The Axis of Evol: Getting to the Root of DNA Repair with Philogeny
In 2005 I wrote an essay about my time in graduate school that was potentially going to be included in a special issue of Mutation Research in honor of my PhD advisor Phil Hanawalt. Alas, publishing my essay ran into complications in regard to the closed access policies of this journal. So in the end, my essay was not published. I had forgotten about it mostly until very recently. And so I decided to convert the essay to a blog post. The essay is sort of about what I did in grad. school and sort of about Phil ...
Abstract:
Phylogenomics is
a field in which genome analysis and evolutionary reconstructions are
integrated. This integration is important because genome data is of great value
in evolutionary reconstructions, because evolutionary analysis is critical for
understanding and interpreting genomic data, and because there are feedback
loops between evolutionary and genome analysis such that they need to be done
in an integrated manner. In this paper I describe how I developed my particular
phylogenomic approach under the guidance of my Ph.D advisor Philip C. Hanawalt.
Since I was the first to use the term phylogenomics in a publication, I have
decided to rename the field (at least temporarily) Philogenomics.
1. Doctor of Philosophy
When I went to
Stanford for graduate school, I was interested in combining evolutionary
analysis and molecular biology in a way that would allow me to study molecular
mechanisms through an evolutionary perspective. Although I had gone to Stanford
ostensibly to work on butterfly population genetics, within two days of
starting a rotation in Phil’s lab, I knew that that was where I wanted to work.
This decision was somewhat traumatic, since the work on butterflies included
spending the summers at 10,000 feet in the Rocky Mountains and possibly chasing
butterflies like a Nabakov wanna-be all over the mountain ranges of the world.
As an avid outdoor person, this was quite appealing. Nevertheless, I chose to
spend 99% of my graduate work in the dingy confines of Herrin Hall, studying
DNA repair. The choice of joining Phil’s lab did have one very positive affect
– and that was on my relationship with my grandfather on my mother’s side.
Benjamin Post was in many ways like a father to me, especially after my father
passed away. He was a physicist from the “old school” and thought that most of
biology was completely useless. Needless to say, when I told him I was going to
graduate school in California (which he considered already one strike against
me) to study butterflies, he decided I was simply a lost cause. Despite all his
talk of Einstein and computers and math when I was a child, I might as well
have been a poet from his point of view. To make matters worse, my grandfather
was a crystallographer, and my brother was getting his Ph.D in crystallography
at Harvard. When I informed my grandfather that I was going to be working on
DNA repair, he seemed somewhat interested. And then I told him, my advisor,
Phil Hanawalt, is relatively well known, and actually used to be considered a
biophysicist. Then my grandfather really perked up. He said, “Hanawalt – is he
related to Don Hanawalt?” It turns out, that my grandfather worked in the same
field as Phil’s father (they both did powder diffraction) and knew him. So my
grandfather said “You may not be doing real science, but at least you are doing
it with the relative of a real scientist.” Thankfully, I was no longer the
black sheep in the family. So, with my grandfather’s approval, I embarked on a
career in DNA repair.
