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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 @03:10PM (#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.
    • by Creedo (548980)
      You think this will stop them? The same old stupid arguments are already popping up. ID proponents are amazingly dense as a whole.
    • Due to a failsafe in the universe, if I were to get a girl pregnant the universe would cease to exist; however, due to a basic property of quantum mechanics, the probability of that happening is zero. Since a universe in which that outcome occurs cannot continue to exist, that outcome cannot occur; the universe continues to exist in the opposite state.
    • by gyrogeerloose (849181) on Thursday May 20, 2010 @03:15PM (#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.

      • by oodaloop (1229816)
        Yeah, but it's hard to argue that it will never happen now.
        • Yeah, but it's hard to argue that it will never happen now.

          Agreed.

          Now, whether that's a good thing or not is somewhat debatable. I can come up with arguments on both sides of that one.

    • Re:Take that, IDers! (Score:5, Interesting)

      by virtualXTC (609488) on Thursday May 20, 2010 @03:38PM (#32283894) Homepage
      Lets not get a head of our selves here, they've only re-programmed a cell, not created artificial life. If you are looking for a fully artificial cell you should focus on what's going on in George Church's lab [masshightech.com].
      • by Peter Trepan (572016) on Thursday May 20, 2010 @04:17PM (#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.

      • Re: (Score:3, Insightful)

        by HiThere (15173)

        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

        • This is not a new species. In fact they had to work their butts off making sure that what they were looking at was what they thought they were looking at because it easily bred. This is not creation of life in any sense of the word, photocopy maybe, but creation? No. The 'Gene Machine' has been out there for a long long while. That they might have made a whole DNA is really not that surprising or impressive. This has been in the works for years and not really a first step anywhere. That said as a scientist
  • Where's my nobel? (Score:3, Insightful)

    by fuzzyfuzzyfungus (1223518) on Thursday May 20, 2010 @03:17PM (#32283562) Journal
    sudo dd if=genome.helix of=/dev/nucleus0
  • Waits for... (Score:5, Interesting)

    by NeutronCowboy (896098) on Thursday May 20, 2010 @03:20PM (#32283584)

    ... the first fully patented life forms. I'm really curious how that would work.... let's say an egg gets a fully artificial set of chromosomes that include patented genes for fixing Thyroid diseases, preventing breast cancer, and purple hair with green skin. Let's also say that that egg develops into a regular person. Is that person property? What happens if they have kids? Do they need to pay royalties?

    I can't wait for this stuff, because it will allow for some truly awesome fixes to truly terrible diseases. But I'm also pretty sure that this will result in legal messes of epic proportions. Monsanto will be a side show compared to that.

    • Re: (Score:3, Insightful)

      by sakdoctor (1087155)

      legal messes of epic proportions

      Only in America.

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

    • Re: (Score:2, Insightful)

      by Anomalyx (1731404)
      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:Waits for... (Score:4, Insightful)

        by Daniel Dvorkin (106857) * on Thursday May 20, 2010 @04:03PM (#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.

        • I dunno, the military types are the ones willing to dive head first into unknown and questionable territory without regard to life, limb, and cost to taxpayers.

          I'm kinda surprised that our special forces don't have cyber eyes with natural night-vision and HUDs yet. Of course, super-soldiers take time to grow.
      • Re: (Score:3, Insightful)

        by HeckRuler (1369601)
        Dude, that's what secret labs are for. Haven't you ever seen the mad scientists trope?
    • by mapkinase (958129)

      "Is that person property? What happens if they have kids? Do they need to pay royalties?"

      This is just silly. "Parents" will probably pay through the nose, but not the person or his kids.

      • Current court cases have made farmers pay if GM crops pollinate their crops, even unknowingly, so making the kids pay is just a few steps away.
        • by jeff4747 (256583)

          [citation needed]

          In the only cases I'm aware of, the defendant claimed their crops were pollinated from the wind, etc. But at trial it was revealed the defendant had bags of the plaintiff's seed.

          (insert Bevis-and-Butthead style joke here)

        • by mapkinase (958129)

          In which world? In the world where the laws about humans and plants are generally the same?

          How do you imagine this argument in court?

          "Your honor, the corn plant seeds are subject to this regulation, babies are nothing more than human seeds, so they should be subject to it to".

    • by bazorg (911295)

      Is that person property? What happens if they have kids? Do they need to pay royalties?

      if we take a look at the universal declaration of human rights I think it's clear that no special rules need to be made to protect the interests on individuals according to the kind of birth or technique involved in their conception. Taking the example of clones, after they're born it really is not possible to say that they are different from anyone else and therefore should have special status. right?

      Article 6 Everyone has the right to recognition everywhere as a person before the law.

    • by Alsee (515537)

      purple hair with green skin

      You really shouldn't say things like that on Slashdot.
      Now a whole bunch of slashdotters are going to have to go wash off their sticky keyboards.

      -

  • Pandora's box has been opened. I'm excited to see what pours out over the next decades. We all know we need radical new technology to fix the energy crisis and reduce climate gas emissions. Hopefully, we can engineer more efficient organisms, providing clean(er) energy and food for the world's ever-growing population.

    • by gyrogeerloose (849181) on Thursday May 20, 2010 @03:29PM (#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.

      • by vxice (1690200)
        Maybe he is the type who thinks horror movies are too fake looking and wants to see it in real life. I mean once Pandora's box is open you can't close it, or at least the cat is out of the bag so you can't fix the problem so why worry about it? Enjoy the ride because you are getting a front row seat to something of spectacular, destruction you know what ever your thing is, why waste such a good gift.
    • by mollog (841386)
      We all know we need radical new technology to fix the energy crisis and reduce climate gas emissions.

      Let's see, we create a problem with misguided policies and practices. Now we fix said problem with a new, complex technology. What could possibly go wrong?

      This planet will become a barren desert and mankind will vanish. Rightfully so.
  • by interkin3tic (1469267) on Thursday May 20, 2010 @03:48PM (#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: (Score:3, Interesting)

      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.

      I'd say it's life once the constructed bacteria show that they're able to reproduce, and keep doing so for a number of generations (which can take place pretty quickly for bacteria.) Until then it's an interesting piece of machinery.

    • by Dr. Eggman (932300) on Thursday May 20, 2010 @04:55PM (#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!
    • Re: (Score:3, Interesting)

      by Flambergius (55153) *

      Is it life? Yes. It's true that life is somewhat difficult to define, but bacteria lies well within any definition I've heard.

      Did they make it? Well, that's a bit more complex.

      Bacteria is basically a self-replicating machine that has software to encode it's own building instructions. Its software gets replaced, so it won't any more build copies of itself, but rather a different machine. That new machine is also a self-replicating machine, just a different one (down to protein level). Now both machines build

    • by lawpoop (604919)

      but it looks like they basically synthesized an entire bacterial genome

      They didn't really synthesize the DNA; they just cut'n'pasted a bunch of existing DNA and inserted it into a new cell. This is like grafting 100 trees together and calling the conglomeration a synthetic tree.

  • by ArbitraryDescriptor (1257752) on Thursday May 20, 2010 @04:32PM (#32284826)
    Article is unclear on this.

    Because current machines can only assemble relatively short strings of DNA letters at a time, the researchers inserted the shorter sequences into yeast, whose DNA-repair enzymes linked the strings together. They then transferred the medium-sized strings into E. coli and back into yeast. After three rounds of assembly, the researchers had produced a genome over a million base pairs long.

    I read this as:

    Sequencer-> Yeast -> E. coli -> Yeast -> Repeat
    Short segments-> Merged segment -> ? -> ??? -> Full M. mycoides Genome

    • by comm2k (961394)
      Probably amplification of the larger DNA fragments.
    • by Chris Burke (6130)

      They always include E. Coli. Shit happens, you know.

    • Yahknow, I tried to figure this one out myself when I was writing the submission. Physorg doesn't elaborate, but their article has since been updated with the release of an official press release by JCVI [jcvi.org] Curiously, E. coli doesn't appear to be mentioned anywhere on their release. Nor is it on the project's site [jcvi.org], at least at casual glance. Perhaps additional information on the process may be found in one of their fact sheets [jcvi.org] (PDF WARNING!)
      • Re: (Score:3, Informative)

        Ah, thanks for that. From the PDF:

        1. The JCVI team designed specific cassettes of DNA that were 1,080 base pairs long with overlaps of 80 base pairs (bp) at their ends to aid in building the longer stretches of DNA. These were made according to JCVI’s specifications by the DNA synthesis company, Blue Heron Biotechnology.

        2. Then the team employed a three stage process using yeast to build the genome using 1,078 cassettes that are 1,080 bp in length. The first stage involves taking 10 cassettes of DNA at a time to build 10,000 bp long segments. In the second stage, these 10,000 bp segments are taken 10 at a time to produce eleven 100,000 bp long segments. Finally, all 11 segments are assembled into a complete synthetic genome as an extra chromosome in a

        yeast cell, by using yeast genetic systems. 3. The complete synthetic M. mycoides genome is then released from the yeast cell and transplanted into M. capricolum recipient cells that have had the gene for a restriction enzyme removed. Following incubation, viable M. mycoides cells are produced in which the only DNA present is the synthetic genome. These cells are controlled only by that synthetic genome.

        Which then makes sense of the chart which states the sequence as:

        1. Oligonucleotide Synthesizer
        2. Yeast
        3. ?
        4. Extract Complete Genome from Yeast

        1. Oligonucleotides in 1,080 bp cassettes (1,078)
        (Assemble109X)

        2. 10,080 bp assemblies (109)
        (Assemble 11X)

        3. 100,000 bp assemblies (11)
        (Assemble 1X)

        4. 1,077,947 bp

        So I guess the ?? in step 3 is the E. coli, which assembles the 10,000bp segments into 100,000 bp segments, which are finally stitched together back i

  • That's new? (Score:3, Insightful)

    by maxwell demon (590494) on Thursday May 20, 2010 @04:34PM (#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!

  • Ugh (Score:3, Interesting)

    by Greyfox (87712) on Thursday May 20, 2010 @11:28PM (#32288836) Homepage Journal
    I am not learning to program in DNA. That's like the assembly language of the molecular biology world. Could someone come up with a nice ruby module so I can just mixin the traits I want?
  • This will really help when we finally get around to terraforming the galaxy. Instead of sending off a huge Noah's Ark to each one, we'll just ship whatever raw materials can't be found on the new planet and build the lifeforms onsite.

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