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Biotech Science

Startup Offers Pre-Built Biological Parts 71

Posted by kdawson from the we-can-assemble-it-for-you-wholesale dept.
TechReviewAl writes "A new startup called Ginkgo BioWorks hopes to make synthetic-biology simpler than ever by assembling biological parts, such as strings of specific genes, for industry and academic scientists. While companies already exist to synthesize pieces of DNA, Ginkgo assembles synthesized pieces of DNA to create functional genetic pathways. (Assembling specific genes into long pieces of DNA is much cheaper than synthesizing that long piece from scratch.) Company cofounder Tom Knight, also a research scientist at MIT, says: 'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"
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Startup Offers Pre-Built Biological Parts More

Startup Offers Pre-Built Biological Parts

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  • So, to reprise a previous question, in an improved form...

    If we synthesize a living organism in totality, does Common Descent become untrue?

    If so, how will we know when Common Descent became no longer true?

    • Haha, what? If we managed to synthesize a completely new organism then any offspring it would have would be descended from those first organisms. Simple concept.

    • Re: (Score:2)

      by jfengel ( 409917 )

      If we synthesize a living organism in totality, does Common Descent become untrue?

      Common descent will have been true, which is the important part. It's a fundamental part of evolutionary history, crucial to understanding what has gone before.

      There's no reason that this planet couldn't have had several parallel threads of common descent. It would have made evolutionary history harder to unravel, adding more noise to a signal that turned out to be pretty clear once we found it.

      It means that future biologists will find the state of evolution on this planet harder to untangle, but that's t

  • I'm ready to place my order (Score:5, Funny)

    by Anonymous Coward on Tuesday October 06, 2009 @01:06AM (#29653931)

    5' 5", 110lbs, female, further details can be found in attached magazine. Do you give volume discounts?

  • Seems that ordinary people may soon be able to do synthetic biology. No wet lab required.

    I could imagine getting into that. Design a few "circuits", send away for them to be built, unpack the slides and.. expose em to ultraviolet light and see if they turn yellow, I guess.

    • Yeah, then your average idiot [slashdot.org] could then order away the correct parts for a virus, either knowing or not knowing what he was doing, and end up really screwing things up. This type of stuff will be difficult, if not impossible to control. I'm not optimistic.

  • Building blocks (Score:5, Funny)

    by cjfs ( 1253208 ) on Tuesday October 06, 2009 @01:10AM (#29653949) Homepage Journal

    The key innovation of the BioBrick assembly standard is that a biological engineer can assemble any two BioBrick parts, and the resulting composite object is itself a BioBrick part that can be combined with any other BioBrick parts.

    Sounds great in theory. In reality, you'll always be missing one of those stupid little yellow bricks and they won't sell them individually.

  • Oh Great (Score:1, Funny)

    by Anonymous Coward

    So instead of "enlarge your penis" emails we will get "get a larger penis" emails.

  • Obligatory reference: (Score:3, Funny)

    by shacky003 ( 1595307 ) on Tuesday October 06, 2009 @01:37AM (#29654065)
    Do the founders wear bras on their heads?
  • TFA:

    I'm interested in transitioning biology from being sort of a craft....to an engineering discipline with standardized methods...

    Good! Geneticists would benefit from getting smarter. Anybody taken a look at Monsanto's work? I don't think "train wreck" quite captures the epic fail quality they've managed to achieve.

  • I want my monkey-man!

  • Plasmids kinda do this already. (Score:3, Interesting)

    by mauthbaux ( 652274 ) on Tuesday October 06, 2009 @02:15AM (#29654197) Homepage

    'I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.'"

    To some extent, this is already done with common bacterial strains, and the plasmid vectors we already use. Most of the plasmids we use in the industry have specific sets of features such as multiple cloning sites, inducible repressors, ORIs, antibiotic resistance sites etc... You need a plasmid that has a kanamycin resistance gene, high copy number, will add a His tag to your product, and lacks cut sites for a particular restriction enzyme? It's likely in the catalogues already. And if what you're trying to assemble is already in the catalogues, it's a target that may not be worth pursing anyway, since you're unlikely to get a publication or a patent off of it.

    The approach he seems to be pushing here seems to be analogous to buying a car piece by piece rather than as a pre-assembled package. The difference is that while average joe has no idea how to fabricate a synchro for his transmission, your average molecular biologist is already quite adept at designing primers and cloning fragments out of a cDNA library. The hard part for the scientists is then characterizing, validating and optimizing the expression of their target; and then later demonstrating the functionality of the product. To continue the analogy, it would be showing that the car ran, was reliable, and was safe for the passengers. Having readily available gene circuits (the famous lac operon for instance) may help with the planning and initial development, but it really won't speed up the bulk of the work we do.

    I'll readily admit that many of the expression/knockout constructs are somewhat ad hoc in nature, but interoperability isn't typically a concern. The thing is that evolution is a pretty laissez faire system where "duct tape and bailing wire" construction is more often the rule than the exception. Nature cares about what works, not about what conforms to standards (codon-amino acid translation being the biggest exception that comes to mind). As a result, expression systems have to be tailored to the organism that they'll be expressed in. For instance, bacteria cannot express functional mammalian genes unless the introns are removed from the sequence first. Sufficiently large yeast proteins will cause an immune reaction because the glycosylation patterns are recognized as foreign. Many genes won't be expressed very well at all unless the regulatory elements in the flanking sequences are also included. Once you start looking at things like inducible expression and tissue-specific expression, things get even more complicated, and more varied between species. In short, it's complicated, and the idea of instituting standards to achieve interoperability between expression systems is pretty much a pipe dream.

    In short, I have my doubts about the plausibility of this plan, and I'll be mighty impressed if he pulls it off.

    • Re:Plasmids kinda do this already. (Score:4, Informative)

      by QuantumG ( 50515 ) * <qg@biodome.org> on Tuesday October 06, 2009 @07:00AM (#29655329) Homepage Journal

      Wow. Retarded reply gets modded up to the highest post.. I'd be surprised, but hey, it's a non-IT article on Slashdot.

      How would you feel if I told you that teenagers have been using biobricks to do some of this "pipe dream" stuff for about 10 years now. That there's an annual international competition to showcase what they come up with and that has been running since 2003? That biobricks are a standard part of genetic engineering of microbes for industrial use? That basically everything you said was so horrendously outdated and ignorant that you sound like someone talking about the impossibility of heavier than air flight in 1913.

      I know things have been bad around here for a long time and we've all come to just accept it, but would it be too much to ask that the moderation system undergo a little bit of review? I'm gunna ask the Taco.

  • Old news. (Score:3, Informative)

    by Hurricane78 ( 562437 ) <deleted&slashdot,org> on Tuesday October 06, 2009 @02:35AM (#29654269)

    It's called "bio bricks", and it's old news.

    I read about before 2006.

  • brrr... (Score:3, Interesting)

    by arcite ( 661011 ) on Tuesday October 06, 2009 @03:18AM (#29654411)
    You not come here! Illegal!

    I just do eyes. Just - just eyes. Just genetic design. Just eyes!

  • Good luck (Score:1, Insightful)

    by Anonymous Coward

    "...transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things."

    Like Software Engineering, then. Good luck with that. -j

  • I'm interested in transitioning biology from being sort of a craft, where every time you do something it's done slightly differently, often in ad hoc ways, to an engineering discipline with standardized methods of arranging information and standardized sets of parts that you can assemble to do things.

    Well, that's nice. I want a pony, too. But that's not how biology works.

    In fact, it's not even how engineering works anymore.

    A century ago, people built big things from small numbers of standardized parts. P

    • Re: (Score:2)

      by Rand310 ( 264407 )

      At the moment, biology is where engineering was a century ago. We NEED standardized parts. We have lots of ground that we could cover very quickly if we didn't have to reinvent the wheel each time we wish to make a small machine.

      We now know there are all these different parts. We want to put them together into small mini-machines with anywhere from 2 to 10 parts working together or so. But each one has to be taken from different sources, put together in a completely arbitrary and new manner in order to

  • ... will notice again how biohazardous materials can be built from these parts and everybody will start panicking at the new tech.

  • The next millionaires?

  • I have a strange desire to have a bunch of 3 inch long cats, as smart as regular cats, smaller brain cells, I guess, all optimized to breed true and live long and prosper. Why? I have this desire to have about 100 of them as pets and be a catherd.
    Can you imagine sitting down with 100 of them all over you, little tiny whiskers, higher frequency purrs. Have to keep them in, I guess, or they would take over

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