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Biotech Supercomputing Science

Mouse Brain Simulated Via Computer 268

Posted by Zonk
from the i-have-some-business-in-nevada-see-you-on-the-net dept.
Mordok-DestroyerOfWo writes "Researchers from the IBM Almaden research lab and the University of Nevada have created a simulation of half a mouse brain on the BlueGene L supercomputer. 'Half a real mouse brain is thought to have about eight million neurons each one of which can have up to 8,000 synapses, or connections, with other nerve fibres. Modelling such a system, the trio wrote, puts "tremendous constraints on computation, communication and memory capacity of any computing platform."' Although there's more to creating a mind than setting up the infrastructure, does this mean that we may see a system for human mental storage within our lifetimes?"
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Mouse Brain Simulated Via Computer

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  • News at 11 (Score:5, Funny)

    by wumpus188 (657540) on Saturday April 28, 2007 @01:31PM (#18912609)
    Researchers ran in terror of a big cat. News at 11.
  • We don't use it any more, 'cause the computer keeps running away and hiding under the desk.
  • Does it run ...? (Score:3, Insightful)

    by rueger (210566) on Saturday April 28, 2007 @01:38PM (#18912669) Homepage
    Assuming that the virtual mouse brain runs on Linux, I propose that we start work now on a virtual mouse trap.... The only question whether we need to develop a virtual spring, or virtual glue.
  • by Anonymous Coward on Saturday April 28, 2007 @01:39PM (#18912673)
    NARF $

  • by atomic-penguin (100835) <(wolfe21) (at) (marshall.edu)> on Saturday April 28, 2007 @01:39PM (#18912679) Homepage Journal

    while (smell($cheese)) {
            squeak();
            scurry();

            if (trapped($cheese)) {
                    untrap($cheese)
            } else {
                    eat($cheese);
                    squeak();
            }

    }


    • Re: (Score:3, Funny)

      by ookabooka (731013)
      untrap($cheese)

      Uh oh. . no semicolon. . if you can even get that to compile you better hope that mouse never has to deal with trapped cheese :-p Also, are you sure its a good idea to have the mouse (if the cheese is not trapped) to eat it, squeak, then immediately squeak again? Is that really necessary? I think you should GPL this and let the genetic algorithm of thousands of developers with thousands of ideas tweak it for the optimum behavior.
    • Re: (Score:3, Insightful)

      by IL-CSIXTY4 (801087)
      Forgive me for being a little pedantic here, but your while loop terminates (as so does, presumably, the mouse) once it stops smelling cheese.
      • Without cheese what is there to live for?

        The mouse would obviously commit suicide in that case. So, the program is correct.

        The funny thing I find is you could refactor your mouse algorithm into a "human male" simply by replacing "smell cheese" with "see hot woman" and "east cheese" with....

  • by Anonymous Coward on Saturday April 28, 2007 @01:40PM (#18912681)
    I opened my mouse and there was just a single chip in there. Why use BlueGene to simulate half of that?
  • Umm (Score:5, Interesting)

    by Tx (96709) on Saturday April 28, 2007 @01:43PM (#18912715) Journal
    FTA:

    Half a real mouse brain is thought to have about eight million neurons

    and

    the researchers created half a virtual mouse brain that had 8,000 neurons


    How can it be half a mouse brain if it has 1/1000 the number of a real half mouse brain? Their simulated neurons also had less synapses than the real thing. So is the 8000 a typo, or am I missing something?
    • Re:Umm (Score:4, Informative)

      by Tx (96709) on Saturday April 28, 2007 @02:01PM (#18912845) Journal
      Just to follow up, according to this article [businessweek.com], Blue Brain*, utilizing a 22.8 teraflop supercomputer, manages to simulate around 10,000 human neurons. I have no idea whether human neurons are significantly more complex than mouse neurons, or whether we just have more of them, but if the latter then maybe the 8000 isn't a typo after all?

      * Previously mentioned [slashdot.org] on slashdot.
      • Re: (Score:3, Insightful)

        by ceoyoyo (59147)
        It depends on how you simulate the neuron.

        If you model it as a black box that sums up inputs and fires if you're over a threshold you can simulate a whole whack of them. If you model it in excruciating detail you might need a supercomputer for each one. If you believe Penrose that quantum mechanical effects are important in neurons then you can't even properly model one with a current supercomputer.

        And then there are the connections. Different types of neurons have different numbers of connections. And
    • Re: (Score:3, Funny)

      by theurge14 (820596)
      They were able to use gzip on the cheese craving neurons.
    • Re: (Score:3, Informative)

      by julesh (229690)
      How can it be half a mouse brain if it has 1/1000 the number of a real half mouse brain? Their simulated neurons also had less synapses than the real thing. So is the 8000 a typo, or am I missing something?

      It's a typo. See original research note here [modha.org].
  • very short article (Score:3, Insightful)

    by mangu (126918) on Saturday April 28, 2007 @01:47PM (#18912741)
    Near the end they say "Imposing such structures and getting the simulation to do useful work might be a much more difficult task than simply setting up the plumbing".


    What did the author mean by that? If they are not simulating any of the actual neural structures in the mouse brain, does it mean they are just simulating a more or less random neural network with eight million neurons? I have seen reports of simulations of actual brain structures in more primitive animals years ago.


    Until they can, as they say, "add structures seen in real mouse brains" there's nothing to see here, move along...

  • by gweihir (88907) on Saturday April 28, 2007 @01:47PM (#18912745)
    There is no connection between the simulation and human mental storage. None at all. Why the nonsensical statement in the article!
  • I always thought it was fascinating how nature has been able to "grow" super computers (our closest analog to brains) and we have been unable to build anything even close to emulating their capabilities. Perhaps, there is a limitation to a mind's ability to understand how itself works. I think that if a person were to have absolute knowledge of how his or her own mind worked, it may just drive that person to madness when he or she realizes the mechanics of it reduce his or her thoughts and actions to mean
    • by ardor (673957)
      Hey, pipe down. Those brains evolved in millions of years, we have been pursuing actual research into these fields for less than 80 years.
    • by ceoyoyo (59147)
      We also haven't been able to build a proper wing that flaps or a system that can metabolize organic material to power itself, or even self replicate, never mind do all of those together.

      The brain might be special but we can't say so until we figure out how to do those other things and simulating a brain STILL eludes us.
    • I always thought it was fascinating how nature has been able to "grow" super computers (our closest analog to brains) and we have been unable to build anything even close to emulating their capabilities. Perhaps, there is a limitation to a mind's ability to understand how itself works.

      Or perhaps it's cause Nature has had 4 BILLION years....... and we've had about 50.... Just perhaps....

      BBH
  • by apathy maybe (922212) on Saturday April 28, 2007 @01:49PM (#18912761) Homepage Journal
    If they can simulate half a mouse's brain, then they can surely simulate a politicians. Now we can start rounding up those scum and replacing them with computers ...
    • by jd (1658)
      For the last ten years, you've really been electing a bunch of PET 3032s, Apple Is and ZX-80s. The speech synthesis was by Superior Software and the suits by US Gold. Sometime in the next few months, we are due to be attacked by a large number of mutant camels, the road system already having degenerated into a maze of twisty passages, all alike.
    • by tsa (15680)
      Just machines that make big decisions
      programmed by fellows with compassion and vision...
        -- Donald Fagen, I.G.Y., from the marvellous LP 'The Nightfly' (1982)

      You see the problem? You replace one human with another.
  • Cheese? (Score:2, Funny)

    by fluch (126140)
    Did it think "Cheese!" .. or was that the other half of the brain?
    - Martin
  • The essentials (Score:5, Informative)

    by Dr. Eggman (932300) on Saturday April 28, 2007 @02:02PM (#18912855)
    If you like the fancy terms, here's the (only 1 page and a cover sheet) pdf the Research report [modha.org] or, better yet here's Modha's blog [hostingprod.com] with about the same info.

    For more information on the Blue Brain Project [bluebrain.epfl.ch] which appears to be the same, or atleast a strikingly similar project but from switzerland, click...err, that link I just placed! Here also [spiegel.de] is a good article to learn more about blue brain. It seems much more detailed than the BBC's snippit.

    Groups of neurons started becoming attuned to one another until they were firing in rhythm. "It happened entirely on its own," says Markram. "Spontaneously."
    Insights like these are absolutly amazing. It's all such facinating research, but I can help feel a twinge of sorrow for the poor thing.

    the main purpose of the artificial brain, say its creators, is to make new types of experiments possible. For example, what happens when damage is inflicted on certain types of cells whose function still isn't determined? How many cells can be switched off until the behavior of the surviving cells around them becomes erratic, or the entire circuit breaks down?
    The poor thing is just circuits and reactions, I know, but I feel sorry that it's literally being torn apart and rebuilt all the time. It's odd, I don't feel this way in similar experiments with real mice; I guess I have a soft spot for computers...
    • Re:The essentials (Score:4, Informative)

      by Animats (122034) on Saturday April 28, 2007 @02:50PM (#18913181) Homepage

      I just found and read the actual paper, too; now I don't have to post the link. (It ought to be a Slashdot requirement that when you post a story about something, you have to link to the real source, not just some news site or blog link.)

      This isn't really about simulating a mouse brain. This is more like running a synthetic benchmark to demonstrate that if they had the wiring diagram for a mouse brain, IBM Almaden has enough CPU power on hand to simulate it. But they don't have a mouse brain wiring diagram; they're just exercising the simulator with some random set of connections.

  • This isn't really anything dramatic. It appears to only differ from what they were already doing with Blue Gene I think a year ago in that now they've made some optimizations to their firing/communication algorithms to be less resource intensive (and correspond less directly to what occurs physically), allowing for simulation of more neurons and firings.

    They don't seem to be simulating any neuroanatomy beyond interconnected neurons, and the initial interconnection pattern is just artificially generated.

    So w
  • by RyanFenton (230700) on Saturday April 28, 2007 @02:17PM (#18912957)
    It's cool that we can create the basic scale of the infrastructure of a (half) mouse brain - but if we're really going to simulate a brain, we need the ability to read the contents of a real one in order to verify our simulation. Otherwise, we have little basis for saying that input X gives the sensation of movement, and would have effect/output Y in terms of changed state/response.

    I wonder what the current state of neuron state reading is - would we ever theoretically be able to read the state of a brain beyond the external outputs? Could we ever get a sinlgle state that would be the 'ROM' of a person's memories and mental state, that you could place in a simulation and have that person's memories 'wake up' in a simulation? I wonder how close we could get.

    Ryan Fenton
    • by Gabrill (556503)
      You're jumping ahead of us. You'd have to emulate sensory organs in order to sense "movement".
      • >>You're jumping ahead of us. You'd have to emulate sensory organs in order to sense "movement".

        Actually, you just need to be able to read the outputs from a sensory organ. There's no rule against testing a simulated brain with a real eye's outputs. You can either record the outputs and send them through to the simulation later, or have realtime IO to a real eye. Same with equalibrium, and other data sources. Oddly enough, it's likely many, many, many orders of magnitude simpler for us to provide
  • by DoofusOfDeath (636671) on Saturday April 28, 2007 @02:25PM (#18912999)
    Developing simulations involves using abstractions and simplifications to deal with the fact that we can't handle the computational complexity of quantum-level simulation of an entire mouse brain.

    I've seen far too many papers where people make a "simulator" for a system, without demonstrating that the simulator has any real connection to reality, and then make grandiose claims about the real system that they're simulating, based on simulation results.

    Call me a cranky old computer scientist, but someone simulating a brain isn't particularly noteworthy. Showing that the simulator is accurate enough to shed light on the ways that brains work, or that the simulated mouse brain can achieve things that we have difficulty achieving with traditional computer software, and I'll be excited.
    • by rbarreira (836272)

      to deal with the fact that we can't handle the computational complexity of quantum-level simulation of an entire mouse brain


      Noone has ever proved (or gave very strong reasons for) the necessity of quantum-level simulations of brains, so I'd say your post is at least a bit misleading...
      • Fair point. Although my main intention was to show the the (necessary) use of abstractions when modeling potentially introduces modeling errors. I wasn't really trying to say that a quantum-level simulation would be the gold standard of accuracy.
  • Mouse, whatever... Wake me up when computer scientists can model an insect [umd.edu] brain!
  • by fahrbot-bot (874524) on Saturday April 28, 2007 @02:33PM (#18913055)
    Researchers from the IBM Almaden research lab and the University of Nevada have created a simulation of half a mouse brain on the BlueGene L supercomputer.

    I would imagine a Beowulf Cluster of these, but I want to be able to sleep tonight...

  • Not even close (Score:5, Informative)

    by quizzicus (891184) <johnbanderson@nOSpam.gmail.com> on Saturday April 28, 2007 @03:10PM (#18913305) Journal
    The subject on this story is a bit misleading. According to the article, the simulation:
    • Simulated only half a mouse brain
    • Ran at about 1/10 the speed of a real mouse brain
    • Only ran for 10 seconds
    • Only simulated generic tissue (didn't contain brain structures found in real mice)
    From the article:

    Imposing such structures and getting the simulation to do useful work might be a much more difficult task than simply setting up the plumbing.

    For future tests the team aims to speed up the simulation, make it more neurobiologically faithful, add structures seen in real mouse brains and make the responses of neurons and synapses more detailed.

    It's not that this isn't noteworthy, it's that mammalian brains are incredibly complex. I would be curious to see if they could faithfully reproduce a fish or reptile brain at this point.


  • to paraphrase Jack Nicholson in "The Departed": "You all are [on your way out]. Act accordingly."

    Advances in nanotech will obsolete the human brain and body probably within fifty years. So if you're younger than forty, you'll probably see it. If you're between forty and sixty, you might or might not depending on how close you are to the upper end of the range and whether you can take advantage of life extension technologies over the next twenty years or so. If you're over sixty - arrange for a suspension co

Wernher von Braun settled for a V-2 when he coulda had a V-8.

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