Bespoke Life

By Sean Carroll | May 20, 2010 2:16 pm

Synthetic Cell Craig Venter and colleagues have achieved a remarkable milestone: they designed a genome, and brought it to life. More specifically, they’ve synthesized a chromosome consisting of over a million DNA base pairs, and implanted it in a bacterial cell to replace the cell’s original genome. That cell then reproduced, giving birth to offspring that only had the synthetic genome. See the Venter Institute press release, discussion in Nature (pdf), more discussion at Edge, and some background from Carl Zimmer. Update: and here is the paper.

Who knows exactly what this means as yet — but it’s important! You can argue if you like about whether it’s really “artificial life” — that argument has already started, and already seems boring. There are also speculations about designing microorganisms to help us solve problems like global warming or (let’s say) massive oil spills. Not completely crazy speculations, either. But there’s a long way to go before anything like that is coming off a biological assembly line. And eventually we’ll be going much further than that, beyond designer microorganisms into much weirder terrain. This isn’t a culmination, it’s just a start.

CATEGORIZED UNDER: Science
  • Torbjörn Larsson, OM

    I think PZ said it best:

    It’s a very small cell that has been created — the mycoplasmas have the smallest genomes of any extant cells. It’s not much, but this is a breakthrough comparable to Wöhler’s synthesis of urea.

    [Yes, in the process view, the most natural and inclusive, it’s life (and so are viruses). The weakest case is when all the original proteins have been replaced by new ones from the different synthetic recipe – PZ claims ~ 30 generations. The strongest case is that this falls under man made (artificial) evolution, hereditary change, so it’s immediate artificial life.

    … as you said, already boring.]

  • Low Math, Meekly Interacting

    I’d call it an important proof-of-concept, and a very impressive technical achievement on its own, which leaves me bemused by all the hyperbole. The needless references to “artificial life” aren’t so much gratuitous as wholly inaccurate. Once you get down to the level of molecules, DNA is DNA, no matter who or what synthesized it, and if you string together a precise copy of a genome, it IS that genome. True, it lacks the epigenomic factors that make life so interesting, which is more of a limitation than anything, and that’s one of the big reasons why this is so exciting. It’s a little bit like the astonishing successes of mammalian cloning: Stick the blueprint you’ve got handy in a sack of the right stuff, and somehow it all sorts itself out well enough to propagate. So, yes, when people get around to more exotic fusions of genomes, or, if we dare speculate that far in advance, rationally-designed gene products, we know we can probably get it to replicate, all while maintaining an astounding level of control over the genetic recipe. So, truly, hats off to them for what they did. I hope the world at large comes to appreciate what was actually accomplished.

  • Mike

    So I guess it’s time to retire those “Extinction is Forever” bumper stickers and stop worrying about biodiversity.

  • Mantis

    Sean: You can argue if you like about whether it’s really “artificial life”

    What’s to argue? Of course it’s not. It’s an engineered life, a GMO. It’s an interesting technical achievement but no big deal. Hopefully they will now establish a pipeline automatically producing such cells in large numbers for testing, that would be much more useful but I am not sure they have the resources to do it.

    A truly artificial life – one designed from scratch – is completely impossible and will remain that way for the foreseeable future.

  • Josh Neal

    This argument about whether are not this constitutes a truly creative work is going to get as pointless and wearying as the 19th century “art imitates life/life imitates art” debate. One can always argue that any creative work is derived from something else.

    Also, @ Mantis:

    “When a distinguished but elderly scientist states that something is possible, he is almost certainly right. When he states that something is impossible, he is very probably wrong” – Arthur C. Clarke

    “Impossible doesn’t mean very difficult. Very difficult is getting a Nobel Prize; impossible is eating the sun.” – Lou Reed

  • jrad
  • znz

    Elements of the discussion seem like semantics antics.

  • jef

    This video touches on the ethics of categorizing synthetic life as machine or living organism.
    http://www.scienceinseconds.com/video.php?vId=140#comments

  • Sili

    I have yet to tuck into PeeZed’s summary, but the more I read about this, the more it makes me think of heart transplants. It’s significant, but it’s hardly new life yet. But I’ll be looking forward to the artificial heartvalves and cyborg lungs.

  • chemicalscum

    @Sili

    Not as relevant to transplant technology as cloning. You already have an example of your genome – in you. You don’t need to synthesize it from scratch.

    For an organic chemist like myself PZ’s comparison to Wöhler’s synthesis of urea is incisively apt. In the long term who knows where it might lead us.

  • Mantis

    Josh designing life from scratch is not very hard it *is* impossible (now and for the foreseeable future), not in the “eating the Sun” sense, in the “making an integrated circuit with stone age tools and knowledge” sense.

    Synthesizing DNA is simple but DNA alone is as dead as a rock, to make it part of life you need an incredibly complex molecular machinery made of hundreds of proteins and RNA molecules, plus sugars, lipids, aminoacids, etc. Our primitive technology cannot even design a single protein doing some trivial task from scratch, yet to make life you need hundreds of them all precisely coordinated.

  • Sili

    chemicalscum,

    I’m a (failed) chemist, too. And I certainly only meant the transplantation as simile.

  • Josh Neal

    Mantis: you seem to have a very strict definition of life, if you’re going to require “hundreds of proteins and RNA molecules, plus sugars, lipids, aminoacids, etc.” I personally lean more toward the much simpler – and more meaningful – view of life as an autocatalytic feedback loop.

    The *interesting* part of creating life is what was accomplished. You’re right that the boring stuff wasn’t done, but so what? If we discovered a vast alien computer network on Mars, just learning how to operate it would constitute a major advance. People like you would complain that we still can’t build Martian computers. True, but not very relevant. And besides – maybe the computers will provide the information on how to build them.

  • OXO

    It going to be a great idea to design a microorganism which will mop up all the free CO2.. NOT!

  • Pingback: And On The Fourth Day, Venter Said, Let There Be A Press Release « Around The Sphere()

  • amphiox

    A truly artificial life – one designed from scratch – is completely impossible and will remain that way for the foreseeable future.

    You are contradicting yourself, Mantis. Something “completely impossible” will remain so FOREVER. That’s what impossible means – it can’t be done, not now, not ever, not by any means, not with infinite resources, infinite time, or infinite capability.

    If there is even an unforeseeable future wherein it might be done, then it is not impossible.

  • amphiox

    If you use the definite of life as a “self-organizing system capable of undergoing Darwinian evolution”, then we already have made artificial life. And it is truly, completely artificial because it only exists in an artificial environment.

    It’s called a computer virus, and it has already escaped our control and run amok.

  • Zwirko

    Josh, you don’t need to design the entire cell from scratch – the DNA will do that for you. Venter’s cell will be be composed entirely from products that were encoded by a synthetic genome after around 30 generations. Does that make it truly synthetic? Does it even matter? Why even bother doing it any other way?

  • Mantis

    Zwirko: “…Does that make it truly synthetic?”
    No, since the DNA is natural with only slight modifications and rearrangements.

    Zwirko: ” Does it even matter?”
    Of course, it means you cannot use the cell to do anything you want, you are limited to genes found in nature and their modifications. This is a critical limitation from practical POV.

    Zwirko: “Why even bother doing it any other way?”
    Truly synthetic life if mastered would be of incredible utility, it could be used to produce or recycle any substance you want, it could produce electrical energy directly by photosynthesis, It could be made more resistant or even immortal if needed, it could be made to interface with electronics, really it could be tailored to any task imaginable.

    Natural life is incredibly impressive but it simply isn’t tailored to human needs (well, humans are to some extent).

  • Zwirko

    I think your getting confused by the use of the phrase “truly synthetic”. You simply don’t need to create everything from scratch. All Venter has done is use a pre-existing cell to “boot up” his synthetic genome. In a few days that cell will contain little or no components from the original.

    Taking the experiment further and actually designing the entire genome to do what you want, then after a few days the cell will no longer be recognisable as the original “shell” that you used to boot up your designed genome.

    I was trying to address the complaint that it’s not really synthetic since the genome-less cell you transplanted into was not synthesised. What Venter’s synthetic genome encodes is not really an issue as to whether its synthetic or not for it would be a completely trivial matter to stick a whole bunch of any genes you so desired into that genome.

  • Mantis

    Zwirko, you don’t seem to understand that we cannot as you say “design entire genome to do what we want,” that is the whole problem. We cannot even design a single working protein(!), much less a whole genome. The only reason Venter succeeded is because his synthesized a copy of a natural genome.

    This of course invalidates your argumentation, even after many divisions the cell remains natural since the genes and their products are exactly the same as those of the natural bacterium.

    And while sticking a whole bunch of any genes you desire into a genome is relatively easy (although it still took Venter and company many years) making such genome work is a completely different matter, for that the genome has to contain a precise mix of hundreds of natural genes such as ribosomal proteins, tRNAs, rRNAs, metabolic enzymes, polimerases, replication machinery, and so on, so again contrary to what you say it is in fact *critical* what Venter’s synthetic genome encodes.

  • fatkid

    Water and carbon, lifes building blocks, came to earth aboard meteorites and comets. If life happens thru the slow grind of nature, why not in a controlled lab?

  • Zwirko

    Mantis, I understand perfectly. The sole point I was making, and what you seem to be not seeing, is that the distinction between what is synthetic and what is not synthetic is not how you are defining it. Whether the genome is a copy of another is not relevant. Whether it’s transplanted into a pre-esxisting cell or not is not relevant either. The genome was synthesised from sequences held in a computer. The biochemistry of the resultant cells – including the rRNA’s, tRNA’s, replication machinery, structural proteins, enzymes and so on – are all products of, and regulated by, the synthetic genome. It is synthetic in every way that is meaningful. It is synthetic.

    The second point I was making is that for applications of this sorts of biotechnology there is no need at all to make everything from scratch. It would be entirely pointless. If we want to make a cell that converts one substance into another and secrete the products for industrial use, then then there is no need to make everything from scratch – we simply take the genes from other organisms. For example, the synthetic genome already produces a reporter protein product. There is no need to design every single gene and figure out how to regulate them all.

    Venter’s project has produced a synthetic cell. I don’t see what you are arguing about here?

  • amphiox

    Mantis, I disagree with how you define “synthetic”. An exact copy of something natural that is made by humans is still synthetic. “Synthetic” diamonds are exactly the same as natural diamonds in their chemical and crystal structure. “Synthetic” insulin is exactly the same as natural insulin.

    They are called “synthetic” because they are made by humans, using human developed technology.

    So you cannot say this is not “synthetic” just because it is a near exact copy of something that already exists naturally. Synthetic = “made by human technology”, and whether or not it is a copy of something else that already exists nature doesn’t matter one bit to the definition.

    Your arguments make somewhat more sense with respect to the question of whether or not this counts as “artificial”.

  • Mantis

    You are mistaking DNA for the genome, DNA is just a carrier, genes and genomes are information and information is only synthetic if it is invented by humans. Information in the genome used by Venter is natural – it’s origin is Nature – and it is this information that defines life, so the resulting bacterium cannot be considered synthetic by any stretch of the word.

    The fact that you copied the information doesn’t make it synthetic, just as the fact that you copied a song doesn’t make you the author.

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Cosmic Variance

Random samplings from a universe of ideas.

About Sean Carroll

Sean Carroll is a Senior Research Associate in the Department of Physics at the California Institute of Technology. His research interests include theoretical aspects of cosmology, field theory, and gravitation. His most recent book is The Particle at the End of the Universe, about the Large Hadron Collider and the search for the Higgs boson. Here are some of his favorite blog posts, home page, and email: carroll [at] cosmicvariance.com .

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