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World's First Game-Playing DNA Computer 166

Posted by simoniker from the why's-the-enzyme-always-allowed-to-go-first? dept.
An anonymous reader writes "NewScientist.com posted an article today about the first game-playing 'computer' powered by DNA logic. An interesting read, although not at all a practical alternative for those looking to replace their PlayStation2 with the next great platform." The machine is "...an enzyme-powered tic-tac-toe machine that... uses a complex mixture of DNA enzymes to determine where it should place its nought or cross, and signals its move with a green glow."
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World's First Game-Playing DNA Computer More

World's First Game-Playing DNA Computer

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  • Shall We Play A Game? (Score:5, Funny)

    by Anonymous Coward on Monday August 18, 2003 @01:22PM (#6724611)
    Obligatory of course. However, maybe this time we can stick with a nice game of chess, eh?

  • Play tic-tac-toe? "Stojanovic has lost to MAYA more than a 100 times." With semi-intelligent players I thought this game was pretty much guaranteed to generate a draw?

  • Game Playing DNA? (Score:5, Funny)

    by mopslik ( 688435 ) on Monday August 18, 2003 @01:25PM (#6724637)

    Bah, my DNA's been playing Life for ages.

  • Ok sure, (Score:5, Funny)

    by arcite ( 661011 ) on Monday August 18, 2003 @01:26PM (#6724654)
    When Leisure Suit Larry get ported, call me.
    • It has been, but becuase you come to /. you might not have heard the news.

      DNA supports sexual reproduction of mammals. And the process through which this takes place is supports a Leisure Suit Larry like enviroment. Perhaps you should consider playing. For complete results insure subject has matured for the appropriate number of years before playing the game.

      Ted

  • can not be defeated? (Score:5, Interesting)

    by Lispy ( 136512 ) on Monday August 18, 2003 @01:27PM (#6724662) Homepage
    From the article: "We could have programmed it to lose sometimes, to make humans happy," he told New Scientist. "But to say 'the automaton can not be defeated' has a nice ring to it."

    Great. Can I quote you after humanity got defeated by DNA-based Uberhumans? But then again, if it's DNA-based we might be able to make holes in it with a bullets, right?

  • Wrong game (Score:5, Funny)

    by WTFmonkey ( 652603 ) on Monday August 18, 2003 @01:27PM (#6724663)
    Naughts and crosses? I though you played tic tac to with xes and os. Man, I've been playing wrong all these years.

  • Silly Human! (Score:5, Funny)

    by rwiedower ( 572254 ) on Monday August 18, 2003 @01:28PM (#6724674) Homepage
    Stojanovic has lost to MAYA more than a 100 times.

    Um, even I couldn't lose to a machine more than a 100 times at tic-tac-toe. It doesn't take a WOPR [imdb.com] to learn that tic-tac-toe is surprisingly easy to grasp. I bet you could train a DNA-powered monkey to the same level of effectiveness as this silly human named Stojanovic.

    • Re:Silly Human! (Score:2, Informative)

      by Dudio ( 529949 )
      Indeed. The Tropicana in Las Vegas used to have a chicken trained to play tic-tac-toe, with cash prizes for anybody who could beat it. I didn't see it when I was just out there for Defcon though, so maybe the novelty wore thin.
      • Tic-Tac-Toe playing chicken is a drawing point for residents of Natchez, MS [natchezdemocrat.com], Reno, NV [rgtonline.com] and Cherokee, NC, which I have personally lost to. On a side note, I did get to watch a de-clawed bear slap the hell out of a hillbilly that day, so it was a good one for my ten-year-old mind at the time.
    • Stojanovic has lost to MAYA more than a 100 times.

      Yes, I suspect that Stojanovic might be throwing games to make the computer seem "smarter" than it may actually be. Manipulating results, I understand, is something that many scientists have become guilty of.

      "We could have programmed it to lose sometimes, to make humans happy,"

      And this seems like it might be their rationalizing the deficiencies of their technology. Sort of like when I tell my girlfriend, "I could have gotten the Porsche, but I thou
    • Whenever testing something, you should test not just expected responses, but also the unexpected. Perhaps he lost so many times because he wanted to see MAYA capitalize on human errors, and make sure that it would win?

      Who cares if the machine will always play to a tie, if it can't convert a win from a stupid human mistake?
    • Now, I'm no scientist, but I thought all monkeys were DNA powered? Aren't we all?

  • CNN article (Score:5, Informative)

    by kaan ( 88626 ) on Monday August 18, 2003 @01:28PM (#6724675)
    here's a similar article [cnn.com] titled "DNA basis for new generation of computers"
  • Game playing comes second only to porn as the driver of new technologies.

    More seriously, this is a good time to look at how to model DNA computers on "normal" computers so that we can start abstracting the tools and techniques needed to design (breed?) the really complex patterns we'll need to exploit DNA technology.

    Good stuff - in 20 years this may seem like the only way to compute, with silicon being as quaint as valve transistors.

    • Re:Very significant development (Score:5, Funny)

      by stratjakt ( 596332 ) on Monday August 18, 2003 @01:40PM (#6724829) Journal
      Well we already got DNA based porn. They're called girls.
      • Now THATS the funniest post Ive read in a while. Got my funny bone, that did.
      • Bah you actually believe in girls? We all think we've seen them, walking around among us, even seemingly interacting with us to give us our change or look at us only to roll their eyes. But we see a lot of things that don't really exist. Examples include searchlights zooming across the sky when there really is nothing moving that fast, and faked images we see all the time on TV and in magazines.

        I ask you this - have you ever touched a girl? I haven't, and none of the guys (a redundant term, since all p

      • And unfortunately most of us guys are big losers at this game and don't like to play.

        No wonder so many geeks rather play computer games instead.

    • Re: Natural step (Score:3, Insightful)

      by CyberDruid ( 201684 )
      Game playing comes second only to porn as the driver of new technologies.

      And since DNA is already involved in porn and sex in so many ways, this was basically the logical continuation. As long as I'm not DNA-spammed by malevolent viruses, I'm happy.

      • And since DNA is already involved in porn and sex in so many ways, this was basically the logical continuation. As long as I'm not DNA-spammed by malevolent viruses, I'm happy.

        Well, we've already got DNA spam; it's called... umm... SPAM.
    • "More seriously, this is a good time to look at how to model DNA computers on "normal" computers so that we can start abstracting the tools and techniques needed to design (breed?) the really complex patterns we'll need to exploit DNA technology."

      I disagree. I believe that if we want to fully exploit DNA technology we should be researching how to build a new computing paradigm out of it. Why model it off of current computers when we have the possibility to create computers that are wildy different and cap

      • Why model it off of current computers...

        Because building the tools needed to build tools takes time, and too much time. If you can model the DNA machines on today's computers, you can simulate enough of an environment to bootstrap the whole process.

        It's like building a compiler for a CPU when all you have is a simulation of the CPU. Then you compile the compiler with itself, and finally get native code that lets you compile the compiler using a compiled compiler instead of a similated compiler. Make s
    • You can look at it that they are in fact modeling DNA computers on "normal" computers. So far, they've managed to make a number of logic gates. In the article in Nature Biotechnology, this group has made YES, NOT, AND, and ANDANDNOT gates. Other groups have made similar molecular gates, but this is the most advanced thing to date. As for replacing your silicon PC, my $0.02 says it ain't gonna happen.
    • While this is true, have you ever noticed that there are no truly good Porn Games?

  • GREAT (Score:5, Funny)

    by Anonymous Coward on Monday August 18, 2003 @01:29PM (#6724700)
    I'll dump some DNA on my wifes face tonight, then say "your move".

  • Summary for those to lazy to RTA (Score:5, Interesting)

    by stienman ( 51024 ) <.adavis. .at. .ubasics.com.> on Monday August 18, 2003 @01:29PM (#6724701) Homepage Journal
    Essentially they have 9 enzymes to specify the nine possible moves of the player. Once a move is chosen the enzyme for that position is added to each of the nine wells. The DNA inside each well is aware of its location, and, of course, each of the player's moves since the enzymes are added to each well.

    The DNA in each well makes a simple logic decision based on all the enzymes it currently detects and turns green to indicate that the dna 'computer' is choosing to move there.

    Overall it's an interesting logic puzzle, not only because it's done in DNA, but because the method involves seperate logic cells which have no means of communication - only the knowledge that they know everything that their brethren know.

    It has weaknesses in that it's easy to fool them all individually so they all light green.

    Probably has many good applications in chemical sniffing and quite possibly future DNA analysis speed ups.

    -Adam

  • Great (Score:5, Funny)

    by Narphorium ( 667794 ) on Monday August 18, 2003 @01:30PM (#6724703)
    I've never been a leet gamer by any means but now I can add enzymes to the long list of organisms that are capable of beating me at computer games.

  • DNA based computer used to solve TSP (Score:5, Interesting)

    by GillBates0 ( 664202 ) on Monday August 18, 2003 @01:30PM (#6724706) Homepage Journal
    I submitted a related story about another article [cnn.com]on CNN today.

    Apparently, Leonard Adleman [usc.edu] of the University of Southern California [usc.edu] used his DNA based computer to solve the travelling salesman problem by exploiting the predictability of how DNA interacts. "Adleman used his computer to solve the classic "traveling salesman" mathematical problem -- how a salesman can visit a given number of cities without passing through any city twice -- by exploiting the predictability of how DNA interacts. Adleman assigned each of seven cities a different strip of DNA, 20 molecules long, then dropped them into a stew of millions of more strips of DNA that naturally bonded with the "cities." That generated thousands of random paths, in much the same way that a computer can sift through random numbers to break a code. From this hodgepodge of connected DNA, Adleman eventually extracted a satisfactory solution -- a strand that led directly from the first city to the last, without retracing any steps. DNA computing was born".

    Apparently, a single gram of DNA can store as much information as a trillion CDs.

    • Re:DNA based computer used to solve TSP (Score:5, Funny)

      by CraigoFL ( 201165 ) <slashdot@kano o k . n et> on Monday August 18, 2003 @01:37PM (#6724782)
      "Apparently, a single gram of DNA can store as much information as a trillion CDs."

      Wow, then I've been doing the equivalent of throwing out my entire record collection every night for years...

    • To me, DNA based computing will be a reality before quantum based computing. It'll at least augment what we have now. Imagine the above, a CPU thats a little bucket of DNA, and you drop someones public PGP key in as a DNA coded deal. It basically tries all possible combinations at once, kaboom.

      WOW

      Or DNA based prOn. Oh wait, I got that already, it's called a wife.
    • Unfortunately, that's not the traveling salesman problem. Finding a path that leads to all cities without hitting any twice is easy. Finding such a path that is provably the shortest possible path is trickier, and a fine thing to do. But the famously unsolved "Traveling Salesman Problem" is to find an algorithm that finds the provably shortest path between N cities in a number of steps that is not proportional to N factorial (or worse). There is no proof that an algorithm better than N! does not exist,
      • Yes and no. It may indeed be true that you can't solve it in less than O(N!). Theres alot of problems similar enough to travelling salesman that if you can provide such a proof that you can't do it in less than N! (or a proof that shows you can), then those problems will fall in line as well.

        If indeed it can be shown the problem may not be solved in less than N!, then the problem becomes hardware to solve. This is why DNA and quantum computing will be handy because of their inherent parallel nature, in

        • "If indeed it can be shown the problem may not be solved in less than N!, then the problem becomes hardware to solve"

          I have to disagree. If it can be shown the problem may not be solved in less than N!, hardware won't save you. Let's say at your current level of computer speed, in the time you have available to work on a given instance of the problem, you can solve it for 100 cities. But now you want to solve it for 110 cities in the same time. You must increase the speed of your computer by a factor o

    • Re:DNA based computer used to solve TSP (Score:5, Interesting)

      by jfengel ( 409917 ) on Monday August 18, 2003 @01:50PM (#6724941) Homepage Journal
      The problem, unfortunately, is that TSP is still an exponential problem. Solving it for seven cities is reasonably trivial. Although DNA is extremely small, an exponential about of it is not. By the time you get to 200 cities, you start requiring masses of DNA larger than the planet.

      DNA based solutions basically call for you to use DNA to sort through every possible combination. Since it's all done in parallel, it can be done fairly fast, as long as you provide enough DNA. However, the only interesting problems are exponential ones (since polynomial problems can already be solved fairly fast), and you're basically trading material for time.

      A 200 city TSP problem really isn't all that much. Some crypto breaking is equivalent to a 1,000 city TSP. The whole point of NP-completeness is that if you can solve one of them you can solve all of them. Traveling salesman is easy to explain, and more interesting than, say, 3SAT. So solving TSP for large numbers would be interesting, but sadly the solutions don't scale.

      More comp-sci background: These problems are NP in that they are "nondeterministic polynomial". That is, you can check a proposed solution in polynomical (read: reasonable) time. If you guess right the first time, you can "solve" the problem immediately. The trick is guessing right the first time. But you don't have to with DNA: you can use the molecules to check all solutions at once, which is equivalent to guessing right the first time.

      The "complete" part means that one NP-complete problem can be reduced to another in polynomial (again, read reasonable) time. So if you can solve TSP, you can solve all the other NP problems, which include scheduling, some cryptography, and a bunch of other interesting stuff.

      Sadly, the numbers get big. 10^20 DNAs weighs only micrograms, but 10^200 DNAs weighs 10^170 tons. That's why we use it for crypto: it's hard to do. Just solving it in parallel doesn't help, because there are too many things to do in parallel.

      There may be uses for DNA computing; note that the article talks more about sensors than math problems. So don't oversell it for math problems.
    • Does the article mention the O-notation efficiency of the DNA TSP algorithm? Even if it can "check all the solutions at once", setting up all the DNA required to actually solve the problem may not run in polynomial time (or polynomial space, which is the same thing.)

      The issue with DNA storage (at least, at this point) is the reliability of said storage. DNA works as a storage mechanism for biological systems (me), because slight replication errors usually don't cause failure; even if they do, it's usually
  • That's O or X in the US of A, baby. :-)

    Crosses and naughts...sheesh.

    • Re:Naught or cross? (Score:1, Funny)

      by Anonymous Coward
      Actually they are Freedom-O's and Freedom-X's. Please report to your nearest Patriotism Terminal for re-education.
  • If you or someone you know is tired of poking their fingers for tic-tac-toe blood samples you should try our new DNA testing supplies...
  • I wonder if I could get some DNA from Kasparov and play a wicked hard game of chess.

  • bah! (Score:5, Funny)

    by the darn ( 624240 ) on Monday August 18, 2003 @01:33PM (#6724736) Homepage
    Slashdotters already play LOTS of games with DNA...mostly solitare, though, as I understand.

  • Well then... (Score:3, Funny)

    by motardo ( 74082 ) on Monday August 18, 2003 @01:33PM (#6724740)
    this gives a new meaning to "Powered by Nvidia"
  • People have been worried about an unleashed nanobot replicating copies of itself and turning the world into a grey goo.

    Grey goo I can live with - an earth sized Xs and Os planet I cannot.

    I for one am getting the first ticket out of here.
  • Shouldn't one of these computers already evolved out the goo found in swamps today? Considering thats how we came about and all...

  • And now... (Score:1, Redundant)

    by GearheadX ( 414240 )
    ...for the obligatory 'imagine a Beowolf cluster of those...' post.

    Thank yew.

  • Interesting b/c its a molecule or b/c it's DNA? (Score:3, Interesting)

    by kaltkalt ( 620110 ) on Monday August 18, 2003 @01:42PM (#6724854)
    Yeh I realize DNA is a molecule. But if this computer were running of off, say, some chemical other than DNA, would it be as interesting? DNA implies life, whereas other chemicals (aside from caffeine) do not. But a DNA computer is no more alive than the silicon-based PC I'm using right now. I know DNA molecules have interesting properties, and I'm not saying this is about clever marketing. But I think the fact that the molecule being used here is DNA makes this much more interesting than it would be if the molecule were anything else. JMHO, though. An alcohol-based PC is a novelty, but a DNA-based PC is amazing....
    • The way cells work is very computational in nature. You have DNA which is comprised of certain sequences of ACTG which are called codons, that are essentially assembler mnemonics. These codons stand for each amino acid, and a couple of special ones that tell it to stop reading, start, etc. The DNA stand is pulled through a structure (ive forgotten the name of it..bio class was awhile back) which reads the codons and sends out calls for amino acids, which then bind together to form proteins. Then the pro

  • Let the jokes begin... (Score:5, Funny)

    by SirDaShadow ( 603846 ) on Monday August 18, 2003 @01:45PM (#6724891)
    >The human player makes his or her moves by dropping DNA into 3 by 3 square

    No comment...

  • Can you imagine... (Score:3, Interesting)

    by twoslice ( 457793 ) on Monday August 18, 2003 @01:48PM (#6724924)
    the kind of viruses that could be created? The thought is mind blowing!
  • The article (yes I RTFA) states that it is interactive, but how long does it take for the 'computer' to make it's move?

  • This chicken [tripod.com] may not be around anymore, but a little Googling will show other references.

    And yes, I can admit to having lost a few games to her, too.

  • Patents? (Score:2, Funny)

    by derfel ( 611157 )
    Hope these guys [myria.com] don't find out about it.
  • ...uses a complex mixture of DNA enzymes to determine where it should place its nought or cross...

    Is it one of those obscure biblical units, like a cubit [kayakforum.com]?

    'Doth Job fear God for nought [biblegateway.com]? --Job i. 9.'

    Maybe it's some kind of animated character [animateclay.com] that ruins pizzas for fun.

  • "A strange game... (Score:4, Funny)

    by sverrehu ( 22545 ) on Monday August 18, 2003 @02:30PM (#6725355) Homepage
    ... the only winning move is not to play."
  • ... cuz if it can, then i'll be impressed with its computing power.
  • ...that you can build a tictactoe playing machine, that learns to play from experience with a bunch of matchboxes and marbles. It's in a Martin Gardner book as well as a Scientific American article.
  • Molecules could, for example, assess faults in a living cell and then either kill or repair it.

    Boy, gives the phrase "Blue Screen of Death" a whole new meaning, right?

    Uh, only there's no screen. And you don't turn blue.

    But what would happen if these mini DNA logic gates all went haywire, or something. Like if they, say mutated, as DNA is sometimes wont to do (granted, IANAG). But say these things went haywire and decided that all your cells must die. What then?

    I, for one, do not want to welcome any DNA
  • "developing simple decision-making solutions that can operate in vivo. Molecules could, for example, assess faults in a living cell and then either kill or repair it."

    Yipes, hope they do not use some Doom mod code I've seen! Code with comments like " this should take all your extra lives away"

  • Aren't games already enough like life forms?

    Tetris for instance is the next best thing to a virus, afterall, think of how simple and yet utterly addictive it was until attention deficit disorder offered us a cure.

    Do we have to make games INTO life forms?


    • This brings up a question I wanted to ask: Would this kind of thing be considered a very basic life form playing a game? Have these guys created a lifeform that plays tic-tac-toe? Or is this way too low-level to be considered life?

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