Cambridge, Mass. - The first conference devoted to the emerging field of synthetic biology brought a range of research projects and professionals together recently at the Massachusetts Institute of Technology.
The tools being generated by the synthetic biology movement are of interest to the biotechnology industry, since they have the potential to create a direct, hands-on genetic-engineering capability. There is also the distinct possibility that BioCAD systems could introduce the same ramping of system functionality coupled with plunging costs that have characterized the electronics industry.
The eclectic roster of 300 participants at Synthetic Biology 1.0 included biologists from various subdisciplines, artificial-intelligence experts, circuit designers, chemical engineers and a small clutch of researchers from the biotech industry.
One of the most interesting topics was the current state of the BioBrick catalog. Randy Rettberg, a computer industry veteran and director of the catalog, discussed the project in terms of the evolution of electronic circuits.
"We are at the beginning parts stage, where individual gates and simple circuits were offered in packages with pins," Rettberg said. "We expect the parts stage to eventually give way to larger integrated DNA modules and finally systems, just as in electronics."
The BioBrick catalog of elementary biochemical "parts" with standard inputs and outputs is being constructed in Tom Knight's wet lab in MIT's Computer Science and Artificial Intelligence Laboratory.
Rettberg is working on an online data book and is initiating a standards process so anyone can build BioBricks and add them to the catalog. He envisions an assembly service with measurement and quality control leading to "open-source biology."
It seemed remarkable that such a varied group had a common language-one that an uninitiated EE would find strangely familiar. Poster presentations were sprinkled with conventional circuit schematics along with chemical formulas and DNA diagrams. Participants discussed their strategies for schematic capture, simulation and tapeout. In this case, tapeout involves a sequence of symbols from the genetic code, which is shipped via the Internet to a DNA synthesis service. Design debugging takes place when the synthesized DNA arrives at the lab. Hopefully, the synthetic DNA will generate a biochemical realization of the original schematic.
There are currently about 300 BioBricks. Another 800 parts have been built by combining those into composite BioBricks. Knight and his collaborators presented results on a next-generation version of the system called BioBricks++. Just as object-oriented programming constructs allowed programmers to quickly combine previous software modules into more complex systems, the BioBricks++ system has standard interfaces for all DNA segments that can be combined in any sequence using commercially available enzymes.
Rettberg is also organizing a summer design contest sponsored by the National Science Foundation and the Defense Advanced Research Projects Agency, where teams of graduate and undergraduate students, led by a faculty member, will genetically engineer a finite-state machine (FSM).
"This contest is as much for the education of the faculty leaders as for the students," he said. "At the beginning of the VLSI revolution, around 1980, all the circuit design capability was in the hands of industry, and the universities fell behind in their capability to design computers and systems. That all changed when Carver Meade and Lynn Conway put together the first VLSI design course." That development then produced student projects directed at reduced-instruction-set computers that eventually revolutionized the microprocessor industry.
The university groups taking part in the contest have various design plans. The Boston University team will try to build a simple counter. The University of Texas at Austin team will try to beat the processing power of silicon by culturing a massive array of identical FSMs. The MIT team is not talking beyond the initial designation of an acronym: Smug, for "Self-replicating Machines of Undeniable Greatness."
The similarity between synthetic biology and electronics may imply that synthetic biology is nothing more than an attempt to build computing machinery with biochemistry instead of silicon. There is one inherent limitation, however: There is no direct way that biochemistry, which involves the generation and diffusion of proteins, could compete with silicon in terms of speed. But as the VLSI generation runs up against enormous complexity and size-generated physical limitations, bioengineered molecular systems may offer a way to exceed them.