CHE.496/2008/Schedule/Foundational technologies

Foundational technologies

 * '''Discussion leader: George M.


 * '''Foundations for engineering biology link
 * Purpose: This article gives us insight into how the field of synthetic biology was thought of and what engineering principles set it apart from traditional biotechnology (i.e., it is an approach to biological engineering).
 * In this article, Drew Endy (a co-founder of the iGEM competition), describes key elements in establishing the foundations for making biology truly engineer-able. This is goal of synthetic biology.  He describes what synthetic biology is in detail from four different groups: biologists, chemists, "re-writers," and engineers.  In the eyes of engineers, biology is a technology (building on genetic engineering, recombinant DNA technology, and automated sequencing).  The goal is to make the design and construction of engineered biological systems easier.
 * Endy points out four challenges that hinder the development of synthetic biology:
 * An inability to avoid or manage biological complexity
 * The tedious and unreliable construction and characterization of synthetic biological systems
 * The apparent spontaneous physical variation of biological system behavior
 * Evolution
 * Endy lists three engineering principles that should be used in developing synthetic biology:
 * Standardization
 * Abstraction
 * Decoupling


 * '''Synthetic biology: promises and challenges link
 * Purpose: This article provides yet another overview of the nascent field of synthetic biology that focuses on the definition of the field, the difference between fundamental and applied synthetic biology, safety and ethical considerations, and differences between research in the US and Europe.
 * Serrano states that current synthetic biology research projects are "toy" or concept projects and do not necessarily solve real-world problems, but that the goal is to be more applied. This will happen as technology advances and enables this development.  The focus of synthetic biology now should be on fundamental research.  Once there are enough working standardized parts, then real applied research can take place.
 * Synthetic biology can be used for both good and bad, just like any technology. Although we can expect huge benefits, there are significant risks and we should expect misuse.  To minimize risk, perhaps there should be logical regulations established at various levels.  Another option may be self-governance.


 * '''The iGEM competition: building with biology link
 * Purpose: This article describes the history of MIT's international Genetically Engineered Machine competition including brief descriptions of BioBricks and the Registry of Standard Biological Parts.
 * The VGEM Team presents its work at the annual iGEM Jamboree in early November. This article gives a little bit of background and flavor regarding the Jamboree and the overall iGEM experience.
 * The most valuable sections of this article are the brief descriptions of BioBricks (including what they are and how they are used) and the Registry (the library of BioBricks at MIT), both of which are essential elements of the iGEM competition. More details about BioBrick construction will be presented later in the course.


 * Problem-based learning exercise
 * One of the major goals of this course is to stimulate the independent, critical thinking and problem-solving that is necessary to operate a student research group such as the Virginia Genetically Engineered Machine Team. To jump-start this, we will work together as a group to try to solve a problem.  Our goal is to produce hydrogen gas from microorganisms.  How should we go about doing this?