User:ClarkeS

Bio
Sean Clarke

saclarke at mit

directory info

I am a Biological Engineering (BE, MIT Course XX) graduate student in the Alm lab (48-324). Our focus is on the evolution of microbial genomes, and I am specifically working on engineering genetic diversity and stress tolerance in Vibrio splendidus. I hope to determine what alleles and loci contribute to environmental stress tolerance and how experimental evolution and resequencing can reveal these.

Past life and credentials
My background is in mechanical engineering and design, but not of things quite as small as BioBricks.


 * B.S.M.E., University of Texas at Austin, biomedical technical area
 * B.A., University of Texas at Austin, Plan II Liberal Arts Honors Program
 * Fulbright grant, Milan, Italy, independent study of industrial and engineering design methods, and classes in biomaterials at the Politecnico di Milano

I've also lived in Long Island, St. Louis, and Washington, DC, all places to which I would move back to prevent ending a sentence with a preposition.

Other research interests

 * Engineering microbial stress tolerance
 * Relating stress tolerance to genome loci
 * Resequencing evolved microbes
 * Scaling of engineered biology to industrial purposes
 * Design and use of replicating biological machines
 * Technologies/vocabularies to make biological engineering easier
 * Ethics and philosophy of science instruction for scientists/engineers
 * Biomimicry, bioscaffolds for material processing
 * Recycling/"cradle to cradle" design of biological systems
 * Usability of biological design software and equipment
 * Biomineralization

Classes

 * BE.400
 * BE.410
 * BE.420
 * BE.430
 * 5.95 Teaching College-Level Science and Engineering
 * 7.81 Systems Biology Excellent class, Alex van Oudenaarden
 * 18.085 Applied Math for Engineers with the indefatigable Gil Strang, who might have taught your parents and is still revising his book daily.
 * 7.56 Graduate Cell Biology, with an emphasis on yeast, Profs. Stephen Bell and Frank Solomon
 * 1.89 Environmental Microbiology with Martin Polz
 * OEB.192 Microbial Evolution with Chris Marx, a great subject that is not taught enough
 * directed evolution seminar

Past Projects

 * My first project at MIT was during the summer of 2005 when I tried the Orthogonal cloning of clpXP from E. coli into yeast. I was more successful at learning molecular biology techniques by making mistakes than at cloning into yeast.  This work is continuing in someone else's more capable hands.

Notes