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Biotech Science

Life Made to Order 203

Roland Piquepaille writes "When he was president of Celera Genomics, Craig Venter was the leader of the private project which deciphered the human genome. Now, he has another goal: create custom-made organisms -- one DNA letter at a time. 'Venter's objective is not merely to tweak existing life forms by inserting genes that confer specific traits -- the main tactic in conventional genetic engineering. Instead he wants to assemble an entire genome, DNA letter by DNA letter, putting together only the genes he wants: those necessary for an organism's survival and those that will allow it to carry out a desired task.' If successful, maybe in a decade, this could yield new sources of energy or novel drugs. Venter is not alone in this quest. Other institutions, private companies or universities, have similar efforts under development. Check this column for a summary of this eye-opening -- but quite long -- Technology Review article."
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Life Made to Order

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  • Here it is (Score:5, Insightful)

    by Henry V .009 ( 518000 ) on Saturday March 29, 2003 @11:29AM (#5622204) Journal
    This is the real nano-technology. First we bio-engineer the tools we need to create whole genomes quickly. At that point, we can make designer bacteria or other organisms. The potential of that sort of technology is nearly unlimited.
    • Re:Here it is (Score:5, Interesting)

      by The Only Druid ( 587299 ) on Saturday March 29, 2003 @11:36AM (#5622231)
      Actually, the irony of your statement is that we're going to need better nano-technology to complete the task. As enthusiastic as these companies are, the problems in intentionally constructing a DNA molecule letter by letter are huge: notably, if you screw up in one spot, you can have tremendous problems.

      Further, there's no "spell check" for them, using current methods. They wouldn't know they had a problem until they start letting it reproduce, only to find that they have an [apparently] inexplicably error, possibly making the organism unviable.

      Whats needed is sophisticated enough nanobots that will be able to not only perform the construction of the DNA, but to "spell check" it by running up and down its length continually, comparing it against the desired pattern.
      • You've pointed out the main problems. We need to create the tools to be able to do this. But like I said, I imagine that those tools we create or modify will be organic (DNA based). Organisms already do so much of those error checking and construction tasks that I think it will be easiest that way.
      • by whovian ( 107062 ) on Saturday March 29, 2003 @12:32PM (#5622449)
        Looks like you're designing DNA!

        Genome Assistant can help
        you compose your artificial sequence.
        First, tell us how you plan to design it....
        -- Clippy

      • Re:Here it is (Score:2, Insightful)

        by jmt9581 ( 554192 )
        I don't really think that nanorobots are necessarily the answer in this case. Spell checking could be done by DNA sequencing, which is currently expensive but there are efforts to develop new techniques [harvard.edu] that would make sequencing cheaper. I think that a new, cheaper sequencing technology will will be released long before DNA-synthesizing nanobots.

        However, I must admit that nanobots constructing DNA would be really frickin' cool. :)
      • > Actually, the irony of your statement is that >we're going to need better nano-technology to >complete the task.

        I could see sort of a "bootstrapping" thing. If a small bacteria is producible, perhaps you can create such a bacteria whose purpose is to assemble a component for a larger bacteria (five different classes make DNA sequences A, B, C, D, E, and five more bind A->B, B->C, C->D, D->E, E->A, or even to "infect" and modify another cell to serve the true purpose of the proje
      • Whats needed is sophisticated enough nanobots that will be able to not only perform the construction of the DNA, but to "spell check" it by running up and down its length continually, comparing it against the desired pattern.

        These exsist, in the form of enzymes. These organisms would have their genome checked in the same manner as you and I; cellular repair enzymes would monitor for problems. They would start with microbes, simple bacteria. Ther would be maintained like a multicellular organism,. though;

      • That's a major problem, which I think will take several years to solve (not with nanobots, but with better hijacking of biological systems). But it is dwarfed by the problem of identifying the right cocktail of proteins necessary to get the DNA to work in a living cell.

        Venter is known in the public genomics community as an ambitions, ruthless, and unprincipled egotist. Example: At the end of Celera's (Venter's company) much publicised private human genome project it was revealed that the genome they had se
      • Re:Here it is (Score:3, Informative)

        by tfoss ( 203340 )
        Oh come on. This is wrong on so many levels.

        ctually, the irony of your statement is that we're going to need better nano-technology to complete the task.

        No. Nanotechnology is completely uninvolved in this. These guys are chemists, biochemists & geneticists not engineers.

        As enthusiastic as these companies are, the problems in intentionally constructing a DNA molecule letter by letter are huge: notably, if you screw up in one spot, you can have tremendous problems.

        No. Making DNA base by base is n

    • and then CleverNickName accidentally lets them loose and they take over the ship. Oy vey!
    • Nano technology is the future, look at a sci-fi example, borg nanoprobes can take over your body in a matter of seconds. Imagine what someone could do with such technology. We could design bacteria that would repair ourcells so that we could live forever, build muscle tissue, regenerate tissue in wounds to prevent and eliminate scarring. Isn't bacteria already genetically engineered for tasks such as these? The production of insulin...
  • Instead he wants to assemble an entire genome, DNA letter by DNA letter, putting together only the genes he wants:

    Neck bolt by neck bolt, green skin, flat head with scar on forehead, demeanor not unlike a geek without caffeine, and bring it all to life with a strategic bolt of lightning that hits the castle on top of the old hill....

    ...Yeah, that's the type of stuff we should be tinkering with!
  • The potential capability of being able to engineer DNA sequences makes a myriad of SF nightmares seem like fanciful daydreams. Consider a DNA equivalent of the "Island of Dr Moreau". What would the biological landscape look like populated by viable hazardous failures that aren't what such a new age alchemist intended? The possibility for creating the butterfly that ends civilization is far too frightening to launch ourselves into this blindly. We've been lucky with a few "accidents" that have benefitted man
    • ...that is a bit scary. I can see it now, a butterfly lands on a guys arm, everyone around him screams and runs..
    • Sjeesh, the government should interfere with you, so that at least
      you would take some time to form a real opinion.
      You don't even know what you're talking about. Brr, it looks scary.
      I don't understand it. It must be stopped.

      Time will tell that this is for the benefit of mankind, and your opinion
      will be in history books. Alongside ideas that the earth is flat, and
      that steam engines hurt the economy.
      And then there is always: you can use a knife to cut bread or to kill someone.

      Please spare us this nonsense pa
      • Okay let me make it clearer for you:

        1. Venter has helped lay out the building blocks, but he doesn't have a real idea how all the parts interact. That's why he wants to put some of the parts together: to see what happens.

        2. For years we've been giving kids anti-biotics. Guess what? Now we've got mutated bacteria that don't respond to the current course of meds.

        3. Ask the folks in Europe if they want any of America's genetically engineered crops or the beef we've fed it too. No?

        There are TOO many unknown
        • All I'm saying is that society will need to decide in a rational way. Not in an emotional one.

          You might be right about some of your concerns. Just like you are right about Oppenheimer, it was the people who decided this was for the benefit of mankind (it was the military, mostly). And it has it good and bad sides. In this case the good sides (including using it as a weapon) were decided to be more important than the bad ones (can't think of any right now).

          "We should not play God" is a completely wrong, mi
  • I would like a side of genetically created fries without the use of a patato with that.
  • by nagora ( 177841 ) on Saturday March 29, 2003 @11:36AM (#5622236)
    Version 1.0 of our anti-cold virus virus has developed an error whereby it instead shuts down the customer's nerve system. The company acknowledges that more debugging of the genetic code should have been done and assures any surviving members of the human race that these issues have been addressed in version 1.1. This is a pre-recorded message as I'm afraid we're all dead at the moment.

    TWW

  • Imagine the new market for customized pets.. It wouldn't be too cool when your pet Balrog-look-alike turns on you though and tears your limbs off.

    I would get a pet ostrich with the head of an antelope.
  • If he has played Starcraft, he will know what genes to avoid absolutely. The Zerg and the Protoss were afterall created the same way ...

  • Consider this: How well have we done writing software to perfection?
    How well have we done predicting all outcomes of chaos?
    I submit not very well. Lets not multiply our error in living creatures.
    • Hmmm.... the article addresses questions similar to yours:

      Not only does designing genomes from scratch allow researchers to engineer new organisms with extreme precision, Venter says, it also allows them to strip the cells of a host of natural functions needed to survive and reproduce in the wild. As a result, synthetic organisms would function only under tightly controlled or rarified conditions such as those inside a biological pollution filter on the smokestack of a fossil-fuel-burning power plant.

      • This is one of the things annoying about Jurassic Park, actually: if they hadn't made predators (i.e. they'd stuck to herbivores), they'd still have some of the largest and most impressive animals in the history of the world, without any of the risks we saw in the books and movies. Basically, the park would have worked with herbivores...
    • (programming/designing) bugs making bugs.

      The problem with life is that it tend to prevail, so the bugs/bacteria/virii you made could be here for years, there is no service pack that fix magically those mistakes (well, computer worms also seems be here to stay, an example of "art" imitating life). A mistake in that kind of things and we all could be history.

    • How well have we done writing software to perfection?

      Actually, pretty well, if you consider the world outside Microsoft. People generally make software as good as it needs to be. Airbus and Boeing planes with hundreds of critical built-in software systems routinely make flights thousands of times each day around the world - when was the last time one of these had an accident caused by a software failure? Air traffic control at airports all over the world, handling at each airport anything from hundreds to

  • along the usual stuff like creating organisms from scratch and superhumans, we can also have smaller cell phones (!). Maybe this time a real one-cell phone?
  • Scary (Score:5, Interesting)

    by Musashi Miyamoto ( 662091 ) on Saturday March 29, 2003 @11:42AM (#5622267)
    I heard about scientists trying to create a new type of organism a little while ago... It scared me then and it scares me now.

    However, I would think that it would be totally possible to generate TONS of energy and other useful things from something like this. It might be possible to generate oil from sunlight. Huge tanks of stuff making food, energy, whatever.

    The ethical complications are interesting.
    If you create a new life form, do you have the right to destroy it? Maybe. If you can re-create it at a whim, why not? But then, what about existing life forms? Eventually scientists might be able to re-create just about any species in a petri dish. Can they then justifiably destroy a species, since they can re-create it at any time?

    Cool sci-fi... or more accurately, cool sci-soon-to-be-not-fi.

    • If you create a new life form, do you have the right to destroy it?

      I can see it now...

      Critic: "You can't kill this creature, it has feelings just like the rest of us."
      Doctor: "Nonsense. I made this creature's DNA, and I don't remember giving any feelings."

    • If you create a new life form, do you have the right to destroy it? Maybe. If you can re-create it at a whim, why not?

      "Right" is a nonsensical word. There's noone out there granting or revocing rights, really, it's all a big con...... *ZAP!*
  • Before I become a programmer the most fun I hadwas with woodworking. I'd been through several jobs/ job fields, but didn't enjoy the work. I think this editorial is really onto somthign that should be examined more closely.

    From personal experince, the average programmer spends 2-3 years at any job. The most common excuses for leaving: lack of challange, lack of requirements flexability, inflexible or unresponsive managment, and red tape(configuartion managment going out of control and issues such as having
    • I suspect you intended to post to the thread about psychology of programmers. Anyway, one thing struck a chord with me in that: being interrupted. The thing hassling me most at my current job is that people interrupt me very often, and its true, it can easily take an hour to get ones concentration / "train of thought" back on its tracks.

  • by Eudial ( 590661 )
    He sounds like one of us who enjoys writing machinecode by hand. (Or atleast the kind who would potentially enjoy doing it)
  • Hey, they are clean, dont bite and arent noisy..

    Hell ill take a dozen!
  • by LinuxParanoid ( 64467 ) on Saturday March 29, 2003 @11:46AM (#5622283) Homepage Journal
    I read the full Technology Review [technologyreview.com] article.

    Craig Venter is propounding the vision. But the real science/engineering described in that article seems to be the following:

    In mid-2002, researchers at SUNY-Stony Brook synthesized a 7,500-letter long Polio DNA sequence, converted it to RNA, then "combined that RNA with enzymes and other molecules in a test tube, and watched as whole polio viruses assembled spontaneously."

    The complicated chemical steps used to synthesize the DNA are error-prone; errors grow linearly with the number of steps "so researchers typically limit fragments to fewer than 80 letters."

    The Stony-brook researchers thus took two years.

    A company called Egea Biosciences has a prototype machine, the device makes a mistake only once for every 10,000 DNA letters, or bases, a 100-fold improvement over conventional techniques that typically have an error rate of one in 100.

    The CEO of that company "says the technology could be extended to yield in a matter of weeks highly accurate strands 100,000 bases in length--long enough to make a very simple bacterial genome."

    That's what I got out of the article. And a recognition that there is a loose analogy to semiconductor manufacturing in there. The Venter name is useful mostly for hype as far as I can tell. Actually, setting a vision is really important so I should cut him some slack, but I more appreciated the tech details above which were buried in the middle of the article.

    --LP

  • Methinks, that if this concept is worked out properly and people can "build" their favourite organisms, I'll be either old enough to have Alzheimer or dead already.
    So thank heaven I don't have to live through the consequences of it...
  • WESLEY!
  • Upsides Only (Score:5, Insightful)

    by Aknaton ( 528294 ) on Saturday March 29, 2003 @11:49AM (#5622299)
    "If successful, maybe in a decade, this could yield new sources of energy or novel drugs."

    Or perhaps biological weapons or a killer virus? It's amazing to me how people only discuss the upside of things like this without mentioning the bad that can come of it as well.
    • Re:Upsides Only (Score:5, Insightful)

      by Daniel Dvorkin ( 106857 ) on Saturday March 29, 2003 @12:08PM (#5622361) Homepage Journal
      The bad has been so thoroughly discussed by hysterical scaremongers that there's really no point. Even on Slashdot, where you'd expect a fairly scientifically (or at least technologically) literate audience, there are ten "don't these foolish scientists realize that There Are Things Man Was Not Meant To Know?!?!?" posts for every "wow, this is really cool" post.
      It's amazing to me how people only discuss the upside of things like this without mentioning the bad that can come of it as well.
      Reminds me of how American fundamentalist Christians like to talk about Christians as though they were a persecuted minority ...
      • Re:Upsides Only (Score:3, Interesting)

        by mkcmkc ( 197982 )
        The bad has been so thoroughly discussed by hysterical scaremongers that there's really no point.

        If the possibilities don't scare you, I don't think you're paying attention. There are a lot of fundamentalists (of whatever ilk) out there that would like to kill large groups of people (if not all of us), and if this becomes technically and economically feasible, we're going to be in real trouble.

        --Mike

    • Re:Upsides Only (Score:2, Interesting)

      by Efreet ( 246368 )
      Given that these organisms will be hand made by scientists using existing genes I would say that, no, there isn't any danger.

      For a very, very long time organisms have been thinking of ways to kill, parisitize, and otherwise screw their competition. Even the simpleist disease virus or bacteria is a master peice of inconcievable sybtlety by the standards of what we can cerate in test tubes this way.

      The organisms in the article, on the other hand will be very, very simple. They won't even have unexpressed
  • Let's just hope that this doesn't end in a closed-casket funeral and laments of "He tampered in God's domain."

  • by Johnso ( 520335 ) on Saturday March 29, 2003 @11:50AM (#5622303)

    Bart: "How would I go about creating a half-man, half-monkey-type creature?"
    Mrs. Krebopple: "I'm sorry, that would be playing God."
    Bart: "God shmod! I want my monkey-man!"
  • What happens if a genetically engineered life form has an unforseen effect on the real world? Or a mutation?
    • That's why you keep organisms that you make carefully contained. You observe them very carefully before even considering taking them out of quarentine. And as for mutations, perhaps you've been watching too many movies that use "mutation" as the convenient ominous and ill-defined bad thing.
  • If successful, maybe in a decade, this could yield new sources of energy or novel drugs.
    Or... Pokémon.
  • but in order to do this you must have tentacles and communicate in colours.

  • by Fritz Benwalla ( 539483 ) <randomregs@@@gmail...com> on Saturday March 29, 2003 @12:04PM (#5622347)

    I would like:

    1. A turkey that grows with a stomach full of stuffing.
    2. A small monkey-like creature that keeps the shower water at a constant temperature.
    3. A virus that makes just one of my "enlarge your penis" spams true, but then then another one that brings it back down for easy storage.
    4. A tiny giraffe. All the convenience of a small dog but you wouldn't have to bend all the way down to pet it.

    Please let me know when I can pick these up. Thank you.

    ---------

  • by TekReggard ( 552826 ) on Saturday March 29, 2003 @12:07PM (#5622355)
    This reminds me of those Sci Fi flicks where scientists really want to create creatures from scratch. So they come up with a bunch of "super creatures" which they'll use to perform tasks better than their human counter parts. Of course, said "super creatures" turn on them and start killing them or rebelling against mankind. You know what I mean, think... Resident Evil? [the movie for example]
  • I just wonder when they're gonna bring back dinosaurs.

    cues jurassic park music
  • Energy? (Score:3, Funny)

    by Cyno01 ( 573917 ) <Cyno01@hotmail.com> on Saturday March 29, 2003 @12:18PM (#5622409) Homepage
    this could yield new sources of energy
    Are they going to engineer hampster like creatures that will never tire to run on little wheels or what?
  • well lets hope nobody spits in your life while they were making it.. just be sure not to put down your occupation as 'cop'
  • by ubiquitin ( 28396 ) on Saturday March 29, 2003 @12:25PM (#5622430) Homepage Journal
    ...involved in the creation of a living thing. An astonishing array of proteins, complex sugars, and lipids are all necessary for even a unicellular organisms to be viable. These aren't as easily assembled as nucleic acids, but they are just as requisite. The public focus inevitably tends toward DNA and RNA, especially by marketers such as Craig Venter, and especially when the story is being told to a non-scientific readership. The real story in biology is always more complex than the headlines would have us believe. Why can't these people make a real contribution to the world of medicine and figure out how SARS [news.com.au] works.
  • Doubling every five hours or so. :)
  • by Tuxinatorium ( 463682 ) on Saturday March 29, 2003 @12:48PM (#5622514) Homepage
    There was a recent slashdot story [slashdot.org] about a controversy over using genetic screening in conjunction with IVF[/URL], which got me thinking. They are going to raise a new perfectly healthy baby, for the purpose of donating the umbilical cord blood to their sick child in order to save his life. So what if they're using IVF to screen out genetically defective embryos? The sole effect of this treatment, when allowed to go ahead, is a benefit to all parties concerned and does harm to no one. (For those of you who believe that the destruction of embryos is immoral because the embryos are people, all I have to say is that one mindless ball of flesh is not any closer to personhood than any other, because the sole characteristic that makes one a person or makes one capable of having a "soul" (if such things exist) is having a mind capable of thought and emotion, which is obviously not a characteristic of anything that has not yet developed any sort of nervous system) But I digress. The whole slippery slope argument about "Designer Babies" is completely bunk because sliding "down" that slope would be nothing but benefit to mankind. The world would, unquestionably, be a better place if genetically-based diseases were eradicated and people had more of a genetic predisposition to be healthy, fit, and intelligent. So what if the benefit only applies to those who can afford it; the same can be said of ALL expensive medical treatments, and yet we don't see anyone advocating banning chemotherapy for that reason. One of the other arguments against so-called "Designer Babies" is that genetic screening will, in many cases, be applied very narrowly (for example, to enhance physical attractiveness) neglecting more important things and actually making the person-to-be less healthy overall. So, hypothetically, the technology could be misused in harmful ways. Big deal. Antibiotics have been and are still being misused resulting in the creation of dangerous antibiotic-resistant diseases that are taking a great toll in some areas, such as Russia's problem with MDR Tuberculosis. Nevertheless, that has never been a good reason to ban antibiotics altogether, and this situation is hardly any different. The industry could be regulated to avoid abuses and malpractice, the same way other medical procedures and prescription drugs are handled today. The difference between this and other medical resources that are legal but regulated is grossly insufficient to warrant the double standard of banning genetic screening/improvement altogether. The third objection to so-called "Designer Babies" is an (IMO irrational) fear, spawned from science fiction, of creating a "super race" of genetically engineered humans, raising the standards for everyone and harming those whose parents couldn't afford the genetic improvement technology. Let me ask you, how is that sort of economic divide any different from the current situation? Rich people can afford to send their students to better schools, and provide them with a more advantageous upbringing in general. This results in a situation where the children of middle class and rich parents have more of a chance to succeed than the children of poor parents, regardless of their innate potential. Does this mean that all private/rich-public schools should be disbanded, and everyone, should be condemned to a crappy education and a disadvantaged upbringing? Heck no. That would certainly satisfy the resentment of the poor, without really helping them, but it would harm everyone else. That is analogous to the issue at hand: Banning genetic screening/improvement would simply hold back part of society from improving themselves, without providing any concrete benefit except satisfying paranoia and class envy. Such a ban would do nothing to serve the common good. Sure, there may be bugs to be worked out, as with all experimental medical treatments. So federal regulation, similar to the function of the FDA for drugs, is probably a goo
  • Chilling Feeling (Score:2, Interesting)

    by mmmjstone ( 456174 )
    Why is it that when I read this article I thought "man creates great organism, great organism is too great, great organism kills man?"

    Maybe it's just the product of too many science fiction movies.
  • I'm not sure of the ethical or moral implications of creating LIFE to be slaves to tasks or for slaughter. I suppose the dolphins in iRaq and cows/chickens already fit this bill, but we don't create them, rather; herd and domesticate them. Isn't this somewhat the premise behind The Matrix and Planet Of Apes? We create or domesticate animals/machines that are sensiant beings, they catch on that they are slaves, form a "god complex" themselves and then rebel. Who's to say these "organisms" don't gain or alrea
  • Does he prefer to be called "Evil Genius" or "Idiot Scientist"?

    ---gralem
  • If they are gonna be making DNA letter by letter, then hopefully someones gonna write a good spell checker.
  • by megabeck42 ( 45659 ) on Saturday March 29, 2003 @01:22PM (#5622649)
    Ahh.. The future,

    "Organisms'r'US, this is Charlene, how may I help you?"

    "Hi, yeah - I'd like to order a Natalie Portman with a side of grits."

    "Mmmhmm, I'll need a credit card and a shipping address - would you like that overnight?"
  • If you're going to highlight as a link a magazine title, make the link one which goes to the magazine. If you want to link to an article, arrange the link so that the article is clearly specified. Make sure the link highlights the noun to which the target refers, please.
  • They are on crack (Score:5, Insightful)

    by minkwe ( 222331 ) on Saturday March 29, 2003 @01:43PM (#5622727) Journal
    Anybody who claims they can do this in a decate (if at all) is either very naive or not thinking straight.

    We don't even know 0.1 % of how viruses function let alone cells. It's really laughable to hear things like these.

    One fundermental question that is still far from being solved and will benefit mankind more is the 'folding problem' --- That is, given an unknown DNA sequence (gene), what is the 3D structure of the protein it produces?

    Once we know that, the next problem is the 'function problem' --- Given the 3D-structure of an unknown protein, what is its function?

    Current attempts at solutions to these problems are merely AdHoc devices which are far from suitable in unique situations.
  • Anyone ever read "Deus Ex Machina" by Pierre Ouellette? A very good thriller where Computertechnology meets biotech meets AI... nice outlook for our future if it becomes possible..
  • They've put up a picture [transload.net] of the thing they're trying to build from the DNA.
  • Interesting detail from article: creation of a new letter for the base-pair alphabet:

    While Evans and others are working on machines that could expand researchers' ability to write genes, chemists at the Scripps Research Institute in La Jolla, CA, are expanding the genetic alphabet itself. "Our repertoire of bases is naturally limited," to the familiar DNA letters A, T, C, and G, says Scripps chemist Floyd Romesberg. Because these letters tell an organism which proteins to make, the types of proteins that

  • The problem with building a genome from scratch is the fidelity of our current synthetic DNA synthesis techniques. The lowest error rate is 1 in 100 bases which is just not going to hack it when the genome you are trying to build is several hundred thousand base pairs. Compare this to the problem your cells have every time they want to divide: they have to faithfully replicate 3 billion bases in a matter of hours. Just one mistake could be fatal to the cell or even worse induce a mutation that causes di
  • What this is not:

    A way to make new pets, better people or 4-assed monkeys. This is unlikely to make any multi-celled organism, much less one you can even see by eye.

    Anything to do with nanotechnology, this is molecular biology as has been done for years.

    Anything useful to make a weapon. That can be done today so, so much easier in any decent biochemistry lab.

    Anything really novel technique- or theory- wise

    What this is:

    A mixture of known techniques, a new machine, and ego. The likelihood of their acco

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