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Biotech Science

The Art, Music And Computer Science Of DNA 95

Posted by timothy
from the meeting-nucleotides-is-easy dept.
Build6 writes "As part of the 50th anniversary of the discovery of DNA's double-helix structure, many news publications are writing about what has been done with the discovery so far; The Economist has a very interesting one about DNA's use in art and music. ... You can read all about it either by picking up a copy of The Economist (it's well worth the money, I've subscribed for over a decade), or online." And Clint Harris writes "As part of its series commemorating the 50th anniversary of 'the first scientific description of DNA' NPR recently aired a story comparing DNA to software (RealAudio or Windows Media). 'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.'"
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The Art, Music And Computer Science Of DNA

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  • Let's not forget... (Score:5, Interesting)

    by graveyhead (210996) <fletch AT fletchtronics DOT net> on Saturday April 26, 2003 @06:05PM (#5816648)
    Software (and now hardware too...) that is inspired by DNA recombination [genetic-programming.com].
  • by Anonymous Coward on Saturday April 26, 2003 @06:05PM (#5816651)
    Is it really a coincidence that a Caduceus/Kerykeion [medhelpnet.com] has a pair of intertwined snakes? (Some people say that's proof of ancient knowledge!)
    • The intertwined snakes on a pole symbol comes from the Bible. While the Isrealites were wandering around in the desert complaining, God got tired of it. So, he sent poisonous snakes to bite them, but also had Moses make a pole with bronze snakes on it. anyone who was bitten could look at the pole and not die. At least it was something similar to that, I might have the details a little wrong.
      • by Anonymous Coward
        Here's the explanation: http://www.medhelpnet.com/caduceus.html [medhelpnet.com]
        • by Anonymous Coward
          Actually that link doesn't give all the information. While it is true that the Cadeuceus was the staff of Hermes and had two intertwined snakes, it doesn't explain why it's associated with the medical profession. Asclepius was the greek god of medicine. According to myth, he carried a staff which he used to heal. That staff had only one snake around it. Somewhere along the way, the Cadeuceus and the staff of asclepius were mixed up.
  • I know... (Score:1, Informative)

    by Anonymous Coward
    the Economist always backs this community on every financial issue. they're well worth the money.
  • by Anonymous Coward on Saturday April 26, 2003 @06:08PM (#5816662)
    ...God's a VB kiddie :)
  • Bad Programming? (Score:4, Interesting)

    by johny_qst (623876) on Saturday April 26, 2003 @06:10PM (#5816672) Journal
    I'm really confused by someone equating obtuse code they can't understand as bad programming. I want more discussion on how the information encoded in genes acts. Not "This is the worst kind of spaghetti code you can imagine..." and posturing like we can't possibly understand it.
    • Re:Bad Programming? (Score:2, Interesting)

      by Anonymous Coward
      Dude, you obviously haven't taken an intro-level biology course. DNA transcription has so many stop-here, skip-here, start-here signals, that many times there's huge chains of "introns", information that just gets excised from the final product. A single mutation can change something from a regular codon (think of them as words) to a stop codon, rendering everything that follows (up to the next start) junk data.

      So, that's how nature writes spaghetti code. Constantly commenting out loops, etc.
      • Re:Bad Programming? (Score:1, Interesting)

        by Anonymous Coward
        Plus the exons (the coding bits left over after you take out the introns) can be alternatively spliced. It's more like a (eukaryote) gene is a set of library calls than a program.
    • A better analogy is to compare the DNA to a binary executable. A decent optimizing compiler generates code that isn't easily comprehensible by humans*. The DNA and the binary executable are intended to the same job - just execute. They are not meant for humans to understand.

      * Or a few C programs at IOCCC [ioccc.org] that pack LOT of functionality into a small program?

  • object oriented genes.
  • by Anonymous Coward on Saturday April 26, 2003 @06:17PM (#5816699)
    As soon as YOUR code has had uptime of 120 years or so, then you can say nature wrote us poorly.
    • "As soon as YOUR code has had uptime of 120 years or so"

      Uhm...it's more like 120 billion years, give or take.

      Of course, I guess that's all considered legacy code by now, isn't it?
  • Bad Programmer? (Score:5, Insightful)

    by trotski (592530) on Saturday April 26, 2003 @06:19PM (#5816705)
    DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

    Wow, that sure is an arrogant statement. The chemical, physical and biological systems of nature are the most complex systems we know of. Nature is influences by a seeingly infinate number of variables. We don't understand much more than we do.

    Our understanding of the world is far too small to be critiszing nature works and it's language. When humanity can create a WORKING system thats 1/1000th as complex as the natural world is when we can even start to make arrogant statements such as this. Today is not yet that day.
    • by Trepidity (597) <delirium-slashdotNO@SPAMhackish.org> on Saturday April 26, 2003 @06:28PM (#5816738)
      Nature designs things in an incredibly complex way, because that's simply how evolution works -- there's certainly no software engineering notion of clean component separation and so on in evolution. So it ends up certainly being complex, working, and possibly even beautiful, but a nearly impossible to decipher mess of spaghetti. Sort of like an old-school assembly programming genius designing an enormous 500,000-line program in assembly -- it'll work beautifully, but nobody will have any idea what the hell is going on, or be able to modify it. Similar problems exist when trying to genetically engineer things; you're always going to mess something up.
    • by milkmandan9 (190569) on Saturday April 26, 2003 @06:51PM (#5816792)
      The chemical, physical and biological systems of nature are the most complex systems we know of.
      Especially if these chemical, physical, and biological systems happen to be female.
    • Re:Bad Programmer? (Score:3, Insightful)

      by Ieshan (409693)
      Here's a quote which, at the heart, sums up *why the programmer analogy is wrong*:

      Natural selection cannot play God, because it is a blind process with no goal in mind and no means to get to a predetermined endpoint.
      -John Alcock, Animal Behavior, 7th ed.

      Programs are tools for a purpose. DNA is not.
      • Out of context the quote you used looks like a creationist argument that evolution can't reach the "goal" of complex life. I almost replied to you based on that misreading. I just had to delete an entire post, lol.

        You're actually saying that DNA is "spagetti-code" because it's created at random. No objections here :)

        -
        • Right - and it's so random that it has no ultimate purpose. All programs have a purpose, DNA doesn't. Long-term changes in DNA happen because of changes in the immense system that DNA is a part of.

          For instance, cheetahs didn't get faster in able to catch prey - one day, a faster cheetah was born who had the potential to survive longer, and he mated more, and spread his "fastness" through DNA - these individuals had greater potential than the rest of the individuals in the population, and the DNA changed in
    • Agreed. I suspect that nature uses a
      lot of goto's as well. Goto's produce
      'code' that is hard for us to
      understand. Perhaps the only efficient
      way to grow the 'wiring' that
      constitutes a human brain is organically
      without concern for complication. I suspect (I
      do not know, I'm not an expert) that as
      long as AI researchers look for an elegant
      solution, they are destined to miss the
      goal. Nature's designer doesn't seem to
      share the human passion for regular
      polygons, straight lines and clearly
      stated theorems. Phys
    • We don't understand much more than we do.

      I love that sentence. Yep, and I don't have much more money than I have either.

      Our understanding of the world is far too small to be critiszing nature works and it's language.

      We shouldn't criticize nature works and it's language? OOOooo! OOoo! NATURE! It's arrogant to talk about NATURE! LOL. Could you possibly be thinking "god's works and god's language"? Why else would you be offended? Well if you mean god then why not come out and SAY god?

      When humanity can
    • The bad programmer paradigm is probably intended to infer our inferiority and nature's superiority in this arena. Ever get a programmer nut whose code you couldn't fathom? Well we all thought he was a nut but turned out he was a genius. The spaghetti code method he used was appropriate because he could handle the complexity. The rest of us are taught OOP and the like in an attempt to simply our own complicated and misunderstood minds and program something useful and maintable by us (when we've forgotten
  • by slulovic (636452)
    Anyone else find it funny that most gene sequences are proprietary, and hence even DNA isn't Open Source? --Scott
  • Genetic Programming (Score:5, Interesting)

    by CBNobi (141146) on Saturday April 26, 2003 @06:31PM (#5816746)
    DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

    How ignorant of you to say that. There was an article in the Feb. 2003 issue of Scientific American about genetic programming - the creation of new devices and electronic circuity by computer.

    It basically involves starting out the core components (resistors, inductors, capacitors, etc) and a design (for a voltage-current converter, perhaps). A supercomputer is able to rewire the circuit through basic evolutionary processes including crossover, copying, and extinction, and come up with a much more efficient circuit.

    The resulting circuitry is so effective and original that there have been designs that earned approval from the patent office. They're so complex, much like nature's genetic code.

    Sure, it might look like spaghetti code - but you mean to tell me, nature is a bad programmer? Heh.

    Google search on genetic programming [google.com]
    Everything2: Genetic programming [everything2.com]
    What is Genetic Engineering? [genetic-programming.com]
    • The last link is about genetic programming; I just typo'ed 'genetic engineering'.

      Carry on...
    • by Saeger (456549)
      The resulting circuitry is so effective and original that there have been designs that earned approval from the patent office.

      And, IMO, it's a very bad idea to hand out patent monopolies for designs that no human invented, especially if no one can even understand how the damn thing works!

      It's not that patents on evolved solutions -- which are both computationally expensive to produce, and to manufacture physically -- wouldn't necessarily promote progress (unless we're talking software algorithms), but t

    • Good point, you have elaborated fairly well on my frost pist.

      I have tried to point this out on multiple occasions, but slashdot readers are hung up on the fact that some people seriously abuse patents. Not everyone does.

      In this case, the patentability of an invention provides a direct comparison between genetic programming (or in fact, any AI that purports to be able to design or invent software or hardware) and human intelligence.

      With such a yardstick, we can directly measure the progress that genetic p
  • James Watson. (Score:3, Informative)

    by I'm a racist. (631537) on Saturday April 26, 2003 @06:32PM (#5816751) Homepage Journal
    I've been pleasantly surprised by all the attention the 50th anniversary of the discovery of DNA has gotten.

    It got to be the Google logo [google.com]. Cold Spring Harbor Laboratories [cshl.org] has been very active in celebrating this. Among a few other things, they've had a really nice lecture series to commemorate the event.

    I'm a little bit closer to the whole thing since I've done some genetics work (mostly at the Columbia [columbia.edu] Genome Center [columbia.edu]). My current work involves some genetic manipulation, but that's not the main focus.

    Also, I happen to personally know James Watson. I first met him when he spoke at my commencement. But, I shouldn't tell that story, because it has some racist (and very amusing) content... which would only get me modded as a troll. I've kind of worked with him a bit since then, and he's really a very nice, down to earth, intelligent guy. He hasn't really let this whole thing go to his head.

    Anyway, it's very nice to see the general public taking a little bit of interest in science. Maybe this will help to turn some of the scientific illiterates into elites [phds.org]...
    • Re:James Watson. (Score:1, Interesting)

      by Anonymous Coward
      Also, I happen to personally know James Watson. I first met him when he spoke at my commencement. But, I shouldn't tell that story, because it has some racist (and very amusing) content... which would only get me modded as a troll. I've kind of worked with him a bit since then, and he's really a very nice, down to earth, intelligent guy. He hasn't really let this whole thing go to his head. Well, if your work was based on the (alleged) theft of someone else's work (Rosalind Franklin), wouldn't you be a lit
      • Not alleged theft, but well established, and admitted. Maurice Wilkins gave Watson and Crick the keys to Franklin's lab, and the locked drawer where she kept her X-ray photos. Of the DNA that she grew. Using the X-ray camera she designed and built herself .

        In their own defence, they tried to dismiss her as a mere "lab tech" (with a Ph.D. and several publications? I don't think so!) and then put her down in their book The Double Helix by wondering repeatedly, in print, whether she'd look any

  • by teamhasnoi (554944) <teamhasnoi AT yahoo DOT com> on Saturday April 26, 2003 @06:34PM (#5816754) Homepage Journal
    I don't see why the scientists don't just look at the REM statements...they'd have that stuff figured out in no time.

    "Geez, it says here that the next 24,000 lines of code are wholly dedicated to picking one's nose!"

    I'm sure that they would find that politicians are the result of millions of unreturned GOSUB commands.


    • > "Geez, it says here that the next 24,000 lines of code are wholly dedicated to picking one's nose!"

      Yes, but it's just a mutation of the scratch-your-arse code.

      Think of it as OOP-style inheritance in action.

  • by Anonymous Coward
    ...I could mate Microsoft Office with Star Office and crossbreed an office suite that is both free and feature complete...
  • no analogies allowed (Score:3, Interesting)

    by hachete (473378) on Saturday April 26, 2003 @07:06PM (#5816830) Homepage Journal
    Well I guess the problem with the posting is the analogy. Comparing genetic "code" to software implies that there's a writer - in this case "nature" - who is either "good" or "bad" in the works that it perpetrates. The aesthetic and/or moral values of "good" or "bad" don't exist in the evolutionary process, only what works. If a sequence works, then the sequence survives. If it doesn't it dies. Consider Linus when he talks of DRM and Linux: he wants Linux to survive so he won't object to DRM being inserted into Linux; he doesn't want Linux's chances of surving limited. OTOH, RMS is a moralist and an idealist. He doesn't want DRM in Linux - in fact, he sees Linux as a weapon *against* DRM. If he succeeds in pre-empting DRM from Linux, then he will have closed off a route of survivability for Linux - in evolutionary terms, a major no-no.

    Of course, this pulls the analogy apart from the inside: no aesthetic or moral judgments, no writer-figure ghosting in the background. What we have is a an autonomous, self-organising system - a far more interesting prospect if you ask me.

    Of course, calling it "spaghetti-code" enables you to insert that programmer-figure into the argument. All spaghetti-code needs re-factoring right? Tweaking to make it "right" make it work "better"? I dunno; the self-autonomous self-organising model has worked quite well up to now...and, lets face it, when has trying to make something "better" produced less bugs than you first started with? Particularly with something you barely understand in the first place and are desperately trying to portray with ill-thought out analogies.

    h.
  • by Anonymous Coward
    Spaghetti code is only dangerous because it's hard to follow and thus understand, a barrier to maintenance and sharing with others. Perhaps the "programmer" simply has the capacity to know and understand the implications of each piece of the code at once - and perhaps also doesn't wish to share the code with other developers.
  • Even though it is composed of major spaghetti code and is attributed to a bad programmer hacking away at it for billions of years, DNA has not suffered a root level exploit yet! Stick that in your trustworthy computting pipe and smoke it.

    • AIDs?
      Black Plague?
      Smallpox?
      Polio?
      Ebola?
      . .. ...
      • Maybe.. but as they say, with physical access you can break anything. Viruses actually insert in extra code.

        A better example of an exploit would be telling someone to take their right hand and pat their head, take their left and rub their tummy.. and then laugh as the buffer overflow makes them fall on their arse.
    • > Even though it is composed of major spaghetti code...

      Well after all, it implements the control program for a machine that makes spaghetti. What kind of code were you expecting?

      > ...and is attributed to a bad programmer hacking away at it for billions of years

      Well, code does tend to become more spaghetti-like the longer it is maintained.

      > DNA has not suffered a root level exploit yet!

      Viruses exploit it all the time.

  • correction (Score:4, Informative)

    by NotAnotherReboot (262125) on Saturday April 26, 2003 @07:20PM (#5816876)
    It was not the 50th anniversary of the discovery of DNA, it was the 50th anniversary of the publication of Watson and Crick's paper saying that DNA possibly has a double helix.

    It's kind of funny, everyone seems to be making this mistake, I heard the vice president of Clonaid talk just yesterday, and he said the same thing. Not that Clonaid is a legitimate company. :p
    • Re:correction (Score:1, Informative)

      by Anonymous Coward
      No, it's more like the 50th anniversary of the paper saying that all DNA possibly has a particular double helix structure. Many people prior to this thought a double helix was possible, some of Franklin's X-ray data (insert Adelaidian plug for Bragg family here) strongly suggested a double helix for one of the forms of DNA (she in fact misunderstood some of her data on the other form so she didn't think it was a double helix, iirc).
  • Twenty years ago... (Score:4, Interesting)

    by jazzbazzfazz (600773) on Saturday April 26, 2003 @07:35PM (#5816917)
    Douglas R.Hofstadter discussed very similar ideas in his book Godel, Escher Bach, an Eternal Golden Braid. It was published in 1979, won a Pulitzer Prize and is virtually certain to change the way you look at pattern recognition and AI, genetics, musical innovation and a host of other areas of human intelligence.

    If you haven't ever picked it up, give it a try. You can read it on a very superficial level and enjoy the dialogs among the characters, flip through it for the Escher prints...but eventually you'll start digging deeper and see things in the same words that you didn't see before. Highly recommended!

    • I second that. I do have to say that the Godel part of the book is more interesting and enlightening than the Escher and Bach parts, though. Only after reading GEB I actually understood what Godels Theorem was about.

      JP

      (I wonder why I can't use &ouml;? Now I have to spell Godel's name wrong.)

  • by Zanthany (166662) on Saturday April 26, 2003 @07:35PM (#5816918) Journal
    The "Sonic Gene" mentioned in the Economist article is not the only one. I attended university where one of the piano professors has been working on a project like this for many years now.

    His name is Brent D. Hugh, and he has downloadable .mp3s here. [mp3s.com] This has been a pet project of his, and it's definitely worth checking out. His personal site is available here [mwsc.edu] as well.

    Happy listening!
  • Ahhh (Score:3, Funny)

    by Timesprout (579035) on Saturday April 26, 2003 @07:49PM (#5816947)
    Now you tell me. I just hired nature last week. She told me she had loads of experience coding on big projects.
  • by theCoder (23772) on Saturday April 26, 2003 @07:59PM (#5816965) Homepage Journal
    #include <unistd.h>

    int main(int argc, char** argv)
    {
    while (1) fork();
    return 0;
    }
    So, you think if I run this long enough it'll evolve into an AI? :)
  • No, more like a poorly programmed AI with a limited rule set.

    SB
  • Perhaps DNA is more akin to highly optimised compiler output, as opposed to the source code.
    It doesn't matter how elegant your implementation is, once an optimising compiler has done it's business the results aren't going to be very pretty to look at (or easy to understand).
    As soon as a talented group of software engineers develops a useful decompiler/dissassembler for them, the geneticists will start to be freed from the low level detail overload and some of the elegance of the design will no doubt b
  • by coloth (630330)
    Everybody knows only bad programmers write spaghetti code. Nature clearly writes fusilli lunghi code. Just look at it!
  • Maybe it's just like obfuscated C and we're to stupid to understand it.
  • Molecular music (Score:2, Informative)

    by zoeblade (600058)

    Dr. Linda Long had been doing something similar [molecularmusic.com] with Music of the Plants and Music of the Body.

  • NPR recently aired a story comparing DNA to software (RealAudio or Windows Media).

    Does that mean that Men are from Real, Women are from Microsoft?

  • Billions of Years? (Score:2, Insightful)

    by pantropik (604178)

    'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.'

    That isn't very efficient. Microsoft did the same thing with the Windows codebase in only 20 years ...

    Seriously, though, I don't think this statement is as arrogant as

  • by drik00 (526104)
    DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

    I dont know that I could imagine a worse metaphor. Anyone that has ever studied the tendencies of human beings to be insanely ethnocentric and myopic should appreciate what I mean. To make an analogy that the simplistic beauty of DNA is anything like "spaghetti code" is hilarious. You're comparing a bad algorithm method with an incredibly complex (yet very beautiful in its simplis

    • I dont know that I could imagine a worse metaphor. Anyone that has ever studied the tendencies of human beings to be insanely ethnocentric and myopic should appreciate what I mean. To make an analogy that the simplistic beauty of DNA is anything like "spaghetti code" is hilarious. You're comparing a bad algorithm method with an incredibly complex (yet very beautiful in its simplisitic design) and far more brilliant system. Most programmers cant write code to do one simple task without having some sort of b

    • Most programmers cant write code to do one simple task without having some sort of bug or malady arise, whereas DNA is able to manipulate individual molecules and chemical reactions in order to create a system magnitudes above anything the most brilliant human could think to design.

      As a molecular biologist/computer progammer, I think you are giving DNA too much credit. Just as a single error in a piece of code can cause it to crash, a single base mutation in an organism's DNA can either a)cause it to abo
  • NPR recently aired a story comparing DNA to software

    (RealAudio or Windows Media). 'For many, the best analogy for the way DNA works is that it's like a computer program at the heart of every cell. Some of its programming tricks bear an uncanny resemblance to ones the human brain has dreamed up...DNA is [like] spaghetti code because nature has been tinkering with the system for billions of years like a bad programmer.

    Did anybody else read this and think:
    "Realsoft and Microsoft might not be too happy bein

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