Individuals are applying the principals of open source software to the worlds of do-it-yourself biology and synthetic biology.

The time of the amateur dilletante scientist seems to be over. It takes the huge, collective organisation of private individuals to challenge this monopoly. GNU/Linux has managed to make a significant challenge but what of open science, not just the actual use of free software as practised by CERN but utilizing the whole philosophy of organizing scientific endeavour on the principles of open source? Some amateur biohackers think they have the answer.

It is early days but perhaps it is only a matter of time before some biological Linus Torvalds sends an e-mail to say that he or she is working on a project but that it won’t be big or professional—and the rest will be history. Many biohackers have clearly been watching the growth of free software communities facilitated by the internet. In an interview with Seed Magazine Mac Cowell, the founder of DIYBIO, saw the obvious parallel:

"I was disappointed with the huge barrier of entry for average people, or for anyone who wants to get involved but is not already in a PhD program. The open-source computer-programming movement became ubiquitous, and computers became a platform that enabled a huge amateur or hobbyist culture of people to push the field further. Many people got organized and started working on projects collaboratively. So why can’t we do that with biology? Why does all biology happen in academic or industrial labs? What’s the barrier to entry for doing something interesting in biology? It’s a four- to seven-year PhD program. There must be another opportunity"

He’s right. Peer reviewed science has become a synonym for getting you papers accepted and published by the ruling orthodoxies. Just try and get a scientific paper published challenging any aspect of the global warming industry and see how far you get. And publication is the key to academic tenure and career progression. Using free software and deploying the principles of open source, no such constraint exists. How many good ideas and projects in the sciences have been stillborn because they were either not fashionable or offended the vested orthodoxies of the day, and what progress has been stymied by a kind of scientific, vendor lock out?

Peer review is one of the core principles of all branches of science but it can be and has been abused, especially in the field of climate change where some of the abuses constitute an absolute scandal and corruption of science itself. Peer review can cause bottlenecks too. Valuable data which could be read, used and tested by others sits for a period of months or a year or more awaiting acceptance and publication in some learned journal. Prior to the ubiquity of the internet that bottleneck virtually went with the territory, but the web has been as effective as a plumber in unblocking it and opening up possibilities for amateur biohackers. We will never know how many potentially great ideas or concepts never saw the light of day because of office politics or vested financial interests. You need only think of Microsoft to know what I’m talking about.
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In the spirit and terminology of the free software community they march under the banner of the mantra, OpenWetWare. Inevitably, these citizen scientists are sometimes called biohackers. I’ll try to avoid using that term as it has negative and misleading connotations. These guys are the whitehats who want to democratise science (I don’t mean dumbing down here. Many, if not most, will almost certainly be products of third-level education), not hack into a biolab database and steal critical data. They want to create their own data and just like Steve Jobs did, they’re doing it in the garage. Literally.

One citizen biologist is trying to modify Jellyfish genes and adding them to yoghurt to detect the presence of Melamine (which was implicated in contaminated baby milk in China). She intends, if successful, to release the design into the public domain. Another citizen scientist in the Unites States has a lab no bigger than one square metre in which she conducted synthetic biology experiments to engineer a microbe capable of performing simple logical operations which presages the idea of biological computing. Clever, but she was beaten to the first prize by another enterprising bio-citizen who designed a bacteria to enable rice plants process nitrogen more efficiently, in a competition run by the science fiction website, io9. Where do these so called garage geneticists get their technology and raw material? Many pick up basic equipment on eBay. As for materials, they have something akin to GNU/Linux software repositories on which to call. MIT has a registry of standard biological parts called biobricks. The remit could almost have been written by a Stallman clone:

"The Registry is based on the principle of “get some, give some”. Registry users benefit from using the parts and information available from the Registry in designing their engineered biological systems. In exchange, the expectation is that Registry users will, in turn, contribute back information and data on existing parts and new parts that they make to grow and improve this community resource."

That’s Freedoms number two and three in anyone’s language Not surprising really, for while Biobricks has no formal affiliation with the FSF, two of its members do. The FSF approves many licences, including the GPLv3, but as yet the Biobricks Foundation (BBF) has not opted for a species of viral licence, though it has taken Science Commons, an offshoot of the Creative Commons, as the basis for developing a legal framework for its activities. You’ll see a link to it on the CC website, listed as one of its programmes. That said, the thinking behind all this is not just quite as ideologically driven as it is for the FSF. It is there but, like free software, there is a desire to accelerate change and invite non-corporate expertise across the distributive medium of the web which is not just changing the world of software but the whole way we all do our business, research and leisure activities.
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The BBF may not feel the need to slay any biological equivalents of Microsoft but the effect of what they advocate and practice is to implicitly undermine the outdated methodology of their software development model, based as it is on proprietary code and moving to a model of rented software and software as a service (SaaS). One of the best and most interesting takes I have read on these issues to date is a Ph.D thesis on open source biotechnology by Janet Hope which is available an an online PDF. It is particularly good on discussing the biological equivalents of the GPL, copyleft and what constitutes source code and binaries (as it is perhaps a little disingenuous to call molecular biology software or DNA code, unless you agree with Richard Dawkins that human beings are wetware and evolution is the software that does the debugging). Highly recommended. Also highly recommended is an introduction to science commons by John Wilbanks and James Boyle which is particularly good at eliciting the problems with “proprietary” science and how they can inhibit the rate of progress, discovery and application—in the same way that proprietary software militates against better coding and distributive free software models like GNU/Linux.
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They seem oblivious that much of modern technology is based on earlier science motivated by people’s insatiable curiosity. Thank God J.J.Thompson discovered the electron when he did (1897) and was not submitted to a board of accountants and business executives demanding he give a presentation on the profits to be made from his curiosity. What Thompson and others began, lead, ultimately, to radios, televisions, lasers and… computers. They exploit quantum tunneling which is a direct result of quantum theory. And thank God no one demanded that Richard Stallman or Linux Torvalds submitted viable business models (won’t be big or professional Mr. Torvalds? Couldn’t possibly fund that). Stallman could only do what he did because he quit MIT to pursue his own ideas about software freedom—and look where we are now. It seems that those who have science budgets by the throat, like Microsoft, know the price of everything and the value of nothing. In their blinkered short termism they miss on an infinity of possibilities.

The internet has changed all that in ways we are still discovering and the free software community is its apogee. It was a stone dropped in a pond. The ripples have spread, and even allowing for hyped-up buzzwords and transient fashions, other disciplines have seen the potential for doing things differently and better. Even if the free software paradigm never completely dislodges entrenched proprietary business models it has ignited an interest and enthusiasm for doing things the open source way. Business will probably never fully adopt that model. It’s only raison d’etre is profit. Nothing wrong with that as such, excepting when the desire for profit intentionally suppresses access to and free promotion of knowledge for others outside the commercial cathedral.
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Combined with projects like Sugar and the OLPC, free and open biology (and other scientific disciplines) may just constitute a way to get some serious science done on the relative cheap without technical, political and financial interference from the usual vested interests. The semantic web, if realised, may have a big role to play here too.

Its origins give cause for hope; Tim Berners-Lee, head of W3C, Lee mooted the idea (an extension of the world wide web, defining the semantics of information understood by people and machines) in the Scientific American in 2001. It has its critics and the idea is yet to come to fruition (if it ever does) but biologists have seen the potential. Nextbio is an interactive life sciences search engine which searches through and correlates experiments, literature and clinical date to assist researchers to make new discoveries. This is done through a conventional search engine interface. You just type in a term or terms as you would do in a conventional search engine like Google. As the Nextbio website itself says it is a platform for researchers to “search, discover and share knowledge locked within public and proprietary data”.

Nextbio is ultimately a commercial undertaking but there is a free basic web application which is ideal for citizen scientists and does not appear to compromise any open source principles. It even allows registered users to personalise their Nextbio experience to share, communicate and collaborate with the Nextbio community. (You’ll need to register to get beyond the initial search page.) It may be free but you seem to get a lot for your money. Hell, Nextbio basic is even available for the iPhone and there is a semantic plugin called Piggy Bank for Firefox. It would be interesting to know if one could use that plugin when on the Nextbio page to do a mashup.

Note: There were a LOT of links throughout the article that I stripped out. If interested in the subject I highly recommend you check out the Full Article