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Biotech Technology

Writing Genetic Code 190

Posted by ScuttleMonkey from the working-with-soylent-green dept.
An anonymous reader writes "The Globe and Mail is reporting on another group of researchers delving into the field of 'synthetic biology.' The project stemming from the efforts of two biology labs in British Columbia and Maryland is attempting to create the first synthetic life form. From the article: 'The project is being spearheaded by U.S. scientist Craig Venter, who gained fame in his former job as head of Celera Genomics, which completed a privately-owned map of the human genome in 2000. Dr. Venter, 59, has since shifted his focus from determining the chemical sequences that encode life to trying to design and build it: "We're going from reading to writing the genetic code," he said in an interview.'" This is certainly not the first group to venture into this territory.
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Writing Genetic Code More

Writing Genetic Code

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  • I for one... (Score:5, Funny)

    by jpellino ( 202698 ) on Sunday December 25, 2005 @11:35PM (#14338202)
    ... welcome our new two-codon overlords.

    • Call me a luddite, but you youngstahs should bone up on your classic SciFi* [imdb.com] before you start joking about this shiznat.

      Hell, if it were up to me, that damned comet debris [slashdot.org] wouldn't be allowed within a parsec of our atmosphere - unless the intention were to incinerate it.

      *Cf the work of Vincent Price [imdb.com] and Charlton Heston [imdb.com].

      • You're preaching to the choir - in 1970 I was 12 years old and the Andromeda Strain came out in paperback. I read - and reread it until it literally fell apart. I have never not had a copy at hand. There has not been a year in my teaching career that I have not used one of its lessons, from the use of sentinel values 'fail-safe' systems to the fluidity of evolution to the magnification of the problem caused by a stray shred of paper...

        It was a joke, but we do need to remember the amazing efficiency of si

  • Python vs Perl vs Ruby vs.. (Score:5, Funny)

    by Anonymous Coward on Sunday December 25, 2005 @11:36PM (#14338210)
    There you go, no more bitching about which is the best coding language, now you can code in the most natural one.
    • Yes, but how many lines of genetic code would it take to do this:

      print "Hello world!"
      • I think you missed a ";" in the end =)

        And of course you have to think a bit deeper, DNA is "binary" so you have to compare it to machine code instead. You cannot simply compare base pairs with a "print" syntax.

        When coding genetically, you have the four bases A, C, T and G, so it's not really binary either.
      • Yes, but how many lines of genetic code would it take to do this:

        print "Hello world!"

        Assuming you are a human poster... about 3 billion
    • "...now you can code in the most natural one."

      Someone told me non-nerds have been doing that for a while, phfff, what would they know.

    • And, speaking of C++... (Score:5, Funny)

      by Chemisor ( 97276 ) on Monday December 26, 2005 @09:31AM (#14339464)
      Well, as a C++ programmer, I am quite used to hearing how C++ is evil because of all the things it can do. Therefore, I am as justified as they are in saying that C++ is better than genetic code for the following reasons:

      Genetic code is too low-level. While C++ comes with a standard library defining containers, iterators, and common algorithms, in genetic code you have to do everything from scratch. In quaternary. With 3D objects. Talk about a learning curve!

      Genetic code has no garbage collector, and not even a simple malloc. In fact, you have to write self-modifying code to avoid memory leaks or dangling references. This makes it very difficult for the beginning programmer to write good code, and encourages bad practices.

      Genetic code is not object oriented. You have to do horrible hacks to encapsulate private information or define interfaces to it. Most programmers just use a "signals-and-slots" method to pass messages, resulting in spaghetti code rivaling the worst abuses of goto.

      Genetic code is too flexible. If you thought bad C++ code was hard to understand due to operator overloading, wait 'till you see the things a bad programmer can do with genetics! And, while in C++ the worst that can happen is a crash, bad genetic code could eat you.

      Genetic code takes longer to develop for. You have to write lots and lots of code to duplicate even the simplest C++ line. Furthermore, compilation times totally suck, approaching twenty years for complex programs!

      Genetic code has an arcane syntax, leftover from the early days of evolution. Just imagine, we're still using constructs nearly three billion years old! If you thought having some C in C++ was bad, wait 'till you see the archean leftovers you are forced to use in your eukaryotic cells!

      Genetic code is dynamically typed and favors the "duck typing" philosophy. This creates an enormous amount of security holes, where special ducks ("poisons") with appropriate appearance but malicious behaviour could be introduced into the system.

      Genetic code is hard to debug. Having no debugger, one has to rely on contrived printf-like trace statements. Unlike printf, the genetic equivalents are limited in number and expressiveness, sometimes making it impossible to figure out what is wrong.

      Genetic code is a bloated pig. Just imagine, you need trillions of bits to define a simple organism, while in C++ I can code NPCs in under a hundred lines of code.

      Genetic code VM is slow. Perhaps not as slow as Java, but it still takes milliseconds to do even simple operations. We could all think so much faster if we were written in C++.

  • Compiler? (Score:5, Funny)

    by r00t ( 33219 ) on Sunday December 25, 2005 @11:37PM (#14338211) Journal
    I hope there is a gcc backend for this. I hate using Visual Studio to write my code.

  • Problems? (Score:5, Insightful)

    by Renraku ( 518261 ) on Sunday December 25, 2005 @11:37PM (#14338214) Homepage
    Just wait until someone writes a piece of code that cures a genetic disease, but must be 'fed' with a certain medication. If not fed with said medication, it will do something real bad.

    • Re:Problems? (Score:3, Insightful)

      by segment ( 695309 )
      This just reminded me of Genetic warfare amongst other things...

      THE HAZARDS OF HUMAN DEVELOPMENTAL GENE MODIFICATION

      ...Attempts at developmental gene modification will certainly be subject to experimental error, but this is not the only source of potentially unfavorable consequences. Certain genes undergo a process of "imprinting" during development, in which the version of the gene inherited from the father or the mother is blocked from contributing to the individual's biological constitution. This phe

      • "Its possible no one would be able to handle certain situations."

        I am not advocating bio-weapons but the Universe itself is a situation no one can handle (eg: Bird Flu, Aids).

        "How does creating a "species" help us again?"

        A species that inhales CO2, exhales H2 and tastes like steak when cooked on a standard BBQ would be handy. Existing benefits can be seen in just about every domesticated species of plant, animal or fungus. Eg: The modern dairy cow, maybe not an entirely new species but they certain
    • If not fed with said medication, it will do something real bad.
      Yeah, it turns into the Fleshreaper [penny-arcade.com]. BTW, great business model for ambitious genetics companies that want to be the Microsoft of the biotech world.

    • Re:Problems? (Score:3, Interesting)

      by ceoyoyo ( 59147 )
      Fantastic. I'm going to steal a little bit of it and reverse engineer it so it doesn't need the medication any more. THEN I'll inject it. What, you want a copy too? Hm... well, I suppose I could upload it to Basetorrent.

  • Unlikely, but exciting if they pull it off (Score:5, Interesting)

    by yog ( 19073 ) * on Sunday December 25, 2005 @11:38PM (#14338216) Homepage Journal
    Bacteria are already used to synthesize organic materials by reprogramming their DNA. For example, some antivirals and antibiotics are manufactured this way; the desired pattern is injected into the bacteria's genome and it will then produce that pattern. Venter's project is really just an extension of that approach.

    I have doubts as to the likelihood of success using present science; in twenty years, perhaps it will be possible, but today it's really casting about in the dark. Even something as elemental as a bacteria is an incredibly complex thing, with a sophisticated genome and complex organelles working in biochemical harmony to reproduce, to "mate" by conjoining with other bacteria, and to adapt and thrive in a very wide variety of conditions.

    Bacteria have been around for billions of years and, as Stephen Jay Gould put it, we are living in the Age of Bacteria [stephenjaygould.org]. In a few short years it seems unlikely that even brilliant scientists can recreate these things. Modify some, yes, but completely create from scratch something that is going to be viable--well, that's going to be interesting to see.

    That said, if they can pull it off the possibilities of its use, for good or evil, are endless. They can be encoded to synthesize all sorts of compounds, eat nasty pollutants, generate fossil fuels, attack disease microbes, or be diseases themselves. Luckily, the human body has a pretty comprehensive immune system that will adapt to just about anything except retroviruses like AIDS that reprogram the immune system itself.

    • Re:Unlikely, but exciting if they pull it off (Score:1, Informative)

      by Anonymous Coward
      I'm pretty sure that most bacteria reproduce Asexually. Therefore they do not mate. Also, I'm not sure that someone with a last name of 'Go[a]uld' has our best interests in mind!

    • Re:Unlikely, but exciting if they pull it off (Score:2, Insightful)

      by Anonymous Coward
      Bacteria don't have organelles; you're thinking of protists.

      Another commenter mentioned that bacteria can't "mate". It was in quotes because its not really mating like we'd think of it; basically, some bacteria, when nearing death by starvation, will attach to another bacteria and inject its RNA or DNA strand into the other bacteria, producing an "offspring" that is a fusion of the two "parents" with the injector being the "male" and injectee the "female".

      I'm not even a bio major, I'm an engineering major.
      • Well, they teach it wrong, then. Bacterial 'sex' involves the transfer of extrachromosomal loops of DNA called plasmids, via a sex pillus also coded by a plasmid. Plasmids can carry, amongst other things, a casette of genes for antibiotic resistance, which is one of the reasons why resistance can spread so rapidly. It has little or nothing to do with near death experiences, and no 'offspring' is created; it's just a transfer of genes.
    • "Luckily, the human body has a pretty comprehensive immune system that will adapt to just about anything except retroviruses like AIDS that reprogram the immune system itself."

      Eventually AIDS, if for some reason we Never find a cure, will probably just run its course. Humans would adapt or AIDS would evolve to be non-lethal, like in chimps. Or it will at least level off.
    • The only way to have the technology to be able to do this in twenty years is to start making the technology today ;-)
    • Well, they know the sequence of many different bacterium. What happens if they were to synthesize the entire DNA chromosome for one of those bacteria and inject it into an plasma membrane whose DNA was removed? Would you call that synthetically creating a bacteria or just synthetically creating all of the programming of the bacteria?

      Now, what happens if you decide to change parts of the DNA chromosome by inserting your own genes or entire pathways that perform interesting and useful functions? If you do the

  • 'Generic' Code (Score:1, Offtopic)

    by Alamei ( 781359 )
    I think I've had too much exposure to .NET recently. Did anyone else read that headline as "Writing Generic Code"?

  • Here comes the pain (Score:4, Funny)

    by redthefed ( 713416 ) on Sunday December 25, 2005 @11:39PM (#14338221)
    I've seen WAY too many sci-fi movies to consider this a good scientific endeavor. If you need me, I'll be in my concrete bunker. :)

  • In Soviet Russia... (Score:5, Funny)

    by Ruff_ilb ( 769396 ) on Sunday December 25, 2005 @11:40PM (#14338228) Homepage
    Genetics code YOU!

    Oh wait... they do...

    Carry on.

  • Recolada (Score:4, Insightful)

    by Eli Gottlieb ( 917758 ) <.moc.liamg. .ta. .beilttogile.> on Sunday December 25, 2005 @11:40PM (#14338229) Homepage Journal
    Good to hear somebody is working on something important.

    If God didn't mean us to create life he would smite these people straight out, so we can kill that objection, BTW.

    The interesting part is going to be how they actually turn their new genome into a living bacteria. They're basically going to have to either assemble the first one from whole cloth or trick some other microbe into producing what they want.

    And even if we can make these things perform useful functions, how to make sure they don't die out from lack of an evolutionary niche or mutate and become pathological?

    • Re:Recolada (Score:3, Interesting)

      by Ruff_ilb ( 769396 )
      And even if we can make these things perform useful functions, how to make sure they don't die out from lack of an evolutionary niche or mutate and become pathological?
      Simple.
      If we know their genome, presumably we can kill them off pretty darn quickly.
      In this case, design flaws ARE a feature.
      Can't wait until Microsoft gets into this field. Those BSOD's must be nasty.

      • If we know their genome, presumably we can kill them off pretty darn quickly.
        In this case, design flaws ARE a feature.
        Can't wait until Microsoft gets into this field. Those BSOD's must be nasty.

        My first thought was: "Don't let Microsoft at it, whatever you produce will get a virus!".

        I wonder if there's any organisation at all that would be able to create a design that could be trusted to be okay to release outside a lab.

        Any organism that you create and release (outside controlled conditions) and that surviv

        • If you provide say, even TEN fail-safes that can mutate, what are the chances that ALL TEN will mutate and allow the organism to survive? What about 100 fail-safes?

          Very, VERY small, I'd bet.
    • likely they'll design something that will take a very basic protein or nutrient and convert it into energy and proteins that it can use in it's own structure and then self replicate. It can then be tested in a solution of it's ideal diet in an otherwise sterile environment where it won't need to compete with bacteria that have the advantage of 3-4 billion years of evolution.

      Once a basic structure is laid out, we can then start modifying it to serve specific purposes or we can try to piss it off by gradually

    • Re:Recolada (Score:3, Insightful)

      by karmatic ( 776420 )
      > If God didn't mean us to create life he would smite these people straight out, so we can kill that objection, BTW.

      If god didn't mean for people to lie, commit adultery, and murderer, he'd just smite them too, right?

      That being said, genetics is a tool. Like any tool, it can be used for good purposes, or bad purposes (ok, almost any tool - it's kind of hard to abuse a Nerf bat - I know, I've tried).
      • > If god didn't mean for people to lie, commit adultery, and murderer,
        > he'd just smite them too, right?

        Glad I don't believe in god.
      • "If god didn't mean for people to lie, commit adultery, and murderer, he'd just smite them too, right?"

        Correct.
      • (ok, almost any tool - it's kind of hard to abuse a Nerf bat - I know, I've tried).

        Obviously you didn't take off the soft foam and beat a person with the hard plastic inside. And if it doesn't come off, just turn the bat around. The handle, even though it's usually covered in foam, is very solid.
    • Actually, no. If God didn't didn't mean us to create life he would let us do it, and then we would smite ourselves with our little new toys :)
      • But don't worry, he'll save the faithful. So really, if you believe, you should be encouraging this. Fewer scientists to argue with!
  • The article does not seem to contain mention of just when this all started. The Globe & Mail is a bit behind- Discover magazine reported on the project in 2001: http://www.discover.com/issues/apr-01/features/fea tsimple/ [discover.com]

  • Here's what we need... (Score:3, Funny)

    by johansalk ( 818687 ) on Sunday December 25, 2005 @11:43PM (#14338241)
    Forget 'curing disease', that's not the future of the species, what we need are perfect blondes and supermodels.

  • Is it Open Source? (Score:5, Funny)

    by $0.02 ( 618911 ) on Sunday December 25, 2005 @11:43PM (#14338242)
    Seriously, are we going to have both propriatory as well as free genetic code organisms? What's the legal status of a living being that's a result/offspring of a crossing/mating between a propriatory and a GPL organism?
    • Well these "programs" are likely to reproduce by themselves, given that they are bacteria... what is the ownership of a (computer) virus? It reproduces itself - and if you're not careful, you might be running an unlicensed copy of that virus. Does that mean that you owe the virus writer a license fee?

      It's late & I'm feeling pretty incoherent - does my analogy even make any sense? :-)

    • Biotech patents are on a much worse situation than software ones. At least, on software we can still do basic research without paying taxes^W roalties to some company.

      That is the real problem, since life seems to not be covered by copyrights. At least until some realy clever lawer get on the way.

  • genetic code? (Score:3, Funny)

    by radicalnerd ( 930674 ) on Sunday December 25, 2005 @11:44PM (#14338252)
    how the @#$! are you going to debug it?

    • Re:genetic code? (Score:1, Funny)

      by Anonymous Coward
      With bug spray and/or a flyswatter.
    • Eventually, with software simulation tools. As soon as we either come up with hardware/algorithms that can perform protein folding and in-silico simulation in a reasonable amount of time, or understand protein functions better to the point that we can use algorithmic "tricks" to simulate it with present-day processing power.
    • Probably we would have to let it debug itself... much as we try to do for ourselves.

      Of course, debugging it would take many hundreds or thousands of generations, but if evolution works, it should happen.

  • Mwahahahahah! (Score:3, Funny)

    by Anonymous Coward on Sunday December 25, 2005 @11:50PM (#14338267)
    Remember all those stuffed suits who said that the GPL was viral? Just wait for their reaction when we prove them right!

    "I'm sorry sir, but from now on your name ought to be GNU/Mr. Jones..."
  • I think the chicken/egg problem they talk about is a pretty interesting point.

    The DNA is only a small portion of the cell. If they want to make a whole synthetic organism, they're going to have to make the other organelles and various membranes--a task I would imagine would be just as difficult as building the DNA.

    Sure, this is a big deal. But I don't think you can call an organism synthetic if all you are doing is injecting synthetic DNA into a pre-existing organism.

    • Re:Is it really that synthetic? (Score:4, Interesting)

      by castoridae ( 453809 ) on Monday December 26, 2005 @01:03AM (#14338482)
      But I don't think you can call an organism synthetic if all you are doing is injecting synthetic DNA into a pre-existing organism.

      Can you call a piece of (traditional computer) software your own (i.e. synthetic) if it mostly runs API functions provided by the (pre-existing) OS or a third-party library?
    • How long until someone comes up with the genetic equivalent of a bootstrap program? Some sequence of DNA that can be tacked on to the end of whatever their current project is, a sequence that will take raw biological material (amino acids? proteins? This is where I say "disclaimer: I am not a biologist") and construct a simple cell capable of then reading the actual organism DNA and replicating it.
    • In order to make an apple pie from scratch, you must first create the universe. - Carl Sagan
  • We *are* the I.D. now
         
    • (...specially the The last Question [mit.edu]. Albeit that one is on a much more philosophical level)

      We *are* the I.D. now

      Human designing synthetical life :
      Yeah that's the proof of I.D. !!!
      See ?
      Life must be created by someone !
      Life cannot be explained by science, only an Architect could have done it !
      It is such much complex in its "irreductible complexity" that we humans will never be able to study it and understa... Oh, wait...

  • Extremely interesting.... (Score:5, Informative)

    by CupBeEmpty ( 720791 ) on Monday December 26, 2005 @12:04AM (#14338309)
    This is something that is really, truly interesting. I am curious as to what they will consider a "human crafted" organism. I work in a virology lab and in the field there are often "frankenstein" viruses that are created to preform certain tasks. I know many people do not consider viruses to be living, but you are getting pretty darn close. Also, the viruses that are created (actually quite often) are usually combinations of parts of DNA sequence from a variety of viruses. Literally just last week I created an engineered virus that will insert the DNA that codes the protein USP18 [nih.gov] into human cell cultures (huh-7.5 cells... modified human hepatoma 7 cells). The goal is actually to support or detract from the conclusion of the linked paper. The virus in question is basically a highly modified form of HIV. It has certain elements that are exactly the same as HIV but there are large portions (the parts that make it really pathogenic) that are removed and other things are added (promoters and insertions sites to allow the USP18 -or whatever- to be inserted).

    The long and short of it is. These "life forms" are significantly different from their naturally occuring cousins. They are this way by nature of human engineering. This argument can also be extended to bacteria that have been highly modified. There are laboratory strains of almost every bacteria that we know of that are significantly different from wild type bacteria. I am curious as to where they will draw the line. From the article is appears that they are paring down mycoplasma to the barest bones.

    The other question is, once you have the DNA how do you kickstart the process. They appear to be inserting it into and E. coli with the nucleus removed. This means that the cellular machinery of the E. coli will be used to translate the DNA into protein and eventually a new synthetic cell. Does this mean that it is human created if we use naturally occuring cellular machinery?

    I don't mean to detract from the research in any way because it is highly interesting and will tell us a lot about how life works on the most basic level, BUT there are a lot of questions out there and I hope that people keep them in mind as we see this field develop over the next several years.

    • The other question is, once you have the DNA how do you kickstart the process. They appear to be inserting it into and E. coli with the nucleus removed. This means that the cellular machinery of the E. coli will be used to translate the DNA into protein and eventually a new synthetic cell. Does this mean that it is human created if we use naturally occuring cellular machinery?


      The way I see it, the existing bacteria is just a DNA-compiler.

      If I write a C-compiler in C, I need to use an existing C-compil
      • The way I see it, the existing bacteria is just a DNA-compiler.

        Specifically, I think the ribosome corresponds nicely to the compiler - it translates the RNA into the final protein product by performing mappings of codons (DNA/RNA triplets) into the amino acids that make up the proteins. I'd think of the bacteria as a whole more as the operating environment - different systems states, etc.

        Now what would be interesting is to re-engineer the ribosome to compile DNA/RNA differently. Check out this [harmantechnologies.com] blog entry
        • This is an interesting analogy but in this case it is not necessarily that useful. The problem is that if a completely original and synthetic organism is made on a DNA level it means nothing unless it can be "compiled" into a new organism. The problem arises because raw DNA even with exact translation means nothing. There is an entire process of post translational modification that occurs to proteins. One single DNA sequence can produce more than one protein based on the activity of the rest of cellular
      • Right so the real question (in the terms of this metaphor) is how did that compiler get coded without a compiler? The chicken/egg problem is that if DNA codes the machinery that allows DNA to code any machinery then how did that process actually occur naturally. It is one thing to use existing machinery to create modified proteins using synthesized DNA (this occurs constantly in biology) but it is another to "create life." This is one of the important questions in this field. These scientists will almos
        • Ah, you have to write your first compiler in assembly. Of course, you need an assembler. You write that in machine code, by punching holes in little cards or flipping switches if you have to.

          Life probably did it the same way. First you had some chemicals that happened to form up into useful structures spontaneously. Then there was one of these structures that would behave differently if a certain other structure were present. And so on, building structures that can then be leveraged to build something
      • But someone had to write the first compiler, by hand, in machine code. The biological analogy is constructing the cellular machinery atom by atom until you've got something that can process DNA code.
        • someone had to write the first compiler, by hand, in machine code.
          My guess is that the first compiler was written in assembly language.
          The first assembler was probably written in machine code, or, more accurately, was probably written in assembly language, and then hand-translated into machine code.
  • "Frankenstien XML on Rails 101 for Dummies, with MySql."

  • Typo (Score:3, Funny)

    by zephc ( 225327 ) on Monday December 26, 2005 @12:40AM (#14338404)
    You misspelled "Dr. Venture"

    "Why is it every time I need to get somewhere, we get waylaid by jackassery?"

  • Building with DNA (Score:5, Insightful)

    by castoridae ( 453809 ) on Monday December 26, 2005 @12:42AM (#14338413)
    I think one of the biggest challenges isn't in synthesizing strings of DNA, per se - it's in knowing what DNA to synthesize. The real holy grail of synthetic biology is to engineer genetic functions to accomplish a particular goal - design to spec. From the average /. POV, this means "programming" genes in some high-level language (C++ DNA lib, anyone?). Take a look at The Registry of Standard Biological Parts [mit.edu] for a first library of genetic "functions".

    As I understand it, the current state-of-the-art in terms of programming DNA is basic logic gates that still tend to lose coherence when connected together. Once this is accomplished (best guess, 3-4 years from now to work out the basic science), all of the sophisticated tools and techniques developed by the IT community over the last decade(s) can be rapidly applied, and that goal of design/build to spec will become possible.
    • I agree that the major challenge is to figure out what DNA to synthesize. And we need some procedural method to explicitly determine the DNA sequence that performs some specific function. Although, I don't know if thinking about these systems as modular electronics is the best way. These systems certainly are modular, but the fact that there are no wires and no clear separation between modular devices means that a full modularization of the entire system into separate parts is a real challenge. It can proba

  • Maybe... (Score:2, Interesting)

    by rodm13 ( 870050 )
    God intends us to make lifeforms of our own. Just finished reading an interesting piece on a person's "Talk with God", here's a link. [Ragged Trousered Philosopher]

    Just noticed that the site's bandwidth is out, here's the Internet Archive's Cache:

    http://web.archive.org/web/20050312133142/http://w ww.fullmoon.nu/articles/art.php?id=tal [archive.org]

    Even if it is fiction, it's an interesting idea nonetheless.

  • anyone else sense disaster? (Score:4, Interesting)

    by SuperBanana ( 662181 ) on Monday December 26, 2005 @01:19AM (#14338515)
    We're going from reading to writing the genetic code," he said in an interview.

    We have a very bad track record when it comes to "our world" and "technology we invent".

    Far as I'm concerned, "God" doesn't enter into it. I don't think we've developed nearly enough of an understanding about our world or microbiology...to even think about this. Our planet is a pretty complex machine, and we're stuck with it for the moment (and to all the escapists, no, I don't want to hear about your colonization ideas. Let's feed, clothe, and shelter our fellow humans before we send the most elite off to establish a "perfect" world...otherwise Earth becomes the home of the poor and disadvantaged.)

    Call me crazy, but this sounds even worse than the whole nanomachine "grey goo" problem. "Grey goo" scenarios mostly revolved around incompetence (ie, we know how to design a perfect nanobot but someone skips "step number 54", or keys in an extra zero.) Here, we've got not only incompetence but also "we're not really sure how this all works." Oh, and to top it all off? The little buggers could just spontaneously mutate all on their own, because biology isn't a perfect machine. Lovely!

    • Call me crazy, but this sounds even worse than the whole nanomachine "grey goo" problem. "Grey goo" scenarios mostly revolved around incompetence (ie, we know how to design a perfect nanobot but someone skips "step number 54", or keys in an extra zero.)

      Actually, "grey goo" would have to be designed. A self replicating nanomachine that can survive in shirtsleeve environmental conditions, scrounge all the resources it needs to replicate itself from the surrounding environment and process them all into the

      • Oh yes, it could. It could happen even by not checking the replicated bots apropriately, getting random errors on the code.

        All you need to have for a grey goo situation is an imperfect self replicating being capable of doing that outdoors. And this will probably be the goal of any nanobots project. The only part missing is to replicate without control.

  • Years ago Omni published a story by Alfred Bester called "Galatea Galante". The title character was genetically engineered from scratch, and her designer coded her genome using a language with a regular syntax similar to computer languages. Bester shows us a few lines of it before remarking in his narrative voice that it would be really, really boring to show any more of it. It might be of interest in this context if anyone could dig it up though.
  • they'll release their genetic code under the GPL, I'd really hate it if went all commercial.
  • Something tells me this code will be very vulnerable to viruses.

  • Interesting Issue with DNA as code (Score:3, Interesting)

    by ndansmith ( 582590 ) on Monday December 26, 2005 @04:07AM (#14338896)
    "Code" is an interesting word to use when talking about DNA. I think it was first termed as such since it seems to be an obvious descriptor of DNA: Information which is stored by the DNA molecule can be interpreted by the living organism as instructions for various proceses. There is obviously information there, and it does require interpretation, so it is "encoded."

    Normally, when I talk about code, I understand that an agent, some sort of intelligent being, has put the information into code. If there is a code, it must have been encoded by someone, and non-intelligent phenomena do not produce encoded information (as far as I can reason). This sounds like a perfect solution for ID adherents, but must be troubling for evolutionists. Is "code" the correct terminology for talking about DNA? How does science explain the fact that all this information came to be encoded and stored in a DNA molecule by the process of natural selection (an unintelligent phenomenon despite the term "selection") such that living tissues can interpret it and put it into action? This issue is primary over natural selection itself, since the ability to pass information to offspring is a necessary condition for natural selection.

    I am simply asking because the issue of humans writing their own custom DNA begs the question about how information came to be encoded in DNA in the first place. I never took biology, so I am quite ignorant and curious about this issue.

    • That's similar to what I've been thinking. If it's possible to trace back every piece of DNA through evolution to a piece of code, then that original DNA, having such properties as to evolve into either a cockroach or a dinosaur, should have been somewhat hard to appear from thin air assembled that way.

      I mean, even with evolution making sense one has first to set initial conditions. It's kind of fuzzy once we get to that point; evolution doesn't explain everything, just pushes the nasty and hard to explain
    • DNA is "code" because each set of three (or is it four) nucleotides forms a codon. When a strand of DNA is transcribed to RNA, and then processed by an enzyme (transcriptase or something? it's been years since i took bio), protiens with one end that fits with that codon hook up to the RNA strand. the other end of that protien carries an amino acid (the components that form proteins), and so each codon gets "decoded" into an amino acid -- chains of which form proteins.

      the information came to be "encoded" be
    • How on earth did you get through school without a biology class????

      Even in my 9th grade biology we learned the basics of how DNA information is transfered to offspring, and in cell division, the imperfect copies that lead to mutations, etc.
    • You might want to read Stephen Wolfram's book, "A New Kind of Science", which explores the idea of complexity arising from very simple sets of rules (The Principle of Computational Equivalence). In this book (which, while long, is not too difficult to read - although the appendices will probably leave you scratching your head), he details a very simple set of 6 rules, which he utilizes to show how such simple rules, being used in a 2D cellular automata, can easily give rise to many complex patterns, includi
  • And you thought Perl was unreadable?
  • If this project is successfull... whe can only hope...

    I wonder if in a couple of years the result will start debating about its origins with theories like evolution vs. intelligent design. :-P
  • Life is unbelievably complex, and for all our recent results and new insights in biology and genetics, we are still only just scratching the surface. A living organism, even the simplest prokaryote, isn't just a set of genes. The truth is, we only have a very rough idea about what genes go into any organism; on top of that we don't know what the functions are of the supposedly non-coding parts of the DNA, we hardly know anything yet about the epi-genetics side of things, and we have no idea about how to set

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