Contents

• Audience
• General Information
• Professor
• Required Texts
• Grading
• Policies
• General Plan of Study
• Detailed Schedule  (PostScript file.)
• Classes
• CourseInfo site
• Homework
• Discussion Papers
• Discussion Summaries
• Mathematica Notebooks
• Group Presentations

This course is part of the FOCUS program on Origins. Each student in this course will also be taking either HST 105 "Science in the Twentieth Century" or SOC 101 "Society and Identity: Origins and Transformations". A fourth course in the program is PHY 047 "Physics and the Universe", which is taken by half the students in place of this course. In addition to these classes, all the students in the program take the same University Writing Course and all students and professors meet once each week for dinner and discussion of epistemological issues common to all of the classes.  It is expected that students will contribute insights gained from these courses , as well as personal experiences, to our discussions of the scientific understanding of the emergence of complexity.

Professor

• Joshua Socolar -- Associate Professor of Physics
• E-mail: socolar@phy.duke.edu. (This is a good way to reach me.)
• Office:  Room 046, Physics Building
• Phone:  660-2557
• Office hours:    By appointment.  I will usually try to make it between 2:30 and 5:00 on Monday, Thursday, or Friday.

• Per Bak:  How Nature Works: The Science of Self-organized Criticality
• Philip Ball:  The Self-made Tapestry: Pattern Formation in Nature
• Richard Feynman:  The Character of Physical Law
• Stuart Kauffman:  At Home in the Universe: The Search for the Laws of Self-organization and Complexity

Policies

• Students must abide by the Duke Undergraduate Honor Code.
• Classroom participation is an essential part of the course.  Students are expected to help maintain an open, constructive classroom environment at all times.
• Students are welcome to talk with each other about homework assignments.  The only rule is that you must fully understand any work you hand in and it must be written in your own words.
• Special cases involving conflicts between the assignments for this class and other commitments or coursework will be treated fairly, but they must be brought to my attention well in advance of the due date.
• Classes will begin promptly at 10:55.
• I am always open to discussing topics of concern or interest outside of class.  Please feel free to contact me at any time about whatever is on your mind.

Our overall goal is to develop insight into the origins of complex structure in the natural world.

During the first half of the semester we will focus on physical and chemical processes that produce a variety of familiar structures, from
soap films to butterfly wing colorings and sand dune ripples.  Without dealing directly with any mathematical descriptions of these systems, we will see what types of models account for such patterns.  We will encounter systems in which simple causes generate complex structures, and others in which complex causes generate simple structures.  Along the way, we will refine our ideas about what constitutes a complex system and what kinds of questions we can ask about such systems.

We will begin by addressing some basic questions about the physical world and the mathematical models we use to describe and understand it.  We will talk briefly about randomness and determinism, energy and entropy, predictability and chaos, and fractals, all concepts that we will revisit several times over the course of the semester.  The texts for this part of the course will be Feynman's chapters adressing the relation between mathematics and physics and the ``arrow of time'', and selected portions of Ball's book describing the current understanding of processes that lead to interesting natural structures.

In the second half of the course, we will focus more directly on the question of whether there are general principles that govern the emergence of complex structure in physical and biological systems.  The emphasis will be on recent approaches to the modeling of biological evolution and the origin of life, as discussed by Bak and Kauffman.  Their approaches are representative of a new trend in thinking about complex systems, an approach that tries to understand complexity as an inevitable emergent phenomenon and finds relevant insights in the behavior of generic, abstract models.
 

• Classes are held on Tuesday & Thursday, 10:55-12:10, Room 234, Physics Building.  It is important that we start each class on time.
• To make the distribution of papers to classmates easier, we will use the CourseInfo system.  The address for this class is http://cinfo.aas.duke.edu/courses/PHYSICS48S.01-F2000.

This is a seminar-style course.  All students are expected to participate in class discussion on a regular basis.
    The heart of the course is the student-led discussion classes.  Each class period will be divided into two 35-minute sections, with a short break between them.  For each section, a student will have prepared a 4-6 page paper and distributed it to the class two days earlier.  We will begin the discussion by having one student (selected on the spot) comment briefly on the paper and then lead a discussion of it.
    The discussion leader's job will be to comment briefly on the themes identified in the paper as being interesting and important, then to direct a general discussion.  In some cases, the point of the discussion may be to expand on the paper by providing new examples and relating the subject to familiar experiences.  In others, it may be to probe our understanding more deeply by suggesting counterarguments or considering situations where the conclusions drawn from the paper don't seem to fit.  In still others, it may be simply to clarify questions and points of confusion.
    Finally, a student will be designated to write a short summary of the discussion and distribute it to the class within two days.  These summaries will provide the starting points for exam questions.
    Other classroom activities will include lecture/discussions led by the professor, a guest lecture/discussion by Prof. Nijhout on butterfly wing patterns, one midterm exam, and small-group presentations.

• Discussion Papers: Each student will be required to prepare two papers for class discussion over the course of the semester.  Your paper should cover the reading assigned for the upcoming class period.  Aside from length limits, the precise form of the paper is up to you.  It can be a direct summary of the reading material, drawing the class's attention to a particularly interesting or difficult point.  It can describe an application of the principles discussed in the text to a topic of personal interest.  It can even be an articulation of questions you have concerning the reading.  In all cases, though, the paper should be written using precise language and the logic of your explanations and arguments should be clear to your classmates.

    Each paper should be 4 to 6 pages long, double-spaced.  Papers should be saved in Rich Text Format (.rft) and uploaded to the appropriate place in the CourseInfo site for the class.  They are due at 8:00pm, two days before the class period in which it will be up for discussion.  All the other students will be required to read it and be prepared to respond to it in class.  Papers turned in up to 24 hours late will be penalized 25%.  Papers turned in later than that will be penalized 50%.
 
• Discussion Summaries:  For each Discussion Paper, one student will be designated to write a summary of the class discussion and post it to the CourseInfo site.  The summary should be written in complete sentences and paragraphs, not as a list.  It should be 1-2 pages long and include a statement of the main issue addressed in the paper, a paragraph describing the central conclusion reached during the discussion, and a paragraph describing one issue that remained unresolved.

    Each student will do two summaries during the semester.  Each summary is due at 8:00pm on the day after the relevant discussion.  Late assignments will be penalized 20%/day unless an extension is granted prior to the due date.
 
• Mathematica Notebooks: These are guided exercises to be carried out on a computer using the Mathematica program.  Mathematica is available on all public cluster computers.  It can also be downloaded from http://www.oit.duke.edu/site/.

(Click on the Software Library button.)
    There will be two graded Mathematica assignments.  For each of these, you must create your own notebook containing your write-up and turn in a hard copy at the beginning of class on the day it is due.  The write-up should include a paragraph describing your approach to the problem, input cells indicating what you did to obtain your results, a few figures (either explicitly requested by me or useful for illustration), and a concluding paragraph summarizing your findings.
    Notebooks are due at the beginning of class on the designated day.  Late assignments will be penalized 10%/day unless an extension is granted prior to the due date.  Collaboration on Mathematica Notebooks is encouraged, but every student is expected to submit an independent solution and understand it.
 
• Group Presentations: At the end of the term you will be placed in 4-person group that will be charged with making a 30-minute presentation on a topic selected by the group in consultation with the professor.  The presentations will focus on an issue raised previously in this course and should include elements drawn from other Origins courses.

    Details of the format for group presentations will be discussed in November.  Assignments are due at the beginning of the relevant class.  Late assignments will not be accepted.