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Show HN: My friend's project to simulate an entire C. Elegans

nemaload.davidad.org

21–30 of 44 posts

Re: Show HN: My friend's project to simulate an entire C. Elegans

#21
post #14

The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…

Do be careful when you get to lobsters.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#22
I like the "optional" hands-on challenges he listed for applicants in the jobs page. It may end up filtering out some talented candidates (not wanting to put in this much effort for one application), but it will certainly call out to the tinkerers and hobbyists who would do those tasks for fun anyway.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#23
post #15
post #14

The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…

The link in the sidebar offers a reasonable elaboration: http://nemaload.davidad.org/about/philosophy

I'm curious, is the goal to prove one or few models wrong? I think while it is extremely sexy, his explanation kind of answers the question for him in a cheesy way - "depends on which lens you look at the problem with".

Doing a nematode-version Turing test is one thing. You could even do it as a nematode in a Chinese box. But isn't there a flaw in comparing how a real nematode's brain reacts to light vs. a nemaload function to a specific computed wavelength of light energy? I think I'm not understanding something.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#24
post #19
post #14

The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…

The jump from honeybee to mouse is enormous - much larger than any of the other jumps except chimpanzee to human. Maybe try lizard in between them.

The rest are a bit out of order too... you'd probably want to try Drosophilia before Zebrafish. But yeah, the leap to mouse is pretty huge. You could potentially try to do Xenopus tropicalis (frog) before mouse, but I'm not sure how well that is mapped as a neural model.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#25
While interesting (especially from a funding perspective!), most of these approaches aren't quite as ground-breaking as one might think. Neuroscientists in academia are doing most of these things. For optogenetics, see Deisseroth's work; for in vivo Ca2+ imaging in nematodes, refer to the work of Bargmann as well as the various Witesides collaborations involving microfluidics; pan-neuronal in vivo imaging is currently being pioneered by Engert at Harvard and a couple of Janelia Farm labs.

These are massive efforts, and involve horrendous heaps of diligent busywork. This makes me the boring naysayer, but please don't be distracted by the startup-like appearance and the peculiar financing situation. It's possible but unlikely that the major obstacle here is simply the combination of available techniques!

Honestly, what I'm most curious about are his thoughts on model-driven interrogation of an in vivo system -- biologists, and even computational neuroscientists, are a bit too hesitant when it comes to letting computers find and test hypotheses. In the age of highly advanced genetic techniques (e.g., binary expression systems in Drosophila or zebrafish) and 2-photon imaging, the process of actually evaluating hypotheses has become a bit old-fashioned...

Re: Show HN: My friend's project to simulate an entire C. Elegans

#26

Sounds really interesting. You could try to secure additional funding for this project via Microryza ( http://www.microryza.com/ ), which is a kickstarter for scientific research.

Side note, I used to do work with CAD systems for simulating/building gene circuits. I can't wait until we move from open tools (Tinkercell, Biobricks, Genome Compiler, etc) to fully-modeled open platforms for organisms. Imagine having the latest build for E.Coli or C.Elegans, or a package manager to organize them, at your fingertips so that you can hack away at new designs. It makes you wonder, with so many people i…

How is "Genome Compiler" an open tool? I hate those guys, it's not even an actual compiler. or open. If they wanted to do something useful, then yeah I would shoot for that package management concept.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#27
post #26

Earlier quoted context omitted.

Side note, I used to do work with CAD systems for simulating/building gene circuits. I can't wait until we move from open tools (Tinkercell, Biobricks, Genome Compiler, etc) to fully-modeled open platforms for organisms. Imagine having the latest build for E.Coli or C.Elegans, or a package manager to organize them, at your fingertips so that you can hack away at new designs. It makes you wonder, with so many people i…

How is "Genome Compiler" an open tool? I hate those guys, it's not even an actual compiler. or open. If they wanted to do something useful, then yeah I would shoot for that package management concept.

Hmm - it seems those guys are not what I remembered/thought they were. I think they were somehow tied to the open bio standards project which is what I was thinking of.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#28
post #19
post #14

The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…

The jump from honeybee to mouse is enormous - much larger than any of the other jumps except chimpanzee to human. Maybe try lizard in between them.

I'm tempted to point out that reptiles are so distinct from either mammals or insects that they wouldn't be a natural stepping stone. But some of my esteemed colleagues advocate jumping from zebrafish to mouse, and I just realized they're probably thinking along similar lines: why try to figure out insects along the way from fish to mammals?

Personally, though, I'm limiting my scope to the worm (at least for now!). The particular path which is best to take beyond that is much less clear.

Re: Show HN: My friend's project to simulate an entire C. Elegans

#29
post #14

The about page [1] is very interesting. "3. Providing a foundation for uploading research .... If it can be done for a worm, the next steps are to attempt a zebrafish, then a fruit fly, then a honeybee, then a mouse, then a dog, then a macaque monkey, then a chimpanzee, and, ultimately, a human. " -- that really fascinate me. Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality throu…

Do be careful when you get to lobsters.

Charles Stross' book Accelerando includes a short story about uploaded lobster brain-scans defecting from the KGB. And they don't like humans. :)

https://en.wikipedia.org/wiki/Accelerando_%28novel%29

Re: Show HN: My friend's project to simulate an entire C. Elegans

#30
I love the internship application page http://nemaload.davidad.org/jobs. The author does expect any candidate to be perfect before meeting, but sets out a small set of criteria for any potential candidate to research.

Probably in the process of researching any of these topics a potential intern would gain a good understanding of the upcoming internship.

Sometimes I wish job interviews were laid out like this.

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