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Biotech Science

DIY Biologists To Open Source Research 147

Posted by Soulskill
from the meatware-hacking dept.
destinyland writes "Falling costs and garage tinkering are creating a grass roots movement of amateur biologists whose research is more transparent than that of academia. They are building lab equipment using common household items and even synthesizing new organisms, and their transparency also allows the social pressure which creates more ethical research. DIY Bio.org fosters lab co-ops for large equipment and provokes important discussions. (Would it be ethical to release a homegrown symbiote that cures scurvy in hundreds of thousands of people?) This movement could someday lead to bottom-up remedies for disease, fuel-generating microbes, or even a social-networked disease-tracking epidemiology. 'In much the same way that homebrew computer science built the world we live in today, garage biology can affect the future we make for ourselves,' argues h+ magazine, which featured the article in their summer issue."
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DIY Biologists To Open Source Research

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  • by nbauman (624611) on Saturday June 20, 2009 @01:57PM (#28403101) Homepage Journal
    From TFA http://hplusmagazine.com/articles/bio/darning-genes-biology-homebody [hplusmagazine.com] :

    h+: There has been a lot of discussion about the dangers of people doing this sort of research at home. Do you think this is over-exaggerated?

    MP: I really do. The chances of someone accidentally creating a dangerous organism and the chances of it surviving in the environment outside a laboratory are vanishingly low.

    Rudy Rucker has a great quote on that, "I have a mental image of germ-size MIT nerds putting on gangsta clothes and venturing into alleys to try some rough stuff. And then they meet up with the homies who've been keeping it real for a billion years or so." The bare facts of it are that there's nothing random about synthetic biology research. When we design a transgenic organism, we're deliberately adding one specific piece of new functionality, maybe a small pathway that leads to a new piece of functionality -- and the organism has to expend energy on producing the new proteins that those new genes code for. Because of this, the synthetic organism is necessarily less competitive than its wild-type relatives who are much better suited for the niche they already occupy in the environment.

    So any accidental release is fated to die out within a few generations, because itâ(TM)s just not competitive enough.

    That's right. When rabbits were introduced in Australia, they died off right away because they were less competitive than their wild-type relatives who were much better suited to the niche they already occupied.

  • by Daniel Dvorkin (106857) * on Saturday June 20, 2009 @02:08PM (#28403167) Homepage Journal

    False analogy. Rabbits were introduced to Australia from the outside, and they were the product of evolution (in an environment much harsher and more competitive than Australia's) not deliberate genetic engineering. If rabbits had been bred from some native Australian animal, and had then turned into the plague they are today, your point would make more sense.

  • by Vesvvi (1501135) on Saturday June 20, 2009 @02:16PM (#28403225)
    It's true that it's possible to accomplish a great deal of biology/biochemistry research using just basic tools: I would say that the single greatest analytical tool in biochemistry is the polyacrylamide gel [wikipedia.org], which can be produced and used with no real specialized training or tools.

    However, we're moving away from such "crude" techniques towards more sophisticated analytical tools, since in many ways biochemistry is now technology-limited. Single-molecule work, such as that pioneered by Carlos Bustamante [berkeley.edu] provide insights that would never be possible with classical methods, and on the other end of the spectrum, we're now working on characterizing the entire network [wikipedia.org] of small metabolite molecules simultaneously and quantitatively [scripps.edu]. This kind of work just isn't easily carried out by amateur enthusiasts.

    That said, there is certainly quite a bit of research that DIY biologists would be capable of performing, especially considering that they could have access to the same kind of resources that professionals do. For example, after amplifying a gene, no researcher will sequence it themselves: it's shipped of to a specialized lab that will do it, for a fee. That sequencing step requires equipment and expertise that's at a higher level than even the pros don't have.

    But regardless of theoretical ability, the professionals retain the advantage that it is their job to work on these projects. The time they can dedicate to their work will be far greater than someone who does it as a hobby.

    Back to the subject of "openness", the professional scientific world isn't nearly as closed-off as the article would have you believe. It is true that there is a persistent fear of being "scooped", but the standards are changing for staking your claim on a particular piece of research.

    It used to be that a full manuscript in a scientific journal was the only thing sufficient to get credit for something. Now, people are gradually embracing online resources are a valid way to communicate, and by extension, to prove that they were the source of any particular bit of publicized material. Even non-finalized material is now more common to make public: Nature has a pre-publication [nature.com] online source for publishing findings, and there are journals devoted entirely to negative results, which was previously unheard-of.

    The walls are coming down, it's just a question of finalizing the transition, and winning over the old guard.

    Disclosure: I am a professional research scientist, one of the younger ones. I have a substantial hardware/software project in the works, which will likely be simultaneously published via classic journal, online website, and software via SourceForge.

  • Not biochemists (Score:5, Interesting)

    by MaizeMan (1076255) on Saturday June 20, 2009 @02:32PM (#28403351) Homepage
    I think you may be drawing too direct a comparison. It used to be that cloning a gene responsibly for a known phenotype was enough for a significant publication. (That was before my time). Now to get prestige in academia you need to map out the surrounding regulatory networks or at least do a lot more work to characterize WHY gene X is creating phenotype Y. I assume the level of complexity required to publish has expanded similarly in biochemistry

    I see the benefits of this DIY work as twofold. First, a huge fraction of genes (in my field, plant biology) are still annotated only as unknown function. Figuring out those functions may not be the path to a career of academic fame and fortune, but I'd really appreciate any group of people who start making a dent in them. But I doubt they'll do a lot of this, they sound a lot more like synthetic biologists. So secondly, in the field of synthetic biology right now a lot of the work being done is very conservative. For example reconstituting a photosystem from an algae in another microbe. If that works it'll be really cool, and tell us a lot about the genetic regulation involved in the process, but it's not as risky as a lot of things these garage biologists are doing. Not risky in a threat-to-human-life-as-we-know-it way obviously, but risky in a this-probably-won't-work way. You try telling a grad student "here's your thesis project, there's a 90% chance it won't work and after four years in the lab you'll have nothing to show for it, you won't publish, you won't graduate, but good luck with that."

    People in garages can afford to fail, and that means they'll potential develop a few useful things that would have been easy to do in a professional lab, but appeared so improbable no one would want to gamble on them.

IF I HAD A MINE SHAFT, I don't think I would just abandon it. There's got to be a better way. -- Jack Handley, The New Mexican, 1988.

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