Author: Jonathan Eisen

My thesis has represented a relatively long and twisting road. In acknowledging the people who have helped make this possible I think it is useful to provide some of the history of each of the projects and my scientific development along the way. I have tried to make these brief and have put them in somewhat chronological order.

I owe my general interest in science and science research to my parents, Howard and Laura Eisen and to my grandfather Benjamin Post. They did not force me to become a scientist, but they did help me learn how to think critically and to appreciate some of the wonders of science.

As an undergraduate at Harvard, I was very fortunate to interact with many great biology researchers and teachers. During that time, I become interested in evolutionary biology and in particular in molecular evolution. The people I am particularly grateful to include: Stephen J. Gould (for his excellent class on evolution which was my first introduction to evolutionary biology as a science); Wayne and David Maddison (who, as Teaching Assistants for Gould’s class, introduced me to computational evolutionary biology); Stephen Austad (for getting me interested in field biology research through the field “laboratories” for his Ecology class); Eric Fajer and Scott Melvin (for giving me my first experience designing a semi-independent research project for their Conservation Biology); Alan Launer (for lending me the equipment to collect fish from the pond, which, according to him, I never returned); William A. Calder III (for giving me my first experience as doing real science research at the Rocky Mountain Biological Laboratory); Fakhri A. Bazzaz (for being an excellent advisor throughout my time at Harvard and afterward, and for giving me a chance to do my first truly independent research project); Peter Wayne, David Ackerly, and Susan Morse for helping me with the jet-lag experiment; P. Wayne, again, for hiring me as a research assistant and teaching me about science research and culture; Jennifer Doudna (for introducing me to molecular evolution and for teaching me how to critically read a scientific paper); Dennis Powers (for introducing me to molecular ecology), Colleen M. Cavanaugh (for too many things to list here including teaching me to keep a good notebook and to do controls for every experiment, for introducing me to microbiology, and introducing me to the powers of a phylogenetic perspective in biological research); Rob Dorit and Hiroshi Akashi who helped me learn how to do some molecular biology experiments; and all my other teachers and colleagues at Harvard including Woody Hastings, Karl Liem, Peter Ashton, and Otto Solbrig. 

And so, with a great debt to all of these people, I moved on to Stanford. Although I have officially worked on DNA repair in Phil Hanawalt’s lab, I have benefited a great deal from many people at Stanford including: Ward Watt (for teaching me about biochemical evolution), Sharon Long (who somehow taught me many valuable lessons in a short rotation project but in particular, for infusing in me the benefits of working on an organism that has good genetic tools available); Shi-Kau Liu (for help in initial projects and for initiating all of my work on RecA); Charlie Yanofsky (for many things but in particular for helping me realize just how powerful it is to have a crystal structure of the protein one is interested in); Kurt Gish, for help with sequencing and cloning; Allan Campbell and Richard Lenski (for helping me discover some of the flaws of adaptive mutation experiments and thus leading me to look for a new project); Patrick Keeling and W. Ford Doolittle for getting me started working on Haloferax volcanii; Mitch Sogin and the Woods Hole Molecular Evolution course (for teaching me how molecular evolutionary methods worked and how to think about evolutionary questions at the molecular level); David Botstein (for convincing me that teaching and research are not incompatible, despite what many Stanford professors try to claim); all the people involved in the SME core, in particular D. Botstein, Rick Myers, David Cox, Bob Simoni, and Brad Osgood; Rick Myers (for encouraging me to develop methods and ideas behind phylogenomics); my brother Mike Eisen for help with virtually everything; Sam Karlin and Volker Brendel for teaching me about mathematical methods in molecular biology, and for making me be more critical of some of the methods used in molecular evolutionary studies; David Ackerly for teaching me about the uses of evolutionary approaches in comparative biology; Russ Fernald for general advice on life and science as well as for valuable discussions on the uses of evolutionary analysis in molecular biology; Marc Feldman, for many helpful discussions about evolution; Steve Smith, David Swofford, and Joe Felsenstein for making the GDE, PAUP, and PHYLIP computer programs freely available; Steve Henikoff and Amos Bairoch for inspiring me to put information about the gene families I work on onto the World Wide Web; and many of the people I have collaborated with over the years including Bob Shafer and Michael Lerman. 

I am particularly grateful to my advisor Philip C. Hanawalt for allowing me the freedom to explore the areas of science that interested me and for being not only a great advisor, but a great human being too, showing me that one can do good scientific research without losing touch with ones humanity. I am also grateful to many of the members of the Hanawalt Lab including David Crowley, Justin Courcelle, and Jennifer Halliday.

Many people provided basic resources that helped me get my work done and get through my time at Stanford more easily including the library staff, in particular Jill Otto; Steve and Pat at the copy center; all the people in the Biostores especially Darnell, Joe and Manual; and all the people in the Biology Department main office.

On a personal level, I want to thank all of my many friends who have helped me get through graduate school whether it was by playing hockey and softball, going for bike rides, going hiking and camping doing many other things. These people include Bob Fisher, Chester Washington, Jochen Kumm, David Pollock, David Goldstein, Joanna Mountain, Mo Badi, Grant Hoyt, Becky Taylor, James Keddie, Healy Hamilton, Sinan Suzen, and Aviv Bergman. Many of these people are both good friends and colleagues.  

I am also grateful to my family, especially my brother Mike Eisen, my sister Lisa Eisen, and my mother Laura Eisen, my mother’s parents Annie and Ben Post, and my little brother Matthew Glenn, my uncle David Post, and my pseudo-brother Saul Jacobson for support and encouragement. And in particular, I want to thank Maria-Ines Benito for being there through all the good and bad times and for listening to me read sections of papers she had no interest in, and for proofreading various papers and for just about everything.

I dedicate this thesis to the memory of my father, Howard J. Eisen.