CS294, Spring 2014

Evolution and Computation


Instructor:  Christos H. Papadimitriou 
Soda 689,  christos@cs, (510) 642-1559

Office Hours:  Mondays and Thursdays 5-6pm, and by appointment

Meets:  Thursdays 5:00-7:00pm, in Soda 320.

Units:  two.

Course  FormatA reading course.  Each meeting will be a two-hour discussion of the week’s readings.   

Purpose:  Evolution is one of the greatest problems in science, as well as a flourishing research endeavor, and sophisticated mathematics have been employed in its development.  Computational formalisms have also been used, albeit mostly for processing, as in genomics and phylogeny.  A leading thinker of the field has recently noticed that evolution has relied for too long on the mathematics of physics, that is, the kind used to study rolling balls.  During this semester, the Simons Institute at UC Berkeley has a semester-long program on Evolutionary Biology and the Theory of Computing bringing together some of the world’s leading scientists in this discipline.  One of the purposes of this course is to make this opportunity more accessible to the department’s students.

Course Requirements: 


·      Each week read the assigned readings, and write a one-page essay whose purpose is to convince the reader that you have comprehensively absorbed the assigned reading and you have thought creatively about it (due:  Thursday 5pm).


·      Attend all meetings, participate in the discussion, and contribute to it.


·      By the end of the semester, write a longer essay on an advanced topic of your choice.


Contents (as it looks right now):


First three weeks, the classics:  Darwin (Get The Origin of Species.  Make sure your copy has the 1959 foreword by Huxley), Weismann, Mendel, more.   Also note the Simons Institute program’s boot camp starting the same day as the course.  Make sure to attend as much as you can, it will be invaluable help in this class.


Next five weeks, molecular and quantitative foundations:  Graur and Li “Fundamentals of Molecular Evolution” second edition, Chapters 1 and 2.  We’ll also read classics likeWatson and Crick, Fisher, Wright, etc.


Next two weeks, Haldane’s “The cost of Natural Selection” and “Why sex and recombination?” by Barton and Charlesworth, among others.  In parallel, we’ll read about organisms (to remember that all this science is about wondrous, amazing, beautiful life…).


Next three weeks:  Computational theories of evolution.  Selection from:  Valiant's theory of evolvability, Evolutionary algorithms, Livnat's theory of mixability, evolutionary game theory, Artificial Life, etc.


Final four weeks:  Selection from other advanced topics.


Wanna smile?  Evolutionists gather around wall stain in the image of Charles Darwin (from The Onion)