Open source synthetic biology

Written byAlla Katsnelson

| 3 min read

I arrived in Cambridge tonight and headed out to a pub near MIT to find the linkurl:iGEM;http://www.the-scientist.com/blog/display/53819/ crew, who were supposed to meet up for an informal get-together before the Jamboree, iGEM's international linkurl:synthetic biology;http://www.the-scientist.com/2006/1/1/30/1/ contest, starts tomorrow (Nov. 3). After peeking into a few bars I spotted a small group of young people wearing green t-shirts decorated with biotech company names and O-H molecules. We're it, they told me -- the Alberta team. They'll be presenting a project on a more efficient system to produce biofuels, one of 59 teams to compete. At the pub next door, I joined a larger group, led by a sweet-faced bearded kid wearing a white hoodie with iGEM's green cell-and-cog logo. Mac Cowell, who is coordinating the event, had come to iGEM in 2005 as part of the Davidson College team from Wisconsin. It was all so exciting, he told me, that after finishing his biology degree he moved to Boston, knocked on the door of Randy Rettberg, iGEM's founder, and asked for a job. He and a technician work with Rettberg on iGEM full-time. Talking to Cowell and his team of volunteers, it quickly becomes clear that iGEM is a movement rather than simply an annual contest. The aim is two-pronged ?to create a well-characterized system of interchangeable cellular "parts" that are a shared resource within the synthetic biology community, and to recruit students to play with them and see what they can make. Not everyone within synthetic biology takes the open-source approach, Andrew Hessel, an iGEM consultant who recruits teams from Canadian universities, told me, but the driving force behind it is iGEM and MIT (Rettberg works with renowned hacker-turned-synthetic biologist linkurl:Tom Knight).;http://knight.openwetware.org/Contact.html Hessel likened the atmosphere to the time when computers were first becoming cheap enough to be affordable by anyone who wanted one, and young, bright kids began to play around with code. What has hobbled genetic engineering so far, according to iGEM devotees, is a lack of modularized parts, leaving researchers to build everything from scratch. That's where the Registry of Standard Biological Parts comes in -- so far, it contains all of the 1500 or so elements built by all the teams from the past four years, and synthesized such that they're easily mixed and matched. The biobricks, as they're called, are stored both as a list of sequences in a computerized database and as vials of plasmids in a couple of freezers. "It's not so important that it's biobricks," Cowell said, as long as there is some standardized system. This spring, Cowell became intimately acquainted with the contents of the freezers -- he spent six weeks making up about 150 kits, each containing every sequence in the Registry, to be sent out to this year's competitors. Ultimately, there won't be a need to send out the whole kit. (And probably it will soon become unfeasible -- this year's event will more than double its contents, adding about 2000 more parts.) But right now, at least a part of the intended effect is shock value, Cowell said -- opening a box of 1500 usable cellular parts really wakes people up to the possibilities. So far, Hessel said, the Registry's contents are not terribly sophisticated -- on the level of 'see spot run,'" -- and a lot of researchers are wary of using tools created by undergrads. Their concern may not be unwarranted, since many of the sequences are not very well characterized, an iGEM volunteer named Melissa, a PhD student at biology at Georgia Tech, pointed out. But the momentum is building, Hessel told me -- "every time we add an iGEM team, or every time a researcher decides to synthesize instead of clone."

Open source synthetic biology

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