Berkeley Engineering Blogs

Welcome to a blog devoted to all things relating to synthetic biology and the international Genetically Engineered Machines (iGEM) competition at the University of California-Berkeley!!

Well, the obvious first question is:  What is synthetic biology?

As an emerging field of scientific research being designed as an academic discipline, synthetic biology has many definitions, depending on who is doing the defining.  Essentially, as an offshoot of the vast field of bioengineering, it aims to engineer novel organisms “from the ground up”—relying on technologies that allow for the standardization of strings of DNA as “parts” (functioning like electrical engineering’s parts for constructing circuits and signal processing) which are known to have certain functions.  Synthetic biologists then use these standardized parts to form “devices” (and, much more complexly, “systems” constructed from a series of these parts and devices, housed in, usually, a bacterium shell referred to as a “chassis“) that will produce a desired output.  For example, the goal of one project under the synthetic biology banner on the Berkeley campus, headed by bioengineer J. Chris Anderson (who is also the assistant professor that spearheads the Berkeley iGEM team) is to create “tumor-killing bacteria,” a system that is designed to produce a certain output (ie: “tumor-killing toxin”) only after it receives certain inputs from its environment.  According to MIT’s Technology Review,

“…to build a cancer-killing bacterium, biologists must create organisms that can perform a series of complicated functions — namely, when in the bloodstream, they have to sense and respond to the tumor environment. Once inside the tumor, the bacteria must infiltrate the cancer cell, and then — and only then — start producing a tumor-killing toxin. The researchers plan to engineer such super-organisms by co-opting parts from different types of bacteria and inserting them into Escherichia coli, a bacterium commonly used in research.”  (Singer 2006) (Full article here:  “Tumor-Killing Bacteria: Scientists are synthetically engineering E. coli that can target and kill cancer cells”)

It is this “ground up approach” that is often pointed at to distinguish this sort of research from genetic engineering and other closely aligned fields.  Other major synthetic biology projects happening on campus include the designed manufacture of the malarial drug artemisinin through adding “new genes and engineering a new metabolic pathway in Escherichia coli bacteria” in Jay Keasling’s lab (Yarris 2004) (Full article here:  “Synthetic Biology Offers New Hope for Malaria Victims”) and the various projects surrounding cellulosic biofuels at the Joint BioEnergy Institute (JBEI) and the Energy Biosciences Institute (EBI) (EBI’s proposal found here:  “Energy Biosciences Institute proposal summary”).

For more information on what is involved with synthetic biology, look here:  OpenWetWare Main Page.  One of the main objectives of synthetic biology is to be opensource, which includes providing tutorials and elaborate explanation of its procedures to a wide public.

Question number two:  What is iGEM?

Officially (according to its main wiki page), “iGEM addresses the question:  Can simple biological systems be built from standard, interchangeable parts and operated in living cells?  Or is biology simply too complicated to be engineered in this way?”  Started as purely a workshop involving only MIT students in 2003, iGEM earned its “i” after it became an international competition in 2005.  It now connects dozens of teams from around the globe, who create projects ranging from “engineering probiotic bacterium to improve its medical applications” (Caltech) to engineering “a common yogurt bacteria, Lactobacillus bulgaricus, so that it will express the 20aa peptide p1025,” which has been seen to improve dental health (MIT) to creating “E. coli that lyse [or burst open] in response to a sound stimulus,” which could make protein purification (an essential process for research in synthetic biology) less abrasive (UC Berkeley).

For more information on iGEM, look here:  OpenWetWare: iGEM.

Third question of my introductory blog entry:  Who am I?

Unlike the other members of the Berkeley iGEM team, my main research objective is to contextualize synthetic biology (whether anthropologically, politically, economically, philosophically, or ethically) and the research done under its heading.  As a “human practices” researcher, a part of the fourth “thrust” or branch of the Synthetic Biology Engineering Research Center (SynBERC, which is one of the funders of iGEM), my goal is to both learn the science involved in doing synthetic biology but mainly to conduct a continual second-order investigation of synthetic biology:  allowing for the comparison and alignment of relationships with other scientific research, observing the culture of learning synthetic biology and of conducting the research, and discussing controversial issues surrounding synthetic biology research.  For example, looking at the introductory information offered above, information widely available and rhetorically formulated by the scientists designing their projects, we can ask an infinite number of second-order questions:  What process is involved with standardizing genetic information and overlaying an electrical engineering structure on biological systems?  What assumptions and generalizations are established with such standardization and how do processes adhering to such standardization actually function?  What does it mean to “engineer novel organisms,” ie:  create life?  What are the limits to what you can create?  Who decides?  What does it mean that everyone has a different definition of “parts” or “devices” or even “synthetic biology?”  As the months wear on, I will use this blog to confront these and many other questions relating to the design and function of synthetic biology.

And for more information on SynBERC’s human practices, look here:  Anthropology of the Contemporary Research Collaboratory.