLD2c
- exe34 2y ago
  loved that show! my favourite part is their dead eyes, knowing everything that is going to happen takes away all the joy and pain out of life, it's exactly like depression!
sitkack 2y ago
The worm has entered the multiverse.

68 points by lamename 2y ago

[dead]

I have this simulation on my computer, it's really interesting to see. Limited inputs, and the same neurons light up every time for the same input. These animals are 'conscious' yet not capable of any kind of higher thought, basically just a early type of organic robot. Fascinating.

dsjoerg 2y ago

Openworm looks interesting but also looks dead so.

Palomides 2y ago
my bystander understanding: the problem is that openworm knows how the neurons are connected, but not how they're weighted and trigger each other, or how it adjusts them, and it seems like there hasn't been enough funding to take it to the next level in the past, like, 15 years it's unclear to me how much of the result from this paper is algorithmic rather than directly founded in measured data, but it's very cool to see more work in this area.
- verteu 2y ago
  They claim their simulation moves in a "zigzag" pattern that's qualitatively similar to the real animal: > During locomotion, the input of sensory neurons exhibited fluctuations due to the zigzag movement of the body’s head (Fig. 5c). The membrane potentials of each individual motor neuron also oscillated in response to the sensory input, especially the head motor neurons (Fig. 5d). The activation of muscle cells revealed traveling waves from the head to the tail (Supplementary Fig. 4), accompanied by alternating contractions and relaxations of dorsal and ventral muscle cells (Fig. 5e). These findings resemble observations in biological experiments
  - RaftPeople 2y ago
    > They claim their simulation moves in a "zigzag" pattern that's qualitatively similar to the real animal: It seems like they need to show it following chemical gradients the way c elegans does, I don't think any of these simulations has been successful at that.
cyberax 2y ago
I remember reading a blog post saying that C. elegans is not a good example of neural networks, for the same reason demoscene is not a good example of computer programming. C. elegans connectome was tweaked and optimized by evolution to be as compact as possible. So just like with demoscene, untangling and simulating it will require deep knowledge of the underlying "physical" platform. More complex organisms might actually be _easier_ to simulate.
- ruthmarx 2y ago
  > C. elegans connectome was tweaked and optimized by evolution to be as compact as possible. It's not like it's compressed or optimized or anything, it's just incredibly simple.
  - cyberax 2y ago
    It's not that simple. A third of the body of C.elegans consists of neural tissue, it's incredibly energy-expensive. So it was optimized a lot, and there are some hidden interactions between neurons that are not directly connected.
    - ruthmarx 2y ago
      > there are some hidden interactions between neurons that are not directly connected. How is that possible? What is the link, the method of communication? If that isn't known how is it known the interaction is taking place? Do you still have the link to the blog post?
      - RaftPeople 2y ago
        > How is that possible? The neuron state is impacted by: neurotransmitters, electromagnetic fields, the chemical soup that it sits in, etc. An interesting example of how non-simple this stuff is: a new study (https://www.nature.com/articles/s42003-024-06778-2 https://www.nature.com/articles/s42003-024-06778-2) where both the intracellular calcium level and the membrane potential were measured at the same time. The result: The membrane potential encoded the presence of an odor The intracellular calcium level encoded the magnitude of the odor
pests 2y ago
The open worm can die too!? /s

fnordpiglet 2y ago

https://github.com/Jessie940611/BAAIWorm https://github.com/Jessie940611/BAAIWorm

xt00 2y ago

Reminds me of "Devs": https://www.youtube.com/watch?v=xEfyT3vLD2c https://www.youtube.com/watch?v=xEfyT3vLD2c

exe34 2y ago
loved that show! my favourite part is their dead eyes, knowing everything that is going to happen takes away all the joy and pain out of life, it's exactly like depression!

sitkack 2y ago

The worm has entered the multiverse.