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Largest DNA-Based Computational Circuit Created

Posted by timothy on from the artificial-one-that-is dept.

angry tapir writes "Researchers from the California Institute of Technology have built [abstract] what they claim is the world's largest computational circuit based on DNA (deoxyribonucleic acid), using a technology that they said could easily scale to even greater complexity." Adds reader cwmike: "The researchers formed 130 different synthetic DNA strands that can be used to compose logic circuits. From this source material, they created one 74-molecule, four-bit circuit that can compute the square root of any number up to 15 and round down the resulting answer to the nearest integer. In their setup, the multi-layered strands of DNA are fashioned (see video) into biochemical logic gates that can perform the basic Boolean AND, OR and NOR operations executed by today's transistor-based computer processors."

14 of 57 comments (clear)

  1. In their dreams! by NoNonAlphaCharsHere · · Score: 4, Funny

    I've been running a MUCH larger DNA-based computational circuit for YEARS now! Course, sometimes it fails me completely.

    1. Re:In their dreams! by Fluffeh · · Score: 4, Informative

      Well, yes, while DNA based computing may sound like something from Science fiction, it looks like this is a small step:

      The researchers formed 130 different synthetic DNA strands that can be used to compose logic circuits. From this source material, they created one 74-molecule, four-bit circuit that can compute the square root of any number up to 15 and round down the resulting answer to the nearest integer.

      then

      Reif also pointed out a few downsides. One is the speed of calculation. The execution of a single gate can take anywhere from 30 to 60 minutes. Executing a four-bit square root could take up to 10 hours.

      So don't be expecting any DNA based mass computing revolution anytime soon.

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      Moved to http://soylentnews.org/. You are invited to join us too!
    2. Re:In their dreams! by SanityInAnarchy · · Score: 4, Interesting

      If you're talking about your brain, that's not what this is. This is using actual DNA to perform computations.

      Oh, by the way, last I checked, it's slow, and this is no exception:

      Reif also pointed out a few downsides. One is the speed of calculation. The execution of a single gate can take anywhere from 30 to 60 minutes. Executing a four-bit square root could take up to 10 hours.

      This isn't like quantum computing -- maybe they can make it faster, but I really don't see this having any inherent advantages over old-school tech like CMOS anytime soon.

      What makes this interesting is the potential to do calculations inside living systems, or to actually interface our code with otherwise strictly biological processes. These "circuits" are just solutions of custom-designed DNA, and each "gate" takes small single-strands of DNA as input, and produce them as output, whether as a "wire" to another gate, or as the final output to be measured to check if the circuit is working. Now imagine putting that in a cell. (Oh, and this is why formal methods matter -- if someone's going to be putting code in your body, it's not enough to debug it, you want that shit proven correct.)

      Disclaimer: While I did take a class (COM S 433 at ISU) which attempted to examine this stuff, this was covered at the very end of the semester, and no one (including the instructors) really had a good idea how these things actually work. I know enough to be dangerous, but there's a good chance I'm wrong about pretty much anything I say here. Read the papers yourself -- it's fascinating stuff.

      --
      Don't thank God, thank a doctor!
    3. Re:In their dreams! by Fluffeh · · Score: 2

      I am not saying that this isn't cool, but even if you had thousands and thousands of these gates, their individual processing power seems miniscule, and given the very lengthy times required to derive a solution to a problem, parallel operations would be limited.

      While I think it is very "nifty" for them to have done this, it doesn't appear (and I am happy to be corrected here) to have any direct applications, nor does it appear to be a stepping stone to anything in anything but the very distant future. Again, while I think it is nifty that they did this, and I hope that it leads to some wonderful breakthrough in the future, it seems that they are simply mucking about, making a set of items that are totally adapted for something else - do parlour tricks.

      If anything, I am more impressed with how far genetics has come rather than the fact that they got a bunch of DNA to do some arbitary maths puzzle.

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      Moved to http://soylentnews.org/. You are invited to join us too!
    4. Re:In their dreams! by buchner.johannes · · Score: 2

      ... last I checked, it's slow, and this is no exception: ... This isn't like quantum computing

      There shall be Quantum-DNA computing then! I hear DNA is prone to hybridisation.

      --
      NB: The message above might reflect my opinion right now, but not necessarily tomorrow or next year.
  2. A single logic gate operation takes 30-60 minutes by parallel_prankster · · Score: 3, Funny

    Thats exactly how my DNA-based computer works too :)

  3. Re:Did you say 'de oxy ribo nucleic ACID'? by RoFLKOPTr · · Score: 2

    That sounds like dangerous stuff! Its an ACID!

    I dropped some DNA last night and tripped some balls.

  4. Re:Did you say 'de oxy ribo nucleic ACID'? by NoNonAlphaCharsHere · · Score: 2

    Chill. Take two tablets of acetylsalicylic acid with a glass of hydric acid and wait for the palpitations to pass.

  5. Science: it's a tough life by Walt+Dismal · · Score: 4, Funny

    I keep telling girls at bars I'm a scientist who just wants to perform a complex calculation using DNA and then they throw a drink in my face for some reason.

  6. 4-bit square root? by sgunhouse · · Score: 2

    Seems pretty trivial to me. They did say round down, so ...

    0 --> 0
    1 --> 1
    2 --> 1
    3 --> 1
    4 --> 2 ...
    8 --> 2
    9 --> 3 ...
    15 --> 3

    For most inputs, the answer matches the highest 1 bit in the number (exceptions: 0, 1 and 9). Wouldn't be hard to make a circuit do that.

    10 hours? As in, 20 operations? Seems excessive...

    1. Re:4-bit square root? by maxwell+demon · · Score: 2

      Actually, if we name the input bits i0 (LSB) to i3 (HSB) and the output bits o0 (LSB) and o1(HSB) then the calculation to do is:

      o1 = i4 OR i3
      o0 = (i4 OR NOT i3) AND (i1 OR i2 OR i3)

      Indeed, not very complicated.

      --
      The Tao of math: The numbers you can count are not the real numbers.
  7. Re:Destroy it! by maxwell+demon · · Score: 2, Insightful

    Just look at the word: "deoxyribonucleic acid".

    First: deoxy. Removal of oxygen. Now we know oxygen is important for life. This will make us all suffocate!
    Then: nucleic. It's nuclear! Not only will we suffocate, we will also be irradiated!
    Then: acid. Not only will we suffocate and get irradiated, we will also get vitriolised!

    You see, three dangers in one! And who knows what hidden dangers are in the ribo part!

    Oh, and they will tell you that we all have it in our bodies anyway. Well, how did it get into our bodies? It's just proof that the contamination is already far too widespread!

    And sometimes you will even get a biologist admit that our death is preprogrammed in the DNA in our body. Therefore, remove all the DNA, and you'll live forever! :-)

    --
    The Tao of math: The numbers you can count are not the real numbers.
  8. Re:Did you say 'de oxy ribo nucleic ACID'? by somersault · · Score: 2

    My DNA tripped last night and my balls dropped.

    --
    which is totally what she said
  9. A computer based on this by imric · · Score: 2

    would give 'computer virus' new meaning.

    --
    Paranoia is a Survival Trait!