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Biotech Supercomputing Science

Mouse Brain Simulated Via Computer 268

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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  • by casings ( 257363 ) * on Saturday April 28, 2007 @01:33PM (#18912625)
    Unlikely, given that we are really no where close to even understanding completely everything about our complex brains.

    Do we even want to, wouldn't that take away some of the mystery behind humans. Afterall if we can figure ourselves out then doesn't that mean that we aren't really all that complex?

    wouldn't that also give us perfect explanations of people's actions making situations predictable violating free will?

    afterall if society is ultimately chaotic in terms of our understanding, then wouldn't this be the ultimate control?
  • 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 @01:42PM (#18912705)
    No one is forcing you to read the textbooks that explain how your brain work. In any case, a bound on complexity was already achieved when we figured out we were made out of atoms, and how many of them.
  • by suv4x4 ( 956391 ) on Saturday April 28, 2007 @01:46PM (#18912731)
    Unlikely, given that we are really no where close to even understanding completely everything about our complex brains.

    Do we even want to, wouldn't that take away some of the mystery behind humans. Afterall if we can figure ourselves out then doesn't that mean that we aren't really all that complex?

    wouldn't that also give us perfect explanations of people's actions making situations predictable violating free will?

    afterall if society is ultimately chaotic in terms of our understanding, then wouldn't this be the ultimate control?


    Don't be afraid to know more. It's coming if you want it or not. It doesn't mean a thing about free will: did you ever believe that your free will belong to your "ghost" or something? You are the sum of your parts and the interaction between them. Nothing scary about this.

    As for the "mental storage" - simulating a brain doesn't mean much about mental storage. Knowing and simulating an Intel chip in a program doesn't mean you can crack open an already produced Intel chip unit and hack few more cores in it.

    Plus, we already make very good use of tools to expand our mental storage: starting with notes, diaries, databases, computer knowledge systems, customer relationship programs, photos albums etc. etc.

    All these act as peripheral devices to our brain, and we should expect tighter integration between the brain and those (for example a wire projecting video directly in your cortex), but nothing that "expands" the brain structure at such a low level as is hinted in the summary.
  • 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!
  • by Poromenos1 ( 830658 ) on Saturday April 28, 2007 @01:49PM (#18912759) Homepage
    Afterall if we can figure ourselves out then doesn't that mean that we aren't really all that complex?

    You think that making something that can figure itself out is simple?
  • by Kandenshi ( 832555 ) on Saturday April 28, 2007 @01:52PM (#18912789)

    Do we even want to, wouldn't that take away some of the mystery behind humans.


    We have a fairly good understanding of the way a rainbow is made, but I can still appreciate it's beauty. Same goes for a wide variety of phenomena.
    We understand the physiological make-up of boobs, but they're still pretty interesting and appreciated by a large % of the population. Just because we understand something, doesn't make them less wonderful and amazing. Besides, most people in the near future wont bother/be able to learn about the exact way a mouse brain works, let alone a human one. So those people can still have that ignorant bliss you promote.

    While it's a bit of a tangent, regarding your free will comment... Psychology does allow us to make probabilistic predictions about how populations of people will behave in a given situation. That seems to rob us of free will? But at the same time, some sort of regular predictable nature has to exist in order for us to make choices. If I can't use some sort of rudimentary psychology to predict how a girlfriend will react to my gift of a pair of tickets to the superbowl, versus tickets to the theater, then how can I be said to be choosing anything? I need to be able to predict how people will behave, or else I can't make informed choices with my own "free will"
  • 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 IL-CSIXTY4 ( 801087 ) on Saturday April 28, 2007 @02:29PM (#18913031) Homepage
    Forgive me for being a little pedantic here, but your while loop terminates (as so does, presumably, the mouse) once it stops smelling cheese.
  • Re:Umm (Score:3, Insightful)

    by ceoyoyo ( 59147 ) on Saturday April 28, 2007 @02:33PM (#18913059)
    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 the connections themselves are quite complex, if you want to get into the gory details.

    So the 8000 might be a typo, but they might be doing a simulation of a very different type than Blue Brain.
  • by vertinox ( 846076 ) on Saturday April 28, 2007 @02:54PM (#18913209)
    Do we even want to, wouldn't that take away some of the mystery behind humans. Afterall if we can figure ourselves out then doesn't that mean that we aren't really all that complex?

    Would it bother you to wake up one day and realize you don't have free will?

    Or perhaps the soul is nothing more than chemical reactions that only came about through random chance?

    Truth be told, the brain exists in a semi-logical universe where rules are applied and must adhere to the laws of physics.

    The question of having free will or a soul makes no difference to how the human mind works on a chemical level. It would work regardless of how we thought on the matter (maybe just different regions) but it would still function.

    So if we find tomorrow exactly how the human brain functions on an atomic level or forget the whole matter entirely, it will change nothing of how it is made and how it actually works.

    And we might as well try to figure it out, because leaving well enough alone would have left us in caves thinking that fire was a bad idea.
  • Re:No randomness? (Score:4, Insightful)

    by rumli ( 1066212 ) on Saturday April 28, 2007 @02:55PM (#18913211)

    Without this you have a deterministic machine, and not a brain.
    Why do so many people refuse to entertain the possibility that they might be deterministic? Seems like people get overly defensive about their free will.
  • by vertinox ( 846076 ) on Saturday April 28, 2007 @03:05PM (#18913269)
    However, there is an alternate theory of consciousness, based on quantum physics [quantumconsciousness.org]. It is inherently non-deterministic and cannot be modeled in a computer.

    I think the biggest argument against this is that synapses do not work on the atomic level. They are made of atoms, but quantum states do not seem to overtly affect organic matter at cellular level.

    Of course I could be wrong about this, but since decisions are usually the next best move [wikipedia.org] it could simply be a matter of weighting what the "intelligence" applies to his rules as next best move.

    The problem with General Artificial Intelligence is that "the next best move" is often open ended and too many possible choices often give our current computation a run for its money unless its put into some form of predefined rules.

    The reason humans do so well is because we have certain criteria encouraging us to do things (hunger, pain, altruism, fear, etc etc)

    Hence, our general intelligence goals aren't that complex (usually... to feel good about oneself and one's life) and that our true intelligence is being able to recognize things that improve upon that given a set amount of rules we know.

    Which makes us very deterministic.

    Even rebelling against the crowd can often be very predictable in humans.
  • by Anonymous Coward on Saturday April 28, 2007 @03:13PM (#18913319)
    Quantum physics *can* be simulated in a computer. It's just that it can requires time exponential in the number of particles (in the worst case). The output is the probability of each possible outcome, which is actually *better* than reality which "outputs" just one outcome without telling you how probable it was.
  • Re:No randomness? (Score:3, Insightful)

    by 2short ( 466733 ) on Saturday April 28, 2007 @03:59PM (#18913557)
    Ignoring the obvious question of whether Penrose is correct...

    What makes you think this machine is not affected by cosmic rays?

  • Re:No randomness? (Score:3, Insightful)

    by snarkh ( 118018 ) on Saturday April 28, 2007 @04:47PM (#18913837)
    This is a very difficult, unintuitive concept, and it completely abolishes the idea that you can predict human behavior, even though you may be able to reach better and better approximations as you reach larger scales.

    How does it remove the possibility of predicting human behavior? Many macroscopic processes (e.g., motions of the celestial bodies) can be predicted very well, despite quantum uncertainty. You would have to argue that human behavior is determined at the quantum level, as Penrose does, not very convincingly, in my view.

    You may also consider the fact that uncertainty does not just arise at the quantum level. for example, it is very difficult to predict weather, despite the fact that quantum effects probably have little role in it. It has to do with the fact, that certain systems are very sensitive to the initial conditions and our ability to measure is limited.
  • Re:No randomness? (Score:3, Insightful)

    by BillyBlaze ( 746775 ) <tomfelker@gmail.com> on Saturday April 28, 2007 @05:46PM (#18914223)
    Hmm, couldn't you just give the simulator a source of entropy, such as a hardware random number generator? Or perhaps implement the simulator in an FPGA, and then overclock it to the point where it's just a little finicky?

    Given the difficulty of distinguishing between pseudo-random and truly random numbers, I don't think that would even be necessary. I would be very surprised if we made a brain simulator with a real entropy source, which was creative, and then replaced that with a pseudo-random number generator, and the creativity evaporated.
  • by DogFacedJo ( 949100 ) on Saturday April 28, 2007 @07:09PM (#18914453)
    Yep, exactly, and I totally consider it a truly bizarre assumption that Penrose holds there.

        I am forced to assume that it is important for his notion of identity, to have a free will that is capable at least of thinking whatever it is possible to think. He likely refines this formally as the ability to 'prove what is provable' - since if we *couldn't* prove certain things that are actually provable, then we clearly wouldn't have the ability to think whatever was thinkable, or possibly to think whatever we want preventing free will. Can't be certain which beef he has that drives his assumption - there are likely several more possible motivations, though Penrose claims at least not to be motivated by spirituality in this argument.

        Any discussion of AI and computability must acknowledge the wonderful Godel Escher and Bach: An eternal Golden Braid by Douglas Hofstadter. ISBN-10: 0465026567 ISBN-13: 978-0465026562
        Hofstadter is less rigorous, and is mostly just trying to show how neat these areas of math are - and how they relate to consciousness, intelligence, identity, knowledge etc... If you haven't read it already I think you'd really, really, enjoy it. He also assumes things more along the lines of how I think - so I can claim his arguments are more 'sound' than Penrose. Penrose does a commendable job of logically carrying his position, but his assumptions are crazy - I accuse him of an 'unsound' analysis. ;}

        Thanks for taking the time to read my post - there's no way I'm getting modded up on something that long.
      I had mod points too (or at least I did earlier today), could have just hit him with the trusty 'overrated'.
    Sigh.

  • by FluxIntegrator ( 1094517 ) on Saturday April 28, 2007 @08:00PM (#18914765)
    Slashdotters are disappointing me on this one. I practically fell out of my chair when I read that half a mouse cortex has been simulated. This is an INCREDIBLE advancement. Furthermore, the fact that synchronous firing (which is probably THE most important feature of neuronal activations in the cortex) was observed is absolutely remarkable. First of all, the human brain is not a quantum computer. The scales as WAY to large, and this has been known for many years . Only crackpot websites have suggested otherwise. There is absolutely NO serious research on quantum computation in the brain. That theory was discarded several years back by serious researchers. Secondly, there are consistent theory of the mind. In particular, Jeff Hawkins Memory-Prediction framework. It is becoming increasingly evident that the mind is simply an extremely powerful predictor, which evolved to protect organisms. And third, recent research has linked synchonous firing to CONSCIOUS attention. Which means that this simulated half a rat brain is most likely the first conscious simulation EVER. This is HUGE. I cannot believe, on a forum such as this, that people would be making jokes that imply that absolutely nothing has been accomplished. This is practically the beginning of the next stage of human evolution. I could say more, but I'll let slashdotters redeem themsevles.
  • by jerald_hams ( 725369 ) on Saturday April 28, 2007 @08:28PM (#18914939) Journal
    Setting up computational infrastructure is an important but extremely unexciting step in neural simulation. The very fundamentals of *what* we should be simulating are still largely unknown. If anyone has read more on the research please correct me, but my guess is they are running simulating 8 million undifferentiated neurons disconnected from real-world input. This isn't a "mouse brain", they just call it such because the number of "neurons" is similar.
  • by FluxIntegrator ( 1094517 ) on Sunday April 29, 2007 @02:37AM (#18916619)
    You have several misconceptions. First of all, this is not simply a "neural net". This is a somewhat biologically accurate model, with structure similar to a real cortex, including microcolumns, in addition it is:

    A massively parallel cortical simulator with (a) phenomenological spiking neuron models; (b) spike-timing dependent plasticity; and (c) axonal delays.

    (see the actual research description here: http://www.modha.org/papers/rj10404.pdf [modha.org])
    Secondly, it is not necessary for a cortex to have left-right brain functionality in order for it to function. This has been demonstrated in live humans.
    And third, the speed, relative to real-time, is irrelevant. It is comparatively a minor task to increase the speed of the simulation by increasing parallelization.
    Now, to respond to your somewhat antiquated understanding of the current state of AI:

    In addition, everything I have seen in tech press on AI since the rules based AI reasoning failures of the 80's has been neural net simulations looking for patterns, such as the mentioned synchronized firings.

    Sounds like you're a couple of years behind (as would be expected on slashdot, which primarily focuses on IT and science, and not neuroscience). Let me bring you up to date a little. Spiking neural networks began to grow in popularity in the mid to late 90's. They are much more biologically realistic then most of the models used in the 80's and early 90's. Also, a lot of research has been done which points to the significance of chaotic attractors, which arising from phase-locked loops in the neuronal structure. The fact that synchronous firing is observed tends to imply similar dynamics are occurring.
    Furthermore, you make the assumption that biological brains are somehow superior to simulated brains, just because they are more chemically complex. That assumption has absolutely no research to back it up. For all we know at this point all of that chemical complexity may be superfluous for evolutionary benefits (and this is direction which evidence suggests).

    Aren't the neural net rules just tweaked until they get interesting behavior like that?

    That's the way it used to be done, so I can understand your confusion here. I think the problem lies in the fact that people are very interested in neuroscience these days. But a remarkable amount of progress has been made. Phenomenological spiking neural networks are quite a bit biologically accurate than the "neural nets" of the 80's and early 90's.

    Don't tell me you think they actually have any idea how they would simulate brain functionality.

    The cortex is arranged into mircocolumns of neurons, which have a very definite structure repeating structure over the surface of the cortex. Jeff Hawkins has recently presented a very convincing argument for structure of the mind, in relation to the structure of the cortex.

    Training neural nets is just something easy to do. Beats actually writing complex code, doesn't it?

    If you're implying that the simulation was not complex, consider that each neuron had its own dedicated computer. And, once again, this is much more complicated than a simple neural network.

    I've never seen any explanation for how either short term or long term memory works, much less reasoning or any other functionality. And that at least is something that would seem able to be modeled and explained. How does man know anything about something they have never encountered before, for example, to acquire language as a child?

    Explanations for both short and long term memory have been out there for quite some time. But neuroscience is not a popular topic of discussion, partly because it can get quite complex. People would much rather be talking about the step in the evolution of Intel processors, or life

  • by WetFreud ( 911489 ) on Sunday April 29, 2007 @06:25AM (#18917529)

    We can have a brain that's fully deterministic at a microscopic level without doing away with free will, if we assume that our brains operate in non-linear conditions [wikipedia.org].
    No, we can't. Chaos doesn't allow for a causal or non-deterministic effect of counsciousnes. It seimply means that the final state of the system cannot be predicted based on initial conditions, usually because these initial conditions can't be measured precisely enough. However, all the steps in the process are still completely deterministic. There is no more need or room for free will in a deterministic and chaotic brain than there is in complex meterological system. Or said another way, in which step in the nonlinear but completely deterministic chain of brain events does "free will" take place?

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