Wednesday, January 02, 2008

In memory of Sam Karlin

I just got an email telling me that Sam Karlin had passed away. Sam, for those who do not know, was one of the luminaries in bioinformatics and mathematical biology. You can learn a bit more about him by going to this site which relates to a workshop that was help in honor of his 80th birthday.

His passing saddens me greatly. Sam was a curmudgeony guy at times, but also a great scientist and teacher. He was one of my mentors when I was in graduate school at Stanford. I was kind of a fish out of water --- trying to learn boinformatics in a lab that studies the cell biology of DNA repair processes. So I took a course from Sam Karlin and Volker Brendel and then spent three years meeting on and off with Sam in his office discussing various aspects of genome and gene sequence analysis. We did not always agree. But I think I learned more about bioinformatics from those meetings with Sam than from anything else I have done in my career.

Sam reminded me a lot of my grandfather (who was a physicist). We would meet to ostensibly talk about RecA (my favorite protein) or DNA composition (Sam's favorite thing at the time) or evolution or something or other. But Sam turned every meeting into some type of lesson about bioinformatics. We rarely got to our end goal, but that did not really matter.

So - in his honor I am going to start a new section of this blog --- the Something about Math in Biology or the SAM in Biology section ... stay tuned.

NOTE Lee Altenberg has a memorial page to him, consisting of his doctoral advisor genealogy:


  1. R.I.P., Sam.

  2. Sam was my PhD supervisor. To me he represented the ultimate scientist who leveraged his unusual mathematical skills to handle real life problems. he could have remained a mathematician, but he chose not to.

    the thesis i wrote is titled "Studies in Enzyme Kinetics". during 3 intensive years i travelled about 12 times between Palo Alto and Rehovot. Both his offices at Stanford and the Weizmann Institue looked like research factories. many visitors, many students, many projects.

    the journey with him took me from solving mathematical probems with total positivity tools, developping migration models in population genetics, innovating on data analysis techniques to study multivariate genetic data and studying, in great depth, enzyme kinetic models originally developped by biologists.

    today, as a statistical consultant, i can attribute to sam my ability to work on very different areas, seeking the highest possible level of professionalism. Sam Karlin represents the ultimate scientist, specially in these days of interdisciplinary initiatives. His influence as a researcher and supervisor cannot be truely grasped. we lost one of the giants in science.


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