Bryn Mawr College
CS 361: Emergence
Spring 2008
Course Materials
Dr. Emily Greenfest-Allen
General Information
Instructor: Emily Allen, PK 246, x6503
E-Mail: egallen at brynmawr dot edu
Lecture Hours: Tuesdays & Thursdays, 11:30 a.m. to 1:00 p.m.
Room: PK 349; Computing Labs in PK 231
Additional Lab Hours: Mon-Wed 1-3 p.m. in Room 231 (additional lab hours will also available, see below)
Laboratories:
- Computer Science Lab Room 231 (Science Building)
- You will also be able to use your own computer to do the labs for this course.
These are the hours when the Lab will not be available:
TBA
Syllabus: PDF version of the basic course information contained on this website + more detailed information on policies and assignments.
Software
Important Dates
January 22: First lecture
May 1: Last lecture
Assignments and Readings
Current Assignment:
- Readings:
For Thursday 4/10
- Read Chapter 20 from Flake (Computational Beauty of Nature). Handed out in class
- Read Chapters 3 - 5 from Carroll (Endless forms most beautiful)
Past Assignments
Web Explorations
- Non-Linear Dynamics at Drexel (FLASH Movies of Choatic Systems)
- Chaos Pro and other Fractal Generating Programs
- Emergence: Complexity and Organization (a journal and society)
Schedule
- Week 1 (January 22, 24)
Topics: PowerPoint: Emergence
-
- Week 2 (January 29, 31
- Topics: PowerPoint: Chaos
- Chaos and Complexity
- Predicatability: Deterministism versus Stochastism
- Simulation:
- Explorations in Chaos and Fractals
-
- Week 3 (February 5, 7)
- Topics: Power Point: Phase Space
- Phase Space and the Fractal Dimension
- The Origin of Life
- Irreducible Complexity: Fact or Fiction?
- Simulation:
-
- Week 4 (February 12, 14)
- Topics: Power Point: CAs
- Cellular Automata
- Universal Computation
- Simulation:
-
- Week 5 (February 19, 21)
- Topics:
- Self-Organization in Biology
- Simulation:
-
- Week 6 (February 26, 28)
- Topics:
- Competition and Cooperation
- Ecological Release and the Origin of Species
- Simulation:
-
- Week 7 (March 4, 6)
Mid-Term Presentations
- Week 8 (March 11, 13)
No classes. Spring Break!
- Week 9 (March 18, 20).
- Topics:
-
- Week 10 (March 25, 27)
- Topics:
- Simulation: None
-
- Week 11 (April 1, 3)
- Topics:
- Simulation:
- Week 12 (April 8, 10)
- Topics:
- Hox Genes
- Genetic Algorithms
- Simulation:
-
- Week 13 (April 15, 17)
- Topics:
- Modularity and Robustness
- Simulation:
-
- Week 14 (April 22, 24)
- Topics:
- Simulation:
-
- Week 15 (April 29, May 1)
Final Project Presentations
Grading
All graded work will be graded on a point scale, with the total worth of the assignment proportional to its complexity and difficulty. At the end of the semester, final grades will be calculated as a weighted average of all grades according to the following weights:
Class Participation: 10%
Journal: 25%
Weekly Exercises: 25%
Mid-Term Presentation: 15%
Term Project: 25%
Total: 100%
Additional Readings
- May, R. M. 1974. Biological Populations with Nonoverlapping Generations: Stable Points, Stable Cycles and Chaos. Science 186:645-647. PDF
- Pereto, J. 2005. Controversies on the origin of life. International Microbiology, 8:23 - 31. PDF
- Koonin, EV. 2007. The cosmological model of eternal inflation and the transition from chance to biological evolution in the history of life. Biology Direct, 2: 15. PDF
Created on January 18, 2008.
from Oltavi and Barabási 2002