Synthetic Biology: Can we reprogram the living world?

The second lecture I attended at Stanford Saturday University on November 5, 2011 was given by Christina Smolke, a professor in the Bioengineering department. It is such a fascinating time to be a student because there are such interesting areas of study, especially in this new frontier of science and engineering called Synthetic Biology. While many of the details of the lecture escaped me (the language here is all gene and protein related), the general ideas and potential benefits were clear enough to get the endorphin high going.

The title of the blog is taken verbatim from Smolke’s talk. She began the lecture outlining some natural chemicals and materials such as Taxol (anti-cancer), Silk, rubber, codeine/morphine, and butanol that humans have used for various purposes. The motivation underlying the question she raised then has to do with producing, for example, codeine, on large scale using natural “microbial factories” (beacuse they are much greener) instead of synthetic ones.  One huge benefit of being able to do this: to treat hard to get at diseases such as brain tumors, by injecting microbial factories in-vivo (Intelligent Therapeutics) to eliminate the tumor (she made a reference to the classic movie Fantastic Voyage).

Currently, these types of ideas are still sci-fi fantasies because the tools are lacking for enabling the applications. The rest of the lecture delved into the details of the state of the art in our understanding of protein coding (transcription) and directions for making proteins (translation). Here is an interesting tidbit. The human genome has 3Billion DNA sequences, of which less than 1% code for about 23,000 proteins. With our current knowledge, we can annotate pretty readily the protein coding regions but the directions for making proteins are not very well understood.  In fact, the functional significance of 99% of the DNA sequences are not well understood. Genome sequencing has revealed that we have about as many coding regions as worms!!

Smolke then talked about the evolution of various techniques for gene sequencing. Essentially, her lab is involved in creating a “library” of the basic building blocks. From this library, the building blocks can them be combined in specific ways to enable the mass production of the various natural chemicals I mentioned at the beginning.

As I was listening to the lecture, I was reminded of the evolution of the VLSI industry (which is where I spent the last dozen or so years) beginning in the 70s. I think Carver Mead did for VLSI what Smolke and her colleagues are doing in the area of Synthetic Biology. Mead essentially came up with a CAD (computer aided design) methodology that uses a library of standard cells which could be stitched together to create very complex integrated circuits. The whole industry took off once these tools were in place.

It was also a wonderful lecture. I sincerely hope Smolke is successful in her endeavors. We are poised to witness some science fiction become fact in the not too distant future.