ECOL 496H/596H:
Complex systems: networks and self-organization in biology

course description & schedule
Optional and required readings for this course
Course syllabus (pdf file)
another graduate course taught by me: ECOL467/567
another graduate course taught by me: ECOL596V
another course taught by me: ECOL597S
Course list for the Department of Ecology and Evolutionary Biology
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Soc. Ins. Lab

This course was taught in Spring 2008.
It will be on offer again, but possibly not until Fall 2011 or later.
If you are a student interested in the course, drop me an email, so I can judge how many people would like to take it.

What is a complex system? What does networks theory have to do with biology? Biologists have discovered that many biological systems, from embryos to ecosystems, can be considered "complex systems", in that many units interact without central control to form complicated patterns. How do such patterns arise? What can we learn from a 'holistic', system-wide approach?

We will discuss current and classic literature on complex systems research at multiple levels, including gene regulatory networks, neural net(work)s, ecological networks, and social networks. We will try to identify the commonalities of these systems and what is so exciting about 'systems biology'. We will also discuss what types of models are used to describe and study self-organization and networks in general.
Students will be allowed to pick some topics for the course that are most relevant to their interests - the schedule below is therefore preliminary and flexible.

Grading: there is no end-of-term paper or exam. The main assignment is to prepare a presentation and discussion session (including a one-page handout) and to write or revise a "Wikipedia" entry related to the topic of your presentation. Grades are also based on participation in discussions, and reading the readings.

open sections of this course: 496H, 596H
Please note that the first class will be on January 23rd (no class on January 16th).

Please email me if you have questions about the course:

Instructor: Anna Dornhaus
I'm a biologist with a special interest in collective behavior and cognition (esp. 'collective intelligence'). I work with social insects, particularly bumble bees, honey bees, and ants.
check out my lab webpage, department webpage, or personal webpage
Feel free to contact me with questions about the course or if you are interested in working in my lab:

Students from this course have created, substantially edited or expanded the following Wikipedia articles:
Ecological Network (EJ)
Blackout Inevitability and Electric Sustainability (ZW)
Self-organization in social insects (JJ)
Quorum sensing (ML)
Tandem running (ML)
Spatial organization in social insects (JJ)
Modular neural networks (JS)
Mechanisms of cellular differentiation (DS)
Weaver ants (TC)
Network theory (MH)
Pattern oriented modeling (AR)
Preventing transmission of infectious diseases (MH)
Evolving cellular automata (SK)
History of Artificial Life (YT)
Non-trophic networks (NF)
Task allocation and partitioning in social insects (FD)
Interactomics (GP)
Prokaryote sociality (WD)
Kin selection and what is r (WD)
Dense heterarchies (MC)
Patterns of self-organization in social insects (MC)
Symmetry breaking in Herding behavior (MC)

Students: please check whether your article was tagged, and address the comments or respond to them. Please read the quality/formatting standards for Wikipedia if your article receives a complaint. Feel free to add to/improve other students' articles. Some of these articles may be better joined together or joined with relevant larger categories. You can also comment on the tags on other student's articles.

Course plan for Spring 2008

Date Topic Presenter Reading
Jan 23 Introduction: What is a complex system? (also admin: assigning topics & dates for presentations, also tipps for presentations) Dornhaus -
Jan 30 Six degrees of separation: what do we know about networks Shikhar Kumar Proulx et al., May
Feb 6 Self-organization: pattern and function arising from a non-ordered system Michele Lanan Nedelec et al., also read Wikipedia entries Complex systems and Self-organization
Feb 13 Ecological networks: can we predict extinction rates from 'connectedness'? Emily Jones Montoya et al.
Feb 20 Pattern formation and cell differentiation in developmental biology Deborah Shelton Levine & Davidson, and check out this video and/or NYTimes article
Feb 27 Systems biology and the 'interactome' Grant Peterson (& Alex Lancaster) Bruggeman & Westerhoff and optionally Wilkins
Mar 5 no class    
Mar 12 Neural Networks: Complex Solutions or Complex Confusion? Jason Slepicka Moody and Ness essays; also see Wikipedia on Neural networks and Artificial neural networks. Optional: review by Abdi
Mar 26 Societies as complex systems - the spread of disease in a 'small world network' Ming Huang Lloyd & May and Naug & Smith
Apr 2 Ecological networks: Tritrophic interactions between parasitoids, hosts, and host plants Nicole Ferguson Heil - please read (at least) up to page 48 (starts with p 41)
Apr 9 Self-organized structures in physical (non-biological) systems and Group size and emergent properties Jenny Jandt & Tuan Cao On self-organization, read Bak & Chen; on group size, read Parrish & Edelstein-Keshet; optionally, Detrain & Deneubourg and/or Michod
Apr 16 Social insects: self-organized symmetry breaking and Communication and task allocation Fred Drumlevitch & Meghan Curry Altshuler et al., O'Donnell & Bulova, and Anderson et al., plus optionally another O'Donnell & Bulova paper
Apr 23 Fast, cheap, and out of control? Engineered complex systems AND Artificial life Zach Wagner & Yun Tao Dobson et al.; Burtsev & Turchin; and optionally Buchli et al. or Reynolds
Apr 30 Cellular societies: collective behavior in bacteria and other microbes Will Driscoll Parsek & Greenberg and Crespi
May 7 Conclusion and discussion - is it all a hype? Alyssa Rosemartin Grimm et al.; please also be prepared to say whether and how 'complex systems science' affects your own research, and/or whether you think it is a useful approach.