Method Rapidly Reconstructs Animal's Development Cell By Cell

An anonymous reader writes Researchers at the Howard Hughes Medical Institute's Janelia Research Campus have developed software that can track each and every cell in a developing embryo. The software will allow a researcher to pick out a single cell at any point in development and trace its life backward and forward during the embryo's growth. Philipp Keller, a group leader at Janelia says: "We want to reconstruct the elemental building plan of animals, tracking each cell from very early development until late stages, so that we know everything that has happened in terms of cell movement and cell division. In particular, we want to understand how the nervous system forms. Ultimately, we would like to collect the developmental history of every cell in the nervous system and link that information to the cell's final function. For this purpose, we need to be able to follow individual cells on a fairly large scale and over a long period of time."

Comments

Wow

[Falos]

When they can track everything every individual cell has ever done, you know it's time to rein in the surveillance state.

Seriously though, promising tech.

Re:Wow

[zlives]

just wait till they can "predict" what every cell is going to do.

Re:Wow

[i kan reed]

It's only really a concern if the cell runs Linux.

Re: Wow

[Anonymous Coward]

You do mean Gnu/Linux don't you?

Can Emacs do this yet?

Re:Wow

[Anonymous Coward]

Remember Sony disabled the other os in playstation long ago.

Re:Wow

[Applehu Akbar]

Because at that point, it will have used up all the iron ore on Earth for its server storage.

Re: Wow

[taylorius]

Don't worry, they'll only use this to track terrorist cells.

Re:Wow

[interkin3tic]

As a cell biologist I have to say, we already can:

Option 1. Die
Option 2. Cancer

Re:Wow

[Darinbob]

Ever cell gets its own IPv6 address too.

Singularity

[tmosley]

Could this give us a method for mind uploading? If we are able to track every cell in the human brain, especially over time, we should be able to emulate it wholesale with one or two more layers of software (electrical and chemical signaling).

Very exciting times we are living in.

Re:Singularity

[wierd_w]

No.

What it MIGHT give you, eventually, is a set of observations on which to model the synhetic generation of nervous systems (and whole organisms if you have the CPU and memory to blow) within a computational model framework.

What can you do with an emulated nervous system?

Outside of medical research and drug candidate evaluations-- perhaps it could be useful for developing BCIs and the like-- but without a considerable amount more data than just what cells turn into what other cells, the model wont be useful for much.

Also, full nervous system emulation is about the worst possible way to approach strong AI. Just saying.

Models like these are useful for making inexpensive testbeds to test hypotheses against, after said models are vetted-- that's what they are for. They arent for doing non-science with.

Re:Singularity

[Scottingham]

No.

This method is currently only for embryology studies. They are only able to track each cell while it is being observed. There are no tracking devices placed into these cells.

What you are proposing would be roughly 100 orders of magnitude more complex. In addition to each cell you'd have to track each synapse connection, which ranges in the 100s of billions.

The only way I could see 'mind uploading' work is if there was some MRI-like machine that could resolve down to the molecular level and was able to take a snapshot of every molecule in its orientation/current velocity. Then, assuming some magical hyper-quantum (whatever) computer could store and then presumably simulate what would happen 'next' with such a snapshot...Then you'd be essentially modeling reality/matter on a quantum scale, and that would be....cool.

Re:Singularity

[Ichijo]

Also, full nervous system emulation is about the worst possible way to approach strong AI.

Please elaborate. Why is it a bad way to approach strong AI, and what would be a better way?

Re:Singularity

[tmosley]

Well damn.

Uploading can also work by doing it gradually, replacing neurons one at a time with artificial ones, or fast links to an emulator. This could actually be done after being placed in a Matrix-like device that replaces signals going into and out of the brain. This has the upshot of not creating copies, meaning that there isn't a "you" that dies in the process.

Re:Singularity

[Scottingham]

Replacing neurons with artificial ones sounds iffy, but other than that I think you're on the right track. So-called 'brains in jars' are probably the way it'll get done. Instead of artificial neurons I could see GM neurons or GM viruses keeping your existing neurons in tip-top shape. Given sufficient sensory stimulation and input there's no physical reason why this could happen indefinitely. Moving from neurons to 'not neurons' is going to be extremely difficult, if not practically impossible.

Re:Singularity

[Immerman]

Actually they are already beginning to experiment with this - IIRC they've managed to emulate "generic" subsections of rat brain to the point where they can wire in a simulated version to restore much of the functionality lost by destroying the original. Very crude, and I doubt personality would would be preserved even with an exact copy. But undeniably cool.

Re:Singularity

[wierd_w]

Think about it this way--

You have a system that does $FOO.

you arent sure how it does $FOO, exactly. You see that inputs go in, some magical process $BAR happens inside, and $FOO comes out.

Strong AI strives to reproduce this $FOO.

The issue, is that the process $BAR is very much dependent on what the system is built from. (In this case, complex organic molecules and saline ions). Understanding $BAR is insanely hard, because $BAR is carried out in a highly parallelized fashion, with many many subprocesses going on, many of which are highly dependent upon the method of construction of the system, and exist soley because of that method of construction.

So, you want to build an artificial system that takes the same imputs, does $BAR, and gets $FOO.

Do you:

1) Slavishly reimplement millions of models in the new medium's physical construction, to emulate the quirks and behaviors of the target system's physical construction, wasting huge amounts of energy and making a system that is actually *MORE* complex than the original....

OR

2) Deconstruct all the mechanisms at work in the physical system that currently performs $BAR to get $FOO, evaluate which of these are hardware dependent, and can be removed/adapted to high efficiency analouges in the new hardware platform-- and produce only the components needed for $BAR to be accomplished, to generate $FOO?

The former will most certainly get you $FOO, but is HORRIBLY INEFFICIENT, and does not really shed light on what is actually needed to get $FOO.

The latter is MUCH HARDER to do, as it requires actually understanding the process, $BAR, through which $FOO is attained. It will however, yeild the higher efficiency synthetic system, AND the means to prove that it is the best possible implementation.

Basically, it's the difference between building a rube-goldberg contraption, VS an efficient machine.

Re:Singularity

[interkin3tic]

Not really. The embryo here is a fruit fly. They're small enough to see the entire thing with a microscope. Vertebrates tend to get too big to image completely with current microscopes really early on in development. A human brain is way too big to image completely with a microscope without slicing it thinner than lunch meat.

Re:Singularity

[Immerman]

Well, if neurons worked like transistors, perhaps. However available evidence is that each neuron operates more like an embedded processor, possessing memory and firing in response to some sort of non-trivial analysis of the state of the 7,000 (average for a human) synaptic connections is possesses. That suggests that in order to make an artificial copy of a mind we'd first have to figure out how to emulate individual neurons and possibly even record their internal states. And of course emulate the various types of synapses and their sensitivity to ambient brain chemistry. And the ambient brain chemistry... things could get complicated.

And of course even if you could perfectly emulate a brain there's still the core problem with "uploading" a mind for most purposes (aka immortality) - much like uploading a file you aren't moving it, you're making a copy. Which means that after the upload you'd get out of the scanner and continue on with your normal mortal life while your new mind-twin begins their new potentially immortal one. Or you die in the process. Either way there's not much in it for the original.

Re:Singularity

[Ichijo]

Slavishly reimplement millions of models in the new medium's physical construction...

You make it sound like implementing one million cells in software is a million times more difficult than implementing just one.

Re:Singularity

[Beezlebub33]

Do you:

1) Slavishly reimplement millions of models in the new medium's physical construction, to emulate the quirks and behaviors of the target system's physical construction, wasting huge amounts of energy and making a system that is actually *MORE* complex than the original....

OR

2) Deconstruct all the mechanisms at work in the physical system that currently performs $BAR to get $FOO, evaluate which of these are hardware dependent, and can be removed/adapted to high efficiency analouges in the new hardware platform-- and produce only the components needed for $BAR to be accomplished, to generate $FOO?

The former will most certainly get you $FOO, but is HORRIBLY INEFFICIENT, and does not really shed light on what is actually needed to get $FOO.

The latter is MUCH HARDER to do, as it requires actually understanding the process, $BAR, through which $FOO is attained. It will however, yeild the higher efficiency synthetic system, AND the means to prove that it is the best possible implementation.

Basically, it's the difference between building a rube-goldberg contraption, VS an efficient machine.

We've been trying, in various ways, to do #2, but can't do it yet. So, we're trying to do #1, analyse it, and then do #2. You say that we should 'produce only the components needed', but really, that's the crux of the matter. We don't know what the components needed are. We can't even simulate a worm yet at either the individual cell OR functional level; see the OpenWorm project (http://www.openworm.org/) for an attempt at the former. We can use that sort of model organism to figure out what the important features are, model those, and move forward, but it seems unreasonable to complain that full nervous system modeling is the wrong approach, when the alternatives haven't worked yet.

What?

[jones_supa]

This sounds quite amazing. What's the catch?

Re:What?

[Anonymous Coward]

It only tracks the nuclei (which will provide very little information about a nervous system) from existing image data. It is not currently not even possible to image how the final nervous system of a fruit fly is setup so that this software could be run. They are too thick and opaque for any current microscopy technique to use while alive. Philipp Keller also developed a microscopy technique for imaging this type of data. I've tried using it on flies, and it doesn't work.

Re:What?

[Immerman]

In fairness fly neurons appear to be far more sophisticated than those of humans - we had the luxury of being able to just keep adding more neurons at minimal cost in order to build more sophisticated structures - as long as those extra neurons on average put more calories in our bellies than they consumed they were a clear win. Flies on the other hand have extremely tight mass and volume constraints, and as a result the individual neurons had to become more sophisticated instead - to the point where an individual fly neuron may serve the function of several independent human neurons (i.e. having multiple independently operating axion&dendrite clusters all connected to the same nucleus), and/or being able to fundamentally alter their responses based on the current activity (flying, feeding, etc) in a sort of "situational multiplexing" of the neuron's functionality - a feature that has no known analogue in mammals.

Re:What?

[Anonymous Coward]

I'm not sure that this brings fairness. Humans have 100 billion neurons to the 100,000 that flies have. Most fly neurons don't have multiple independent parts, and the ones that do have 2-4 parts. The electrophysiology backing up the claim on "independence" is spotty at best too.

Here's the catch

[kid_wonder]

Cell Division

1 cell becomes 2 cells -- which cell does it follow?

Re:Here's the catch

[Impy the Impiuos Imp]

Both -- track the entire tree. Seems like an obvious thing to try...on retrospect.

Once you know this, you can start looking for conttol mechanisms at the DNA and chemistry level.

Re:Here's the catch

[Fly Ricky - The Wine]

Someday we might be able to roll back to an earlier version.

Re:Here's the catch

[one eyed kangaroo]

Cell Division

1 cell becomes 2 cells -- which cell does it follow?

My understanding is that it can follow both. "Once a cluster of supervoxels has been identified as a cell nucleus, the computer uses that information to find the nucleus again in subsequent images." That sounds like extraordinarily cool technology. Tracking the embryonic development of cells is currently very hard. For really simple organisms, each embryonic cell can be tracked to one or more fixed descendent cells in known locations. For most organisms however, where a given embryonic cell ends up is a non-deterministic process.

Wait

[HangingChad]

Wasn't this the opening scene for Jurassic Park?

ctrace

[Anonymous Coward]

cell trace - yea!!!!!!!!

Interesting

[Anonymous Coward]

I wonder how thick the imaging works over.

For a mouse, how far can they image the development.

Re:Interesting

[Immerman]

Hmm, I seem to remember some folks a while back figuring out how to replace the fats in neurons to render a brain transparent. If they could figure out how to do that, even partially, without killing the organism in the process, then it could dramatically increase the power of this tracking.

Fly neurons?

[Doug Merritt]

Very interesting; is there a technical book (or chapter) or paper with a good overview of this comparative aspect of fly neurons?

I was just starting to look around to see what's available on comparative neuroscience in general, based on an interest in the most salient functional differences from human neurons, so anything related to that more general topic would also be welcome.

Re:Fly neurons?

[Immerman]

Can't offer one offhand - there was a TED talk on it not too terribly long ago though, and they may have a few references.

Could you use this for body building?

[tjstork]

I know it sounds vain but it does also have practical applications for people with muscular deficiencies owing to immobility. From what I've gathered, no one really knows what happens, precisely, to cause muscles to "grow". Sure, there's a hundred different theories tossed around on body building forums, but a lot of sounds more like pseudo-biological nonsense rather than real science. There's precious little experiment in the field and my lay understanding is that it is because the only method of looking at muscles is biopsy.

You guys are all stupid

[Anonymous Coward]

Everybody knows the nervous system can't develop if you're watching.

That's incredible

[Anonymous Coward]

Each AND every?