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Biotech Open Source Science

Open Source Software Meets Do-It-Yourself Biology 113

Posted by Soulskill
from the releasing-your-genome-under-the-gpl dept.
destinyland writes "This article profiles a growing movement — DIY biology — that's made possible in part by open source tools. Using programs like BioPerl and BioPython, DIY biologists write their own code (computer and genetic), designing their own biological systems and altering the genome. A protein-folding simulator, Folding@home, is now the most powerful distributed computing cluster in the world, and as the movement evolves, cooperatives are also springing up where hobbyists pool resources and create 'hacker spaces' to reduce costs and share knowledge. 'As the shift to open source software continues, computational biology will become even more accessible, and even more powerful,' this article argues — while intellectual property and other bureaucracies continue to hobble traditional forms of research."
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Open Source Software Meets Do-It-Yourself Biology

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  • Depends (Score:3, Insightful)

    by robbyjo (315601) on Tuesday January 26, 2010 @12:45PM (#30907022) Homepage

    Many of these biology experiments require very expensive machines, such as microarray machines, as mentioned by the article. I don't know if purchasing refurbished machines is a wise choice since we don't want data quality to be compromised. Also, don't forget about service plans when the machines break or producing inconsistent output. Not to mention various reagents, other chemicals, and supplies such as microarray chips that make the experiment yields high quality data. These easily reach hundreds of dollars a piece. Also, purchasing such chemicals will get you labeled as a terrorist.

    Another issue is gathering the samples. If you're collecting yeast, that would be simple. Arabidopsis, other small plants, mice, or other small animals, you probably need quite some space. Humans? That won't be simple at all. You have to clear privacy issues, getting the research review board to sign papers, etc. Sample collection alone can cost you lots of money and time. You can always resort to publicly available data. But chances are that you won't be able to impress scientists much for going that route. Also, most of the important discoveries are already done on this data. Most likely, all you can do is to confirm existing results or to provide some tangential additional info.

  • Re:Uhhh... (Score:5, Insightful)

    by fuzzyfuzzyfungus (1223518) on Tuesday January 26, 2010 @12:47PM (#30907050) Journal
    On the plus side, doing dangerous things that are more dangerous to others than to yourself is substantially harder than just doing dangerous things.

    Until we get to the point where you can just buy a programmable matter synthesizer with a voice interface that will accept the command "50grams aerosolized anthrax, weapons grade" the only real danger of DIY Biology will be a few scientist wannabees ending up in the ER on a stiff antibiotic drip after spilling the wrong bacterial culture on themselves.

    DIY Bio is novel, and sciencey, which makes it OOH Scary; but, if you just want to hurt some people, good old-fashioned all-american firearms are way easier, cheaper, and substantially more refined.
  • Any progress? (Score:5, Insightful)

    by vlm (69642) on Tuesday January 26, 2010 @12:49PM (#30907092)

    Any progress since the last time this was on slashdot? No? Thought so.

    Downloading computational biology software, that you have no idea how to use, makes you a molecular biologist, the same way that downloading finite element analysis software that you don't know how to use, makes you a mechanical engineer, downloading a SPICE simulator that you don't know how to use, makes you an electrical engineer, or downloading Pr0n that you can't re-enact makes you a sex expert. At least the Pr0n is easier to apply than a FEM or SPICE package, it being a "pictorial diagram", the disadvantage being that it requires a member of the appropriate sex (and species!) to re-enact.

  • Re:Uhhh... (Score:2, Insightful)

    by izomiac (815208) on Tuesday January 26, 2010 @12:55PM (#30907182) Homepage
    Meh, most lab research in biology fail on the first few attempts. DIY biology is likely to have an even higher failure rate, especially with stuff that hasn't been done a thousand times before. Beyond that, if grey goo or a super bug was feasible the natural bacteria would've done it ages ago.
  • by mollog (841386) on Tuesday January 26, 2010 @12:57PM (#30907204)
    This concept of DIY biology is far, far older than science, itself. People have been manipulating livestock, crops, even our own genome, for a long time now. But the author of this article is right about new tools making the process that much more accessible and powerful.

    The build-out of world trade over the last century has wrought some damaging changes to the world ecology. Invasive species, pernicious plant diseases, and the like are spreading world-wide. Government efforts in this realm have been sporadic and often do more harm than good. The ability of smaller, private organizations to conduct sophisticated science on a smaller budget will be a boon to the restoration of endangered species, for example.

    But, I tagged this article with the whatcouldpossiblygowrong tag. Danger ahead.
  • Re:Any progress? (Score:5, Insightful)

    by laughingcoyote (762272) <barghesthowl.excite@com> on Tuesday January 26, 2010 @01:03PM (#30907286) Journal

    Sure. And downloading an IDE you have no idea how to use doesn't make you a programmer, either. But it can certainly be a good first step in that direction. Knowing how to use those tools properly is part of what a (molecular biologist|mechanical engineer|electrical engineer) does, so if you're interested in doing that, you'll want to learn. The way to learn something complex is to see it, fumble around with it, make some mistakes, figure out what caused them, take a look at the documentation, mess up again, take another look, and so on. How will you ever start that process without first getting your hands on the tool?

  • by the gnat (153162) on Tuesday January 26, 2010 @01:09PM (#30907362)

    Vijay Pande is a Stanford professor and funded primarily by the same agencies that fund most of the biomedical research in this country - most importantly, the NIH. (Disclaimer: they fund my work too.) He has full-time scientists (i.e. people who spent most of their 20s in school) and computer engineers writing code and assistance from hardware vendors (ATI/AMD and NVIDIA, at least). FAH is a great example of how to leverage distributed computing resources and volunteer effort, and it's an excellent technical solution to what is potentially a very expensive problem, but the intellectual effort is *not* distributed. I don't mean any of this as a criticism (I wish I had five petaflops at my disposal too), but this is not an example of "hobbyists" performing research free of bureaucracy. (In fact, the umbrella project for much of Pande's work now has a relatively large bureaucracy at Stanford, which surely wasn't suffering from a lack of bureaucracy to begin with.)

  • Re:Uhhh... (Score:3, Insightful)

    by Chris Mattern (191822) on Tuesday January 26, 2010 @01:14PM (#30907432)

    I actually flagged this article "graygoo" myself, but in fact, it's not as likely as a lot of people think. The microbial ecology of the earth is a battlefield, with each micro-organism looking to expand its niche at the expense of others. Our would-be gray goo organism isn't going to take over the earth--it's going to get mugged for its lunch money and its carcass eaten by whatever can find nutrient value in it.

  • Re:Uhhh... (Score:3, Insightful)

    by PitaBred (632671) <slashdot@pitabre ... org minus distro> on Tuesday January 26, 2010 @01:20PM (#30907498) Homepage

    Why would anyone write computer programs for fun? Fun is completely in the eye of the beholder

  • Kidding, right? (Score:4, Insightful)

    by Corson (746347) on Tuesday January 26, 2010 @01:27PM (#30907610)
    "many DIYers knowledge of these fields is so complete that the best among them design and conduct their own experiments at stunningly low costs. With adequate knowledge and ingenuity, DIYbiologists can build equipment and run experiments on a hobbyist's budget." That must be a (bad) joke. Forget the open-source/custom-made software and discount price hardware acquired on eBay, biology is first and foremost about wet lab. And not only it costs *a lot* but one needs licenses to purchase certain products. I have worked in biomedical research for almost ten years and I know that if you're in academia then you can purchase, say, enzymes and genetic vectors at their catalog price; but if you're industry then you get hit with 5-6 digit licensing fees. The only way to do at home what they claim to be doing is by using stuff from their academic research labs. Besides the risks involved (those cell line are actually cancer cells and engineered bacteria are mutant germs, not to mention the radioactively labeled nucleic acid probes that might end up in the toilet) the logistics are a nightmare. Storing liquid nitrogen in your basement? Discarding ethidium-bromide and acrylamide gels? Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days. Drosophilla flys can't be frozen like bacteria. How do you discard biohazardous materials and mutagen/teratogen substances at home? There are many reasons why DIY biology is a very bad idea; it's a disaster waiting to happen.
  • Re:Uhhh... (Score:3, Insightful)

    by interkin3tic (1469267) on Tuesday January 26, 2010 @02:17PM (#30908452)

    Probably a bit pedantic, but grey goo [wikipedia.org] means nanobots out of control. You're thinking of biological threats, like artificial superflu or ebola reston [wikipedia.org] mutated to become pathogenic to humans or something similar, which I guess would be green goo?

    Grey goo technically wouldn't be a product of DIY biology, that would be DIY nanotech.

    Probably a bigger concern is invasive GMO taking over, but this I think is a bigger concern from say Monsanto, which has more money to put into making GMOs and seems a lot less concerned with ethics or long term consequences than individual researchers. If they were to find some genes that allowed plants to outcompete any wild plant, and it got out into the wild, it might be difficult/expensive to contain. Outside of several plant labs you can find Arabidopsis [wikipedia.org] that "got out", some could be harmless GMOs. I could easily see monsanto making a superplant arabidopsis and then being careless with the seeds.

    I should state that I'm not a plant biologist, don't work at monsanto, and have no idea what if any legal or technical restrictions are in place to prevent that, they could be good ones. I'm just saying I'm more worried about dangerous biological threats coming out of corporate labs than someones garage.

  • by Grond (15515) on Tuesday January 26, 2010 @02:48PM (#30908806) Homepage

    In fact, I'd be all for a general extension to patent law to explicitly allow violation of any patent for the purpose of non-commercial research where any devices made in violation of a patent are not sold or distributed.

    What's the need? If the research is non-commercial and no infringing products are sold or distributed, why would the patentee bother suing? It's non-commercial, so the defendant probably has little money and it would likely be a PR disaster. They didn't sell or distribute any infringing products, so damages are likely to be minimal. These are the main reasons why non-profit research is already basically in the clear.

    So why not go ahead and codify the de facto research exemption into the law as you suggest? The reason is that it would be exploited like crazy (see the FDA safe harbor for an example). Companies would set up non-profit research arms to do their research, license-free, and then bring the results to market. It's very difficult (maybe impossible, given powerful corporate interests) to design a law that's narrow enough not to be exploited, broad enough to achieve its goal, yet also doesn't invite litigation or burdensome regulatory oversight.

  • Re:Kidding, right? (Score:3, Insightful)

    by Hatta (162192) on Tuesday January 26, 2010 @03:29PM (#30909342) Journal

    The only way to do at home what they claim to be doing is by using stuff from their academic research labs.

    Not really. You can get E. coli that express recombinant enzymes and purify it yourself. And patents don't cover stuff for personal use, so you're clear there.

    Besides the risks involved (those cell line are actually cancer cells and engineered bacteria are mutant germs

    None of which have a chance to survive outside of carefully controlled laboratory conditions.

    not to mention the radioactively labeled nucleic acid probes that might end up in the toilet

    I doubt anyone's using radioactive probes at home, probably more fluorescence, chemiluminescence, etc.

    Storing liquid nitrogen in your basement?

    Not really a problem if you pony up for the right container.

    Discarding ethidium-bromide and acrylamide gels?

    There are non-toxic stains for agarose gels. Polymerized acrylamide is not that toxic either.

    Biological experiments are different from software development, they need follow up and supervision through the end, which may take 2-4 days. Drosophilla flys can't be frozen like bacteria.

    For people dedicated to the hobby, there's no reason they can't deal with that.

    How do you discard biohazardous materials and mutagen/teratogen substances at home?

    This is a valid concern. The best way is to find ways to perform experiments that don't require hazardous materials. There is a lot of biology that does require hazardous materials, but there's also a lot that doesn't.

  • by martin-boundary (547041) on Tuesday January 26, 2010 @05:32PM (#30911046)
    Your linked paper is a report by a bunch of non-lawyers asking working scientists whether they think their work is adversely affected by IP law, and you consider that useful why?

    We already know that most people break IP laws all the time, often without realizing it. Would you also quote a paper that claims the copyright threat is overblown, because the vast majority of music downloaders self-report that they aren't being sued?

    The real problem is that the IP laws exist in the first place: they are a Sword of Damocles [wikipedia.org] upon researchers, whether they look up or not.

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