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

I think it's fair to say that the hope is to combine the state of the art technology to discover more scientifically than has been before known.

Additionally, this pushes technology. The hope is to push the technology far enough a system such that not only do the components work, but you can build actual useful engineering systems with them.

David's start is at 14 and not post 20 as most grad students. At minimum, he will end up making something like Mathematica like Wolfram and at max, he will change the world.

The Big and Little Oh of this story are both extreme events.

I like to describe my techniques as "not novel, just new." I'm absolutely building on the work of many others in academia. I've spent time with Engert at Harvard, Rex Kerr at Janelia, and some of Deisseroth's students, among others (including Boyden, Ramanathan, Manuel Zimmer in Vienna, Aravi Samuel, George Church, and more). I've only briefly met Bargmann and I loved the advice she gave me: "Hmm. That's probably not going to work, but...it's really worth trying."

Unfortunately, most academic scientists are not in a position to risk their careers on such a bold and encompassing proposal. However, I benefit from this in some ways, because academics who are interested in this problem often work on a small piece of it instead of going for the whole thing, and are then incentivized to share that piece with me to integrate with all the other pieces, so they can see their contribution realize its full potential.

I wouldn't underestimate the technical demands of the project - it certainly would have been unthinkable 10 years ago. Sydney Brenner once famously wrote: "Progress in science depends on new techniques, new discoveries, and new ideas, probably in that order." However, you're right to point out that it's really the abstract methodology of delegating experimentation to a machine which truly distinguishes my technical proposal from related work. I have to admit that I haven't worked out in detail what the math will look like, though <http://arxiv.org/abs/1103.5708>; is a pretty good start. The tricky bit is defining the probability space (that is, the family of models under consideration). As a probability space, it must have a measurable structure. But for efficient and effective inference, it should also have additional structure, like a vector space. Yet any particular choice of vector space representation will trade off dimensionality against non-convexity, so it's desirable to have multiple representations of the same space. I've been taking a "cross that bridge when I come to it" approach, as I'm occasionally reminded by academics that if all I manage to do is collect a bunch of time series data about hundreds of neurons simultaneously, that would still probably be scientifically interesting and novel, even with ordinary, human-driven analyses.

I do not think funding is David's problem :-).

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 independently studying and creating observed and simulated data, are there centralized places to aggregate and share these?

...and was fired from it.

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

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.

Do be careful when you get to lobsters.

> Isn't that awesome? But ... "the philosophical assumptions fail, and human immortality through uploading is fundamentally impossible".

To boil it down: They assume roughly that simulating the state and functionality of the neurons is sufficient to reproduce consciousness.

If there's something more to consciousness - say for example that consciousness requires the specific organisation of matter of the human brain - then uploading, at least into software, will fail.

Doesn't seem to be same thing. OpenWorm is computer simulation, while the OP plans to build a model based on observing an actual living individual [1].

[1] http://nemaload.davidad.org/about

Yes, I know Stephen Larson and some of the other OpenWorm guys. In fact, I'm even a member of their organization on GitHub <https://github.com/openworm?tab=members>. Once both projects are a bit more developed, I expect ample opportunities for substantive cooperation; but for now, I'm focusing on data collection challenges, while they're focusing on simulations, visualizations, and data management.

The challenges are great because it's not just another meaningless programming test. Instead it's "week 1" of the internship, where you learn the background necessary to start work on the project. And even if you don't get the position, all those tasks are useful for a grad student in neuroscience or bioinformatics.

Yeah, I haven't updated the site in a while. (This really wasn't the best time for a Hacker News blitz. I was just telling my friend that Nemaload hadn't been on HN yet, as far as I knew, and he simply decided to fix that pronto.) But there have been plenty of developments since November (when I think I last updated the site). I have access to a few candidate strains for pan-neuronal calcium imaging (though the genetic engineering is still an ongoing optimization process) and have collected a couple of large datasets, one on a light-sheet microscope and one on a light-field microscope. Much of the data is useless, and we're still working on the algorithms to extract signals from it, as well as the infrastructure for opening it up for distribution. But there will certainly be more publicly visible activity soon (June at the latest).