My work focuses on approaches that apply novel combinations of existing and new methods to learn more about how living systems work. My specific interests tend toward metabolic networks and the engineering of biology, but I’m excited to apply my experience to a wide variety of challenges in the land of predictive biology.
From the bench to bioinformatics
My research career started with two very fortunate undergraduate opportunities. My first research gig was a summer stint in the lab of Ethan Bier at UCSD, pushing flies and learning how to run restriction digests. After that I did research on the epigenetic regulation of gene expression in the lab of Marietta Dunaway at Cal.
I did my PhD research in the laboratory of Randy Hampton at UCSD. There I studied how HMG-CoA reductase, an enzyme that’s the target for pretty much all of the cholesterol-lowering drugs, is regulated by a “quality control” pathway. This was bench biology, spending my days in the lab, developing a structural transition assay and an aggregation assay that helped me figure out that a small molecule signal made HMG-CoA Reductase change shape to look like a “broken” protein, after which the cell’s cleanup systems gobbled it up. This was also my first exposure to computational tools, as I used everything the San Diego Supercomputer Center’s Biology Workbench had to offer to guide my research.
From UCSD I joined the Artificial Intelligence Center at SRI International, home of Apple’s Siri, among other things. There I worked on bioinformatics, computational, and synthetic biology projects, including the Orphan Enzymes Project, on which I was the PI. You can also see my work on the EcoCyc and BioCyc web sites. Research at SRI was a great opportunity to collaborate with biologists, computer scientists, fuels chemists, engineers, and more. My office was also next door to a group who specialized in blowing things up and upstairs from the guy who invented the mouse.
For the next couple years I worked in Clover Collective, a small research company where we applied quantitative and design-influence thinking to address scientific challenges. Clover Collective published two papers from the Orphan Enzymes Project, which you can get to from my publications page.
I’m now at Zymergen, where we use data science, automation, and biology to “improve the economics of existing products, bring new products to market faster, and develop novel ones.”
Specifically my work includes extending the reach of biological manufacturing and helping create our approach to biological design as part of our work in the DARPA Living Foundries program.
Writing about other things
I’ve also been writing for and about gaming since 1997.
You can read more at my gaming site and my old column at ChannelFireball.com. I enjoy crossing over between my gaming and science writing – I occasionally used statistical methods and clustering to explore and explain gaming strategy to a weekly audience that ranges from junior high kids through professors.