2015 Complexity and Modeling Program Readings

2015 Complexity and Modeling Program Navigation Home Logistics CAMP Participants Surveys Preprogram Faculty Schedule Readings Software Word Wall Complexity Puns Project Page

Readings and Materials

Santa Fe Institute Website

Complexity Resources

Epstein's "Why Model" goes here
Introduction to Complexity Online Videos
Complexity Explorer Terms Glossary
Santa Fe Institute Online Courses on Complexity
A huge online archive of Santa Fe Institute YouTube Videos
Background Reading on Complexity

Rock, Paper, Scissors

Rock Paper Scissors in Bacteria & Biodiversity - Kerr et al.‎

RPS on a Small World Network - Szabo, Szolnoki, Izsak

Emergent Behavior of Rock Paper Scissors - Kircher

Chaos Theory

Deterministic Nonperiodic Flow - Lorenz‎

Ants

The Ant System: Optimization by a Colony of Cooperating Agents - Dorigo, Maniezzo, Colorni

Modeling Complexity in Evolution

Schedule and handouts

• Schedule
• Netlogo - day 1 - drift and mutation
• Netlogo - day 2 - cooperation
• Instructions for online economic game

NetLogo files

• [Day 1 - drift and mutation]
• [Day 2 - cooperation]

Readings

In order to help you prioritize, the first reading for each day is the most important, while the second is important and the third is less important.

Day 1:

1. McShea, Daniel W and Brandon, Robert N. 2010. Biology's first law: the tendency for diversity and complexity to increase in evolutionary systems. University of Chicago Press, Chicago. Chapter 1.
2. Zimmer, Carl. 2013. The Surprising Origins of Life's Complexity. Scientific American 309:84--89. doi:10.1038/scientificamerican0813-84
3. Doolittle, W. Ford. 2012. Evolutionary biology: A ratchet for protein complexity. Nature 481:270--271. doi:10.1038/nature10816

Day 2:

1. Szathmáry, Eörs and Maynard Smith, John. 1995. The major evolutionary transitions. Nature 374:227--232. doi:10.1038/374227a0
2. Godfrey-Smith, Peter. 2006. Local Interaction, Multilevel Selection, and Evolutionary Transitions. Biological Theory 1:372--380. doi:10.1162/biot.2006.1.4.372
3. Okasha, Samir. 2010. Levels of selection. Current Biology 20:R306-7. doi:10.1016/j.cub.2010.01.025

Epidemiology

Global Epidemic and Mobility modeler: [1]

Readings:

Article on the role of airline network in predicting global epidemics.

Maps and cartograms of disease evolution in the US via air traffic.

Curriculum & Tools

Netlogo Mystery Pattern‎

Walk & Turn (doc)‎

Swords & Shields (doc)

Lorenz Attractor Netlogo Program

Suggested Readings

Why Model? - Joshua M Epstein,

Jim Crutchfield, The Dreams of Theory

Melanie Mitchell, Complexity: A Guided Tour

Thomas D. Seeley, Honey Bee Democracy

Suggested Videos

Video Catalog of SFI Lectures

Iain Couzin, Understanding Human Behavior

Hunting the Hidden Dimension, NOVA documentary on fractal geometry

The Secret Life of Chaos, BBC documentary on chaos theory

Emergence, Abridged NOVA ScienceNOW documentary on emergent phenomena

Progect GUTS Intro to Complex Adaptive Systems