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:Each distinct BioBrickTM standard biological part is a nucleic acid-encoded molecular biological function (e.g., turn on/off gene expression), along with the associated information defining and describing the part.
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 called The 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.
Phil Odence Vice President of Business Development for Black Duck Software, makers of enterprise app development tools that address management, compliance and security challenges associated with open source. In that role Phil is responsible for expanding Black Duck’s reach, image and product breadth by developing partnerships in the multi-source development ecosystem. He came to Black Duck from Empirix (formerly RSW Software and Hammer Technologies) a leader in carrier VoIP, contact center and Web application testing and monitoring. He served there as Vice President of Business Development successfully developing the firm’s alliance program, creating strategic partnerships, starting up new businesses and supporting M&A activities. Prior to Empirix, Phil was a partner at High Performance Systems, a computer simulation modeling firm where he was responsible for consulting and partnerships with leading management consultancies, including McKinsey and A.T. Kearney.
He began his career with Teradyne’s digital logic simulation group in several sales and marketing management roles. He has an AB in Engineering Science and an MS in System Simulation from Dartmouth College.
Black Duck counts a long list of well-known technology companies as partners. These include IBM, Novell, Red Hat, HP, Intel and Microsoft.
When not at work, Phil can be found running barefoot, which he documents in his entertaining Barefoot? Phil blog.