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Digital DNA Circuits

Posted by michael on from the synergistic-merger dept.

TheSync writes "ScienceNews has a story about digital DNA circuits. The circuits use proteins that activate or deactivate genes on the DNA for control. Since an inverter and an AND gate have been created, any digital logic circuit can now be done in DNA. Moreover, evolution can help make circuit elements work better. There is even a "databook" of BioBricks circuit elements and BioSPICE for biocircuit simulation."

40 of 157 comments (clear)

  1. And, not by Anonymous Coward · · Score: 2, Interesting

    But does this mean we can store data in DNA using hundreds of bases (latch), instead of a few bases directly?

  2. Oh! by Quasar1999 · · Score: 2, Interesting

    So that's how the neuro-gel packs work in Star Trek... and all this time I thought it was crap!

    Seriously though... what's the delay on these things? Comparable to silica versions?

    --

    ---
    Programming is like sex... Make one mistake and support it the rest of your life.
    1. Re:Oh! by g4dget · · Score: 5, Informative

      Transcription and translation happen at about 45 nucleotides per second in bacteria, meaning it takes at least a few seconds to get a signal through a genetic "gate" or "switch".

    2. Re:Oh! by The_K4 · · Score: 4, Informative

      Yes, but if you have several trillion copies of your program you can run them all in parellel. Think of cytography....you could make a bioprogram that's designed to find the 128 bit key. There's 2^128 possible solutions. So if you have a whole bunch of these 2^1000 bio-programs in a solution, you can quickly find the 128 bit key. Look here under DNA computing for an example of why this stuff is useful, even if it is slow compared to silicon.

    3. Re:Oh! by aqkiva · · Score: 3, Informative

      The original post of 45 nt/s is correct for transcription and translation (the speed of RNA polymerase and ribosomes). 1000 nt/s is for replication (the speed of DNA polymerase).

    4. Re:Oh! by g4dget · · Score: 2, Insightful
      No, you are just confusing lots of issues. DNA computing has little to do with genetic networks. It's also unproven whether DNA computing can actually do anything useful.

      And while DNA is compact, 2^128 and 2^1000 are really big numbers. 2^128 is about 10^38, and 2^1000 is about 10^300. A pound of hydrogen has about 10^27 atoms, so even if you use one hydrogen atom per key, you need nearly a billion tons of hydrogen just to get 2^128 atoms, let alone a billion DNA molecules.

      All this attention from computer scientists to "biocomputing" is mostly hype, and it's probably due to lucrative DARPA grants running out for the old kind of work. There are interesting questions to be asked there and interesting applications to be found, but biologists and mathematicians have been asking those for decades already.

  3. Huh? by blackmonday · · Score: 2, Funny

    This one wins my vote for absolute nerdiest post ever!

  4. imagine that by g4dget · · Score: 5, Funny

    And people have known about them only for, oh, a few decades.

  5. but then... by Tuxinatorium · · Score: 3, Interesting

    but then, that's not much more compact than a 90-nanometer transistor. Do you know how huge a polymerase protein is?

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    1. Re:but then... by g4dget · · Score: 5, Interesting

      But proteins go into a little 3D bag, while transistors need to be packed near a flat surface with current VLSI technologies.

  6. DNA computing and Cryptography by jwdb · · Score: 2, Interesting

    Does anyone know of any research into DNA computing and cryptography? I'd expect, given the massively parallel capabilities of DNA, it would be a very useful tool for a brute force attack...

    Imagine coding all possible keys as dna, mixing in the message, and pulling out the only possible and logical match -> your decrypt.

    Or am I just dreaming?

    Jw

    1. Re:DNA computing and Cryptography by rwiedower · · Score: 4, Interesting

      Even your body doesn't rely upon chemical reactions to accurately predict certain outcomes. Studies have shown that nerve fibers in your arm will often send a "the ball is coming" signal to your brain well in advance of the actual signal reaching your fingers. This sort of predicative function makes complex tasks like walking and talking much easier, but when it catches up to you (like when you fall on the bottom step of a flight of stairs because you forgot how many steps there were) you crash and burn.

      The point is, that chemical reactions are very slow. If they were faster, your brain (and your neurons in your arm) wouldn't have to guess. Because they're so slow they'd be very poor at brute force attacks, regardless of the sheer number of cells.

      So, yes, you're dreaming.

    2. Re:DNA computing and Cryptography by Code-Ex · · Score: 2, Informative

      Try this page

  7. Illuminate Me by rwiedower · · Score: 2, Interesting

    Okay, this may seem short-sighted, but if silicon circuits are so much faster, why not simply design silicon-to-carbon interfaces rather than try to redesign the wheel? Unless there's some level of functionality that's not applicable on the silicon side, I don't see why the results of a process couldn't be approximated. In the article, for instance:

    It's far easier to describe the schematics of these circuits than to build them for operation inside a cell. For instance, to hook up one gate to the next, the amount of protein produced by the first gate must be the right amount to activate the next gate. And at every step, the output protein must be either very high or very low, to avoid false positives or negatives. It's also necessary to tweak many parameters, such as the strength with which the various proteins and the messenger RNA bind to different parts of the DNA sequence.

    If the end result is accomplished simply by having the right protein the right place at the right time, why not build the circuit in silicon and simply train the cell to produce the appropriate protein based on the result of a calculation? Perhaps my ignorance is becoming too glaring...

    1. Re:Illuminate Me by Mr.+Spectre · · Score: 2, Interesting

      Okay, this may seem short-sighted, but if silicon circuits are so much faster, why not simply design silicon-to-carbon interfaces rather than try to redesign the wheel? If the end result is accomplished simply by having the right protein the right place at the right time, why not build the circuit in silicon and simply train the cell to produce the appropriate protein based on the result of a calculation?

      They are hacking the instructions written the code that cells already understand. This might allow for programming a cell to produce a particular protein only under certain circumstances determined by the hacked code. How is creating a silicon-to-carbon interface going to get a cell to do what you want it to?

    2. Re:Illuminate Me by rwiedower · · Score: 2, Insightful

      I wasn't saying the interface would solve the problem. I was saying that if I designed a cell to respond to an external stimulus with a certain protein production, I'd have a handy interface. Instead of building a cell to light up in the presence of a complex chemical compound, I could then simply have a cell send a protein to a circuit which could then send a signal to a led. Or, vice-versa, I could program a complex series of actions into a processor which would then interface with said S-2-C cell which would produce the proper proteins to achieve the desired effect.

      The article certainly goes beyond the idea of having one cell act a certain way. They implied that multiple cells could be chained together like some sort of rube-goldberg contraption. It's the chaining together that seems inefficient to me, when you could use silicon for the complex stuff and an interface cell to make the conversion. Kind of like a digital-to-analog switch, only between silicon and carbon. You still need to hack the cells, but you don't need to create complex machines. That was all I was wondering.

    3. Re:Illuminate Me by ciroknight · · Score: 2, Insightful

      There are applications of this FAR beyond those of silicon. What if you designed a circuit to detect the presents of certain viruses? You could make chemical/biological weapon detectors the size of CELLS! Also, think of what it can give us in a way of examining solutions to problems in our bodies.. you could design circuits to output certain chemicals/protiens when certain chemicals are in our blood stream. We could build cells that help filter out cancerous elements, PRODUCE INSULIN so that people would never need the shot again. This is just the tip of the iceburg on what all is possible with this new technology.

      Personally I'de love to sit and tinker with them, a cell program that could provide anti-histimenes when they build up in my system would be really nice, never worry about allergys again. Pipedream maybe, but it looks really sound and possible to me.

      --
      "Victory means exit strategy, and it's important for the President to explain to us what the exit strategy is." G.W.Bush
  8. Death.. by Anonymous Coward · · Score: 3, Funny

    So, now will death be refered to as a power outage?

    1. Re:Death.. by hesiod · · Score: 2, Funny

      > So, now will death be refered to as a power outage?

      Well, it sort of is. As I understand it, death is usually just a lack of oxygen to the brain (explains why guillotine victims seemed to be alive a few moments after being decapitated -- there was still blood/oxygen/power in the head, feeding the brain.

  9. [insert supreme being/philosophy etc.] called... by Dutchmaan · · Score: 5, Funny

    He wanted to remind you that he has held the copyright for DNA for billions of years now..

    He's been in contact with his lawyers and is tallying your bill as we speak.

  10. Could you program these bacteria� by Anonymous Coward · · Score: 5, Funny

    ... to play the game of life?

  11. Self-improving circuits by 16977 · · Score: 5, Interesting

    The most interesting thing about this announcement is that this guy has been able to use evolution to improve his circuits. I don't expect molecular computers to surpass electronic computers, at least right away -- although they could theoretically perform faster than electronic computers in the short term, any advantage is offset by the time needed to convert the information to human-readable form (by finding and correctly reading the DNA sequence). As the article says, it's better to take advantage of the fact that you can "work with" bacteria. But if DNA computers could repair and upgrade themselves, they would have an advantage that electronics currently does not have. Electronics already is under intense artifical selection, and it can reproduce itself after a fashion, but unlike copper and aluminum, DNA computers can be randomly mutated, and the close homology between computers ensures that some of those mutations will be beneficial.

    1. Re:Self-improving circuits by rwiedower · · Score: 2, Interesting

      DNA, maybe. DNA is fairly good at reproducing without errors. RNA, on the other hand, isn't that good with errors, but is much quicker. (Ask any virus.)

      My thought is this: as soon as the process becomes complex, errors introduced into each cell could produce vastly different results. And the debug process would be tortuous. There'd be no guarantee that a single mutation couldn't bring down the whole system.

  12. New female DNA logic circut states by Timesprout · · Score: 5, Funny

    YES
    NO
    MAYBE

    --
    Do not try to read the dupe, thats impossible. Instead, only try to realize the truth
    What truth?
    There is no dupe
    1. Re:New female DNA logic circut states by Lemmeoutada+Collecti · · Score: 3, Funny

      Can't be too sure of that MAYBE state either. It posesses the following sub states:

      MAYBE.You should have noticed already
      MAYBE.NO but I don't want to be the one to say it
      MAYBE.You had better know I mean YES
      MAYBE.Let's just be friends
      MAYBE.Are you being sensitive to my needs
      MAYBE.DON'T EVEN THINK OF PLAYING QUAKE RIGHT NOW OR YOU WILL BE SINGLE

      And there are a lot more potential substates yet to be catalogued in the interface.

      --

      You can have it fast, accurate, or pretty. Pick any 2.
  13. Don't know how 'wow'-ing this really is... by Necromancyr · · Score: 4, Interesting

    Reports of this sort have been coming out for a few years now - basically, all they are doing is a controlled induction of a promoter. It's nothing amazing. Chaining one promoter to express another promoter ad infinitum (or to restrict expression) is already done in nature and used extensively to create transgenic cell lines, bacteria, etc. Hell, they've already developed means to do basic computations with DNA that are more applicable/advanced then this in some respects.

  14. Evolution of Programming Languages? by jdh-22 · · Score: 2, Interesting

    Does this mean that a new bread of modern inovative programming languages will be needed? I am sure that most expirenced programmers would definatily like to do something differently to make the development process more efficient, and faster.

    Any suggestions on what you would like to see if a new language was developed for this platform?

    --
    Every Super Villan uses Linux.
  15. proteins by lazira · · Score: 2, Interesting

    Have there been studies in alternate programming methods/languages for DNA, like there were for quantum computers? DNA logic doesn't need to be sequential- each protein can affect many things at once. It seems rather unwieldy to try to apply conventional logic building blocks, as each gate would require a unique protein and inhibitor- you can't use the same block twice.

  16. Nooooo not again... by fireflew · · Score: 2, Funny

    Gives a new meaning to 'my computer died'.

  17. Grey goo theory? Super sperm? by macshune · · Score: 3, Funny
    Will Bill Joy's "grey goo" theory turn out to be just a bunch of DNA-computer-packin' malevolent super sperm?

    Will women have to worry about guys with DNA-computer enhanced sperm, so unprotected sex could mutate a woman into a ninja turtle?

    Will I be able to code myself urine that tastes like apple cider and poop that tastes like swiss chocolate?

  18. Teletubbies not so far fetched... by Billy+the+Mountain · · Score: 3, Funny

    If you could embed this into human cells, I bet you could convert my stomach into a 1280 X 1024 display!

    BTM

    --
    That was the turning point of my life--I went from negative zero to positive zero.
  19. NOT gate by Bowling+Moses · · Score: 3, Informative

    Sounds similar to work being done by the Arnold group at Caltech. They've apparently (haven't read the article yet) made a NOT gate using directed evolution. They're more interested in developing and applying the directed evolution technique than in biological computers, it seems. Lab website's here. And the lab website's got their own articles available for free in .pdf form. Screw you, Elsevier!

  20. Spaghetti Code by Obiwan+Kenobi · · Score: 5, Interesting

    I was listening to NPR the other day which focused on DNA as a computer.

    The guy interviewed correllated the DNA genetic map to spaghetti code, a programmers worst nightmare. Apparently all through the genetic make-up of our bodies are "fuction calls" (to put it simply) and pathways that reference other calls and other pathways, over and over upon itself for a hundred million lines.

    Its not the listing of the GTAC code (ie, genetic map) that's really necessary. Though of course it plays a part. Its the understanding of such code, what it does and what it controls, where power lies.

    The guys interviewed all guessed it would be a hundred years or more before we began truly understanding what "functions" do what in the DNA strand and how it affects the organism in question.

    Food for thought.

    1. Re:Spaghetti Code by DocDendrite · · Score: 2, Insightful
      The guy interviewed correllated the DNA genetic map to spaghetti code, a programmers worst nightmare. Apparently all through the genetic make-up of our bodies are "fuction calls" (to put it simply) and pathways that reference other calls and other pathways, over and over upon itself for a hundred million line
      This seems a little strange to me. I am a fourth-year PhD student in Molecular Biology and I see a lot of Biology misinformation on slashdot.

      What the NPR interviewee said does appear true. However, be aware its not the DNA that's actually performing any operations. Genetic control sequences (called promoters, enhancers, and silencers) are well characterized. It is the product of other genes (i.e. proteins) that perform the operations on DNA and are subject to regulation via these control sequences.

      Now what is truly complex is that proteins can bind to other proteins and affect their activity. Lengthy circuits of proteins "touching" one another (called signal transduction pathways) becomes incredibly complex with the exponential level of crosstalk and pathway intersections that can occur. That is where true Bioinformatic power lies....not so much the Folding Projects you see on distributed computing systems.

      The design of the "DNA computation" in the original story is contigent upon the aforementioned processes. It does not work on some natural computing power of DNA.

      -DD
  21. Re:[insert supreme being/philosophy etc.] called.. by Cobralisk · · Score: 2, Funny

    http://www.copyright.gov/circs/circ15a.html#durati on Sorry dude, its expired

    --
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  22. The article link by Obiwan+Kenobi · · Score: 2, Insightful

    Is right here. Highly suggested reading/listening.

  23. Keep working by smittyoneeach · · Score: 2, Insightful

    I don't think we'll have serious applications in bioware in the next decade.
    The sequencing work done to date is phenomenal. Not trying to sell anyone short. However, the complexity when you move from the genome to the proteome can be fairly described as staggering, so I'm weighing in on the conservative side on this one.

    --
    Get thee glass eyes, and, like a scurvy politician, seem to see things thou dost not.--King Lear
  24. Woman Are Quantum Computers by ari_j · · Score: 2, Funny

    Women actually have these three states (yes, no, and maybe), but here are the correct definitions: YES - a superposition of maybe and no
    NO - a definite no
    MAYBE - a superposition of yes and no

  25. Origins of this stuff by WillWare · · Score: 3, Informative
    Tom Knight and some other MIT people were talking about this kind of stuff in 1996-97. This was the same group interested in amorphous computing at the time. They saw it all as one big research agenda, and amorphous computing fell under the DOD funding umbrella for autonomous battlefield surveillance widgets.

    These guys were poking around with some genuinely interesting ideas. Their idea was that if you relaxed the requirements on manufacturing quality, you could make nodes that were super-cheap with a modest (but today-considered-unacceptable) failure rate. They set forth a collection of programming axioms that treated a sea-of-nodes as a continuous computational "gunk". Very cool stuff.

    --
    WWJD for a Klondike Bar?
  26. Oh, the irony... by nickgrieve · · Score: 4, Insightful

    In the course of her work with Watson and Crick, Rosalind Franklin had to do a serious amount math by hand (Patterson analysis to create Patterson maps). Later, after her work on DNA she was forced to hire a computer (an 18yr old girl) to do the leg work on the data she gathered on the Tobacco Mosaic Virus.

    Today I read here http://www.sciencenews.org/20030426/bob11.asp (Computer circuits made of genes may soon program bacteria)

    "Silicon circuits perform complex operations using a handful of simple components known as logic gates. Genetic- circuit engineers are now building the same devices inside cells."

    I wonder, what she would have thought, to know that very thing she was studying could some day be used to do the math that took up so much of her time.