Archived Assignments

Week 1

Read: Aderem, A. 2005. Systems Biology: Its Practice and Challenges. Cell 121:511-513. PDF

Read: Goldstein, J. 1999. Emergence as a construct: history and issues. Emergence 1:50-73. PDF

Read: Kadanoff, L. P. 1993. Chaos: a view of complexity in the physical sciences. in From Order to Chaos. L.P. Kadanoff, ed. World Scientific, New Jersey: pp. 399-429. (photocopy handed out in class)

Journal:

What is Chaos?

In your opinion, what was the most interesting example examined in the paper and why?

List one (1) thing discussed by the author that you either did not understand or would like to have discussed in more detail.

Week 2

Read: excerpt from Behe, M. 1996. Darwin's Black Box: The Biochemical Challenge to Evolution.

Read: Shapiro, R. 2007. A Simpler Origin of Life. Scientific American, June 47-53. PDF

Journal:

What is you opinion on the idea of irreducible complexity?

Which theory of the origin of life do you support and why? Creationism (Intelligent Design)?  Replicator First?  Metabolism First? Have you another idea?

List one (1) issue raised by either author that you would like to discuss in more detail in class.

• Lab: Lab 1 Due
  • Key to Lab

Week 3

Read: "Cellular Automata" in Flake, G. W. 1998. The Computational Beauty of Nature. pp.231-259. (photocopy provided)

Journal: Direct Link to Course Blog

We've now read a bit about two types of models: mathematical models (differential and linear equations for chaotic systems) and cellular automata. The mathematical models are sort of a top-down representation of a system: they model the behavior of the systems, ignoring the individual elements that comprise the system.  In contrast, cellular automata are more bottom-up model, we use simulate the basic elements to gains some insight into the behavior of the system. What are the pros and cons of each of these modeling approaches?  How does this relate to reductionist versus systems science?

Give an example of a system (not used in the reading) you think would be well modeled by a cellular automata (biological, social, or physical).

List one (1) point mad by or a topic introduced by the author that you would like to discuss in more detail in class.

• Lab Due: Exercise 2: Conway's Game of Life

Week 4

Read: Chapters 1-3 of Self-Organization in Biology (handout provided in class)

Read: Chapters 4-6 of Self-Organization in Biology (handout provided in class)

Journal: Direct Link to Course Blog1

• Lab Due: Exercise 3: Conway's Game of Life

Week 5:

MID-TERM PROJECT

• Lab: Due: Exercise 4: More NetLogo

• Readings:
  • • Read Stewart, I. 2003. Self-organization in evolution: a mathematical perspective. Phils. Trans. R. Soc. London, A. 361: 1101-1123. PDF
    • Read Coyne, J. 2007. Sympatric Speciation. Current Biology, 17: R787-R788. PDF
    • Read Pennisi, E. 2006. Speciation standing in place.  Science, 311:1372-1374. PDF
  • • Read Rhodda, G.H. et al. 1997.  The disappearance of Guam's wildlife: new insights for herpetology, evolutionary ecology, and conservation.  BioScience, 47: 5656-574 PDF
    • Read Carroll, S.P. 2007. Natives adapting to invasive species: ecology, genes, and the sustainability of conservation. PDF

• Journal: Direct Link to Course Blog

Week 7:

• Readings
  • Read Marshall, C. 2006. Explaining the Cambiran "Explosion" of Animals. Annual Review of Earth and Planetary Science Letters, 34: 355- 84. PDF
  • Read Thomas, R. D. K. et al. 2000. Evolutionary exploration of design options by the first animals with hard skeletons.  Science, 288: 1239-1242. PDF

Week 8:

• Readings:
  • Fitness Landscapes: 2 papers by Niklas, Karl