6.048-6.877J/HST.949J Computational Evolutionary Biology
 
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Staff
Prof. Robert C. Berwick
berwick@csail.mit.edu
32-D728, x3-8918
Office hours: tba

Course Support
Lynne Dell
ldell@mit.edu
32-D664, 617-452-3679

Course Time & Place
Lectures: M 2:00-5:00 PM
Room:33-422,  map

Level & Prerequisites
6.047 or permission of instructor

Course Description

Evolution from a computational, modeling, and engineering perspective. Could the current H1N1 influenza virus ("swine flu") evolve into a more dangerous form? Why might 'survival of the fittest' really be 'survival of the luckiest'? Has there been natural selection for a ‘language gene’? When does ‘maximizing fitness’ lead to evolutionary extinction?  Did humans ever mate with Neanderthals? Has there been natural selection for a 'language gene'? How can we use evolutionary biology to design new drugs?
Extensive hands-on laboratory exercises in model-building and analyzing evolutionary data. Note: graduate version requires a more substantial final project and additional laboratory assignments. 4 Engineering Design Points.

Textbooks

Required (available at the MIT Coop or through Amazon):
Sean Rice, Evolutionary Theory: Conceptual and Mathematical Foundations. Sinauer, 2004. ISBN 0-87893-702-1.

General Policies on Required Work, Grading, and Collaboration

Class days in blue, holidays in green, add/drop dates in orange.

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Announcements:

• Welcome! For Lecture 1: Please read Lewontin, "Directions"; and Rice, ch. 1.
• For a 'popular' background, read R. Berwick, 'Feeling for the organism,' a review of Dawkins, "Climbing Mt. Improbable," 1996.

Course Schedule at a Glance
Week
Topic
Slides & Reference Readings
Laboratory/Assignment
9/14
Introduction: the basic dynamical forces of evolution & complications of the simple model
Laboratory 1/Pset 1 OUT TUES
9/21
Forces of evolution: Why Dawkins is wrong; Genetic drift or survival of the luckiest; The neutral theory of evolution
Rice, ch. 1, pp. 17–36; Rice, 36-50.
Lecture 2 notes.

9/28

The Fisher-Wright "diffusion" model for evolution

Rice, ch. 3, pp. 73–78;
Lecture 3 notes.

Laboratory 1 DUE
Laboratory 2 OUT
10/5
The Fisher-Wright model, cont'd.; Price's theorem

Rice, ch. 5, pp. 129–140.
10/13
 Coalescent theory I (Mon class on Tues!)
Rice, ch. 5, pp. 141–164.
 Laboratory 2 DUE
10/19
Coalescent theory II; did we mate with Neanderthals?

Rice, ch. 3, pp. 80–93.
Laboratory 3 OUT
10/26
How to (not) catch the flu
Notes, lectures 4-6
 
11/2 Molecular evolution I   Laboratory 3 DUE
Laboratory 4 OUT
11/9
Molecular evolution II
  
Choose final project
11/16
Evolution at the molecular level; comparing the chimp and human genomes
Lewontin, On inferring the number of evolutionary events.
 
11/23
Detecting natural selection
Laboratory 4 DUE
11/30
Detecting natural selection: was there selection for a 'language gene'?
12/7
Final project
presentations

 

 
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