2014 Complexity and Modeling Program Readings

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General Agent-Based Modeling

Aligning Simulation Models - Axtell et al.

Agent-Based Generative Social Science - Epstein‎

Modeling Civil Violence - Epstein‎

Complexity of Langton's Ant - Gajardo, Moreira, and Goles

Tasmanian Devils

Polygons.PNG

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

Flocking

Statistical Physics is for the Birds - Feder

Autonomous Boids - Hartman & Benes‎

Flocks, Herds, and Schools - Reynolds‎

Peppered Moths: Melanism and Evolution

Fine-tuning the Peppered Moth Paradigm - Grant

The Peppered Moth: Decline of a Darwinian Disciple - Majerus

The Peppered Moth: The Proof of Darwinian Evolution - Majerus

Chaos Theory

Deterministic Nonperiodic Flow - Lorenz‎

Networks

Food Webs - Dunne

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