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== Reference ==
Bar-Yam, Y. (1997). Dynamics of Complex Systems. Addison-Wesley, ISBN-13: 978-0813341217.

== DOI ==

== Abstract ==

== Extended Abstract ==

== Bibtex ==

== Used References ==
Additional Reading

Chapter 0

keywords: system theory; autopoiesis; biological systems; chaotic behavior in systems;
cybernetics;linear systems;social systems;system analysis;systems engineering; com-
plexity (philosophy)

[0.1] Herbert A. Simon, The Sciences of the Artificial, 3d ed. (MIT Press: Cambridge,
1996). See the last chapter for an alternate overview of this text.

There are a remarkable number of popular or semipopular books on various con-
cepts in the study of complex systems. For a number of reasons these books have ap-
peared instead of textbooks. They are of two types: books written by observers of the
field, and books written by researchers presenting their ideas to a popular audience.

There are both positive and negative aspects of this approach,the ultimate benefit of
which will be judged by others. Here we provide a few references to this literature:

[0.2] James Gleick, Chaos: Making a New Science (Penguin: New York, 1987).
Concept and personality history, focusing on chaotic and nonlinear dynamics

(Section 1.1), and fractals (Section 1.10) but relevant to the study of complex
systems in general.

[0.3] Douglas R. Hofstadter, Gödel, Escher, Bach (Vintage: New York, 1989).
Semipopular and creative romp emphasizing mathematical and philosophical
aspects of logic (Section 1.9).

[0.4] Roger Lewin, Complexity: Life at the Edge of Chaos (Macmillan: New York,
1992).

[0.5] M. Mitchell Waldrop, Complexity: The Emerging Science at the Edge of Order
and Chaos (Simon & Schuster: New York, 1992).

[0.6] John L. Casti, Complexification: Explaining a Paradoxical World through the
Science of Surprise (HarperCollins: New York, 1994).

[0.7] Brian Goodwin, How the Leopard Changed its Spots: The Evolution of
Complexity (Charles Scribner’s Sons: New York, 1994).

[0.8] Stuart A. Kauffman, At Home in the Universe (Oxford University Press: New
York, 1995).

[0.9] John H. Holland, Hidden Order: How Adaptation Builds Complexity (Helix
Books, Addison-Wesley: Reading, Mass., 1995).

[0.10] Peter Coveney and Roger Highfield, Frontiers of Complexity: The Search for
Order in a Chaotic World (Fawcett Columbine: New York, 1995).

[0.11] Per Bak, How Nature Works: The Science of Self-Organized Criticality
(Copernicus, Springer-Verlag: New York, 1996).

More technical references include some with classic and others with modern
approaches:

[0.12] James Grier Miller, Living Systems (McGraw-Hill: New York, 1978).

[0.13] George J. Klir, Architecture of Systems Problem Solving (Plenum: New York,
1985).

[0.14] Gérard Weisbuch, Complex Systems Dynamics (Addison-Wesley, Reading,
Mass., 1991).

[0.15] Thomas J. Sargent, Bounded Rationality in Macroeconomics (Carendon,
Oxford, 1993). Title is inadequate.

[0.16] Mikhail V. Volkenstein, Physical Approaches to Biological Evolution (Springer-
Verlag: Berlin,1994). Touches on many classic contributions in complex systems.

A series of books under the collective title “The Santa Fe Institute Studies in the
Sciences of Complexity” published by Addison-Wesley, collects various workshops
and lectures sponsored by the Santa Fe Institute on subjects relevant to complex sys-
tems. This series illustrates the great diversity of concepts and applications of this
field. We do not include a full list of these books here.A few volumes in this series are
mentioned below as appropriate.

Chapter 1

Section 1.1

keywords: chaotic behavior in systems

[1.1.1] Predrag Cvitanovic, ed. Universality in Chaos: A Reprint Selection, 2d ed.
(Adam Hilger: Bristol, 1989).

[1.1.2] Robert L. Devaney, A First Course in Chaotic Dynamical Systems: Theory and
Experiment (Addison-Wesley: Reading, Mass., 1992). Excellent undergradu-
ate-level textbook on basic mathematics of iterative maps and chaos.

[1.1.3] Robert L. Devaney, Introduction to Chaotic Dynamical Systems, 2d ed.
(Addison-Wesley, Reading, Mass., 1989). More advanced mathematical
treatment than [1.1.2].

[1.1.4] Steven H. Strogatz, Nonlinear Dynamics and Chaos. With Applications to
Physics, Biology, Chemistry, and Engineering (Addison-Wesley: Reading,
Mass., 1994). Undergraduate textbook on nonlinear dynamics that arise
from differential equations.

[1.1.5] Edward Ott, Chaos in Dynamical Systems (Cambridge University Press:
Cambridge, 1993).

Section 1.2

keywords: probabilities; combinatorial probabilities; correlation (statistics); distribu-
tion (probability theory); games of chance (mathematics); limit theorems (probabil-
ity theory); random variables; stochastic processes; stochastic sequences; random
walks (mathematics)

Probability and statistics is a traditional field of study in many fields with vary-
ing emphasis depending on whether it is used for analysis of data, for modeling of sys-
tems, or for more abstract formal concepts.A reference that is particularly relevant to
our purposes is:

[1.2.1] N. G. van Kampen, Stochastic Processes in Physics and Chemistry (North-
Holland, Amsterdam, 1981). Outstanding graduate text on the concepts and
applications of stochastic processes. Somewhat more formal than this text,
while still providing a useful conceptual framework.

Section 1.3

keywords: thermodynamics; statistical physics; statistical mechanics; phase transfor-
mations (statistical physics); statistical thermodynamics

Thermodynamics/statistical physics is a traditional field of physics covered by
undergraduate and graduate textbooks with various approaches and flavors.
Examples include:

[1.3.1] Kerson Huang, Statistical Mechanics, 2d ed. (Wiley: New York, 1987).
Undergraduate text.

[1.3.2] Edward A. Guggenheim, Thermodynamics: An Advanced Treatment for
Chemists and Physicists (North-Holland: Amsterdam, 1967). Graduate text
with elegant review of basics.

[1.3.3] Lev Davidovich Landau and E. M. Lifshitz, Statistical Physics (Course of
Theoretical Physics, vol. 5) 2d ed. (Pergamon: Oxford, 1969). Classic ad-
vanced text.

Section 1.4
keywords: chemical reaction, conditions and laws of; chemical kinetics
The two-state system analysis is based on classic transition-state theory covered
in many physical chemistry books as a model for chemical reaction kinetics.

Section 1.5

keywords: cellular automata

[1.5.1] Stephen Wolfram, ed. Theory and Applications of Cellular Automata (World
Scientific, Singapore, 1983). Many of the original articles are collected in
this book. Includes an extensive bibliography.

[1.5.2] Doyne Farmer, Tommaso Toffoli and Stephen Wolfram, eds. Cellular
Automata (North-Holland: Amsterdam, 1984). A conference proceedings
volume.

[1.5.3] Tommaso Toffoli and Norman Margolus, Cellular Automata Machines: a
New Environment for Modeling, (MIT Press: Cambridge, Mass., 1987). Many
useful concepts and methods discussed.

Section 1.6

keywords: phase transformations (statistical physics); ferromagnetism; Ising model
Most books on statistical physics (Section 1.3) include a discussion of the Ising
model. See especially:

[1.6.1 H. Eugene Stanley, Introduction to Phase Transitions and Critical Phenomena
(Oxford University Press: New York, 1971).

[1.6.2] Giorgio Parisi, Statistical Field Theory (Addison-Wesley, Reading, Mass.,
1988). Advanced formal treatment.

Section 1.7

keywords: simulation methods; mathematical models; computer simulation; Monte
Carlo method

[1.7.1] M. P. Allen and D. J. Tildesley, Computer Simulations of Liquids (Oxford
Science Publications: Oxford, 1987). Readable, practical guide to modern
simulation strategies.

[1.7.2] Malvin H. Kalos and Paula A. Whitlock, Monte Carlo Methods, vol. 1: Basics
(Wiley & Sons: New York, 1986).

Section 1.8

keywords: information theory; statistical communication theory

[1.8.1] C. E. Shannon, “A Mathematical Theory of Communication,” in Bell Systems
Technical Journal, July and October 1948; reprinted in C. E. Shannon and W.
Weaver, The Mathematical Theory of Communication (University of Illinois
Press: Urbana, 1963). The original manuscript on this subject is still the best
discussion. Note the change in the first word of the title from original to
reprint.

Section 1.9

keywords: logic, symbolic and mathematical; machine theory; computer science;
Turing machines

[1.9.1] Ira Pohl and Alan Shaw, The Nature of Computation: An Introduction to
Computer Science (Computer Science Press, Potomac, Md., 1981). Pleasant
introduction to concepts and language of computer science.

[1.9.2] John N. Crossley, What is Mathematical Logic? (Oxford University Press:
Oxford, 1972). Dense overview.

[1.9.3] Elliott Mendelson, Introduction to Mathematical Logic, 2d ed. (Van
Nostrand: New York, 1979).

[1.9.4] Herbert B. Enderton, A Mathematical Introduction to Logic (Academic Press:
New York, 1972).

[1.9.5] H. (Hartley) Rogers, Theory of Recursive Functions and Effective
Computability (McGraw-Hill: New York, 1967; MIT Press: Cambridge,
1987). Formal discussion of the theory of universal computation.

Section 1.10

keywords: fractals; renormalization group;scaling laws (statistical physics); multigrid
methods numerical analysis

The subject of fractals has strong overlaps with the topic of chaos (Section 1.1)
due to the connection between multiscale phenomena and chaotic dynamics dis-
cussed in Chapter 9. Thus, see also the references in Section 1.1.

[1.10.1] Benoit B. Mandelbrot, The Fractal Geometry of Nature (W. H. Freeman:
New York, 1983). The original source.

[1.10.2] R. J. Creswick, H. A. Farach and C. P. Poole, Jr., Introduction to
Renormalization Group Methods in Physics (Wiley: New York, 1992). A rela-
tively accessible discussion of renormalization methods.

[1.10.3] Albert-Laszlo Barabasi, H. Eugene Stanley, Fractal Concepts in Surface
Growth (Cambridge University Press, New York, 1995).

[1.10.4] F. Family and T. Vicsek eds. Dynamics of Fractal Surfaces (World Scientific:
Singapore, 1991). A collection of articles on the application of scaling ideas
to surfaces. The principal relevance to us is the scaling treatment of spatial
and temporal properties of these systems. References on the application of
scaling to polymers are given in Chapter 5.

[1.10.5] James H. Bramble, Multigrid Methods (Longman: Harlow, Essex, 1993;
Wiley: New York, 1993).

[1.10.6] William L. Briggs, A Multigrid Tutorial (SIAM: Philadelphia, 1987).

Chapter 2

keywords: neurophysiology; brain—localization of functions; neural networks (neu-
robiology); cognitive neuroscience;artificial intelligence;neural networks (computer
science); pattern-recognition systems

Discussions of neural function from a biological perspective:

[2.1] Michael S. Gazzaniga, Richard Ivry and George R. Mangun, Fundamentals of
Cognitive Neuroscience (W.W. Norton: New York, 1997).

[2.2] Eric R. Kandel, James H. Schwartz, Thomas M. Jessell eds. Principles of Neural
Science, 3d ed. (Elsevier: New York, 1991).

[2.3] Gordon M. Shepherd, Neurobiology (Oxford University Press: New York,
1983).

[2.4] Scientific American (September 1992). Issue devoted to the biological ap-
proach to brain function, specifically cellular function and brain imaging.
Almost any book on neural networks, of which there are a number, will offer a
basic introduction to various types of neural networks including the attractor net-
work and the feedforward network, variations on these networks and other simple
models. Unfortunately, the field is polarized, with distinct camps taking different ap-
proaches and claiming priority on ideas, realism or other issues. The complexity of bi-
ological neural systems enables various approaches to coexist without much more
than acknowledging each other. A collection of articles that are central to the devel-
opment of various threads in the field of neural networks is contained in:

[2.5] J. A. Anderson and E. Rosenfeld eds. Neurocomputing (MIT Press, Cambridge,
Mass., 1988).

While it is important to resp ect the value of all approaches, the treatment em-
phasized in this chapter originates from J. J. Hopfield. This approach emphasizes sim-
plicity of the microscopic components so that collective behavior can be more easily
(but still not trivially!) understood. Books expanding on this:

[2.6] Daniel J. Amit, Modeling Brain Function: The World of Attractor Neural
Networks (Cambridge University Press, Cambridge, 1989). A systematic de-
scription of the analysis of attractor networks using techniques developed in
statistical mechanics. The early chapters motivate the use of the attractor net-
work from a biological perspective and introduce the models.

[2.7] Marc Mezard, Giorgio Parisi, and Miguel Angel Virasoro, Spin Glass Theory
and Beyond (World Scientific: Singapore, 1987).

Specific references:

[2.8] P. Baldi and S. Venkatesh, “Number of Stable Points for Spin-Glasses and
Neural Networks of Higher Orders,” Phys. Rev. Lett., 58, 913 (1987). The max-
imum number of stored independent bits cannot be greater than 2N 2, or 2N
uncorrelated patterns—note that the synaptic matrix is not required to be
symmetric.

Chapter 3

Section 3.1

keywords: sleep; sleep—physiological aspects

Discussions of sleep phenomenology and models of its function are contained in:

[3.1] James A. Horne, Why We Sleep: The Functions of Sleep in Humans and Other
Mammals (Oxford University Press, Oxford, 1988). Excellent review focusing
on sleep-deprivation studies. Counters notion that sleep serves physiological
restorative function.

[3.2] Andrew Mayes, ed. Sleep Mechanisms and Functions in Humans and Animals:
An Evolutionary Perspective (Van Nostrand Reinhold (UK): Wokingham,
1983). See particularly Chapter 1 by W. B. Webb for the evolutionary perspec-
tive on sleep criticized in this chapter.

[3.3] William Fishbein, ed. Sleep, Dreams and Memory: Advances in Sleep Research
vol. 6, (Spectrum Publications Medical and Scientific: New York, 1981). This
and the next reference suggest that sleep serves a role in memory.

[3.4] David B. Cohen, Sleep and Dreaming: Origins, Nature and Functions
(Pergamon: Oxford, 1979).

[3.5] J. Allan Hobson, The Dreaming Brain (Basic Books: New York, 1988).
Dissociation of neural function from sensory information is discussed on pp.
209–210.

[3.6] Ernest L. Hartmann, The Functions of Sleep (Yale University Press: New
Haven, 1973). Mention of the similarity of aspects of dreams to cognition of
postlobotomy patients, pp. 136–138.

Specific references:

[3.7] F. Crick and G. Mitchison, “The Function of Dream Sleep,” Nature 304, 111
(1983).

[3.8] J. J. Hopfield, D. I. Feinstein and R. G. Palmer, “‘Unlearning’ Has a Stabilizing
Effect in Collective Memories” Nature 304, 158 (1983).

[3.9] T. Geszti and F. J. Pázmándi, “Learning within Bounds and Dream Sleep,” J.
Phys. A20, L1299 (1987); “Modeling Dream and Sleep,” Physica Scripta T25,
152 (1989).

[3.10] L. M. Mukhametov, “Sleep in Marine Mammals,” in A. A. Borbély and J. L.
Valatx, eds. Sleep Mechanisms (Springer-Verlag, 1984) pp. 227–238. Studies
of dolphins sleeping half brain at a time. Among other arguments, refutes
the evolutionary perspective of ref. [3.2].

[3.11] M. A. Wilson and B. L. McNaughton, “Reactivation of Hippocampal
Ensemble Memories During Sleep,” Science 265, 676 (1994).

Section 3.2

keywords: knowledge,theory of;intellect; perception; human information processing;
artificial intelligence; philosophy of mind; cognitive science; memory; psychology of
learning

[3.12] Marvin Minsky, Society of Mind (Simon and Schuster, New York, 1985).

Specific references:

[3.13] L. Standing, “Learning 10,000 pictures,” Quarterly Journal of Experimental
Psychology 25, 207 (1973). Testing recognition.

[3.14] R. D. Hawkins, T. W. Abrams, T. J. Carew, and E. R. Kandel, “A Cellular
Mechanism of Classical Conditioning in Aplysia: Activity-Dependent
Amplification of Presynaptic Facilitation” Science 219, 400 (1983);

E. R. Kandel and R. D. Hawkins, Scientific American (September 1992) pp. 78–86,
Experimental studies of the biology of neurons showing synapses that cou-
ple three neurons; e.g. implementing the logical AND operation.

Chapter 4

keywords: proteins; proteins–conformation; protein folding

Note: the problem of identifying time scale can also be seen in other fields. In
computer science see keyword: computational complexity.

[4.1] Jack Kyte, Structure in Protein Chemistry (Garland: New York, 1995).

[4.2] Carl Branden and John Tooze, Introduction to Protein Structure (Garland: New
York, 1991).

[4.3] Alan Ferscht, Enzyme Structure and Mechanism, 2d ed. (Freeman: New York,
1985).

[4.4] Thomas E. Creighton, Proteins: Structures and Molecular Principles (Freeman:
New York, 1983).

Chapter 5

keywords: macromolecules; polymers; polymer solutions; biopolymers
Books on the scaling properties of polymers:

[5.1] Pierre-Gilles de Gennes, Scaling Concepts in Polymer Physics (Cornell
University Press, Ithaca, N.Y., 1979).

[5.2] Masao Doi and Sam F. Edwards, The Theory of Polymer Dynamics (Oxford
University Press, Oxford, 1986).

A discussion of parallel-processing simulations is found in:

[5.3] B. M. Boghosian, Computers in Physics 4, 14 (1990).

Specific references:

[5.4] P. G. de Gennes, “Kinetics of Collapse for a Flexible Coil,” Journal de Physique
Lettres 46 L639 (1985).

[5.5] B. Ostrovsky, M. A. Smith and Y. Bar-Yam, “Applications of parallel comput-
ing to biological problems,” Annual Review of Biophysics and Biomolecular
Structure 24, 239 (1995).

[5.6] Y. Bar-Yam, “Polymer Simulation Using Cellular Automata: 2-d Melts, Gel-
Electrophoresis and Polymer Collapse,” in G. Bhanot, S. Chen, and P. Seiden
eds. Some New Directions in Science on Computers (World-Scientific:
Singapore, 1996).

Chapter 6

keywords: evolution; evolution (biology); heredity; adaptation(biology); variation
(biology); natural selection; genetics; population genetics; cytoplasmic inheritance;
egoism; genetic algorithms

[6.1] Charles Darwin, On the Origin of Species (By Means of Natural Selection) (a
facsimile of the first edition, 1859) (Harvard University Press: Cambridge,
Mass., 1964). The original discussion is still enlightening, and shows the
strong phenomenological basis for the conceptual developments.

[6.2] Douglas J. Futuyma, Evolutionary Biology, 2d ed. (Sinauer Assoc., Sunderland,
Mass., 1986). Outstanding discussion of phenomena in biological evolution
and their relation to conceptual issues in the theoretical understanding of
evolution.

[6.3] Robert N. Brandon and Richard M. Burian, eds. Gen e s ,O rganisms, Populations:
Controversies Over the Units of Selection (MIT Press, Cambridge, Mass.,1984).

[6.4] Richard Dawkins, The Selfish Gene, 2d ed. (Oxford University Press: Oxford,
1989). Presents the extreme reductionist view criticized in this chapter.

[6.5] Stephen Jay Gould, Wonderful Life: The Burgess Shale and the Nature of History
(Norton, New York, 1989). Punctuated equilibria. See also ref. [0.11]

[6.6] Stuart A. Kauffman, The Origins of Order: Self Organization and Selection in
Evolution (Oxford University Press: New York, 1993). A complex systems per-
spective.

[6.7] Karl Sigmund, Games of Life: Explorations in Ecology, Evolution, and Behavior
(Oxford University Press: Oxford, 1993). Many fine points on mathematical
treatment of evolution.

[6.8] William Day, Genesis on Planet Earth: The Search for Life’s Beginning, 2d ed. (Yale
University Press: New Haven, Conn.,1984). Molecular to cellular evolution.

Artificial life references include:

[6.9] Christopher G. Langton, ed. Artificial Life: The Proceedings of an
Interdisciplinary Workshop on the Synthesis and Simulation of Living Systems
(Addison-Wesley, Reading, Mass., 1989). See also the sequels in the same se-
ries, Artificial Life II–IV. See the video for Artificial Life II.

[6.10] Christopher G. Langton, ed. Artificial Life: An Overview (MIT Press,
Cambridge, 1995).

For genetic algorithms, see:

[6.11] John H. Holland, Adaptation in Natural and Artificial Systems, 2d ed. (MIT
Press: Cambridge, Mass., 1992).

[6.12] Melanie Mitchell, An Introduction to Genetic Algorithms (Bradford, MIT
Press: Cambridge, Mass., 1996).

For discussions of the philosophy of egoism—self-interest vs. altruism, see:

[6.13] David P. Gauthier, ed. Morality and Rational Self-interest (Prentice-Hall:
Englewood Cliffs, N.J., 1970).

[6.14] Robert M. Axelrod, The Evolution of Cooperation (Basic Books: New York,
1984). Shows the marginal stability of the most primitive form of coopera-
tion (tit for tat); i.e. upon introduction of spatial correlations (correlations
in selective forces).

[6.15] David P. Gauthier, Morals by Agreement (Clarendon: Oxford, 1986).

Chapter 7

keywords: developmental biology; embryology; pattern formation (biology); chemi-
cal reactions

[7.1] Lee A. Segel, Modeling Dynamic Phenomena in Molecular and Cellular Biology
(Cambridge University Press: Cambridge, 1984).

[7.2] James D. Murray, Mathematical Biology (Springer-Verlag, New York, 1989).

[7.3] Hans Meinhardt, The Algorithmic Beauty of Sea Shell Patterns (Springer-
Verlag: New York, 1994).

[7.4] H. F. Nijhout, “Pattern Formation in Biological Systems,” in Lynn Nadel and
Daniel L. Stein, eds. 1991 Lectures in Complex Systems (Addison-Wesley:
Reading, Mass., 1992). A brief presentation.

[7.5] Przemyslaw Prusinkiewicz and Aristid Lindenmayer with James S. Hanan, The
Algorithmic Beauty of Plants (Springer-Verlag: New York, 1990). L-systems.

Chapter 8

keywords: Kolmogorov complexity

[8.1] http://www.fmb.mmu.ac.uk/~bruce/combib/. An extensive bibliography on
complexity.

[8.2] Gregory J. Chaitin, Algorithmic Information Theory (Cambridge University
Press: Cambridge 1987).

[8.3] W. H. Zurek, ed. Complexity, Entropy and the Physics of Information (Addison-
Wesley: Reading, Mass., 1990).

[8.4] Ming Li and Paul Vitanyi, An Introduction to Kolmogorov Complexity and Its
Applications (Springer-Verlag: New York, 1993).

Specific references:

[8.5] J. E. Lovelock, Gaia, A New Look at Life on Earth (Oxford University Press:
Oxford, 1979).

[8.6] E. R. Cohen and B. N. Taylor, “The 1986 Adjustment of the Fundamental
Physical Constants,” Rev. Mod. Phys. 59, 1121 (1987). Value of the electron
magnetic moment.

[8.7] Neville H. Fletcher, The Chemical Physics of Ice (Cambridge Univ. Press:
London, 1970). Excellent review of basic knowledge of the low temperature
properties of ice.

[8.8] Charles H. Bennett, “The Thermodynamics of Computation—A review,”
International Journal of Theoretical Physics 21, 905 (1982).

Chapter 9

keywords: civilization—history,civilization—philosophy; social history; social change;
technology and civilization; organization; management; management science; eco-
nomic history; international economic relations; man—origin

For modeling using system dynamics, a method that was not discussed in this
text, see:

[9.1] George P. Richardson and Alexander L. Pugh III, Introduction to System
Dynamics Modeling with DYNAMO (MIT Press: Cambridge, Mass., 1981).

Books on the structure of corporations and the recent changes in civilization
include:

[9.2] Henry Mintzberg, The Structuring of Organizations: A Synthesis of the Research
(Prentice-Hall, Englewood Cliffs, 1979). Remarkable phenomenologically-
driven discussion.

[9.3] David Mitchell, Control Without Bureaucracy (McGraw-Hill, London, 1979).
Experience-driven discussion.

[9.4] Gregory Stock, Metaman: The Merging of Humans and Machines into a Global
Superorganism (Simon & Schuster: New York, 1993). Includes an extensive set
of references.

== Links ==
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