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Great you can download your very own E. coli bacterium

Microbiology is going open source

The same concepts that have lead to open source rockin' the software world have spawned the beginning of a revolution in biotech. An organization called Biofab, funded by the NSF and run through teams at Stanford and Berkeley, is applying open development approaches to creating building blocks (BioBricksTM from BioBricks Foundation) for the bio products of the future. Now, the first of those building blocks (based on E. coli) are just rolling off the production line. This, according to the organizers, represents "a new paradigm for biological research."

At its basis, Free and Open Source Software (FOSS) is about sharing and collaborating. The purpose of the open source licenses of which RMS (as Richard Stallman is known to fellow hackers) conceived was to ensure that users of software could have the freedom to use, modify and share the software as they wished. What has evolved is an enormous stock of freely available building blocks (about half a million by Black Duck's count) that make for faster, better, cheaper creation of software.

This goal is behind Biofab, to create biological building blocks that can be assembled into an unimaginable plethora of applications. Somewhat in contrast to the philosophical grassroots motivations that have gotten software development to this point, it's being driven by economic motivations, and there's some real money behind the project from the outset. It can cost tens of millions of dollars to create a single microbe that can do useful work because the current process is like creating a software application using machine language.

The geniuses behind Biofab are clearly modeling much of what they do on the FOSS model. Stanford's Drew Endy, Biofab director, talks about what they are building and a "biological operating system." In fact the name (Biofab International Open Facility Advancing Biotechnology) is oddly recursive like GNU (which stand for GNU is Not Unix). OK, but biology and software? You can't download even microscopic bugs over the internet can you? Well, since Watson and Crick discovered the double-helix, you kinda can. Sequences of genes in nucleic acids are known as "genetic codes" and are basically the programs that runs the cells with which they are associated, and BioBricks foundation decribes a BioBrick, as follows:


Sure sounds like software to me. In fact it's enough like software that the BioBrix guys figured out they needed and developed a very OSI-like license calledThe BioBrick Public Agreement. I gave it a quick read and it reads very much like a software license, a fairly permissive one with no reciprocal clauses that I could see. (By the way, it would violate the OSI requirement of unrestricted use with a "do no harm" clause, but that seems like a good thing given the bioweapon potential.)

The microbiology community sits where the software community was a few decades ago. A few big corporations with a lot of stake in keeping technology proprietary and a grass roots movement to open and shake things up a bit. My guess is that with the analogous trail having been blazed in the software world, things will unfold more quickly in biology. I'll be monitoring from the sidelines to see how it all plays out.

Near the end of composing this blog, I stumbled across an outstanding book, Biobazaar: The Open Source Revolution and Biotechnology by biologist/lawyer, Janet Hope. The author delves deeply into what she calls the "irresistible analogy" between open source software and microbiology. Biology aside, it is well worth the read just for concise history of open source she provides in Chapter One and the detailed treatment of open source licenses in Chapter Five. 

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