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Scientists Build Possibly The First Man-Made Genome

Posted by Zonk on Thu Jan 24, 2008 04:40 PM
from the quite-a-crafting-combine dept.
Biotech Science
hackingbear writes "Wired is reporting that researchers have created the longest synthetic genome to date by threading together four long strands of DNA. 'Leading synthetic biologists said with the new work, published Thursday in the journal Science, the first synthetic life could be just months away — if it hasn't been created already. [...] The ability to synthesize longer DNA strands for less money parallels the history of genetic sequencing, where the price of sequencing a human genome has dropped from hundreds of millions of dollars to about $10,000. Just a few years ago, synthesizing a piece of DNA with 5,000 rungs in its helix, known as base-pairs, was impossible. Venter's new synthetic genome is 582,000 base-pairs.' As a programmer, I'm most excited by the possibility of a new platform and the programming jobs that will be created by it."
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Submission: Scientists Build First Man-Made Genome by hackingbear (988354)
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  • Thanks for the SuperFlu, Craig! (Score:3, Insightful)

    by nebrshugyo (1216152) * on Thursday January 24 2008, @04:43PM (#22173610) Journal
    If Venter and company royally screw-up, and create some bug that kills us all, or turns the biosphere to a pile of gray goo, nobody's going to make any money off of dandy, new, commoditized designer life forms. Where do I complain?

    • Re:Thanks for the SuperFlu, Craig! (Score:5, Insightful)

      by Fallingcow (213461) on Thursday January 24 2008, @04:46PM (#22173670) Homepage
      I'd be more worried about the tech becoming common enough and easy enough to use that anyone with $100,000 and some spare time can make a super-virus, or a bacterium that is extremely hardy and destroys wheat or rice crops, or any number of other nasty things.

      • Ewww! (Score:5, Funny)

        by monkeyboythom (796957) on Thursday January 24 2008, @04:53PM (#22173764)

        As a programmer, I'm most excited by the possibility of a new platform and the programming jobs that will be created by it.

        As a regular guy, I am NOT excited by the thought of thousands of fat, greasy programmers drooling over a test tube and a well worn copy of "Weird Science."

        As my friend Han was so fond of saying, "I've got a bad feeling about this."

        • As a regular guy, I am NOT excited by the thought of thousands of fat, greasy programmers drooling over a test tube and a well worn copy of "Weird Science."

          As my friend Han was so fond of saying, "I've got a bad feeling about this."
          Tell the programmer to keep his hands to himself.
      • Ahhh, I see, you're one of those people who hears the term "Super-empowered Individual" and thinks of it as a bad thing. Whereas I'm kinda of the opinion that the problem with our society is the dis-empowerment of the individual.

        Guess you think concealed-carry licenses are a bad idea too.

        • I guess you think every individual on the planet should have nuclear weapons? I mean, that would be "super-empowered individuals," right?

          • Re: (Score:3, Insightful)

            by QuantumG (50515)
            Well, the thing about nukes is that you need a good delivery device.. oh, and they're pretty conspicuous, so you'd need a secret silo too. That's, umm, really a lot of capital investment. That said, if more concerned citizens had access to "the button" then we'd hardly have any threat of military coup would we?

    • Re:Thanks for the SuperFlu, Craig! (Score:5, Insightful)

      by KublaiKhan (522918) on Thursday January 24 2008, @04:53PM (#22173756) Homepage Journal
      If 'grey goo' could happen from nanotech or biotech, then bacteria would have done it already.

      So far, all that's happened is some assorted earthtone sludge.

      • Re:Thanks for the SuperFlu, Craig! (Score:4, Insightful)

        by Cheesey (70139) on Thursday January 24 2008, @06:43PM (#22175270)
        You forgot about all the other life on Earth.

        We are the grey goo. The plants and the bacteria had a good go at spreading all over Earth, but we spread further and faster than any previous life. The "grey goo scenario" is limited by the assumption that energy is abundant, and indeed energy (food) shortages are all that stops us covering every inch of the world.

        I, for one, welcome my fellow grey goo overlords.

  • But, but... (Score:4, Funny)

    by Wylfing (144940) <[brian] [at] [wylfing.net]> on Thursday January 24 2008, @04:44PM (#22173634) Homepage Journal

    But Jesus, and the Bible!

    • Re:But, but... (Score:5, Funny)

      by CaptainPatent (1087643) on Thursday January 24 2008, @04:47PM (#22173674) Journal

      But Jesus, and the Bible!
      Yes, don't worry...
      We'll be able to genetically replicate those soon too

      • Re: (Score:3, Informative)

        by KublaiKhan (522918)
        The official position of the Catholic Church, IIRC, is that animals do not have a soul--so no problem there; just define any artificially created lifeforms as non-human animals, and then you'll have no theological problems.

        Not sure about how the other 5/6 of the world's population would think about it, though.

          • Well, the easy out there is that Animals are not entirely sentient.
            You know it's funny, that's exactly what the dolphins and chimpanzees say about humans.

  • Impossible? (Score:4, Insightful)

    by XxtraLarGe (551297) on Thursday January 24 2008, @04:44PM (#22173636) Journal

    Just a few years ago, synthesizing a piece of DNA with 5,000 rungs in its helix, known as base-pairs, was impossible.
    Yet, somehow we've managed to have life on earth...

    • Re:Impossible? (Score:4, Informative)

      by bumby (589283) on Thursday January 24 2008, @04:51PM (#22173742)
      unless you believe in "intelligent" design, life on earth wasn't synthesized. At least not by the definition of the word in this domain.

      • Re:Impossible? (Score:5, Funny)

        by esampson (223745) on Thursday January 24 2008, @04:56PM (#22173830) Homepage

        I have my own theory; so many things in this world annoy me that they couldn't have happened by random chance. Instead they are proof of some supreme cosmic being who shaped the world just to piss me off.

        I call my theory Belligerent Design. (with all credit to Lore Sjoberg for that joke).

          • Whenever I think somebody, anyone, not just supreme cosmic beings, is trying to piss me off, I think: am I really that important? Why, exactly, would anyone make an effort to piss me off? Nah, probably just a coincidence.
            You're trying to piss me off aren't you?

          • It's not paranoia if they're really out to get you (Score:4, Funny)

            by Goldarn (922750) on Thursday January 24 2008, @05:51PM (#22174638)

            Whenever I think somebody, anyone, not just supreme cosmic beings, is trying to piss me off, I think: am I really that important?
            I used to wonder about this. Then I realized that, since the cosmic beings/universe/whatever are trying to piss my off, then I am, ipso facto, that important. It did wonders for my self-esteem.

            Still, I can't help but wonder... is the entire universe against me? Or just the part where light has reached since my birth? Don't laugh; it's an important question.
    • I think the key word in that sentence is 'synthesizing'. They weren't saying it wasn't possible for it to happen. Just that we couldn't do it ourselves. :)
    • We could not synthesize DNA with over 5,000 base pairs until recently. Obviously, natural DNA has more base pairs than this. Yes, you are correct, life exists on earth, and we did not create it. Glad that's sorted out.

  • The question that needs to be asked is (Score:3, Funny)

    by Pojut (1027544) on Thursday January 24 2008, @04:44PM (#22173640) Homepage
    will they use this technology to create a life form who is programmed to create other life forms?

    Up in the sky! It's a bird! It's a plane! IT'S A NET!!!*

    *My apologies for this horrendously bad joke
    • The odds are very good that has already happened. Compare the estimated life of the universe to the estimated life of your star system.

  • I mean, imagine the possibilities. The ability to create synthetic, self replicating machines that produce whatever material we could need. Tailor drugs and chemicals by using "Biotechnology".

    Or should I be afraid of the first "programmed virus" that can actually infect human beings?

    I don't know. As usual, it seems to have two sides. What comes out of it is up to us, I guess. In other words, if I believed in God, I'd hope he has mercy with us.
  • If that can be achieved (much like a Florida geneticist once made THC-producing orange trees) then you'll single-handedly kick the War on Drugs' ass. That would be a worthy cause right there.

  • Wonderful (Score:4, Insightful)

    by pnewhook (788591) on Thursday January 24 2008, @04:46PM (#22173672)

    As a programmer, I'm most excited by the possibility of a new platform and the programming jobs that will be created by it.

    Geez. The LAST thing society needs is a bunch of synthesized clones running around with hacked up spaghetti code for genes.

  • At last! (Score:3, Funny)

    by erroneus (253617) on Thursday January 24 2008, @04:47PM (#22173680) Homepage
    I will have my four-legged chicken! (The drumstick is my favorite part)

  • An omission (Score:4, Insightful)

    by leob (154345) on Thursday January 24 2008, @04:48PM (#22173702)
    The article does not say if it's methylated in the right places.

    • Re:An omission (Score:4, Informative)

      by reverseengineer (580922) on Thursday January 24 2008, @06:21PM (#22175018)
      The parent poses an important question, and as it turns out, Mycoplasma genitalium was a clever choice in that regard: its genome is so streamlined as to lack the machinery to methylate its DNA. In prokaryotes like M. genitalium, methylation is mostly used to distinguish self from non-self DNA, quite useful (restriction enzymes can be used to carve up non-self DNA then), but not strictly necessary; in eukaryotes, it plays a vital role in regulation of gene transcription, so appropriate methylation is very important.

      Analyses of M. genitalium suggest it may have orginally had methylation capabilities, but has lost them over time: http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=206970&blobtype=pdf [nih.gov]

      In our analysis, restriction enzyme digestions of M. genitalium genomic DNA, using MspI and HpaII, did not support the fact that CpG methylation currently exists in this genome as evidenced by the identical pattern produced by both restriction enzymes (data not shown). Whether the disparity in CpG dinucleotides in the M. genitalium genome is the result of a now extinct CpG methylase activity or related instead to the codon usage of this organism will require further analysis.

  • whatcouldpossiblygowrong? (Score:5, Funny)

    by $RANDOMLUSER (804576) on Thursday January 24 2008, @04:49PM (#22173708)

    "As a programmer, I'm most excited by the possibility of a new platform and the programming jobs that will be created by it."
    As a programmer, when I think of the quality of the HTML on most websites, and then read the above sentence, I throw up in my mouth a little.
    • Elitist much? Shortsighted perhaps?

      Things don't start off perfect, or even good. They get there by wading through the mistakes and learning from the garbage you see. When you lose, don't lose the lesson.

      • Re: (Score:3, Informative)

        by $RANDOMLUSER (804576)
        Dude. HTML is a completely known entity. There are VALIDATERS for it, and the quality of most HTML is rubbish. An influenza [wikipedia.org] virus has only 10 genes, meaning it doesn't take much "code" to make some really bad bad shit.

        • Re: (Score:3, Interesting)

          by spleen_blender (949762)
          My point isn't to praise in any way the people that aren't performing to that standard. It is the fact that they exist almost as a reminder as to what not to do. Sort of a "without night there is no day" kind of thing.

          You make a good point with the dangers that loom. You should read if you haven't "The Singularity Is Near" by Ray Kurzweil. It has some good ideas as to how to deal with this topic with nanotech and AI.
  • counted....

    It used to be in the prehistoric computing days, engineers got paid by number of lines cranked out. Now, it looks like gene engineers will bask in that opportunity.

    But, hopefully, they don't crank out shitty code. Or, well REALLY have "The First man-Made Gnome" (which is what I read at first...). This could be a different take on Project Genesis.
  • welcome our new synthetic overlords. (It had to be done.)
  • The final line of the paragraph scares me to death - I haven't met a programmer whom I'd turn loose on a DNA construction. It would be like handing a loaded, fully-automatic weapon, with the safety ground off, to a three-year-old; or asking them to complete a fully distributed ERP system written in assembler.
    Just because we CAN do something doesn't mean we SHOULD. Perhaps if we constructed a complete corpus of biological effects, and dependencies of all currently known sequences (yeah right, like we're go
  • ... intelligent design, science will be safe from religious ridicule.

  • Procedural Abstraction (Score:4, Insightful)

    by Aram Fingal (576822) on Thursday January 24 2008, @04:58PM (#22173858)
    In the article, Venter says that they will need something similar to high level programming tools in order to accomplish useful modifications. I think that there is already plenty of evidence that genetic systems have procedural abstraction. In talking about gene activation, Biologists often use the term "ordered cascade" to describe what's happening when one gene activates a few more and those genes, in turn, activate other genes. If you think about it, it's exactly like subroutines of a program. Construction of the bacterial flagellum, for example, starts with the activation of one gene, which activates others, leading to the contribution of about 25 genes. These genes contribute various parts of the flagellum and activation of the cellular machinery to put it together and attach it to the cell wall.
    • will need something similar to high level programming tools in order to accomplish useful modifications. I think that there is already plenty of evidence that genetic systems have procedural abstraction.

      Sounds to me like programming in Prolog.

      For those who don't know... A Prolog program is a set of patterns and actions. When a pattern is "matched" it action occures. The set is unordered. A more modern and more widely used version of this is the language "Erlang". I think Erlang points to the way we wi

  • So 582k? (Score:4, Funny)

    by Guysmiley777 (880063) on Thursday January 24 2008, @05:09PM (#22174038)
    582k ought to be enough for anybody.

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