Synthetic biology – what is next?

Synthetic biology is the engineering of biology, re-designing existing biological systems and designing new ones, for a myriad of purposes. The most obvious killer apps are the improved synthesis of drugs and other medicines and the synthetic generation of biofuels.

Right now the most exciting aspect of synthetic biology –suggesting that the field is getting some traction – is that three key community constituents are getting more heavily involved: traditional academic researchers (SB 4.0 conference videos and agenda), undergraduates and high school students through the annual iGEM (international genetically engineered machines) competition (1200 students from 112 teams are expected at this fall’s iGEM Jamboree at MIT, and a growing group of non-institutionally affiliated enthusiasts, diybio’ers, the 2000s version of the Homebrew Computer Club, for both wetlab (an interesting recent example) and computer modeling, simulation and data management projects.

Venture capitalists are slowly starting to realize that synthetic biology could be a huge growth industry and could be the next generation of biotechnology. Amyris is probably the best-known synthetic biology company, estimating to launch its biofuel (ethanol) business publicly in Brazil and the US in 2011.

The long road to automation
Other waves in the history of biotechnology have shown that life sciences problems tend to be much more complex, take much longer than expected to solve and ultimately underdeliver results. There is no reason to think that synthetic biology would be any different, but it is obviously not futile to work on the challenges. When the synbio community analogizes their status to the heterogeneous screws and bolts of the construction industry circa 1864, they are not kidding.

The DNA synthesis process is astonishingly unautomated, unstandardized and expensive ($0.50-$1.00 per base pair) at present (it would be $15-30 billion to synthesize the full genome of a human (ignoring ethical, legal, etc. issues)).

Synthetic biology is a new field and the demand for synthesized DNA is still small; the 2,000 or so iGEM community members are the biggest market. Ginkgo Bioworks is working to deliver robotic synthesized DNA assembly and other startups would be likely to spring up in this area. Ginkgo has also helped to expand and improve one of the main synbio tools, the Registry of Standard Biological Parts.

Synthetic biology advances

The realization of synthetic biology, one of the cornerstone fields in this century’s life science revolutions, is a step closer this year with three important advances.

First, synthetic biology movement leader Drew Endy has arrived at Stanford from MIT. Knowing that people and tools are critical to the area’s development, he is assembling a world class curriculum and department to tackle the challenges of synthetic biology, estimating that Stanford is four years behind.

Second, more than 85 worldwide university teams have entered this year’s iGEM (international genetically engineered machines) competition. 900 students are estimated to be at MIT for the November 8-9 presentation of their work and the contest’s culmination. Previous year’s novel synthetic designs have included wintergreen and banana-scented E. coli bacteria, creating virtual-machine like computational platforms in cells and microbial cameras or light programmable biofilms.

Third, record attendance is expected at the fourth annual Synthetic Biology conference will be taking place October 10-12 at the Hong Kong University of Science and Technology.

Biology investigation, modeling, simulation and building
Synthetic biology is starting to have more process and rigor, particularly as articulated by Martyn Amos in Genesis Machines. Several areas have been simultaneously improving and coming together: biological system and process enumeration, 3D software modeling and simulation, and biological machine building. As CAD and EDA allowed semiconductor designers to achieve new levels of productivity and automate complex circuit design and test, so too are software tools aiding biology.

Bio-SPICE (Biological Simulation Program for Intra- and Inter-Cellular Evaluation) is an open source framework and software toolset for the modeling and simulation of spatio-temporal processes in living cells. The innovation process for synthetic biologists is now:

• investigate the biological phenomenon or mechanisms
  
• mathematically model the existing or novel phenomenon
• use software simulation to test the model
• build it in the lab with standardized off the shelf biological parts of synthesized DNA