Open Questions: Self-Organization and Complex Systems

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See also: Chaos theory and dynamical systems - Combinatorics, graph theory, and computation

Introduction

Networks

Artificial life

Cellular automata

Genetic algorithms

Evolutionary computation

Neural networks

Complex adaptive systems

Percolation

Renormalization theory

Spin glasses

L-systems

Self-organized criticality


Recommended references: Web sites

Recommended references: Magazine/journal articles

Recommended references: Books

Introduction



Recommended references: Web sites

Site indexes

WWW Virtual Library: Complex Systems
Provides links to Web resources on a wide variety of subjects, such as artificial life, cellular automata, chaos, critical systems, fractals, genetic algorithms, neural networks, non-linear dynamics, and self-organization. Related to the Complexity On-Line site.
Galaxy: Complex Systems
Categorized site directory. Entries usually include descriptive annotations.
Erik's Favorite Mosaic Links
External links (somewhat old) to pages on complex systems, artificial life, genetic programming, genetic algorithms, robotics, neural networks, nanotechnology, etc. (Erik Winfree)
The Net Advance of Physics: Complexity
An index of tutorial and research articles located at the physics preprint archive. Topics include quantum computation, chaos and dynamics, complexity, neural networks, and spin glasses.


Sites with general resources

Center for Complex Systems Research
The Center, located at the University of Illinois at Urbana-Champaign, is a research group which studies phenomena of multivariante systems with a large flow. It develops and uses methodologies such as non-linear dynamics and chaos, neural nets, cellular automata, genetic algorithms, and artifical life models.
The Santa Fe Institute
The Santa Fe Institute is a private, non-profit, multidisciplinary research and education center, founded in 1984. Its main focus is research on complex adaptive systems. The research, bibliography, publications and working papers pages are especially interesting.
Serendip: Complex Systems
A variety of educational articles and interactive exhibits. Has links to additional resources.
Complexity On-Line
Resources related to complex systems such as cellular automata, L-systems, and fractals.
Complex Systems Bibliography
A large database of books, articles, and papers.
Complexity International
"A refereed journal for scientific papers dealing with any area of complex systems research."
Self-Organization FAQ
Frequently asked questions, maintained by Chris Lucas.
Self-Organized Criticality
Brief articles on the subject with a few links.
International Society for Artificial Life
Primarily for active researchers in artificial life, cellular automata, and related areas.


Surveys, overviews, tutorials

Complex system
Article from Wikipedia.
CompLexicon
Brief articles on various terms and topics in complexity theory.
A frustrating view of complexity
October 2008 article from Science News. "The unifying theme of complex systems, a researcher argues, is frustration."
Complex Systems
A ScienceWeek "symposium" consisting of excerpts and summaries of articles from various sources.
Complexity & Organic Evolution
Good overview of complexity theory in general and as applied to the issue of extinction events in geologic history. Part of the Hooper Virtual Paleontological Museum.


Networks

The physics of the Web
July 2001 article from Physics World, by Albert-László Barábasi. "Statistical mechanics is offering new insights into the structure and dynamics of the Internet, the World Wide Web and other complex interacting systems."


Cellular automata

Mathematics Archives - Cellular Automata
Annotated list of links.
Galaxy: Cellular Automata
Categorized site directory. Entries usually include descriptive annotations.
Cellular automaton
Article from Wikipedia.
Cellular Automata
A tutorial by David Green.
Bibliography of Cellular Automata
Large bibliography of articles, but formatted for computer rather than human use. Hosted by the Institute for Mathematics and its Applications.
Cellular Automata FAQ
Questions and answers on many topics in cellular automata.


Genetic algorithms, evolutionary computation

Mathematics Archives - Computer Algebra, Cryptology, and Genetic Algorithms
Annotated list of links
Galaxy: Genetic Algorithms
Categorized site directory. Entries usually include descriptive annotations.
Evolutionary algorithm
Article from Wikipedia. See also Genetic programming, Genetic algorithm.
The Genetic Algorithms Archive
Repository of information on genetic algorithms and evolutionary computation, related to an email discussion list on the topic. Lots of good content, such as archives of list discussions, source code, external links.
Evolutionary Computation at PNNL
Extensive collection of resources provided by the Pacific Northwest National Laboratory. Includes overview, online demos, general information.
Encore: The Hitch-hiker's Guide to Evolutionary Computation
Large list of links to material on genetic algrorithms, genetic programming, and related fields such as artificial intelligence, artificial life, cellular automata, fuzzy systems, nanotechnology, neural networks.
Genetic Algorithms
Matlab routines for genetic algorithms, and visualizations made by Juha Haataja of the Center for Scientific Computing in Finland.
The Golem Project
Also known as Golem@Home. A cooperative distributed computing project to investigate evolutionary computation.
International Society for Genetic and Evolutionary Computation
Professional association. Site includes information on books, journals, and external links.
The Digital Life Laboratory
"The Digital Life Laboratory at the California Institute of Technology is a research group focusing on the dynamics of simple living systems, in particular their evolution."


Artificial life

Galaxy: Artificial Life
Categorized site directory. Entries usually include descriptive annotations.
Galaxy: Adaptive Systems and Artificial Life
Categorized site directory. Entries usually include descriptive annotations.
Artificial life
Article from Wikipedia.
Alife - Biotopia
An online game illustrating some principles of artificial life, part of the BBC Evolution Website. Contains a good list of external links related to the topic.


Neural networks

Galaxy: Neural Nets
Categorized site directory. Entries usually include descriptive annotations.
Neural network
Article from Wikipedia.
Neural Network FAQ
Questions and answers from comp.ai.neural-nets.
Introduction to Neural Networks
Downloadable tutorial by P. van der Smagt.
Neural Nets by Kevin Gurney
Tutorial notes, available in both HTML and PostScript form.
Bibliographies on Neural Networks
Directory of many useful bibliographies. Part of the Collection of Computer Science Bibliographies.


Recommended references: Magazine/journal articles

Biology's Gift to a Complex World
John Holland
The Scientist, September 2008
How studying biological interactions and evolution yields techniques for predicting the outcome of complex interactions.
Machines that Think
Brad Lemley
Discover, January 2001, pp. 74-79
New algorithmic techniques based on complex self-orgainizing systems that are derived from various biological models are being used in practical applications. These techniques have characteristics that in humans would be called "artistic" or "creative".
Swarm Smarts
Eric Bonabeau; Guy Th´raulaz
Scientific American, February 2000, pp. 72-79
The behavior of ants and other social insects may provide a model for a new type of computation for solving complex problems.
From Complexity to Perplexity
John Horgan
Scientific American, June 1995, pp. 104-109
Skepticism is growing over the scientific content of notions such as "artificial life" and "self-organized criticality". At the very least, dreams of a "unified theory" of complex systems seem far from being fulfilled.
Charge and Spin Density Waves
Stuart Brown; George Grüner
Scientific American, April 1994, pp. 50-56
When certain metals are cooled to near absolute zero their electrons become ordered into what is known as charge-density waves. Spin-density waves are a similar phenomenon invoving electron spin rather than charge. Both phenomena are examples of self-organized criticality, which also occurs in sand piles and earthquake fault networks.
Genetic Algorithms
John H. Holland
Scientific American, July 1992, pp. 66-72
Living things "evolve", in order to better adapt to their environments, by processes of randomly altering and recombining DNA. It is possible to use a similar process in computer algorithms in order to improve their ability to solve specific problems.


Recommended references: Books

Gary Flake -- The Computational Beauty of Nature: Computer Explorations of Fractals, Chaos, Complex Systems, and Adaptation
MIT Press, 2000
Flake develops the idea that simple iterated rules can produce rich and complex behavior. Appropriate mathematical and computational science details are introduced as needed to support the narrative. The main topics dealt with are as stated in the book's subtitle. In particular, this includes cellular automata, neural networks, and various kinds of genetic algorithms. Source code (in C) may be downloaded for programs that illustrate many of the concepts.
[Book home page]
Henrik Jeldtoft Jensen -- Self-Organized Criticality: Emergent Complex Behavior in Physical and Biological Systems
Cambridge University Press, 1998
The term "self-organized criticality" refers to the idea that sufficiently complex systems which are just at the boundary between stability and instability may exhibit surprising, yet somewhat predictable, regularities of behavior. The canonical example is a pile of sand. The book presents mathematical and computer models of this example and others, such as earthquakes, forest fires, and biological evolution.
Per Bak -- How Nature Works: The Science of Self-Organized Criticality
Springer-Verlag, 1996
The author is one of the originators of the idea of self-organized criticality. The book presents a non-mathematical treatment of the theory for a general audience. Chaos is equated with randomness, and is distinguished from complexity, which is a situation that occurs just at the boundary or chaos. Many phenomena exhibit a statistical pattern called "1/f noise". Bak tries to explain this pattern, and considers complex systems (in addition to sandpiles), such as landscape formation, earthquakes, biological evolution, traffic jams, and free-market ecomomies.
Peter Coveney; Roger Highfield -- Frontiers of Complexity: The Search for Order in a Chaotic World
Fawcett Columbine, 1995
The authors offer a long, detailed, but non-technical account of many of the most popular topics in complexity theory. This includes computation, cellular automata, spin glases, neural networks, genetic algorithms, chaos theory, real and artificial life, and neurobiology.
John L. Casti -- Complexification: Explaining a Paradoxical World Through the Science of Surprise
HarperCollins, 1995
Casti, a mathematician who has written frequently on mathematical topics for a general audience, gives his take on the usual topics in complexity theory. This includes catastrophe theory, chaos theory, artificial intelligence, and emergent phenomena.
Stuart Kauffman -- At Home in the Universe: The Search for the Laws of Self-Organization and Complexity
Oxford University Press, 1995
Kauffman is one of the leading researchers in the study of self-organization and complexity as applied to biology. This book offers a thorough but non-technical account of his work. The main concerns are with the origins of life and the detailed mechanisms of biological evolution.
Jack Cohen; Ian Stewart -- The Collapse of Chaos: Discovering Simplicity in a Complex World
Penguin Books, 1994
The authors are (respectively) a biologist and a mathematician. But the book itself isn't really so much either biology or mathematics as it is philosophy. The science it draws on is mostly biological: DNA, evolution, living organisms. The philosophy it advocates is a championing of "emergence" over "reductionism".
Stuart A. Kauffman -- The Origins of Order: Self-Organization and Selection in Evolution
Oxford University Press, 1993
This is a much longer and weightier book that the author's later At Home in the Universe. It covers much the same ground -- applications to biology of the theories of chaos and self-organization -- but without making concessions necessary for a "general audience". Nevertheless, following it requires only patience, not a lot of heavy-duty mathematics.

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