Syllabus | Phil 410 - Constructive approaches to the emergence and evolution of life - Fall 2003

Mark Bedau
Vollum 141
751-7337 | bedau@reed.edu

Course meetings
Biweekly lecture/conference: Tu/Th 2:40-4:00.
Occasional evening lab/conferences will be scheduled during the term.

A 300-level philosophy course or permission of the instructor.

Philosophy is concerned with the essential nature of the most fundamental aspects of reality, such as life and mind. Philosophy traditionally relies on a priori thought experiments and conceptual analyses, but these methods have limitations. A priori thought experiments yield uncertain and inconclusive results when directed to complex systems. And conceptual analysis of complex phenomena sometimes reveals more about the quirks of our contingent conceptual schemes than about the nature of actual phenomena.

The course is an introduction to constructive methods for understanding the nature of real complex systems. The focus will be on natural systems that are alive and that emerge and evolve spontaneously in the material world. The constructive methods covered include cellular automata, random trees, genetic algorithms, and agent- or individual-based (or botton-up) models of evolution. These methods are constructive in the sense that they explain phenomena by synthesizing instances of them. Constructive methods typically are implemented as computer simulations, and they can be viewed as computational analogs of traditional thought experiments in philosophy.

The course has two parts. The first part is an introduction to important constructive models of living phenomena. Computer programming is not required, but all students will do computer experiments. The second part of the course explores how constructive methods can be applied to understand the emergence and evolution of life.

Required work
1. miscellaneous homework exercises, including computer experiments.
2. class presentation on computer experiment (group presentations okay)
3. 7-10 pp. report on computer experiment and library research (individual work)
4. class presentation on philosophical research (group presentations okay)
5. 10-15 pp. research paper on philosophical topic (individual work)

Required books
- Margaret Boden, ed. The philosophy of artificial life. Oxford UP.
- Stephen Wolfram. Cellular automata and complexity. Addison Wesley.
- Daniel Dennett. Darwin’s dangerous idea. Touchstone.
- John Holland. Emergence: from chaos to order. Helix Books.
- Stewart Kauffman. Investigations. Oxford UP.
- Lynn Margulis & Dorion Sagan. What is life? U California Press.
- John Maynard Smith & Eors Szathmary. The origins of life: from the birth of life to the origin of language. Oxford UP.

Recommended books
- William Poundstone. The Recursive Universe. (out of print)
- Stephen Gould, Full house. Harmony Books.

Software to be used
- LifeLab
- MaxLife
- Bugs
- MacTierra
- Avida
- Mathematica

Course web site

Part 1 – constructive methods

Langton, Artificial life [in Boden]

The game of life (LifeLab, MaxLife)
Poundstone. The recursive universe. Chapters 11 and 12.

Cellular automata (Lifelab, Mathematica)
Wolfram, A New Kind of Science (selections below):
- Preface, Chs. 1, 2, pp. 105-113 (in Ch. 3), pp. 167-168 (in Ch. 4), Chs. 6-8, Ch. 12

Evolving sensorimotor agents (Bugs)

Bedau, The edge of disorder.

Bedau & Packard, The evolution of evolvability via adaptation of mutation rates.

Evolving self-replicating programs (Tierra, Avida)
Ray, An approach to the synthesis of life [in Boden]
A Guided Tour of an Avida Ancestor and its Hardware (available on the web at http://dllab.caltech.edu/avida/v2.0/docs/cpu_tour.html).
Wilke and Adami, The biology of digital organisms.
Lenski et al., The evolutionary origin of complex adaptive features.

Class presentations on computer experiments (the week before fall break)

Part 2 – the emergence and evolution of life

Holland. Emergence.
Papers on emergence:
- Boden, Autonomy and artificiality [in Boden].
- Clark, Happy couplings [in Boden].
- Hendricks-Janse, In praise of interactive emergence [in Boden].
- Bedau, Downward causation and autonomy of weak emergence.

Margulis & Sagan. What is life?
Maynard Smith & Szathmary. The origins of life.
Papers on life:
- Matthews, Aristotle on life [in Boden].
- Godfrey-Smith, Spencer and Dewey on life and mind [in Boden].
- Pattee, Simulations, realizations, and theories of life [in Boden].
- Sober, Learning from functionalism--prospects for strong artificial life [in Boden].
- Bedau, The nature of life [in Boden].

Dennett, Darwin’s dangerous idea.
- Preface, Chs. 1-8, §4 of ch. 10, chs. 12-14, ch. 17, ch. 18.
Kauffman, Investigations.
- Preface, Chs. 1-6, ch. 8, Epilogue.
Papers on evolution:
- Adami et al., Evolution of biological complexity.
- Bedau, Adaptation.
- Bedau, Evolutionary creativity.

Class presentations on emergence, evolution, and life (last week of classes)