Self-Organization in Science and Society

 

Spring 2016  STSH 4580 Mon-Thurs 12-2, Sage 2701. Instructor: Ron Eglash.

To contact instructor:
Office Hours: Mon 10:00-12:00 and by appointment, 5502 Sage. Email: eglash@rpi.edu, phone: 276-2048. Course webpage: www.rpi.edu/~eglash/eglash.dir/selforg.html

Description
Self-organization has become an increasingly important phenomenon in both the natural sciences and engineering. Self-assembly of molecular structure is critical to nanotechnology; self-regulating ecosystems are modeled in biology, and so on. But recursive loops in which things govern themselves are also foundational to society: democracy is the people governing the people; social networks on the internet arise by self-assembly, and many indigenous societies use self-organization to create sustainable ways of life. This course will introduce students to models of self-organization in natural science and engineering, and examine their potential application to society, politics, and ethics. No prerequisites are required.

Learning Outcomes

Academic Honesty

While ideas are available to everyone, credit for ideas, and the particular text used to express them, belongs to their originator. Plagiarism occurs when a student attempts to pass the ideas or words of someone else as their own. It is surprisingly easy to do. For example, students who are not writing in their first language will sometimes try to use a sentence from another written text, simply because they are worried about their grammar. Plagiarism also occurs when a quotation is reworded in an attempt to avoid citation—always make sure the sources of your quotations are specifically cited. The internet makes plagiarism particularly tempting, since you can copy and paste from the web to your paper. Recycling your own paper from another course would not be plagiarism, but it would be academic dishonesty and thus subject to the same penalties, which include failing the course (a grade of “F”).

Special Needs
Please contact me if you have special needs such as disability or religious holidays.

Requirements:
Evaluation will be based on the 4 short “reading reflection” papers (10% each), the research project paper (30%), the research project presentation (10%), and class participation (20%). Note that the syllabus tells you the reading that will be discussed for that day. You need to have done the reading before you arrive, and you are required to bring the reading to class so that we can discuss the texts in detail. To get participation credit for a class meeting you are required to be physically present, AND post a discussion question or comment on our board here. Many class sessions you will need your laptop as well to play with simulations and other tools.

Short papers and research project:
Short “reading reflection” papers should be about 5 pages (double-spaced, with proper citations); these allow you to demonstrate your understanding of the material. The final research project paper should be 8-10 pages (double-spaced, with proper citations); the instructor will help you find a suitable topic for your research.  Research projects can be done by groups, in which case the paper will be longer, and each individual is responsible for a different section of the paper. Working in a group is a great way to  bring together more than one discipline (eg math and anthropology, or computing and environmentalism). Research project presentations may also be done by the group.

Texts:

Mitchell, Melanie. Complexity: a Guided Tour. Oxford University Press, 2009

Eglash, Ron. African Fractals: Modern Computing And Indigenous Design. Rutgers University Press1999.

Course Schedule:

Part I: Foundations of Self-Organization

 

Jan 25: Intro
Lectures: intro to self-org, history of self-org
in-class video: http://www.pbs.org/wgbh/nova/nature/emergence.html.
Readings: Mitchell ch 1
Further examples in video:

Jan 28: fractals--technical background 1
Reading assignment 1: Mitchell ch 7
Reading assignment 2: Take a tour through Yale's "Panorama of Fractals and Their Uses"
Lecture: Fractal Dimension  
In class: Video “Hunting the Hidden Dimension” http://www.youtube.com/watch?v=ZbK92bRW2lQ

Feb 1: fractals--technical background 2
Reading: Mitchell ch 17

Lecture: Embedding dimension  
Homework: find a fractal and measure its dimension. It can be a leaf you found, a photo of a city, grandma's quilt, anything you like. If you have windows or lunix you can use freeware: http://www.fractalyse.org/. Note that it needs .tiff files (but some file converters will add some form of compression--using gimp or photoshop will help that issue). The "analyze" menu gives you several choices for dimension measures, I find that "Correlation" usually works best. I am not sure if there is a freeware version for the mac -- try: http://paulbourke.net/fractals/fracdim/.
Make sure to bring your laptops as we will experiment in the classroom with software for creating fractals.

koch curve plant sprial baobab fern

Feb 4: fractals--social aspects

Readings: I have included both "beginner" and "advanced" readings -- read any 2 that you find suitable, in any combination you like (you can do two from one category or across categories):

Economics:
beginner: http://aidwatchers.com/2010/09/beautiful-fractals-and-ugly-inequality/
advanced: http://ageconsearch.umn.edu/bitstream/127794/2/Cornell_Dyson_wp0342.pdf

Literature:
beginner:http://users.math.yale.edu/public_html/People/frame/Fractals/Panorama/Literature/PollardGott/PollardGott.html
advanced: http://www.depauw.edu/sfs/backissues/113/wenaus.html

Social science:
beginner: http://mayagis.smv.org/The%20Broken%20Past%20Fractals%20in%20Archaeology%20P503L835G32T2000.pdf
advanced: http://www.colbud.hu/apc-aa/img_upload/4d11dfd490c468ca39fcefabae592944/GalJournalLinguisticA2005.pdf

and just for fun two more reading options in literature:

Diamonds within diamonds: Ethnic Literature and the Fractal Aesthetic
The Fractal Nature of Gary Snyder's Mountains and Rivers without End

in-class video: http://www.ted.com/talks/geoffrey_west_the_surprising_math_of_cities_and_corporations.html

lectures: fractal poverty traps fractal eye movements and art

Feb 8 Chaos-- technical background 1
Reading: Mitchell ch 2, Nonlinear dynamics as low-dimensional self-organization.
Lecture: Intro to chaos theory
In class: Video, “The Strange New Science of Chaos.”

Feb 11 Chaos-- technical background 2
Reading: Hofstadter, D. “Strange Attractors: Mathematical Patterns Delicately Poised Between Order and Chaos.” (pp. 363-395 in the hardcopy original pages). You can also get a scanned copy here.
In-class: we will experiment with:

logistic map: https://community.csdt.rpi.edu/projects/773/run

sonic version: https://community.csdt.rpi.edu/projects/355/run

exercises

Lecture: Cybernetics

Feb 15 no class

Feb 18 Chaos social 
Lectures: Intro to STS
Readings: Chaos theory and international relations (also online at http://foreignpolicy.com/2013/05/23/can-chaos-theory-teach-us-anything-about-international-relations/)
Chaos theory and social science: The Problem of the Attractor A Singular Generality between Sciences and Social Theory.
Rossler attractor exercise

Feb 22 Cellular automata
Mitchell ch 8-10. In class: experiment with CA at http://www.ccd.rpi.edu/eglash/temp/Life32v111.zip or http://sourceforge.net/projects/golly/
Lecture: Intro to Life32
Lecture: Measuring Complexity 
In-class video: http://www.ted.com/talks/stephen_wolfram_computing_a_theory_of_everything.html

Feb 25 Flocking
Mitchell ch 12 (information in living systems).
Young " How the Science of Swarms can help us fight cancer and predict the future"
Optional: Couzin, I.D. & Krause, J. (2003) Self-organization and collective behavior in vertebrates. Advances in the Study of Behavior 32, 1-75.

In class: http://www.youtube.com/watch?v=uIH-p1OSRZw wildebeest migration – start at 1:20 and observe how split evolves over time.
Deborah Gordon: http://www.ted.com/talks/deborah_gordon_digs_ants.html
Flocking simulation at http://www.heatonresearch.com/aifh/vol2/flock_3d.html; also at http://threejs.org/examples/#webgl_gpgpu_birds
Mosh pit sim: http://mattbierbaum.github.com/moshpits.js/
Lecture: self-organization in vetebrate collective behavior

Feb 29 Autocatalytic sets: Readings

Mar 3 Self-organized criticality and 1/f noise

Readings:

  • Gardner, "White, Brown and Fractal Music"
  • Bak and Chen, "Self-Organized Criticality"
  • Eglash, "Inferring representation type"
  • Optional: http://www.pnas.org/content/92/15/6689.full.pdf

    In-class exercise: show sub-critical, super-critical, and critical systems using simulations at http://www.shodor.org/interactivate/activities/ABetterFire/
    Lecture: 1/F noise

    Mar 7 Evolution revolutions
    Mitchell ch 5 (evolution), 18 (evolution complexified by autocatalytic sets)
    Lecture: Darwin: an STS perspective

    Part II: Applications in African Studies

    Mar 10 --  1st paper due

    Mar 14 --spring break

    Mar 17  -- spring break

    March  21

    March 24 

    March 28

    Part III: Self-organization: from natural to social ecologies

    March 31 Second paper due (drop here)

    April 4

    April 7

    April 11

    April 14

    April 18

    April 21

    Part V The Politics of Self-Organization

    April 25

    April 28 Third paper due (drop here)

    May 2

    May 5

    May 9

    May 13 (no class) Final research paper due (drop here).

    Some texts you might find useful in your research projects for this course:

    Politics of self-organization
    Haila, Yrjö et al. How Nature Speaks: The Dynamics of the Human Ecological Condition. Duke University Press 2006.

    Chesters, Graeme and Welsh, Ian.  Complexity and Social Movements: Protest at the Edge of Chaos. Routeldge 2006.

    Geyer, Robert Complexity, Science and Society, Oxford: Radcliffe Publishing 2007.

    http://www.marxists.org/subject/science/essays/kropotkin.htm

    Complexity theory
    R. Lewin, Complexity: Life at the Edge of Chaos. Macmillan Publishing Company, New York, 1992

    Complexity: the Emerging Science at the Edge of Order and Chaos by Mitchell M. Waldrop 1992

    How Nature Works: the Science of Self-organized Criticality by P. Bak

    At Home in the Universe : the Search for Laws of Self-organization and Complexity by Stuart Kauffman

    Hidden Order: How Adaptation Builds Complexity by John H. Holland

    The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems and Adaptation by Gary William Flake

    Recursion and self-replication
    Hofstadter, D. R., Gödel, Escher, Bach: an Eternal Golden Braid, NY: Basic Books, 1979.

    Robert A. Freitas Jr., Ralph C. Merkle, Kinematic Self-Replicating Machines, Landes Bioscience, Georgetown, TX, 2004; http://www.MolecularAssembler.com/KSRM.htm

    Networks
    Six Degrees : the Science of a Connected Age by Duncan J. Watts