Keasling: Synthetic Biology Class

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Revision as of 19:23, 9 October 2005 by Kalil (talk | contribs)

Draft September 9, 2005 T. Kalil/J. Goler

This is a wiki for a proposed course: “Implications and Applications of Synthetic Biology” Feel free to edit if you have something productive to say!


Explore strategies for maximizing the economic and societal benefits of synthetic biology and minimizing the risks.

Create “seedlings” for the future research projects in synthetic biology at UC Berkeley.

Increase multidisciplinary collaboration at UC Berkeley on synthetic biology.


Instructor: Keasling, Arkin TAs: Howard, Yasuo, Goler(?) Listing: BioEngineering, ChemE, (MOT)

Composition of class: How diverse (in terms of subject area) should the students be for this class? In addition to science/engineering – would it make sense to have law, public policy, business, ERG, etc. students? Make sure we have a strategy for recruiting those students. (2/3 Science 1/3 biz/policy)

Resources: What resources are required to make the course successful?

Lead In - Observe and pick people for iGEM 06

Three modules

1. Introduction to synthetic biology (Keasling, Arkin, et. al) – primarily on current and future capabilities, as opposed to technical details

2. Applications of synthetic biology

a. energy – Tad Patzek

b. energy – JGI termite gut project?

c. “Dual-use” approaches (developed/developing country markets) – Lisa Conte – Napo Pharmaceuticals

d. pharmaceuticals, specialty chemicals – Amyris

e. Marine biotech - ?

f. Other company talks (e.g. Diversa, Genecor, etc.)

3. Ethical, legal, and policy implications of synthetic biology

a. Steve Mauer (Goldman School) Open Source Biology

b. Blue Heron – Regulation of gene synthesis

c. Steve Block, Stanford, Rogert Brent, MSI – National security implications of genetically-engineered pathogens

d. Gerry Sussman – How can synthetic biology be harnessed for biodefense?

e. John Wilbanks – Executive Director, Science Commons

f. What should a national strategy for synthetic biology look like? Drew Endy

This is a list of possible student projects. Please add to it!

1. Dual-use strategies: Identify a synthetic biology “platform” or product with “dual-use” applications for both developed and developing country markets

2. Energy: What is the energy balance of proposed schemes to produce biofuels from genetically-engineered organisms? What are the relevant technical targets that would need to be met for bioenergy to make sense from an economic and thermodynamic point of view?

3. Marine biotechnology: Marine natural products represent a largely untapped and promising resource for drug development. As scientists with the Harbor Branch Oceanographic Institution observe:

The marine environment may contain over 80% of the world's plant and animal species, and during the past decade over 5000 novel compounds have been isolated from marine organisms. The diversity of chemical compounds in the marine environment may be due in part to the extreme competition among organisms for space and resources … It is hypothesized that sessile marine organisms (for example, sponges, octocorals, tunicates and algae), have developed a diverse array of chemical compounds known as "secondary metabolites" or natural products for defense and competition.

It is worth noting that this research group alone has discovered 235 bioactive compounds and has had over 117 patents issued over the last 10 years.

Researchers in synthetic biology may be in a position to increase the payoff from this research. Once pharmaceuticals (or possibly specialty chemicals) have been derived from marine natural products, “synthetic biology” approaches developed at Berkeley could lower the cost of producing them at high volumes. This, in turn, would increase the economic and social value that we place on marine biodiversity, in addition to its incalculable intrinsic value. Potential projects:

a. Develop a list of the most promising pharmaceuticals, specialty chemicals, etc. that could be biosynthetically derived using genes from marine organisms. Identify current stage of commercialization. [Examples discussed in the literature include: a cancer therapy made from algae; a painkiller derived from the toxins in cone snail venom; anti-viral drugs Ara-A and AAZT and anti-cancer agent Ara-C developed from a Caribbean coral reef sponge; and Dolostatin 10 (extracted from an Indian Ocean sea hare and undergoing clinical trials for the treatment of breast cancer, tumours, and leukemia. A publication called Natural Products Report has review articles on marine and other natural products. See

b. Determine whether any of these are candidates for cost-effective biosynthesis using existing platforms (e.g. pathways for isoprenoids)?

c. Does an analysis of possible high-value marine products for biosynthesis suggest new pathways that would produce precursors for a broad range of them?

d. What models exist to re-invest some of the revenue generated from marine products into marine biodiversity efforts?

More TBD