View source for 2014 Complexity and Modeling Program Readings

{{2014 Complexity and Modeling Program}}

[[Image: SFIcamp20143.jpg]]

==Readings and Materials==

===Resources===

'''[http://fractalfoundation.org/ Fractal Foundation]''' <br>
'''[http://santafe.edu/ Santa Fe Institute Website]'''<br>
'''[http://www.complexityexplorer.org/online-courses/11 Introduction to Complexity Online Videos]'''<br>
'''[http://www.complexityexplorer.org/explore/glossary Complexity Explorer Terms Glossary]'''<br>
'''[http://www.complexityexplorer.org/online-courses Santa Fe Institute Online Courses on Complexity]'''<br>
'''[https://www.youtube.com/user/santafeinst A huge online archive of Santa Fe Institute YouTube Videos]'''<br>
'''[http://www.complexityexplorer.org/explore/resources Background Reading on Complexity]'''<br>
'''[http://tuvalu.santafe.edu/projects/musicplusmath/ Music + Math Website!]'''<br>

===General Agent-Based Modeling===

[[Media:Axtell,_et_al_-_Aligning_Simulation_Models.pdf | Aligning Simulation Models - Axtell et al.]]

[[Media:Epstein_-_Agent-based_Generative_Social_Science.pdf | Agent-Based Generative Social Science - Epstein‎]]

[[Media:Epstein,_Steinbruner,_Parker_-_Modeling_Civil_Violence.pdf | Modeling Civil Violence - Epstein‎]] 

[[Media:Gajardo,_Moreira,_Goles_-_Complexity_of_Langton's_Ant.pdf | Complexity of Langton's Ant - Gajardo, Moreira, and Goles]]

===Tasmanian Devils===

[[Media:Polygons.PNG |Polygons.PNG]]

===Rock, Paper, Scissors===

[[Media:Kerr,_et_al_-_Local_dispersal_promotes_biodiversity_in_rock-paper-scissors.pdf | Rock Paper Scissors in Bacteria & Biodiversity - Kerr et al.]]‎ 

[[Media:Szabo,_Szolnoki,_Izsak_-_RPS_on_Small_World_Networks.pdf | RPS on a Small World Network - Szabo, Szolnoki, Izsak]]

[[Media:Kircher_-_Emergent_Behavior_of_Rock-Paper-Scissors_Game.pdf‎ | Emergent Behavior of Rock Paper Scissors - Kircher]]

===Flocking===

[[Media:Feder_-_Statistical_Physics_is_for_the_Birds.pdf | Statistical Physics is for the Birds - Feder ]]

[[Media:Hartman,_Benes_-_Autonomous_Boids.pdf | Autonomous Boids - Hartman & Benes]]‎

[[Media:Reynolds_-_Flocks,_Herds,_and_Schools.PDF | Flocks, Herds, and Schools - Reynolds]]‎

===Peppered Moths: Melanism and Evolution===

[[Media:melanism.pdf | Fine-tuning the Peppered Moth Paradigm - Grant ]]

[[Media:Darwiniandisciple.pdf | The Peppered Moth: Decline of a Darwinian Disciple - Majerus ]]

[[Media:Swedentalk220807.pdf | The Peppered Moth: The Proof of Darwinian Evolution - Majerus ]]

===Chaos Theory===

[[Media:Lorenz_-_Deterministic,_Non-periodic_Flow.PDF | Deterministic Nonperiodic Flow - Lorenz]]‎

===Networks===

[[Media:Dunne_-_Encyclopedia_of_Complex_Systems,_Food_Webs.pdf | Food Webs - Dunne]]

===Ants===

[[Media:Dorigo,_Maniezzo,_Colorni_-_The_Ant_System_-_Optimization_by_a_colony_of_cooperating_agents.pdf‎ | The Ant System: Optimization by a Colony of Cooperating Agents - Dorigo, Maniezzo, Colorni ]]

===Modeling Complexity in Evolution===

==== Schedule and handouts ====

* [[Media:schedule.pdf|Schedule]]
* [[Media:netlogo_day1_drift-mutation.pdf|Netlogo - day 1 - drift and mutation]]
* [[Media:netlogo_day2_cooperation.pdf|Netlogo - day 2 - cooperation]]
* [[Media:game_instructions.pdf|Instructions for online economic game]]

==== NetLogo files ====

* [[https://www.dropbox.com/s/tctj53o64p2u5k2/GenDriftBasic.nlogo Day 1 - drift and mutation]]
* [[https://www.dropbox.com/s/mwyno2gpuhdcfxi/Altruism_basic.nlogo 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:

# [[Media:McShea.Brandon_2010_BiologysFirstLaw_Chapter1.pdf|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.]]
# [[Media:Zimmer_2013_SciAm.pdf|Zimmer, Carl. 2013. The Surprising Origins of Life's Complexity. ''Scientific American'' 309:84--89. doi:10.1038/scientificamerican0813-84]]
# [[Media:Doolittle_2012_Nature.pdf|Doolittle, W. Ford. 2012. Evolutionary biology: A ratchet for protein complexity. ''Nature'' 481:270--271. doi:10.1038/nature10816]]

Day 2:

# [[Media:Szathmary.MaynardSmith_1995_Nature.pdf|Szathmáry, Eörs and Maynard Smith, John. 1995. The major evolutionary transitions. ''Nature'' 374:227--232. doi:10.1038/374227a0]]
# [[Media:Godfrey-Smith_2006_BiolTheory.pdf|Godfrey-Smith, Peter. 2006. Local Interaction, Multilevel Selection, and Evolutionary Transitions. ''Biological Theory'' 1:372--380. doi:10.1162/biot.2006.1.4.372]]
# [[Media:Okasha_2010_CurrBiol.pdf|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:
[http://www.gleamviz.org/]

Readings:

[http://www.pnas.org/content/103/7/2015.full.pdf+html Article on the role of airline network in predicting global epidemics.]

[http://www.cpt.univ-mrs.fr/~barrat/bmb68.pdf Maps and cartograms of disease evolution in the US via air traffic.]

==Curriculum & Tools==

[[Media:NetLogo_Mystery_Pattern.pdf | Netlogo Mystery Pattern]]‎

[[Media:A1-Complex_Adaptive_Systems-W&T.doc | Walk & Turn (doc)‎]]

[[Media:C1-Swords&Shields.doc‎ | Swords & Shields (doc)]]


[http://projectguts.org/files/Lorenz_0.nlogo Lorenz Attractor Netlogo Program ]

==Suggested Readings== 

[[Media:Why_Model.pdf‎ |Why Model? - Joshua M Epstein, ]]
 
[http://www.santafe.edu/media/workingpapers/10-12-033.pdf Jim Crutchfield, The Dreams of Theory]

[http://www.amazon.com/Complexity-Guided-Tour-Melanie-Mitchell/dp/0195124413/ref=sr_1_1?ie=UTF8&qid=1309386862&sr=8-1 Melanie Mitchell, Complexity: A Guided Tour]

[http://www.amazon.com/Honeybee-Democracy-Thomas-D-Seeley/dp/0691147213  Thomas D. Seeley, Honey Bee Democracy]

==Suggested Videos==

[http://santafe.edu/research/videos/catalog/ Video Catalog of SFI Lectures]

[http://itunes.apple.com/itunes-u/understanding-human-behavior/id381962164 Iain Couzin, Understanding Human Behavior]

[http://www.youtube.com/watch?v=ZbK92bRW2lQ Hunting the Hidden Dimension, NOVA documentary on fractal geometry]

[http://www.youtube.com/watch?v=cPjv5gIUeU8 The Secret Life of Chaos, BBC documentary on chaos theory]

[http://www.pbs.org/wgbh/nova/nature/emergence.html Emergence, Abridged NOVA ScienceNOW documentary on emergent phenomena]

[http://projectguts.org/files/Fileshare_Area493/videoTutorials/introCAS.mov Progect GUTS Intro to Complex Adaptive Systems]