Can computers reproduce? Can DNA compute? Can evolution give us hints on solving big problems? Is life's blueprint inefficient? This course looks at the way computers are shaped by biological thinking, and the way that biologists make use of computational theories. Topics range from artificial life to identification of genes to the susceptibility of machines to viruses.

Final Exam: Thursday, December 14, 1:30 p.m.; location TCL 206

Lectures:

• Lecture 1, September 7. Introduction. The course syllabus and Honor Code.
• Lecture 2, September 12. Computation. Models and measures of things that compute.
• Lecture 3, September 19. String biology. The "central dogma" of biology.
• Lecture 4, September 21. String bio II, and synthetic biology.
• Drew Endy's Tired of Evolving? talk.
• Lecture 5, September 26. Sequencing and Assembly.
• Lecture 6, September 28. Blast searching, string matching.
• Lecture 7, October 3. Evolution.
• Lecture 8, October 5. Genetic algorithms.
• Lecture 9, October 12. Information theory.
• Lecture 10, October 17. Algorithmic information theory (and the beginning of Life)
• Lecture 11, October 19. Cellular Automata.
• Lecture 12, October 24. Exam review.
• Lecture 13, All Hallow's Eve. Transistors to memories.
• Lecture 14, November 2. Flip-flops and counters.
• Lecture 15, November 6. Neurons and perceptrons.
• Lecture 16, November 8. Neural nets and Vision.
• Lecture 17, November 14. Filters, Growth, and L-Systems
• Lecture 18, November 16. L-systems, Kolam, and Growth.
• Lecture 19, November 21. Protein folding & Puzzles
• Lecture 20, November 28. DNA-based computation: Len Adleman
• Lecture 21, November 30. DNA computation II: Through Self-Assembly.
• Lecture 22, December 5. Viruses.
• Lecture 23, December 7. Life as an Algorithm.

• Lab 1. Getting acquainted lab.
• Lab 2. Turing machine lab.
• Coming Soon: The Incredible Fredkin Page.
• Lab 3. Gene-finding with PERL.
• Lab 4. Genetic Algorithms.
• Lab 5. Entropy.
• Lab 6. Life and other CA's.
• Lab 7. Digital Logic.
• Lab 8. L-Systems.
• The Large Prime printout for lab 9.
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