Tuesday, December 02, 2008

10th Anniversary of my Defense -- A Retrospective

On December 2, 1998 I defended my dissertation entitled "Exploration of microbial genomic sequences via comparative analysis", the somewhat vague title referring to a collection of projects that I worked on in Gary Olsen's (pictured) laboratory at the University of Illinois at Urbana-Champaign, most notably the CRITICA genefinder (which was, until a year or so ago, still in use at JGI), and one of the earliest genomic studies of thermostability.

My thesis committee consisted of Carl Woese, Tony Crofts, and Stan Maloy (now at SDSU; I run into him at seminars occasionally). 
I don't have any pictures of the defense or the lunch afterwords after owning to a sad accident -- my parents' camera had a broken lens, and in that pre-digital era, they didn't know anything was wrong until they tried to develop the film. Still, the day sticks with me in memory. I gave what was probably the best presentation of my career (probably because I had practiced ten times or so), and the questioning was very friendly (the serious questioning had been several years before at my prelim). 

I've worked a number of jobs moving to various cities in the name of science since those days -- a postdoc in Computer Science at the University of Waterloo,  a senior bioinformatics scientist at a now-defunct biotech firm in Montreal,  living in downtown DC while working in the microbial genomics departments of TIGR and its successor JCVI,  and now in San Diego, where I'm working at the west-coast campus of JCVI. Who knows where the next ten years will take me?


John Tsang said...

Can't believe it's 10 years Badger! i thought your job talk at Waterloo was decent, though I didn't understand much of the biology jargon at the time :)

Jonathan Badger said...

Yeah -- I also remember not understanding all the CS jargon -- "Order n log n time", "NP-Hard", etc. that all you CS people peppered your conversations with.

John Tsang said...

Now knowing the jargon of both, I think biology has way more. CS people only deal with the abstract or limited physical things (like memory). In biology gene names alone constitute its own nomenclature.... (Hunchback, Wingless... I guess it's mostly drosophila, but still...). I guess the degree-of-freedom of space-time processes created by evolution is too much for the human language! :)