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Biotech

Computing Inside a Living Cell 41

Posted by samzenpus
from the you're-going-to-need-a-smaller-chair dept.
First time accepted submitter Rozanne writes "The new issue of Stanford Medicine magazine has a story on Stanford professor Drew Endy's creation of microscopic computers out of biological components for use inside living cells. His work is a mash-up of molecular biology and computer engineering: Instead of a computer made of silicon, metal and plastic, it's a computer made of DNA, RNA and enzymes. Endy says biologists are typically confounded at first when he explains how the computers work and how they could be used."
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Computing Inside a Living Cell

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  • by Anonymous Coward

    For all his talk, Drew Endy hasn't actually pushed the synthetic biology field forward, and it was always questionable whether his vision of "standardized biological parts" would be the best way to engineer biology. His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processe

    • by Gravis Zero (934156) on Friday November 01, 2013 @12:33AM (#45297609)

      His analogies to computer engineering are mostly false, as biology operates according to physical and chemical rules. Not Ohm's Law. Not digital logic. You can engineer biology to mimic digital logic, but it's truly analog governed by biomolecular interactions and stochastic dynamical processes.

      (human) brains are both analog and digital simultaneously. [yale.edu]

      even if you argue it's really all analog, the fact that you can mentally process digital logic means that you are digital computer... with lots of extra features. :)

      • the fact that you can mentally process digital logic means that you are digital computer

        Wish I had mod points...

      • by mcgrew (92797) *

        even if you argue it's really all analog, the fact that you can mentally process digital logic means that you are digital computer

        Any analog computer [wikipedia.org] can process digital logic. The difference between analog and digital is with analog you have noise, with digital you have rounding errors (and those rounding errors can be simulated in an analog computer).

        You can make a simple analog computer (actually more like an electric slide rule) with a couple of batteries, a couple of potentiometers, a voltmeter and a l

    • by Daniel Dvorkin (106857) on Friday November 01, 2013 @12:45AM (#45297675) Homepage Journal

      Yeah. I don't know enough about his work to comment, but when I read the part about how all this computational stuff is just too confusing for those poor biologists, my bullshit alarms went off. Speaking as a bioinformaticist, whose job it is to bridge the bio/CS gap all the time, I've observed that computer scientists often have at least as hard a time grasping biology as biologists have grasping computer science. Endy's kind of smugness does no one any good.

    • by ath1901 (1570281)

      I would love to. Care to share some interesting links?

  • by DigiShaman (671371) on Thursday October 31, 2013 @10:05PM (#45297061) Homepage

    Mutation is the result of DNA change. Often from external sources such as radiation or chemicals. The change could be good, bad, or nothing readily noticeable. So that said, how can you rely on the results of a biological computer that's prone to mutation and thus corrupting the results?

    • Re:Mutation (Score:5, Informative)

      by sqrt(2) (786011) on Thursday October 31, 2013 @10:15PM (#45297099) Journal

      At its lowest level, the hardware we use today to store data is prone to errors. Your HDD functions perfectly well misreading data hundreds of times a second. You don't even notice until it becomes especially bad; when the errors overwhelm the ability to check and correct the data. A certain amount of errors are expected, and correctable. The simplest method is a simple checksum. Report the intended length of the message you're sending and the receipient then checks to make sure at least the length is correct. Then you can build in redundancy and error correction through more sophisticated means. These problems have largely been solved in the abstract, so they're not dependent on any particular media.

  • by antifoidulus (807088) on Thursday October 31, 2013 @10:10PM (#45297077) Homepage Journal
    Now we can finally start betting on sperm races. All you need to do is the following:

    1. Put a tiny bit of compute power in each sperm cell that identifies the sperm.

    2. Proceed to give odds, take bets
    3. Fuck

    4. Profit! After the egg has been fertilised you can use the tracking chip in the sperm to see which one "won".
  • by tutufan (2857787) on Thursday October 31, 2013 @10:27PM (#45297169)
    but can it mine bitcoins?!
    • but can it mine bitcoins?!

      yes... but very slooooowly. it takes about 15 minutes per cycle.

      Speed-wise at least, IBM won’t feel threatened by the biocomputer. “The microbial processor operates in the millihertz time frame — about one cycle every 1,000 seconds, or about four times per hour,” Endy says, “But in biology it doesn’t always matter; slow can be beautiful.”

      • by gl4ss (559668)

        what he is saying is that practicality doesn't matter and you could build fluid based computers that act faster in the same size...

  • ...to Cell processors.
  • by Anonymous Coward

    About 15 or 20 years ago, there was a lot of biological computing going on where they would attempt to use bacteria to solve NP-hard problems and also crack encryption in n time (basically by replicating the bacteria and getting n^3 or o^n bacteria reproducing and breaking a code. They used large vats of bacteria instead of acres of cores. And now this. Its either 2013, or 1993, or 2033.

  • where do you plug in the keyboard? :)

  • by Gravis Zero (934156) on Friday November 01, 2013 @12:14AM (#45297553)

    With electronic signal amplification, a very small change in electrical flow is sufficient to open and close gates that control massive rivers of electrons. “The biological transistor, what we call a ‘transcriptor,’ does the same thing.

    He has formally donated the transcriptor and biological logic gates to the public domain via the BioBrick Public Agreement. That means anyone is free to use them. A similar declaration for the biological Internet is in process.
    The only piece of biocomputer technology Stanford and Endy have patented is the biological digital memory.
    “Some other groups have patented technologies claiming to accomplish a similar goal,” explains Endy. “If we have a patent, we can assure the technology is free and available to all simply by not pursuing our patent rights. But if we don’t have a patent, someone else could claim the technology and restrict its use.”

    finally someone that invents a great technology and understands that patents stifle innovation!

    bold tag! :)

    • by gl4ss (559668)

      actually patents don't work quite like that.
      they could just have published it as prior art as well, thereby guaranteeing that any patent could have been fought in court easily.

      (of course the trick to patents is that you don't really have to have invented how to do the actual thing nowadays to get one.. even when you should).

      but now the patent exists, it can pass to some other hands. otoh, it's unlikely it wont expire before any practical application..

      • actually patents don't work quite like that.

        incorrect. they shouldn't work like that but they do.

        they could just have published it as prior art as well, thereby guaranteeing that any patent could have been fought in court easily.

        it's extremely difficult to invalidate a patent and very expensive to fight, even if there is clear and blatant prior art. this is why a bunch of companies just pay for a license instead of fighting it. we have a legal system, not a justice system.

  • This sounds like the scenario to the novel Blood Music [wikipedia.org] by Greg Bear.
    • Exactly what I thought. Now we need to be careful not to let the researchers inject the modified cells back into themselves.

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