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Biotech Science

Synthetic Genome Drives Bacterial Cell 174

Posted by timothy
from the sharpen-your-pitchforks dept.
Dr. Eggman writes "Physorg.com brings us news of a synthetic genome, produced by the J. Craig Venter Institute, being used in an existing bacterial cell for the first time. Using a combination of biological hosts, the technique produces short strings of DNA by machine which are then inserted into yeast to be stitched together via DNA-repair enzymes. The medium sequences are passed into E. coli and back into yeast. After three rounds, a genome of three million base pairs was produced." (More below.)
"Specifically, the genome of M. mycoides was synthesized from scratch. This synthetic genome was then inserted into the cells of a bacteria known as Mycoplasm capricolum. The result is a cell, driven by a synthetic genome, producing not the proteins of Mycoplasm capricolum, but of M. mycoides. The institute has far-reaching plans for its synthetic life program, including designing algae that can capture carbon dioxide, make new hydrocarbons for refineries, make new chemicals or food ingredients, and speed up vaccine production." The BBC has coverage of the hybrid cell as well.
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Synthetic Genome Drives Bacterial Cell

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  • Take that, IDers! (Score:3, Insightful)

    by oodaloop (1229816) on Thursday May 20, 2010 @02:10PM (#32283454)
    I don't know how many times I've heard the young earth creationists and intelligent designers say that since man can't make life, life must be special. Dear FSM, I wish I could send this article to all those IDiots on all the message boards to which I've posted over the years.
  • Re:What... (Score:4, Insightful)

    by Creedo (548980) on Thursday May 20, 2010 @02:15PM (#32283526) Journal
    Obvious troll, but I'll bite. How is this any different than the rampant and completely unsupervised genetic twiddling that has been happening in nature for the last few billion years?
  • by gyrogeerloose (849181) on Thursday May 20, 2010 @02:15PM (#32283528) Journal

    Not that I disagree with your sentiments when it comes to ID proponents (they're morons) but I don't think this really counts as "making life." Not yet, anyway. It's a step in that direction, though.

  • Where's my nobel? (Score:3, Insightful)

    by fuzzyfuzzyfungus (1223518) on Thursday May 20, 2010 @02:17PM (#32283562) Journal
    sudo dd if=genome.helix of=/dev/nucleus0
  • Re:What... (Score:1, Insightful)

    by drachenstern (160456) <drachenstern@gmail.com> on Thursday May 20, 2010 @02:20PM (#32283580) Journal

    Shall we ask Monsanto?

  • Re:What... (Score:3, Insightful)

    by Monkeedude1212 (1560403) on Thursday May 20, 2010 @02:20PM (#32283604) Journal

    This sounds exactly like Jurassic Park, except replace Dinosaurs with Yeast and Frogs with E. Coli.

    Need I explain what happens next?

  • Re:What... (Score:4, Insightful)

    by ColdWetDog (752185) on Thursday May 20, 2010 @02:24PM (#32283660) Homepage

    Obvious troll, but I'll bite. How is this any different than the rampant and completely unsupervised genetic twiddling that has been happening in nature for the last few billion years?

    FTFA

    "This becomes a very powerful tool for trying to design what we want biology to do. We have a wide range of applications [in mind]," he said.

    Perhaps there is a difference between random changes directed solely to furthering of DNA propagation ...

    and the short term goals of greedy men?

    whatcouldpossiblygowrong?

  • Re:What... (Score:3, Insightful)

    by UdoKeir (239957) on Thursday May 20, 2010 @02:27PM (#32283708)
    Beer that gives you the shits?

    Oh wait, that's already been invented [wikipedia.org].
  • by gyrogeerloose (849181) on Thursday May 20, 2010 @02:29PM (#32283738) Journal

    Pandora's box has been opened. I'm excited to see what pours out over the next decades.

    Uh, I think you need to read up on your Greek mythology a bit more. Opening Pandora's Box [wikipedia.org] was not such a good thing.

  • Re:Waits for... (Score:3, Insightful)

    by sakdoctor (1087155) on Thursday May 20, 2010 @02:29PM (#32283746) Homepage

    legal messes of epic proportions

    Only in America.

    Though it will spawn the new industry of genetic engineering tourism.

  • by Anomalyx (1731404) on Thursday May 20, 2010 @02:31PM (#32283782)
    Umm.. yeah, this is a far cry from creating life

    I may be a young-earth creationist, but arguing the concept to anyone who only wants to push their own view is 99% of the time pointless, so I won't elaborate any further besides just saying that modifying an existing life form (that's all this is, really) doesn't count as "creating life". Quite far from it, actually.
  • Re:What... (Score:3, Insightful)

    by virtualXTC (609488) on Thursday May 20, 2010 @02:31PM (#32283796) Homepage

    whatcouldpossiblygowrong?

    People use to say the same thing about computers... and still do about robots. The question a rational person asks is "what is the risk vs possible return."

  • Re:Waits for... (Score:2, Insightful)

    by Anomalyx (1731404) on Thursday May 20, 2010 @02:36PM (#32283860)
    Not to be the party pooper here, but I do doubt this will get expanded to humans. Messing with Human DNA would take massive amounts of experimentation (since we don't really know squat about how it works, when you compare what we do know to what we don't know), with massive amounts of harmful effects (and deaths) on said test subjects. Without even debating the ethics of it here, I highly doubt that such experimentation would be welcomed by society.
  • Re:What... (Score:4, Insightful)

    by redbeardcanada (1052028) on Thursday May 20, 2010 @02:45PM (#32284040)
    Damn straight - we need these bio-engineered life forms to protect us from the robots when they finally make their move...

    That's what you meant by risk vs. return right?
  • by interkin3tic (1469267) on Thursday May 20, 2010 @02:48PM (#32284092)

    I guess we should wait until the actual Science article comes out, but it looks like they basically synthesized an entire bacterial genome, as opposed to the normal way of having a bacteria copy it's own genome with it's own enzymes, and then they put it into a different bacterial strain.

    Is that "making" a cell artificially? They didn't make most of the bacterial cell themselves, the bacteria did that. They didn't design the genome from scratch, they just copied an existing one that nature made and modified it a bit. I'm not sure that constitutes actually making a cell artificially. If you buy a mac at a store, print out the ones and zeros to make windows vista, manually retype them, make a boot disk, and install that on the mac and it worked, that would be an impressive feat, sure, but did you "make a completely new computer?" (Best comparison I could come up with, sorry about that in advance). I don't think this can be considered making life yet.

    Second, is this "life?" Life seems to be impossible to define, but it's pretty certain that "genome was stitched together in a lab and inserted into a dummy cell" is unique to this thing, nothing else we'd call life has that feature. Does that disqualify it as life and make it something else?

    To their credit, Venter doesn't seem to be claiming they made new life, but they are aiming for that eventually, and I'm curious as to what slashdot thinks about when we can actually say we've created artificial life.

  • Re:What... (Score:3, Insightful)

    by asukasoryu (1804858) on Thursday May 20, 2010 @02:50PM (#32284114)

    The question a rational person asks is "what is the risk vs possible return."

    The typical American asks "What is the possible return" and ignores the risk in pursuit of personal gain.

  • by gyrogeerloose (849181) on Thursday May 20, 2010 @03:00PM (#32284306) Journal

    Or maybe he was being so subtly ironic that I missed the point entirely.

  • Re:Waits for... (Score:4, Insightful)

    by Daniel Dvorkin (106857) * on Thursday May 20, 2010 @03:03PM (#32284360) Homepage Journal

    It can be done, and that means it will be done. The first applications will be medical; synthetic gene therapy could offer cures for many diseases we currently have no way to treat, and only "it's bad 'cause it's got DNA in it!!!" Luddites will object. Yes, there will be harmful side effects, including death, but people with terminal cancer, or parents of children with terrible birth defects, will be willing to take the risk. Once the therapeutic principles are established, we'll inevitably see more frivolous applications. And at that point, whether or not it's "welcomed by society" will be irrelevant -- as long as there are people with the money to pay for it, someone will do it.

    That being said, we're a long way from that point. There's a hell of a lot of difference between building a bacterial genome and modifying a human one at will.

  • by Yergle143 (848772) on Thursday May 20, 2010 @03:05PM (#32284402)

    It's different for a a lot of reasons. I'll just focus on three. The bio-weapon fear: the viruses and bacteria that we harbor have co-evolved with us. Viruses and bacteria shape evolution in a myriad of subtle ways but one way to look at even the most pathogenic forms is that their habitat is you and me. So despite the suffering inflicted by TB, Ebola, HIV etc. fundamentally it is not in the best interest of the microbe to cause the extinction of its habitat -- although it probably happens. The bio-weapon fear is that pathogens can now be created whose long term interest is not in the "cruel but fair" hands of Darwinian Evolution but in the possibly malevolent (or hopefully beneficent) hands of a bona-fide "CREATOR/DESTROYER". Let's hope Venter is nice. The second: the lateral gene transfer mechanism has been shown to play a role on evolution. However now it is possible to accelerate this "artificial sex" to rates that far exceed the norm. Plant-Animal hybrids here we come -- and let's use our imagination. Plant a seed, up grows the plant, a flower fruits, a butterfly emerges which lays -- seeds. Pretty kewl huh. Three: Genetic twiddling -- there are some parts of the cell that evolution just doesn't take a chance in messing around with. It is now possible to mess around.
    My two cents: weeds win...the reason algae for fuel doesn't work is weeds. If you go to Indiana you don't see the Monsanto soybeans growing wild in a ditch. And there are no wild packs of Shih Tzus. I'm not sharpening the pitchfork yet.

  • Re:What... (Score:4, Insightful)

    by Maxo-Texas (864189) on Thursday May 20, 2010 @03:08PM (#32284436)

    Oh come on, the likely hood of an oil spill in the gulf is 1/10,000. Do we really want to block drilling based on the 1/10,000 chance of a 200 million barrel leak that could kill all life in the gulf and do substantial damage to most of the eastern seaboard and destroy the fishing industry in four states and potentially do a lot of damage to the atlantic ocean and carribean as well? Be reasonable.

  • Re:What... (Score:4, Insightful)

    by Daniel Dvorkin (106857) * on Thursday May 20, 2010 @03:09PM (#32284452) Homepage Journal

    The typical American asks "What is the possible return" and ignores the risk in pursuit of personal gain.

    Given the amount of Luddism that is invariably displayed with respect to genetic engineering, I'd say that in this particular case the reverse is true. There's a level of ignorance driven fear on this topic that I haven't seen since the days when a lot of people genuinely believed that computers were malevolent "thinking machines" that would try to take the world away from their human creators.

  • Re:Waits for... (Score:3, Insightful)

    by HeckRuler (1369601) on Thursday May 20, 2010 @03:17PM (#32284582)
    Dude, that's what secret labs are for. Haven't you ever seen the mad scientists trope?
  • by Peter Trepan (572016) on Thursday May 20, 2010 @03:17PM (#32284596)

    The grandparent post was modded as flamebait, but the religious flame war is in real life. From the parent's article:

    However, with this step forward comes a new set of ethical considerations, say experts. “We need to be critically aware of the profound implications of creating synthetic life,” said Karl Giberson, director of the Forum on Faith and Science at Gordon College in Wenham. “I don’t think this is something to be scared of. I don’t think Mother Nature is being violated in some egregious way. But this is an area of science with important ethical considerations, and religious sensibilities and higher priorities need to be on the table, under discussion.”

    It's a pretty moderate response, but even so, it conflates ethics and religion, implying that the ethical decisions should be based on theology. The grandparent is right - this is going to be a culture war thing.

  • by domatic (1128127) on Thursday May 20, 2010 @03:23PM (#32284720)

    It would prove that it doesn't require a divinity to create life. That doesn't demolish the stated premise of ID but it is a blow to the implied premise of ID, namely "We all know that it was Yahweh but came up with this as a roundabout way of not actually saying it."

  • That's new? (Score:3, Insightful)

    by maxwell demon (590494) on Thursday May 20, 2010 @03:34PM (#32284870) Journal

    including designing algae that can capture carbon dioxide

    The natural algae already do this. Even more, they produce oxygen at the same time!

  • by interkin3tic (1469267) on Thursday May 20, 2010 @03:44PM (#32285036)

    That would be a good readout that it is functional, and undoubtedly they did that already. Working with a single bacterium is I guess possible, but pretty much everyone just works with whole colonies.

    They wouldn't have had much to screen from to see if they got the genome in had they not gotten a colony rather than a single cell.

    Anyway, the reason "reproducing" isn't a good standard for defining life is there are many live things, such as mules, which aren't capable of reproducing, and some non-living things which are capable of reproducing to various degrees. For example fire spreads by catching other things on fire, and it's questionable whether prions are alive or not though they can reproduce.

  • by Dr. Eggman (932300) on Thursday May 20, 2010 @03:55PM (#32285206)
    Personally, I would prefer to wait until we produce a novel self-replicating "machine" (biological or otherwise) before we call it artificial life. Synthetic life, however, yes I would qualify this as. At least, in the sense that it is the artificial construction of a known quantity/concept through synthesis between related assets. That is to say, this and its project, like much of genetic engineering, is a cut and paste job. This achievement is the latest in a reduction of the cut and paste; the latest in a process of producing successively more fine grained reassembly jobs towards any of the goals of a the development of a novel mechanism (directed evolution or generative engineering which I like to call "gengineering"), a synthesis of of existing mechanisms in a singular form (recombinant and splicing GM), or imitation of an existing form. We're not to artificial life yet, but somewhere down the row of increasing granularity lies an invisible line which, when crossed, will I be satisfied in calling it such.

    As an aside, I really was conflicted whether to state my opinion here or mod you up to increase the chances of getting more opinions. Ultimately, I decided yours is strong enough to stand on its own. Good luck in getting to 5!
  • by SpinyNorman (33776) on Thursday May 20, 2010 @04:00PM (#32285288)

    I'd say it may well be creating life. It's not exactly designing life (and not exactly NOT designing life either...).

    Consider:

    1) The cell they injected the new DNA into had the old DNA removed first - hence it has dead.

    2) The new DNA started out as chemicals in a bottle - certainly dead too.

    3) The new DNA put into the cell "rebooted" / reanimated it so that it started dividing again. Certainly back alive now!

    This experiment may not LOOK that impressive, but consider that the exact same technique can be used to computer modify any type of life you want in any way. Want a hen with teeth - no problem. Replace the feathers with scales ... just a matter of computer programming, then "print" the DNA and animate it.

    Note also that while it's "only" the DNA that's being created, not the INITIAL cell, that the copies the cell it makes of itself as it divides are of course made under control of this synthetic DNA, so the 2nd, 3rd, etc generation cells could be considered themselves synthetic.

  • by HiThere (15173) <`charleshixsn' `at' `earthlink.net'> on Thursday May 20, 2010 @04:46PM (#32285962)

    I don't think you're an artist, a writer, or a programmer. If you are, you need to turn around an look at yourself.

    This is a first step into the grey area. Creation isn't an area of sharp divisions. Almost everything worthwhile is based on extensive predecessors. This is taking one kind of cell, and converting it into another (closely related) kind. This *IS* creation. It's not creating all that much, but it's creating a new species. (Whatever that means at the level of yeasts.) The new species has the DNA of one old species, and the support system (prions, etc.) of the other one. We know a lot more about the DNA level than we do about the prion level, but prions are in charge of ensuring that proteins fold properly. Change the folding properties, and the proteins act differently. Which means the cell acts differently.

    Another step is the insertion of newly designed genes into an existing system. Another step is trying to build a minimal system from scratch. (These are all being worked on simultaneously.)

    So this is another step into the area between selective breeding and creating life de novo. (Although even there I'm not implying that the atoms were synthesized. But one could require that step, too. It's just that I don't see any reason anyone would ever bother.)

    The categories we think in don't have sharp edges, though we usually pretend they do. This is the creation of life, but it's just barely into the fuzzy area. Even so, it's ended up with a new species, and that wasn't the goal.

    (OTOH, I'm not a biologist. It's possible that yeasts don't have prions acting as chaperones for protein folding. In which case I may be wrong about it being a new species, unless they made an error in their DNA synthesis.)

  • Re:Story I heard (Score:2, Insightful)

    by NeutronCowboy (896098) on Thursday May 20, 2010 @05:19PM (#32286360)

    And science is only ever an approximation to the truth, it doesn't try to be anything else (though people try to make it more than it is).

    The only people who try to make science into more than it is are religious people. Scientists are keenly aware of the approximations in their search for truth.

    BTW, how nice of your God to keep moving the goal posts. It used to be: you can't create life out of dirt. Now you have to create dirt, too? And I presume that the goal posts will keep moving until they arrive at "Use your own space/time continuum."

  • by Attila Dimedici (1036002) on Thursday May 20, 2010 @05:57PM (#32286796)
    I love people who argue, "See, we created life, that proves that life doesn't need a creator."
  • by Anonymous Coward on Thursday May 20, 2010 @08:23PM (#32288062)

    It's not just that though, field crops are adapted to grow quickly and use lots of water and nutrients which we provide. In the wild they tend to grow quickly, use up the local water and nutrients, and die quickly. And in order to be resistant to roundup and other things they have to essentially armor their metabolic processes. This makes those processes less efficient, so they are often outcompeted by other plants when there is no poison.

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