Berkeley Engineering Blogs

On an e-mail discussion list for synthetic biology, the question was posed, in regards to what iGEM teams produce specifically: “how is this organism going to be contained, if it’s use is suggested for release in the real world?”  The author then makes an excellent distinction between the actors involved in using synthetic biology: there are the “good guys,” the “greedy guys,” and the “bad guys.” The vast majority of recent discussion surrounding things going dangerously wrong within synthetic biology focuses on these bad guys and forgets about the others.  Even if we could distinguish what makes a bad guy bad, we would miss the point entirely, as they make up a miniscule percentage of those dealing with genetically engineered organisms. It is easy to think about keeping the tools of synthetic biology away from those who would want to intentionally do anyone harm (although, once again, how does one go about defining who such “malicious forces” are?), and certainly a basic level of regulation is necessary for restricting access in general. 

The real question, and the more difficult one to answer, is what sorts of regulations can be set up within the extremely diverse synthetic biology community (which includes academics, industry affiliates, garage “bio-hackers”–discussed at length here–and others) to restrict the possibilities of accidental contamination? 

How is containment dealt with with the UC Berkeley iGEM wet lab team’s project? Even though the argument could be made that this project is directed at ameliorating the process of doing synthetic biology instead of actually existing in the “real world,” what steps can be taken within the iGEM community towards preparedness? Would you agree with Drew Endy that the problem of containment is properly dealt with within current requirements of the iGEM competition?

Here, more than a month after “lysophonix” was deemed unrealistic for completion in time for the iGEM competition, we find the team has gathered together the research completed and has decided to change the focus of the project. A biologically encoded lysis device is still in operation in the team’s new project, coined “Clonebots,” but it now focuses more precisely on the in vivo assembly of parts (which is now regularly referred to as the “manufacture of parts” within the lab) and the easy accessibility of those parts (or product).  

The sound promoters were found to be faulty, which thus led the team to reformat their project for the competition. This is interesting in light of Drew Endy’s past comments that the only way synthetic biology will work and be understood is through the investigation and analysis, on the part of the scientists themselves, of experiments that failed or did not go to plan and the presentation of that analysis to others conducting synthetic biology research. iGEM would seem a perfect place for such presentation of the analysis of complexities involved in attempts and re-attempts to get biological systems to produce what we want them to produce, but it would seem that the environment and situation of the competition could restrict positive inquiry in “failures” as it simultaneously tries to support positive inquiry through “successes.” At the heart of the synthetic biology being done by countless teams across the globe for iGEM is the desire to be recognized at the Jamboree in November–and focusing a project’s presentation on why it did not work according to plan could realistically be an obstacle of access to such recognition. 

But how frequently do scientific experiments go completely to plan?  Synthetic biology focuses its efforts, at least given some of its self-description, on the production of “novel systems,” and biology is an unquestionably largely unknown frontier (though, arguably, less unknown in relation to E. coli or yeast). Unexpected outcomes would appear to be the norm with such a set of parameters. And wouldn’t understanding how to troubleshoot a biological system be the basic requirement for a mapping of electrical engineering onto biology or for engineering biological systems?