April 2-6: Chapter 10 in Origins of Life.
Apr 4 (Wed):
Evolving
virtual creatures
from Karl Sims.
Apr 6 (Fri):
Evolving
autonomous agents
from Frank Dellaert and Randall Beer.
Apr 9 (Wed):
Evolution and manufacturing of
crawling robots.
Apr 11 (Fri):
Swimming creatures
from Tu and Terzopoulos.
April 16-20: Chapter 11 in Origins of Life.
Apr 16 (Mon):
Thomas Ray's
Tierra
system of evolving programs.
Apr 20 (Fri):
Robert Axelrod and the
Iterated Prisoner's
Dilemma.
April 23-27: Chapter 12 in Origins of Life.
Apr 23 (Mon):
Craig Reynolds on
Co-Evolution for game
of tag.
Course Description
This course covers a broad array of techniques for computer simulation of biological systems. The course material will draw from biology, artificial life, robotics, computer graphics and other research areas. Some of the course topics include self-replication, artificial chemistry, multi-cellular development, simulation of evolution, cellular automata, mass-spring simulators, L-systems for plant development, animal locomotion (walking, swimming, jumping), flocking and herding behavior in groups, predator/prey systems, parasites, and foraging behavior.Students will carry out several programming projects during the course. Basic programming skills are recommended for students entering the course, but no previous background in biology is necessary. There will be three or four small programming projects during the first part of the course. During the second half, students will propose and work on a large project of their choice. Projects can be done individually or in teams of two students.
Books and Articles
Required textbook:
"The Origins of Life: From the Birth of Life to the Origin of Language"
John Maynard Smith and Eors Szathmary
We will use the above book to ground our discussions on the biological aspects of the course topics. It will be a point of departure to learn about the different levels of complexity in biological systems (molecules, cells, multi-cellular creatures, species, etc.) Reading material on simulation techniques will be taken from research papers from a variety of areas.
Course Topics
Self-Organization
- self-replication (von Neumann, Christopher Langdon, others)
- complexity at edge of chaos
Molecules
- artificial chemistry
- metabolism
- molecular hypercycles
- RNA folding
- DNA codon optimality
Membranes and Cells
- membrane formation
- cell models
- cell cytoskeletons
- immune systems
Cell aggregation (courtesy of Kurt Fleischer)
Development
- multicellular development
- slime mold aggregation
- pattern formation
- gene cascades/networks
- cell simulation of development (Fleischer and Barr)
- L-systems for plant development
Plant growth (courtesy of Przemyslaw Prusinkiewicz)
Evolution
- evolution
- speciation
- Dawkins on major events in evolution
- genetic algorithms
- blind watchmaker
- co-evolution (Karl Sims, Craig Reynolds, Danny Hillis)
- sexual selection
Locomotion
- modes of locomotion
- Braitenberg vehicles
- evolution of walking and hopping motion (Karl Sims)
- swimming (Terzopoulos)
Walking simulation (courtesy of Karl Sims)
Physics Simulation Techniques
- partial differential equations (PDE's)
- reaction-diffusion
- cellular automata (life, spiral waves, etc.)
- mass-spring systems
Tentacle motion (courtesy of Andrew Cantino)
Multi-Organism Interaction
- communication
- Prisoner's dilemma, tit-for-tat
- predator/prey
- flocks, schools, swarms
- ant foraging
- parasites
- digital creatures (Thomas Ray)
Flocking with collision avoidance (courtesy of Craig Reynolds)
Related Web Links
Flocking resources, compiled by Craig Reynolds.Mass-spring locomotion at sodaplay. (Be sure your browser can run Java!)
Evolved virtual creatures from Karl Sims (locomotion and competition).
Dr. Prusinkiewicz's research on plant development.