@book{AAAS88, author = {AAAS}, title = {D\AE DALUS: Special Issue on Artificial Intelligence}, publisher = {AAAS}, address = {Canton, Mass.}, year = {Winter 1988}, key = {ai,ai-critic,ai-connect,ai-history}, note = { {\it ~\\ Amounts largely to an in-print debate between mainstream AI and the new connectionist school. Many of the issues apply equally well to Artificial Life.} } } @article{Aladyev74, author = {Aladyev, V.}, title = {Survey of Research in the Theory of Homogeneous Structures}, journal = {Mathematical Biosciences}, volume = 22, year = 1974, key = {CA,automata-theory}, note = { {\it ~\\ Survey of primarily Russian work on cellular automata and related structures.} } } @book{Alberts83, author = {Alberts, B. and Bray, D. and Lewis, J. and Raff, M. and Roberts, K. and Watson, J.D.}, title = {Molecular Biology of the Cell}, publisher = {Garland}, address = {New York}, year = 1983, key = {refs-general}, note = { {\it ~\\ A thorough introduction to the mechanics of the cell. See also \cite{Watson87}.} } } @article{Albrecht78, author = {Albrecht-Buehler, G.}, title = {The Tracks of Moving Cells}, journal = {Scientific American}, volume = 238, number = 4, pages = {69-76}, year = {April 1978}, key = {bio-behavior}, note = { {\it ~\\ Description of similarities in the behavior of the daughter cells resulting from a cell-division.} } } @book{Albus82, author = {Albus, J.S.}, title = {Brains, Behavior, and Robotics}, publisher = {Byte Books}, address = {Peterborough, NH}, year = 1982, key = {ai-robotics,brain-model}, note = { {\it ~\\ Neurologically astute model for simulating intelligence.} } } @book{Aleksander83, author = {Aleksander, I. and Burnett, P.}, title = {Reinventing Man: The Robot becomes Reality}, publisher = {Holt, Rinehart and Winston}, address = {New York}, year = 1983, key = {ai-robotics,refs-general,ethics-rights}, note = { {\it ~\\ An excellent book on the fundamental principles involved in robotics. Especially good coverage of the social implications of robotics.} } } @article{Amoroso71, author = {Amoroso, S. and Cooper, G.}, title = {Tesselation Structures for Reproduction of Arbitrary Patterns}, journal = {Journal of Computer and System Sciences}, volume = 5, number = 5, year = 1971, key = {CA,automata-theory,,automata-selfrepro,self-repro}, note = { {\it ~\\ Automata theory relating to pattern reproduction.} } } @article{Anderson83, author = {Anderson, P. W.}, title = {Suggested Model for Prebiotic Evolution: The Use of Chaos}, journal = {Proc. Natl. Acad. Sci}, volume = 80, pages = {3386-3390}, year = 1983, key = {origins}, note = { {\it ~\\ A ``spin-glass'' model for the origin of life.} } } @article{Aoki84, author = {Aoki, I.}, title = {Internal Dynamics of Fish Schools in Relation to Inter-fish Distance}, journal = {Bulletin of the Japanese Society of Scientific Fisheries}, volume = 50, number = 5, pages = {751-758}, year = 1984, key = {schooling}, note = { {\it ~\\ Dynamic properties of fluctuations in nearest neighbor distance are determined by using power spectra.} } } @book{Apter70, author = {Apter, M. J.}, title = {The Computer Simulation of Behavior}, publisher = {Hutchinson University Library Press}, address = {London}, year = 1970, key = {computers-psychology}, note = { {\it ~\\ Application of computers to psychology. Many issues important to artificial life are raised here, and the author even speculates about artificial life at the end of the book.} } } @article{Arbib66a, author = {Arbib, M. A.}, title = {Simple Self-Reproducing Universal Automata}, journal = {Information and Control}, volume = 9, pages = {177-189}, year = 1966, key = {automata-selfrepro}, note = {{\it ~\\ Arbib's novel contribution to the pool of self-reproducing structures. This is a CA-like system in which a more realistic approximation to a chemical-bond is achieved than in von Neumann's model.}} } @incollection{Arbib66b, author = {Arbib, M. A.}, title = {Self-Reproducing Automata - Some Implications for Theoretical Biology}, booktitle = {Towards a Theoretical Biology}, volume = 2, editor = {Waddington, C. H.}, publisher = {Edinburgh University Press}, pages = {204-226}, year = 1966, key = {automata-selfrepro}, note = {{\it ~\\ }} } @article{Arbib67, author = {Arbib, M.}, title = {Automata Theory and Development: Part {I}}, journal = {J. Theor. Biol.}, volume = 14, pages = {131-156}, year = 1967, key = {automata-theory,automata-biol}, note = { {\it ~\\ Automata theory as it relates to the process of development.} } } @book{Arbib69, author = {Arbib, M.}, title = {Theories of Abstract Automata}, publisher = {Prentice-Hall}, address = {Englewood, CA}, year = 1969, key = {automata-theory}, note = { {\it ~\\ Formal automata theory with an eye towards modeling biological phenomena.} } } @article{Ashby47, author = {Ashby, W. R.}, title = {The Nervous System as Physical Machine, with special reference to the Origin of Adaptive Behavior}, journal = {Mind}, volume = 56, pages = {44ff}, year = 1947, key = {adaptation,man-machine}, note = {{\it ~\\ }} } @article{Ashby48, author = {Ashby, W. R.}, title = {The Homeostat}, journal = {Electronic Engineering}, volume = 20, pages = {380ff}, year = 1948, key = {adaptation}, note = {{\it ~\\ Early cybernetic work on a goal-seeking or `teleological' system.}} } @book{Ashby52, author = {Ashby, W. R.}, title = {Design for a Brain}, publisher = {Wiley \& Sons}, address = {New York}, year = 1952, key = {ai}, note = {{\it ~\\ A classic book representing ``the path not taken'' by AI.}} } @book{Atkins84, author = {Atkins, P. W.}, title = {The Second Law}, publisher = {Scientific American Library, W. H. Freeman}, address = {New York}, year = 1984, key = {life-thermodynamics,ref-general}, note = {{\it ~\\ An excellent layman's account of the Second Law of Thermodynamics. Contains a chapter devoted to the thermodynamics of life with a cellular automaton model of the generation of complex structures.}} } @article{Axelrod81, author = {Axelrod, R. and Hamilton, W.D.}, title = {The Evolution of Cooperation}, journal = {Science}, volume = 211, pages = {1390-1396}, year = 1981, key = {evolution,coop-behave}, note = { {\it ~\\ A classic paper on the evolution of altruistic behavior which won {\em Science} magazine's `best paper of the year' award.} } } @book{Axelrod84, author = {Axelrod, R.}, title = {The Evolution of Cooperation}, publisher = {Basic Books}, address = {New York}, year = 1984, key = {evolution}, note = { {\it ~\\ A fine treatment of the selective value of cooperation. Includes a chapter on the iterated prisoner's dilemma and the results of a computer contest organized by Axelrod to test strategies for dealing with the dilemma.} } } @book{Babloyantz86, author = {Babloyantz, A.}, title = {Molecules, Dynamics, and Life: An Introduction to the Self-Organization of Matter.}, publisher = {Wiley Interscience}, address = {New York}, year = 1986, key = {life-dynamics}, note = {{\it ~\\ Thermodynamic analysis of ``how inert matter can acquire self-organizing properties once thought unique to living things''.} } } @article{Backus78, author = {Backus, J.}, title = {Can Programming be Liberated from the von Neumann Style?}, journal = {Comm. ACM}, volume = 8, pages = {613-641}, year = 1978, key = {computers-parallel}, note = { {\it ~\\ Classic analysis of the primary problem with serial programming - the dreaded ``von Neumann bottleneck'' - and suggestions for a programming style that avoids it.} } } @phdthesis{Bagley67, author = {Bagley, J.D.}, title = {The Behavior of Adaptive Systems which Employ Genetic and Correlation Algorithms}, school = {The University of Michigan}, year = 1967, key = {genetic-algorithms}, note = { {\it ~\\ } } } @book{BaiLin84, editor = {Bai-Lin, H.}, title = {Chaos}, publisher = {World Scientific}, address = {Singapore}, year = 1984, note = { {\it ~\\ A collection of reprints of early papers on chaos. Includes papers by Lorenz, May, Feigenbaum, and etc.} } } @article{Barricelli62, author = {Barricelli, N.A.}, title = {Numerical Testing of Evolution Theories: {I} \& {II}}, journal = {Acta Biotheoretica}, volume = 16, year = 1962, key = {evolution-model}, note = {{\it ~\\ An early computer model of evolution featuring a cellular automaton.} } } @phdthesis{Barto75, author = {Barto, A.G.}, title = {Cellular Automata as Models of Natural Systems}, school = {The University of Michigan}, year = 1975, key = {CA,models}, note = { {\it ~\\ Investigation of when it is and is-not appropriate to use cellular automata when modeling natural systems.} } } @article{Bays87, author = {Bays, C.}, title = {Candidates for the Game of Life in Three Dimensions}, journal = {Complex Systems}, volume = 1, number = 3, pages = {373-400}, year = 1987, key = {CA-LIFE}, note = { {\it ~\\ 3D CA rules with dynamics similar to Conway's game of Life \cite{Gardner70,Berlekamp82}.See also \cite{Dewdney87b}.} } } @techreport{Beeler73, author = {Beeler, M.}, title = {Patterson's Worm}, institution = {MIT AI Laboratory}, type = {AI Memo}, number = 290, year = 1973, key = {lattice-model,pattern-formation}, note = { {\it ~\\ Description of simple system for exploring optimal exploration pattern for a simple organism ``feeding'' on a lattice. See also \cite{Gardner73}.} } } @article{Benes80, author = {Benes, J.}, title = {Whither Cybernetics: Past Achievements and Future Prospects}, journal = {Kybernetes}, volume = 9, number = 4, pages = {283-288}, year = 1980, key = {cybernetics}, note = { {\it ~\\ Recent survey of the field of cybernetics.} } } @book{Berlekamp82, author = {Berlekamp, E. and Conway, J.H. and Guy, R.}, title = {Winning Ways for Your Mathematical Plays}, publisher = {Academic Press}, address = {New York}, year = 1982, key = {CA-LIFE,automata-theory,automata-selfrepro}, note = { {\it ~\\ In two volumes. Volume II contains the proof that the game of {\em LIFE} is computation universal and describes the construction of a self-reproducing configuration.} } } @book{Bernal67, author = {Bernal, J.D.}, title = {The Origin of Life}, publisher = {World Publishing}, address = {New York}, year = 1967, key = {origins}, note = { {\it ~\\ } } } @book{Bernard62, editor = {Bernard, E.E. and Kare, M.R.}, title = {Biological Prototypes and Synthetic Systems}, publisher = {Plenum}, address = {New York}, year = 1962, key = {refs-general}, note = { {\it ~\\ Proceedings of the Second Annual Bionics Symposium held at Cornell University, August 30-September 1, 1961. From the cybernetics era. Includes articles by Foerster on ``Bio-Logic'', Lofgren on self-repair, and McCulloch on `Biomimesis'.} } } @phdthesis{Bethke81, author = {Bethke, A.D.}, title = {Genetic Algorithms as Function Optimizers}, school = {The University of Michigan}, year = 1981, key = {genetic-algorithms}, note = { {\it ~\\ A nice application of the GA that illustrates the power of recombination and ``implicit-parallelism''.} } } @book{Blum51, author = {Blum, H.F.}, title = {Time's Arrow and Evolution}, publisher = {Princeton University Press}, address = {Princeton}, year = 1951, key = {life-thermodynamics,origins}, note = { {\it ~\\ Thermodynamics of life and its origin. Third edition published in 1968.} } } @book{Boden77, author = {Boden, M.}, title = {Artificial Intelligence and Natural Man}, publisher = {Basic Books}, address = {New York}, year = 1977, key = {ai,ethics-rights}, note = { {\it ~\\ History and philosophy of Artificial Intelligence.} } } @phdthesis{Booker82, author = {Booker, L.}, title = {Intelligent Behavior as an Adaptation to the Task Environment}, school = {The University of Michigan}, year = 1982, key = {genetic-algorithms}, note = { {\it ~\\ The genetic algorithm is applied to simulated organisms based on Holland's classifier systems \cite{Holland86a} to adapt their behavioral responses to complex environments.} } } @article{Booker88, author = {Booker, L. and Goldberg, D.E. and Holland, J.H.}, title = {Classifier Systems and Genetic Algorithms}, journal = {Artificial Intelligence}, year = {1988 - in press}, key = {genetic-algorithms}, note = { {\it ~\\ Tutorial overview.} } } @techreport{Bosworth72, author = {Bosworth, J. and Foo, N. and Zeigler, B.P.}, title = {Comparison of Genetic Algorithms with Conjugate Gradient Methods}, institution = {The University of Michigan}, number = {T.R. no. 012520-5-T}, year = 1972, key = {genetic-algorithms}, note = { {\it ~\\ } } } @book{Boyd85, author = {Boyd, R. and Richerson, P.J.}, title = {Culture and the Evolutionary Process}, publisher = {University of Chicago Press}, address = {Chicago}, year = 1985, key = {evolution-culture}, note = { {\it ~\\ A good text on the extra-genetic process of cultural evolution.} } } @book{Braitenberg84, author = {Braitenberg, V.}, title = {Vehicles: Experiments in Synthetic Psychology}, publisher = {MIT Press}, address = {Cambridge}, year = 1984, key = {refs-bottomup,coop-behave}, note = { {\it ~\\ A classic book on the synthesis of complex behavior from the interactions of simple components.} } } @article{Braitley72, author = {Bratley, P. and Millo, J.}, title = {Computer Recreations: Self-Reproducing Programs}, journal = {Software-Practice and Experience}, volume = 2, pages = {397-400}, key = {self-rep}, year = 1972, note = { {\it ~\\ } } } @article{Breder51, author = {Breder, C.M.}, title = {Studies in the Structure of the Fish School}, journal = {Bull. Am. Museum Nat. Hist.}, volume = 98, pages = {7ff}, year = 1951, key = {schooling,coop-behave}, note = { {\it ~\\ Study of schooling phenomena and their sensitivity to environmental factors.} } } @article{Breder59, author = {Breder, C.M.}, title = {Studies in the Social Grouping of Fishes}, journal = {Bull. Am. Museum Nat. Hist.}, volume = 117, pages = {399ff}, year = 1959, key = {schooling,coop-behave}, note = { {\it ~\\ Special forms, environmental influences, structural details, and the evolution of fish groups are discussed.} } } @incollection{Bremmerman62, author = {Bremmerman, H.J.}, title = {Optimization through Evolution and Recombination}, booktitle = {Self-Organizing Systems}, editor = {Yovits, M.C. and Jacobi, G.T. and Goldstein, G.D.}, publisher = {Spartan Books}, address = {Washington, DC}, pages = {93ff}, year = 1962, key = {genetic-algorithms}, note = { {\it ~\\ One of a number of pioneering papers that initiated the evolutionary approach to optimization.} } } @article{Breslow82, author = {Breslow, R.}, title = {Artificial Enzymes}, journal = {Science}, volume = 218, pages = {532-537}, year = 1982, key = {wetware}, note = { {\it ~\\ Description of syntheticly engineered molecules with catalytic properties.} } } @unpublished{Broadwell87, author = {Broadwell, P.}, title = {Plasm: A Fish Sample}, key = {refs-bottomup,schooling,coop-behave,models-computer}, note = { {\it ~\\ Computer simulation of an aquarium in which the ``fish'' respond to each other according to local rules for behavior. Demonstrated at the Artificial Life Workshop, Sept. 21-25, 1987, Los Alamos.} } } @article{Brown87, author = {Brown, D.}, title = {Competition of Cellular Automata Rules}, journal = {Complex Systems}, volume = 1, number = 1, pages = {169-180}, year = 1987, key = {CA}, note = { {\it ~\\ Different rules in a heterogeneous CA compete with their neighbors for ``territory'' in the lattice (c.f. \cite{Edelman87}).} } } @article{Bryant77, author = {Bryant, P.J. and Bryant, S.V. and French, V.}, title = {Biological Regeneration and Pattern Formation}, journal = {Scientific American}, volume = 237, number = 1, year = {July 1977}, key = {pattern-formation,biol-behavior}, note = { {\it ~\\ Discusses the role of cellular interactions in development.} } } @article{Burger80, author = {Burger, J. and Brill, D. and Machi, F.}, title = {Self-Reproducing Programs}, journal = {Byte}, volume = 5, key = {self-rep}, year = 1980, note = { {\it ~\\ } } } @article{Burks61, author = {Burks, A.W.}, title = {Computation, Behavior, and Structure in Fixed and Growing Automata}, journal = {Behavioral Science}, volume = 6, pages = {5-22}, year = 1961, key = {automata-theory,automata-biol}, note = { {\it ~\\ Automata theory suited for the modeling of natural growth and development.} } } @incollection{Burks66, author = {Burks, A.W.}, title = {Automata Models of Self-Reproduction}, booktitle = {Information Processing}, publisher = {Information Processing Society of Japan}, pages = {121-123}, year = 1966, key = {automata-selfrepro}, note = { {\it ~\\ } } } @book{Burks70, author = {Burks, A.W.}, title = {Essays on Cellular Automata}, publisher = {University of Illinois Press}, address = {Urbana}, year =1970, key = {CA, refs-general,refs-bottomup,automata-selfrepro,automata-biol}, note = { {\it ~\\ A classic collection of papers on cellular automata intended as a companion to von Neumann's {\it Theory of Self Reproducing Automata} \cite{vonNeumann66}. Includes papers by Burks, Thatcher, Moore, Myhill, Ulam, and Holland.} } } @article{Burks73, author = {Burks, A.W.}, title = {Logic, Computers, and Men}, journal = {Proceedings and Addresses of the American Philosophical Association}, volume = 46, pages = {39-57}, year = 1973, note = { {\it ~\\ } } } @inproceedings{Burks74, author = {Burks, A.W.}, title = {Cellular Automata and Natural Systems}, booktitle = {Cybernetics and Bionics}, editor = {Keidel, W.D. and H\"{a}ndler, W. and Spreng, M.}, publisher = {R. Oldenbourg}, address = {Munich}, pages = {190-204}, year = 1974, note = { {\it ~\\ Cellular Automata as a useful bridge between natural systems and formal computational systems.} } } @article{Burks75, author = {Burks, A.W.}, title = {Logic, Biology, and Automata - some Historical Reflections}, journal = {Int. J. Man-Machine Studies}, volume = 7, pages = {297-312}, year = 1975, note = { {\it ~\\ ``[A] historical study of the relation of logic (including automata theory and inductive logic) to the biological sciences, broadly conceived''.} } } @techreport{Burks81, author = {Burks, A.W.}, title = {Programming and Structure Changes in Parallel Computers}, institution = {Logic of Computers Group, The University of Michigan}, year = 1981, note = { {\it ~\\ Discussion of the merits of self-restructuring, parallel computers. This was the keynote address at the Conference on Parallel Computers, held in N\"{u}rnberg Germany, June 1981.} } } @inproceedings{Butler78, author = {Butler, J.T.}, title = {Analysis of Cellular Automata Growth Models}, booktitle = {Proceedings of 1978 ACM Computer Science Conference, Detroit Michigan, Feb. 1978}, publisher = {Association for Computing Machinery}, address = {New York}, year = 1978, key = {CA,automata-biol}, note = { {\it ~\\ } } } @article{Cairns-Smith66, author = {Cairns-Smith, A.G.}, title = {The Origin of Life and the Nature of the Primitive Gene}, journal = {J. Theor. Biol.}, volume = 10, pages = {53-88}, year = 1966, key = {origins-clays,alt-mat}, note = { {\it ~\\ Early article on his life-from-clays hypothesis.} } } @incollection{Cairns-Smith68, author = {Cairns-Smith, A.G.}, title = {An Approach to a Blueprint for a Primitive Organism}, booktitle = {Towards a Theoretical Biology}, volume = 1, editor = {Waddington, C.H.}, publisher = {Edinburgh University Press}, pages = {57-66}, year = 1968, key = {origins-clays,alt-mat}, note = { {\it ~\\ An early presentation of the ``life-from-clays'' hypothesis.} } } @book{Cairns-Smith73, author = {Cairns-Smith, A.G.}, title = {The Life Puzzle: On Crystals and Organisms and on the Possibility of a Crystal as an Ancestor}, publisher = {University of Toronto Press}, address = {Toronto}, year = 1973, key = {origins-clays,alt-mat}, note = { {\it ~\\ } } } @book{Cairns-Smith82, author = {Cairns-Smith, A.G.}, title = {Genetic Takeover and the Mineral Origins of Life}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1982, key = {origins-clays,alt-mat}, note = { {\it ~\\ A full exposition of Cairns-Smith's theory that life originated with replicating clays.} } } @book{Cairns-Smith85a, author = {Cairns-Smith, A.G.}, title = {Seven Clues to the Origin of Life}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1985, key = {origins-clays,alt-mat}, note = { {\it ~\\ A layman's version of {\em Genetic Takeover} \cite{Cairns-Smith82}.} } } @article{Cairns-Smith85b, author = {Cairns-Smith, A.G.}, title = {The First Organisms}, journal = {Scientific American}, volume = 252, number = 6, pages = {90-100}, year = {June 1985}, key = {origins-clays,alt-mat}, note = { {\it ~\\ Another readable exposition of life-from-clays and genetic takeover.} } } @book{Calvin69, author = {Calvin, M.}, title = {Chemical Evolution: Molecular Evolution towards the Origin of Living Things on the Earth and Elsewhere}, publisher = {Oxford University Press}, address = {London}, year = 1969, key = {origins,life-extra}, note = { {\it ~\\ } } } @article{Caraco82, author = {Caraco, T. and Bayham, M.C.}, title = {Some Geometric Aspects of House Sparrow Flocks}, journal = {Anim. Behav.}, volume = 30, pages = {990-996}, year = 1982, key = {schooling,coop-behave}, note = { {\it ~\\ Analysis of the 3D structure of a bird-flock.} } } @techreport{Cardelli85, author = {Cardelli, L.}, title = {Crabs: the bitmap terror}, institution = {Bell Laboratories}, year = 1985, key = {models-computer}, note = { {\it ~\\ An ``unofficial'' Bell-Labs report detailing the escapades of tiny bitmap ``creatures'' which chew up window systems and interact with one another on screen.} } } @book{Casjens85, editor = {Casjens, S.}, title = {Virus Structure and Assembly}, publisher = {Jones and Bartlett}, address = {Boston}, year = 1985, key = {self-assembly}, note = { {\it ~\\ Describes self-assembly of virus.} } } @article{Caspar62, author = {Caspar, D.L. and Klug, A.}, title = {Physical Principles in the Construction of Regular Viruses}, journal = {Cold Spring Harbor Symp. Quant. Biol.}, volume = 27, pages = {1-24}, year = 1962, key = {self-assembly}, note = { {\it ~\\ Virus self-assembly} } } @article{Caspar63, author = {Caspar, D.L.}, title = {Assembly and Stability of the Tobacco Mosaic Virus Particles}, journal = {Adv. Prot. Chem.}, volume = 18, pages = {37-121}, year = 1963, key = {self-assembly}, note = { {\it ~\\ Virus self-assembly} } } @incollection{Caspar76, author = {Caspar, D.L.}, title = {Switching in the Self-Control of Self-Assembly}, booktitle = {Structure-Function Relationship of Proteins}, editor = {Markham, R. and Horne, R.W.}, publisher = {Elsevier/North-Holland}, address = {New York}, pages = {85-98}, year = 1976, key = {self-assembly}, note = { {\it ~\\ Describes the role of ``conformational switching'' to control the sequence of self-assembly of biological components. See the article by Goel and Thompson in these proceedings for a model incorporating conformational switching.} } } @phdthesis{Cavicchio70, author = {Cavicchio, D.J.}, title = {Adaptive Search using Simulated Evolution}, school = {The University of Michigan}, year = 1970, key = {genetic-algorithms}, note = { {\it ~\\ Adaptive evolution in a population of devices (pattern recognition programs) is discussed and criteria for effective reproductive plans are presented.} } } @article{Chaitin70, author = {Chaitin, G. J.}, title = {To a Mathematical Definition of `Life'}, journal = {ACM SICACT News}, volume = 4, pages = {12-18}, year = 1970, key = {models-math}, note = { {\it ~\\ A definition of life based on the notion that a living organism is its own simplest description.} } } @incollection{Chaitin79, author = {Chaitin, G. J.}, title = {Toward a Mathematical Definition of `Life'}, booktitle = {The Maximum Entropy Formalism}, editor = {Levine, R.D. and Tribus, M.}, publisher = {MIT Press}, pages = {477-498}, year = 1979, key = {models-math}, note = { {\it ~\\ Application of algorithmic complexity theory to the quantitative measurement of organization in living organisms and other complex systems.} } } @book{Chapuis58, author = {Chapuis, A. and Droz, E.}, title = {Automata: A Historical and Technological Study}, publisher = {B.T. Batsford Ltd}, address = {London}, year = 1958, key = {automata-history,refs-general}, note = { {\it ~\\ A thorough, scholarly study of the history of clockwork automata, full of pictures and technical details.} } } @book{Clark59, editor = {Clark, F. and Synge, R.L.M.}, title = {The Origin of Life on Earth}, publisher = {Pergamon Press}, address = {London}, year = 1959, key = {origins}, note = { {\it ~\\ } } } @book{Codd68, author = {Codd, E.F.}, title = {Cellular Automata}, publisher = {Academic Press}, address = {New York}, year = 1968, key = {CA, automata-selfrepro,automata-theory}, note = { {\it ~\\ Codd's PhD thesis in which he details an 8-state, self-reproducing, universal computer/constructor.} } } @phdthesis{Conrad70a, author = {Conrad, M.}, title = {Computer Experiments on the Evolution of Coadaptation in a Primitive Ecosystem}, school = {Stanford University}, year = 1970, key = {evolution,models-computer,ecosystem}, note = { {\it ~\\ This was the first in a series of studies of evolution in artificial ecosystems. Further papers in the sequence are listed below.} } } @article{Conrad70b, author = {Conrad, M. and Pattee, H.H.}, title = {Evolution Experiments with an Artificial Ecosystem}, journal = {J. Theor. Biol.}, volume = 28, pages = {393-409}, year = 1970, key = {evolution,models-computer,ecosystem}, note = { {\it ~\\ } } } @incollection{Conrad74, author = {Conrad, M.}, title = {Molecular Automata}, booktitle = {Physics and Mathematics of the Nervous System}, editor = {Conrad, M. and Guttinger, W. and Dal Cin, M.}, publisher = {Springer-Verlag}, address = {Berlin}, pages = {419-430}, year = 1974, key = {computers-molecular}, note = { {\it ~\\ Discusses possibility for implementing molecular-scale computations.} } } @article{Conrad77, author = {Conrad, M.}, title = {Evolutionary Adaptability of Biological Macromolecules}, journal = {J. Molec. Evol.}, volume = 10, pages = {87-91}, year = 1977, key = {adaptation, evolution}, note = { {\it ~\\ This paper discusses the idea that the amenability of a biological organization to evolution can hitchike along with the advantageous traits whose appearance it facilitates.} } } @article{Conrad79, author = {Conrad, M.}, title = {Bootstrapping on the Adaptive Landscape}, journal = {BioSystems}, volume = 11, pages = {167-182}, year = 1979, key = {adaptation, evolution}, note = { {\it ~\\ Another discussion of the evolutionary self-facilitation of evolvability.} } } @article{Conrad81, author = {Conrad, M.}, title = {Algorithmic Specification as a Technique for Computing with Informal Biological Models}, journal = {BioSystems}, volume = 13, pages = {303-320}, year = 1981, key = {models-computer}, note = { {\it ~\\ Algorithms as proper subjects for biological experiments.} } } @book{Conrad83, author = {Conrad, M.}, title = {Adaptability}, publisher = {Plenum Press}, address = {New York}, year = 1983, key = {adaptation}, note = { {\it ~\\ This book gives an extensive analysis and discussion of the concept of evolvability and the evolutionary self-facilitation principle - how the structure of biological systems becomes organized for more effective evolution through the process of evolution.} } } @article{Conrad85, author = {Conrad, M. and Strizich, M.}, title = {{EVOLVE II}: A Computer Model of an Evolving Ecosystem}, journal = {BioSystems}, volume = 17, pages = {245-258}, year = 1985, key = {models-computer, evolution,ecosystem}, note = { {\it ~\\ Continuation of the artificial ecosystem series. For EVOLVE III see \cite{Rizki85}.} } } @book{Crick81, author = {Crick, F.}, title = {Life Itself (Its Origin and Nature)}, publisher = {Simon and Schuster}, address = {New York}, year = 1981, key = {life-general, origins,life-extra}, note = { {\it ~\\ Crick's views on the nature and origins of life. Includes a discussion of his ``Directed Panspermia'' hypothesis of an extraterrestrial origin for life.} } } @book{Darwin, author = {Darwin, C.}, title = {On the Origin of Species}, publisher = {John Murray}, address = {London}, year = 1859, key = {evolution,refs-general,adaptation}, note = { {\it ~\\ The first edition. No bibliography on life would be complete without this entry!} } } @book{Davis65, editor = {Davis, M.}, title = {The Undecidable}, publisher = {Raven Press}, address = {New York}, year = 1965, key = {automata-theory}, note = { {\it ~\\ Collection of articles on formally undecidable propositions. Contains translations of some of G\"{o}del's famous papers.} } } @book{DavisL87, editor = {Davis, L.}, title = {Genetic Algorithms and Simulated Annealing}, publisher = {Pitman}, address = {London}, year = 1987, key = {genetic-algorithms}, note = { {\it ~\\ A collection of articles describing current results using genetic and/or annealed search.} } } @article{DavisJM75, author = {Davis, J.M.}, title = {Socially Induced Flight Reactions in Pigeons}, journal = {Anim. Behav.}, volume = 23, pages = {597-601}, year = 1975, key = {schooling}, note = { {\it ~\\ Description of the `contagion of flight'.} } } @article{DavisJM80, author = {Davis, J.M.}, title = {The Coordinated Aerobatics of Dunlin Flocks}, journal = {Anim. Behav.}, volume = 28, pages = {668-673}, year = 1980, key = {schooling,coop-behave}, note = { {\it ~\\ Dynamic behavior of bird-flocks.} } } @book{Dawkins76, author = {Dawkins, R.}, title = {The Selfish Gene}, publisher = {Oxford University Press}, address = {Oxford}, year = 1976, key = {evolution-theory,refs-general}, note = { {\it ~\\ Classic book on the gene as the unit of selection. Final chapter proposes ``memes'' - the cultural equivalent of genes - as another form of self-interested replicator in nature.} } } @book{Dawkins83, author = {Dawkins, R.}, title = {The Extended Phenotype: The Gene as a Unit of Selection}, publisher = {Oxford University Press}, address = {Oxford}, year = 1983, key = {evolution-theory}, note = { {\it ~\\ Extension of the ideas presented in ``The Selfish Gene''.} } } @book{Dawkins86, author = {Dawkins, R.}, title = {The Blind Watchmaker}, publisher = {W.W. Norton}, address = {New York}, year = 1986, key = {evolution-theory,refs-general,computer-model}, note = { {\it ~\\ A thorough and careful explication of the nature of Darwinian evolution. The paperback edition contains an order form for the {\em Blind Watchmaker} program for the Apple Macintosh computer, described in Dawkins' contribution to these proceedings.} } } @phdthesis{DeJong75, author = {DeJong, K.A.}, title = {Analysis of Behavior of a Class of Genetic Adaptive Systems}, school = {The University of Michigan}, year = 1975, key = {genetic-algorithms}, note = { {\it ~\\ } } } @article{DeJong80, author = {DeJong, K.A.}, title = {Adaptive System Design: A Genetic Approach}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-10}, number = 9, pages = {566-574}, year = 1980, key = {genetic-algorithms}, note = { {\it ~\\ } } } @book{Dennett78, author = {Dennett, D.C.}, title = {Brainstorms: Philosophical Essays on Mind and Psychology}, publisher = {Bradford Books/MIT Press}, address = {Cambridge}, year = 1978, key = {ai-philos,ai-critic}, note = { {\it ~\\ A very nice book on philosophical issues regarding mind and computation.} } } @article{Derrida86a, author = {Derrida, B. and Pomeau, Y.}, title = {Random Networks of Automata: A Simple Annealed Approximation}, journal = {Europhys. Lett.}, volume = 1, number = 2, pages = {45-49}, year = 1986, note = { {\it ~\\ This and the following article extend and analyze Kauffman's random boolean nets \cite{Kauffman69}.} } } @article{Derrida86b, author = {Derrida, B. and Flyvbjerg, H.}, title = {Multi-Valley Structure in Kauffman's Model: Analogy with Spin Glasses: Letter to the editor}, journal = {J. Phys. A: Math.Gen.}, volume = 19, pages = {L1003-L1008}, year = 1986, note = { {\it ~\\ } } } @book{Descartes87, author = {Descartes, R.}, title = {M\'{e}ditations on First Philosophy}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1987, note = { {\it ~\\ Classic treatise in which Descartes compares the human body to a mechanical clock. This edition also has selections from the objections with replies. Translated by John Cottingham with an introduction by Bernard Williams.} } } @article{Dewdney84a, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {In} the game called {Core War} hostile programs engage in a battle of bits}, journal = {Scientific American}, volume = 250, number = 5, pages = {14-22}, year = {May 1984}, key = {models-computer}, note = { {\it ~\\ Description of a computer game in which short pieces of code reproduce and compete for occupation of memory.} } } @article{Dewdney84b, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {Sharks} and fish wage an ecological war on the toroidal planet Wa-Tor}, journal = {Scientific American}, volume = 251, number = 6, pages = {14-22}, year = {December 1984}, key = {models-computer}, note = { {\it ~\\ Description of program for simulating predator-prey dynamics.} } } @book{Dewdney84c, author = {Dewdney, A.K.}, title = {The Planiverse: Computer Contact with a Two-Dimensional World}, publisher = {Poseidon Press}, year = 1984, key = {refs-general}, note = { {\it ~\\ Entertaining and enlightening book on what life would be like in a 2D universe.} } } @article{Dewdney85a, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {A} Core War bestiary of viruses, worms and other threats to computer memories}, journal = {Scientific American}, volume = 252, number = 3, pages = {14-23}, year = {March 1985}, key = {models-computer}, note = { {\it ~\\ Review of self-propagating programs.} } } @article{Dewdney85b, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {A} circuitous odyssey from Robotropolis to the electronic gates of Silicon Valley}, journal = {Scientific American}, volume = 253, number = 1, pages = {14-19}, year = {July 1985}, key = {models-computer}, note = { {\it ~\\ Description of a program for wiring up simple simulated robots using actuators, sensors, motors, and etc. in order to perform simple task in a simulated environment. Should be extended to allow interactions between robots.} } } @article{Dewdney85c, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {Exploring} the field of genetic algorithms in a primordial computer sea full of flibs}, journal = {Scientific American}, volume = 253, number = 5, pages = {21-32}, year = {November 1985}, key = {models-computer, genetic-algorithms}, note = { {\it ~\\ Description of a program for experimenting with genetic algorithms.} } } @article{Dewdney87a, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {A} program called {MICE} nibbles its way to victory at the first {Core War} tournament}, journal = {Scientific American}, volume = 256, number = 1, pages = {14-20}, year = {January 1987}, key = {models-computer}, note = { {\it ~\\ Results of the first international competition.} } } @article{Dewdney87b, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {The} game of {Life} acquires some successors in three dimensions}, journal = {Scientific American}, volume = 256, number = 2, pages = {16-24}, year = {February 1987}, key = {models-computer, CA-LIFE}, note = { {\it ~\\ Description of Carter Bays' 3D extensions of Conway's game of LIFE. See also \cite{Bays87}.} } } @article{Dewdney87c, author = {Dewdney, A.K.}, title = {{Computer Recreations}: {Braitenberg Memoirs} - {Vehicles} for probing behavior roam a dark plain marked by lights}, journal = {Scientific American}, volume = 256, number = 3, pages = {16-24}, year = {1987}, key = {models-computer}, note = { {\it ~\\ Discussion of programming techniques for implementing Braitenberg's vehicles \cite{Braitenberg84}. } } } @article{Dixon83, author = {Dixon, R.}, title = {The Mathematics and Computer Graphics of Spirals in Plants}, journal = {Leonardo}, volume = 16, pages = {86-90}, year = 1983, key = {models-graphics,plants,pattern-formation}, note = { {\it ~\\ } } } @article{Dobzhansky72, author = {Dobzhansky, K.}, title = {Darwinian Evolution and the Problem of Extraterrestrial Life}, journal = {Perspect. Biol. Med.}, volume = 15, pages = {157-175}, year = 1972, key = {evolution,refs-general}, note = { {\it ~\\ Discussion of the impossibility of predicting the future course of evolution due to its sensitive and unpredictable dependence on ``accidental'' genetic and environmental events.} } } @article{Drexler81, author = {Drexler, K.E.}, title = {Molecular Engineering: An Approach to the Development of General Capabilities for Molecular Manipulation}, journal = {Proc. Nat. Acad. Sci. USA}, volume = 78, number = 9, pages = {5275-5278}, year = 1981, key = {nanotech}, note = { {\it ~\\ An early characterization of {\em nanotechnology}.} } } @article{Drexler82, author = {Drexler, K.E.}, title = {Mightier Machines from Tiny Atoms May Someday Grow}, journal = {Smithsonian}, pages = {145-154}, year = {November 1982}, key = {nanotech}, note = { {\it ~\\ Short overview of nanotechnology.} } } @book{Drexler86, author = {Drexler, E.}, title = {Engines of Creation: Nano-Technology}, publisher = {Anchor-Press/Doubleday}, address = {New York}, year = 1986, key = {nanotech}, note = { {\it ~\\ A popular treatment of nanotechnology.} } } @incollection{Drexler87, author = {Drexler, K.E.}, title = {Molecular Machinery and Molecular Devices}, booktitle = {Molecular Electronic Devices {II}}, editor = {Carter, F.}, publisher = {Marcel Dekker}, address = {New York}, year = 1987, key = {nanotech}, note = { {\it ~\\ } } } @book{Dreyfus79, author = {Dreyfus, H.}, title = {What Computers Can't Do: The Limits on Artificial Intelligence}, publisher = {Harper \& Row}, address = {New York}, year = 1979, key = {ai,ai-critic}, note = { {\it ~\\ Classic book arguing against the traditional AI approach to machine intelligence.} } } @book{Dyson81, author = {Dyson, F.}, title = {Disturbing the Universe}, publisher = {Harper Colophon}, address = {New York}, year = 1981, key = {refs-general}, note = { {\it ~\\ Freeman Dyson's thoughts about the nature of life, the universe and everything.} } } @book{Dyson85a, author = {Dyson, F.}, title = {Origins of Life}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1985, key = {origins}, note = { {\it ~\\ Dyson's theory that non-replicating, metabolizing fauna must have preceeded replicating organisms. Includes a brief survey and analysis of other origin theories.} } } @article{Dyson85b, author = {Dyson, F.}, title = {Space Butterflies and other Speculations}, journal = {Science 85}, year = {November 1985}, key = {self-rep}, note = { {\it ~\\ Proposal for simple, self-reproducing machines to explore the planets and stars.} } } @article{Edelman82, author = {Edelman, G.M.}, title = {Selective Networks capable of Representative Transformations, Limited Generalizations, and Associative Memory.}, journal = {Proc. Nat. Acad. Sci.}, volume = 79, pages = {2091-2095}, year = 1982, note = { {\it ~\\ Description of the ``Darwin'' machine.} } } @book{Edelman87, author = {Edelman, G.M.}, title = {Neural Darwinism: The Theory of Neuronal Group Selection}, publisher = {Basic Books}, address = {New York}, year = 1987, key = {evolution}, note = { {\it ~\\ Presentation of Edelman's theory that high-level functions compete for neuronal support.} } } @article{Eigen71, author = {Eigen, M.}, title = {Self-Organization of Matter and the Evolution of Biological Macromolecules}, journal = {Naturwissenschaften}, volume = 10, year = 1971, key = {origins, evolution, wetware}, note = { {\it ~\\ Theoretical discussion of evolution, natural selection among molecules, and the origin of life.} } } @incollection{Eigen73, author = {Eigen, M.}, title = {The Origin of Biological Information}, booktitle = {The Physicist's Conception of Nature}, editor = {Mehra, J.}, publisher = {D. Reidel Publishing Co.}, pages = {594-632}, year = 1973, key = {origins, evolution, wetware}, note = { {\it ~\\ } } } @book{Eigen79, author = {Eigen, M. and Schuster, P.}, title = {The Hypercycle: A Principle of Natural Self-Organization}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1979, key = {origins, evolution,theory-bio}, note = { {\it ~\\ Theory of the emergence of hierarchies of auto-catalytic networks} } } @article{Eigen81, author = {Eigen, M. and Gardiner, W. and Schuster, P. and Winkler-Oswatitsch, R.}, title = {The Origin of Genetic Infromation}, journal = {Scientific American}, volume = 244, number = 4, pages = {88-118}, year = {April 1981}, key = {origins, evolution}, note = { {\it ~\\ A good, general introduction to Eigen's theories on quasi-species, hyper-cycles, and the origin of life.} } } @book{Eigen82a, author = {Eigen, M. and Winkler, R.}, title = {The Laws of the Game: How the Principles of Nature Govern Chance}, publisher = {Harper Colophon}, address = {New York}, year = 1982, key = {refs-general,coop-behave,CA-LIFE}, note = { {\it ~\\ A wide ranging description of how chance and low-level rules lead to complex behavior.} } } @article{Eigen82b, author = {Eigen, M. and Schuster, P.}, title = {Stages of Emerging Life - Five Principles of Early Organization}, journal = {J. Molec. Evol.}, volume = 19, pages = {47-61}, year = 1982, key = {origins,refs-general}, note = { {\it ~\\ The five are: formation of stereoregular heteropolymers, selection through self-replication, evolution of quasispecies, emergence of cooperative catalytic hypercycles, and evaluation of translation products through compartmentalization.} } } @article{Elsasser81, author = {Elsasser, W.M.}, title = {A Form of Logic Suited for Biology}, journal = {Prog. Theor. Biol.}, volume = 6, pages = {23-61}, year = 1981, key = {bio-logic}, note = { {\it ~\\ One presentation of the notion that the underlying ``bio-logic'' of living systems is independent of the particular physical law that governs the behavior of the material primitives of the system. Argues for a kind of ``creative-selection'' which is different from Darwinian selection.} } } @article{Epstein83, author = {Epstein, I.R. and Kustin, K. and De Kepper, P. and Orban, M.}, title = {Oscillating Chemical Reactions}, journal = {Scientific American}, volume = 248, number = 3, pages = {112-123}, year = {March 1983}, key = {pattern-formation,chaos,dynamics,self-org}, note = { {\it ~\\ Chemical examples of the way in which simple, local reactions can lead to complex global behavior.} } } @book{Fahlman79, author = {Fahlman, S.E.}, title = {NETL: A System for Representing and Using Real-World Knowledge}, publisher = {MIT Press}, address = {Cambridge}, year = 1979, key = {ai,ai-connect}, note = { {\it ~\\ Fahlman's implementation of a semantic network - a distributed knowledge representation scheme.} } } @book{Farley77, author = {Farley, J.}, title = {The Spontaneous Generation Controversy from Descartes to Oparin}, publisher = {John Hopkins University Press}, address = {Baltimore}, year = 1977, key = {origins,refs-general}, note = { {\it ~\\ } } } @proceedings{Farmer84, editor = {Farmer, J.D. and Toffoli, T. and Wolfram, S.}, title = {Cellular Automata: Proceedings of an Interdisciplinary Workshop at Los Alamos, New Mexico, March 7-11, 1983}, publisher = {North-Holland}, address = {Amsterdam}, year = 1984, key = {refs-general, CA}, note = { {\it ~\\ A collection of papers on the theory and applications of cellular automata.} } } @article{Farmer86a, author = {Farmer, J.D. and Kauffman, S.A. and Packard, N.H.}, title = {Autocatalytic Replication of Polymers}, journal = {Physica D}, volume = 22, pages = {50-67}, year = 1986, key = {models-computer, origins}, note = { {\it ~\\ A model of the emergence of autocatalytic networks using the concept of a reaction graph.} } } @article{Farmer86b, author = {Farmer, J.D. and Packard, N.H. and Perelson, A.S.}, title = {The Immune System, Adaptation \& Learning}, journal = {Physica D}, volume = 22, pages = {187-204}, year = 1986, key = {models-computer, adaptation}, note = { {\it ~\\ A dynamic model of the immune system based on Jerne's network hypothesis. Comparisons are drawn with Holland's Classifier Systems \cite{Holland86a,Holland86b}.} } } @book{Farmer86c, author = {Farmer, J.D. and Lapedes, A. and Packard, N.H. and Wendroff, B.}, title = {Evolution, Games and Learning}, publisher = {North-Holland}, address = {Amsterdam}, year = 1986, key = {refs-general,evolution}, note = { {\it ~\\ Proceedings of the Fifth Annual International Conference of the Center for Nonlinear Studies, Los Alamos, New Mexico, May 20-24, 1985. Also Published as {\em Physica D}, Vol. 22, 1986.} } } @book{Fasan70, author = {Fasan, E.}, title = {Relations with Alien Intelligences}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1970, key = {ethics-rights}, note = { {\it ~\\ Written during the height of {\it CETI} enthusiasm (Communication with Extra-Terrestrial Intelligence - see \cite{Shklovskii66}). Similiar considerations apply to intelligences or life-forms of our own manufacture.} } } @book{Feigenbaum63, editor = {Feigenbaum, E.A. and Feldman, J.}, title = {Computers and Thought}, publisher = {McGraw Hill}, address = {New York}, year = 1963, key = {ai,ai-history}, note = { {\it ~\\ A description of the state of the art of AI as of 1960.} } } @book{Feinberg80, author = {Feinberg, G. and Shapiro, R.}, title = {Life Beyond the Earth}, publisher = {William Morrow}, address = {New York}, year = 1980, key = {origins,life-extra}, note = { {\it ~\\ Discussion of likelihood and nature of life in the solar system and beyond.} } } @book{Fisher58, author = {Fisher, R.}, title = {Genetical Theory of Natural Selection - $2^{nd}$ edition}, publisher = {Dover}, address = {New York}, year = 1958, note = { {\it ~\\ A reprint of Fisher's classic 1929 mathematical analysis of the process of evolution by natural selection.} } } @article{Fodor81, author = {Fodor, J.A.}, title = {The Mind Body Problem}, journal = {Scientific American}, volume = 244, number = 1, pages = {114-123}, year = {January 1981}, key = {ai-philos}, note = { {\it ~\\ Hardware of the brain {\it vs.} behavior of that hardware.} } } @book{Fogel66, author = {Fogel, L.J. and Owens, A.J. and Walsh, M.J.}, title = {Artificial Intelligence through Simulated Evolution}, publisher = {John Wiley \& Sons}, address = {New York}, year = 1966, key = {ai, evolution, adaptation, genetic-algorithms}, note = { {\it ~\\ This work has been criticized as involving overly simple evolution of finite automata, but it was of pioneering significance at the time. For a review see \cite{Lindsay68}.} } } @book{FoxRF88, author = {Fox, R.F.}, title = {Energy and the Evolution of Life}, publisher = {W.H. Freeman}, address = {New York}, year = 1988, key = {origins,life-thermodynamics}, note = { {\it ~\\ A solid exposition of the relevance of energy flow to models of life and its origins.} } } @article{FoxSW59, author = {Fox, S.W. and Harada, K. and Kendrick, J.}, title = {Production of Spherules from Synthetic Proteinoid and Hot Water}, journal = {Science}, volume = 129, pages = {1221ff}, year = 1959, key = {origins}, note = { {\it ~\\ Fox {\em et al}'s original paper on proteinoid spheres.} } } @article{FoxSW60, author = {Fox, S.W.}, title = {How did Life Begin?}, journal = {Science}, volume = 132, pages = {200ff}, year = 1960, key = {origins}, note = { {\it ~\\ Fox's theory of the origin of life based on proteinoid spheres.} } } @book{FoxSW65, editor = {Fox, S.W.}, title = {The Origins of Pre-Biological Systems and Molecular Structures}, publisher = {Academic Press}, year = 1965, key = {origins}, note = { {\it ~\\ } } } @book{FoxSW77, author = {Fox, S.W. and Dose, K.}, title = {Molecular Evolution and the Origin of Life}, publisher = {Marcel Dekker}, address = {New York}, year = 1977, key = {origins,refs-general}, note = { {\it ~\\ Good review of the work of Sidney Fox.} } } @book{FoxSW86, editor = {Fox, S.W.}, title = {Selforganization}, publisher = {Adenine Press}, address = {Guilderland, New York}, year = 1986, key = {origins, self-org}, note = { {\it ~\\ Proceedings of the Liberty Fund conference on self-organization held in Key Biscayne, Florida, 1984.} } } @phdthesis{Foy74, author = {Foy, J.}, title = {A Computer Simulation of Impulse Conduction in Cardiac Muscle}, school = {The University of Michigan}, year = 1974, key = {models-computer,coop-behave}, note = { {\it ~\\ Simulation of the generation of periodic pulse-waves in an excitable, refractory medium, and analysis of perturbations which lead to a transition from the periodic to a chaotic regime reminiscient of fibrilation.} } } @phdthesis{Frantz72, author = {Frantz, D.R.}, title = {Non-linearities in Genetic Adaptive Search}, school = {The University of Michigan}, year = 1972, key = {genetic-algorithms}, note = { {\it ~\\ } } } @article{Freitas77a, author = {Freitas, R.}, title = {The Legal Rights of Extraterrestrials}, journal = {Analog}, volume = 97, pages = {54-67}, year = 1977, key = {ethics-rights}, note = { {\it ~\\ Much of this discussion could be applied to {\em artificial} terrestrial life as well.} } } @article{Freitas77b, author = {Freitas, R.}, title = {Metalaw and Interstellar Relations}, journal = {Mercury}, volume = 6, pages = {15-17}, year = 1977, key = {ethics-rights}, note = { {\it ~\\ Relations with other life-forms} } } @article{Freitas80, author = {Freitas, R.}, title = {A Self-Reproducing Interstellar Probe}, journal = {J. of the British Interplanetary Soc.}, volume = 33, pages = {251-264}, year = 1980, key = {self-rep}, note = { {\it ~\\ Detailed plans for the construction of a self-reproducing fleet of interstellar probes. Includes a discussion of such questions as whether it is morally right for a reproducing star-probe to enter a foreign solar system and convert part of that system's mass and energy for its own use.} } } @article{Freitas83a, author = {Freitas, R.}, title = {Roboclone}, journal = {Omni}, volume = 5, pages = {44-47}, year = 1983, key = {self-rep, soc-impact}, note = { {\it ~\\ Popular account of self-reproducing machines and their possible applications.} } } @article{Freitas83b, author = {Freitas, R.}, title = {Building {Athens} without the Slaves}, journal = {Technology Illustrated}, volume = 3, pages = {16-20}, year = 1983, key = {self-rep, soc-impact}, note = { {\it ~\\ Self-reproducing machines could ``expand human horizons dramatically, increase productivity, and cause an explosion of wealth before the end of this century''.} } } @article{Gardner70, author = {Gardner, M.}, title = {{Mathematical Games}: {The} Fantastic Combinations of John Conway's New Solitaire Game `{Life'}}, journal = {Scientific American}, volume = 223, number = 4, pages = {120-123}, year = {October 1970}, key = {CA-LIFE}, note = { {\it ~\\ The original description of Conway's game of LIFE.} } } @article{Gardner71, author = {Gardner, M.}, title = {{Mathematical Games}: {On} Cellular Automata, Self-Reproduction, The Garden of Eden and the Game of {`Life'}}, journal = {Scientific American}, volume = 224, number = 2, pages = {112-117}, year = {February 1971}, key = {CA, CA-LIFE,automata-selfrepro,automata-theory}, note = { {\it ~\\ Follow-up article on LIFE and other CA rules.} } } @article{Gardner73, author = {Gardner, M.}, title = {{Mathematical Games}: {Fantastic} patterns traced by programmed `worms'}, journal = {Scientific American}, volume = 229, number = 5, pages = {116-123}, year = {November 1973}, key = {lattice-model,pattern-formation}, note = { {\it ~\\ Description of Patterson's Worm system. Also see \cite{Beeler73}.} } } @article{Gardner78, author = {Gardner, M.}, title = {Mathematical Games: {A} Mathematical Zoo of Astounding Critters, Imaginary and Otherwise}, journal = {Scientific American}, volume = 238, number = 6, pages = {18-28}, year = {June 1978}, key = {models-math}, note = { {\it ~\\ Organisms with mathematically interesting structure.} } } @book{Gardner83, author = {Gardner, M.}, title = {Wheels, Life, and Other Amusements}, publisher = {W.H. Freeman}, address = {New York}, year = 1983, key = {refs-general, CA-LIFE}, note = { {\it ~\\ The last three chapters are devoted to Conway's game of LIFE.} } } @book{Gatlin72, author = {Gatlin, L. L.}, title = {Information Theory and the Living System}, publisher = {Columbia University Press}, address = {New York}, year = 1972, key = {models-math,theory-biol}, note = { {\it ~\\ An interesting analysis of the information-theoretic structure of DNA, together with a theory about the selection pressure on the DNA-to-protein channel. This work deserves to be followed up now that vastly more DNA sequence information is available.} } } @book{Gebstadter79, author = {Gebstadter, E.B.}, title = {Copper, Silver, Gold: An Indestructible Metallic Alloy}, publisher = {Acidic Books}, address = {Perth}, year = 1979, note = { {\it ~\\ This self-referential reference refers to a self-referential imaginary book \cite{Gebstadter79} which is, however, cited elsewhere \cite{Hofstadter79}. Could this be a self-reproducing, self-referential reference?} } } @article{Gleick87a, author = {Gleick, J.}, title = {Artificial Life: {Can} Computers Discern the Soul?}, journal = {The New York Times}, year = {Thursday, Sept. 29, 1987}, key = {reviews}, note = { {\it ~\\ Science Section: good review of the first Artificial Life Workshop, despite the title.} } } @book{Gleick87b, author = {Gleick, J.}, title = {Chaos}, publisher = {Viking}, address = {New York}, year = 1987, key = {chaos,dynamics,refs-general}, note = { {\it ~\\ A very good layman's introduction to the theory of chaotic dynamical systems and the people who have pioneered the understanding of the role of chaos in physics, chemistry, and biology.} } } @article{Godel31, author = {G\"{o}del, K.}, title = {Uber Formal Unentscheidbare Satze der {\em Principia Matematica} und verwandter Systeme {I}}, journal = {Monatshefte fur Matematik und Physik}, volume = 38, pages = {173-98}, year = 1931, key = {automata-theory}, note = { {\it ~\\ G\"{o}del's famous proof of the formal undecidability of certain mathematical truths. Translation by Elliot Mendelsohn printed in \cite{Davis65}.} } } @article{Goel74, author = {Goel, N.S.}, title = {Cooperative Processes in Biological Systems}, journal = {Prog. Theor. Biol.}, volume = 2, pages = {213-302}, year = 1974, key = {theory-biol,coop-behave,self-org}, note = { {\it ~\\ } } } @article{Goel78, author = {Goel, N.S.}, title = {Computer Simulation of Engulfment and Other Movements of Embryonic Tissues}, journal = {J. Theor. Biol.}, volume = 71, pages = {103-140}, year = 1978, key = {theory-biol,self-org,models-computer}, note = { {\it ~\\ } } } @article{Goel86, author = {Goel, N.S. and Thompson, R.L.}, title = {Organization of Biological Systems: Some Principles and Models}, journal = {Int. Rev. Cytol.}, volume = 103, pages = {1-88}, year = 1986, key = {theory-biol,models-computer}, note = { {\it ~\\ } } } @article{Goel87, author = {Goel, N.S. and Thompson, R.L.}, title = {Microcomputer Modeling of Biological Systems}, journal = {The World \& I}, volume = 2, pages = {162-173}, year = 1987, key = {models-computer}, note = { {\it ~\\ } } } @book{Goel88a, author = {Goel, N.S. and Thompson, R.L.}, title = {Computer Simulation of Self-Organization in Biological Systems}, publisher = {Croom Helm}, address = {London}, year = 1988, key = {refs-general,models-computer,self-org,self-assembly,evolution}, note = { {\it ~\\ A review of computer models of self-organization in biological systems. Chapters cover computer models for protein folding, self-assembly of virus, aggregation of cells, protein biosynthesis, and the evolution of macromolecular machinery. Numerous citations.} } } @article{Goel88b, author = {Goel, N.S. and Thompson, R.L.}, title = {Movable Finite Automata {(MFA)} Models for Biological Systems {II}: Protein Biosynthesis}, journal = {J. Theor. Biol.}, year = {1988 - in press}, key = {models-computer}, note = { {\it ~\\ See \cite{Thompson88} for part I, as well as Goel and Thompson's contribution to these proceedings.} } } @phdthesis{Goldberg83, author = {Goldberg, D.E.}, title = {Computer-Aided Gas Pipeline Operation using Genetic Algorithms and Rule Learning}, school = {The University of Michigan}, year = 1983, key = {genetic-algorithms}, note = { {\it ~\\ Example of the emergence of a default-hierarchy in one of the first applications of classifier systems and genetic algorithms to a real-world optimization problem.} } } @article{Goldberg88, author = {Goldberg, D.E. and Holland, J.H.}, title = {Genetic Algorithms and Machine Learning: {Introduction} to the Special Issue on Genetic Algorithms}, journal = {Machine Learning}, volume = 3, year = {1988 - in press}, key = {genetic-algorithms}, note = { {\it ~\\ Collection of articles detailing current research using GA's.} } } @book{Goldberg89, author = {Goldberg, D.E.}, title = {Genetic Algorithms in Search, Optimization, and Machine Learning}, publisher = {Addison-Wesley}, address = {Reading, Mass.}, year = 1989, key = {genetic-algorithms}, note = { {\it ~\\ An introductory textbook and guide to current research. Contains examples, exercises, and sample programs as well as proofs of most of the major GA theorems on crossover and implicit parallelism.} } } @article{Goodman71, author = {Goodman, E.E. and Weinberg, R. and Laing, R.}, title = {A Cell Space Embedding of Simulated Living Cells}, journal = {Bio-Medical Computing}, volume = 2, pages = {121-136}, year = 1971, key = {CA, lattice-model,models-computer}, note = { {\it ~\\ } } } @incollection{Goodwin68, author = {Goodwin, B.}, title = {The Division of Cells and the Fusion of Ideas}, booktitle = {Towards a Theoretical Biology}, volume = 1, editor = {Waddington, C. H.}, publisher = {Edinburgh University Press}, pages = {134-139}, year = 1968, key = {refs-general}, note = { {\it ~\\ } } } @proceedings{Grefenstette85, editor = {Grefenstette, J.J.}, title = {Proceedings of an International Conference on Genetic Algorithms and their Applications}, organization = {Carnegie-Mellon University, July 24-26, 1985}, publisher = {Lawerence Earlbaum Assoc.}, address = {Hillsdale, NJ}, year = 1985, key = {genetic-algorithms}, note = { {\it ~\\ Proceedings of the first workshop on genetic algorithms.} } } @proceedings{Grefenstette87, editor = {Grefenstette, J.J.}, title = {Genetic Algorithms and their Applications: Proceedings of the Second International Conference on Genetic Algorithms}, organization = {MIT, July 28-31, 1987}, publisher = {Lawerence Earlbaum Assoc.}, address = {Hillsdale, NJ}, year = 1987, key = {genetic-algorithms}, note = { {\it ~\\ } } } @article{Guttman66, author = {Guttman, B.S.}, title = {A Resolution of Rosen's Paradox for Self-Reproducing Automata}, journal = {Bulletin of Mathematical Biophysics}, volume = 28, year = 1966, key = {automata-selfrepro,automata-theory}, note = { {\it ~\\ A response to \cite{Rosen59}.} } } @book{Haken77a, author = {Haken, H.}, title = {Synergetics - An Introduction: Nonequilibrium Phase Transitions and Self-Organization in Physics, Chemistry, and Biology}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1977, key = {dynamics,chaos,theory-biol,models-math,refs-general,self-org,pattern-formation}, note = { {\it ~\\ This is the first volume in the Springer Series on ``Synergetics'': Haken's name for the study of complex dynamics in nonequilibrium systems.} } } @book{Haken83, author = {Haken, H.}, title = {Advanced Synergetics: Instability Hierarchies of Self-Organizing Systems and Devices.}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1983, key = {dynamics,chaos,theory-biol,models-math,refs-general,self-org,pattern-formation}, note = { {\it ~\\ More on chaos and structure in nonequilibrium systems.} } } @book{Hameroff87, author = {Hameroff, S.R.}, title = {Ultimate Computing: Biomolecular Consciousness and Nanotechnology}, publisher = {Elsevier}, address = {New York}, year = 1987, key = {nanotech,computers-molecular}, note = { {\it ~\\ Review of nanotechnology and the possibility for molecular-scale computation.} } } @article{Hamilton64, author = {Hamilton, W.}, title = {The Genetical Evolution of Social Behavior}, journal = {J. Theor. Biol.}, volume = 7, pages = {1-31}, year = 1964, key = {evolution-theory}, note = { {\it ~\\ Classic paper on the evolution of altruistic behavior.} } } @book{Harary72, author = {Harary, F.}, title = {Graph Theory}, publisher = {Addison-Wesley}, address = {Reading Mass.}, year = 1972, key = {refs-general}, note = { {\it ~\\ The standard text on graph theory - a useful tool for describing and analyzing interaction ``networks''.} } } @article{HayL80, author = {Hay, L.}, title = {Self-Reproducing Programs}, journal = {Creative Computing}, volume = 6, pages = {134-136}, year = {July 1980}, key = {self-rep}, note = { {\it ~\\ } } } @book{Hebb49, author = {Hebb, D.O.}, title = {The Organization of Behavior}, publisher = {Wiley \& Sons}, address = {New York}, year = 1949, key = {brain-model,ai,ai-history}, note = { {\it ~\\ Hebb's ``cell-assembly'' model, in which aggregates of neurons form the physiological basis of concepts.} } } @article{HermanGT69, author = {Herman, G.T.}, title = {Computing Ability of a Developmental Model for Filamentous Organisms}, journal = {J. Theor. Biol.}, volume = 25, pages = {421-435}, year = 1969, key = {L-systems, automata-theory}, note = { {\it ~\\ Analysis of computational capacity of L-systems \cite{Lindenmayer68}.} } } @article{HermanGT70, author = {Herman, G.T.}, title = {Role of Environments in Developmental Models}, journal = {J. Theor. Biol.}, volume = 29, pages = {329-342}, year = 1970, key = {development,L-systems}, note = { {\it ~\\ } } } @article{HermanGT73, author = {Herman, G.T.}, title = {On Universal Computer Constructors}, journal = {Information Processing Letters}, volume = 2, pages = {61-64}, year = 1973, key = {automata-selfrepro,automata-theory}, note = { {\it ~\\ Proof that computation/construction universality is {\em not} sufficient to eliminate cases of trivial self-reproduction.} } } @book{HermanGT75, author = {Herman, G.T. and Rozenberg, G.}, title = {Developmental Systems and Languages}, publisher = {North-Holland}, address = {Amsterdam}, year = 1975, key = {L-systems,development}, note = { {\it ~\\ The first and a very useful textbook on L-systems.} } } @article{Hewitt77, author = {Hewitt, C.}, title = {Viewing Control Structures as Patterns of Passing Messages}, journal = {Artificial Intelligence}, volume = 8, pages = {323-364}, year = 1977, key = {refs-bottomup,computers-parallel}, note = { {\it ~\\ Influential description of a method for implementing distributed control structures: the ACTOR paradigm.} } } @inproceedings{Hewitt80, author = {Hewitt, C.}, title = {The Apiary Network Architecture for Knowledgeable Systems}, booktitle = {Proceedings of Lisp Conference}, organization = {Stanford University}, year = 1980, key = {computers-parallel}, note = { {\it ~\\ Description of a hardware architecture to support the ACTOR paradigm.} } } @article{Hillis82, author = {Hillis, W.D.}, title = {New Computer Architectures and their Relationship to Physics, or Why Computer Science is No Good}, journal = {International Journal of Theoretical Physics}, volume = 21, number = {3/4}, pages = {255-262}, year = 1982, key = {CA,computers-parallel,refs-bottomup}, note = { {\it ~\\ Why computer science should begin to look at physics.} } } @article{Hillis84, author = {Hillis, W.D.}, title = {The Connection Machine: A Computer Architecture based on Cellular Automata}, journal = {Physica D}, volume = 10, pages = {213-228}, year = 1984, key = {CA,computers-parallel,refs-bottomup}, note = { {\it ~\\ An early description of the connection machine concept. This article contains many interesting comments on the motivations for massively parallel processors. Reprint of MIT AI-Lab Memo 646 (1981).} } } @book{Hillis87, author = {Hillis, W.D.}, title = {The Connection Machine}, publisher = {MIT Press}, address = {Cambridge}, year = 1987, key = {CA,computers-parallel,refs-bottomup,refs-general}, note = { {\it ~\\ Danny Hillis' PhD thesis describing the massively parallel (65,000 processor!) machine that is now being produced by his company: Thinking Machines Corp. Hillis refers to the human brain as ``the competition''.} } } @article{Hillis88, author = {Hillis, W.D.}, title = {Intelligence as an Emergent Behavior; or, The Songs of {Eden}}, journal = {D\AE DALUS}, volume = 117, number = 1, pages = {175-189}, year = {Winter 1988}, key = {ai,evolution-culture}, note = { {\it ~\\ A metaphorical tale on the mutually beneficial co-evolution of brains and minds, the moral being that {\em both} are based on self-interested replicators in some sense. See also Dawkin's description of `memes' in \cite{Dawkins76}.} } } @book{Hinton81, editor = {Hinton, G. and Anderson, J.A.}, title = {Parallel Models of Associative Memory}, publisher = {Lawrence Earlbaum and Associates}, address = {Hillsdale, NJ}, year = 1981, key = {ai-connect,computers-parallel}, note = { {\it ~\\ A collection of papers on distributed representations for memory.} } } @book{Hofstadter79, author = {Hofstadter, D.R.}, title = {G\"{o}del, Escher, Bach: An Eternal Golden Braid}, publisher = {Basic Books}, address = {New York}, year = 1979, key = {refs-general,refs-bottomup,ai,ai-critic,ai-philos,automata,computers-psychology, coop-behave}, note = { {\it ~\\ Hofstadter's Pulitzer Prize winning treatise on the self-referential nature of life, language, intelligence, and computation. See especially Chapters X, XI, XII, XIV, XVI, XVII, and XX. Also, the ``Ant Fugue'' which follows Chapter X.} } } @techreport{Hofstadter82, author = {Hofstadter, D.R.}, title = {Artificial Intelligence: Subcognition as Computation}, number = 132, institution = {Indiana University Computer Science Dept.}, year = 1982, key = {refs-bottomup,ai-connect,ai-critic,ai}, note = { {\it ~\\ A well-written exposition on the difference between the top-down, computer-program metaphor adopted by traditional AI and the bottom-up, emergent-phenomena approach partially embraced by the new ``connectionist'' school. Reprinted as Chapter 26 of \cite{Hofstadter85}.} } } @book{Hofstadter85, author = {Hofstadter, D.R.}, title = {Metamagical Themas: Questing for the Essence of Mind and Pattern}, publisher = {Basic Books}, address = {New York}, year = 1985, key = {refs-general}, note = { {\it ~\\ A collection of Hofstadter's ``Metamagical Themas'' columns from {\em Scientific American}, elaborated upon with post-scripts several additional articles. See especially sections I, V, and VI.} } } @article{Hogeweg80, author = {Hogeweg, P.}, title = {Locally Synchronized Developmental Systems, Conceptual Advantages of the Descrete Event Formalism}, journal = {Int. J. General Systems}, volume = 6, pages = {57-73}, year = 1980, key = {models-computer}, note = { {\it ~\\ } } } @article{Hogeweg81, author = {Hogeweg, P. and Hesper, B.}, title = {Two Predators and a Prey in a Patchy Environment: An Application of {MICMAC} Modeling}, journal = {J. Theor. Biol.}, volume = 93, pages = {411-432}, year = 1981, key = {models-computer,dynamics-ecology,ecosystem}, note = { {\it ~\\ A system for the simulation of ecological dynamics.} } } @article{Hogeweg83, author = {Hogeweg, P. and Hesper, B.}, title = {The Ontogeny of the Interaction Structure in Bumble Bee Colonies: A {MIRROR} Model}, journal = {Behav. Ecol. Sociobiol.}, volume = 12, pages = {271-283}, year = 1983, key = {models-computer,dynamics-ecology,ecosystem,coop-behave}, note = { {\it ~\\ A later system for the simulation of ecological dynamics.} } } @article{Hogeweg85, author = {Hogeweg, P. and Hesper, B.}, title = {Socioinformatic Processes, a {MIRROR} Modeling Methodology}, journal = {J. Theor. Biol.}, volume = 113, pages = {311-330}, year = 1985, key = {models-computer,ecosystem,coop-behave}, note = { {\it ~\\ } } } @article{Hogeweg88, author = {Hogeweg, P.}, title = {Cellular Automata as a Paradigm for Ecological Modelling}, journal = {Applied Math. \& Computation}, volume = {in press}, year = 1988, key = {CA,models-computer,ecosystem,coop-behave}, note = { {\it ~\\ } } } @article{Holland62, author = {Holland, J.H.}, title = {Outline for a Logical Theory of Adaptive Systems}, journal = {JACM}, volume = 9, pages = {297-314}, year = 1962, key = {adaptation,genetic-algorithms}, note = { {\it ~\\ Early work on genetic algorithms. Reprinted in \cite{Burks70}.} } } @incollection{Holland67, author = {Holland, J.H.}, title = {Nonlinear Environments Permitting Efficient Adaptation}, booktitle = {Computer and Information Sciences II}, publisher = {Academic Press}, year = 1967, key = {adaptation}, note = { {\it ~\\ Considerations of effects of complexity of environment on the process of evolution.} } } @article{Holland73, author = {Holland, J.H.}, title = {Genetic Algorithms and the Optimal Allocation of Trials}, journal = {SIAM J. Comput.}, volume = 2, number = 2, pages = {88-105}, year = 1973, key = {genetic-algorithms}, note = { {\it ~\\ A mathematical analysis of genetic algorithms and their ``implicit parallelism''.} } } @book{Holland75a, author = {Holland, J. H.}, title = {Adaptation in Natural and Artificial Systems}, publisher = {University of Michigan Press}, address = {Ann Arbor}, year = 1975, key = {genetic-algorithms}, note = { {\it ~\\ An early treatment of the genetic algorithm and classifier systems.} } } @incollection{Holland76a, author = {Holland, J. H.}, title = {Studies of the Spontaneous Emergence of Self-Replicating Systems using Cellular Automata and Formal Grammars}, booktitle = {Automata, Languages, Development}, editor = {Lindenmayer, A. and Rozenberg, G.}, publisher = {North-Holland}, pages = {385-404}, year = 1976, key = {automata-selfrepro}, note = { {\it ~\\ A study demonstrating the necessity of stable sub-configurations for the emergence of reproducing entities in any reasonable time.} } } @incollection{Holland76b, author = {Holland, J. H.}, title = {Adaptation}, booktitle = {Progress in Theoretical Biology {IV}}, editor = {Rosen, R. and Snell, F.M.}, publisher = {Academic Press}, address = {New York}, pages = {263-293}, year = 1976, key = {adaptation}, note = { {\it ~\\ } } } @incollection{Holland86a, author = {Holland, J.H.}, title = {Escaping Brittleness: The possibilities of general purpose learning algorithms applied to parallel rule-based systems}, booktitle = {Machine Learning II}, editor = {Mishalski, R.S. and Carbonell, J.G. and Mitchell, T.M.}, publisher = {Kaufman}, pages = {593-623}, year = 1986, key = {models-computer,adaptation,genetic-algorithms}, note = { {\it ~\\ An overview of classifier systems and the genetic algorithm.} } } @book{Holland86b, author = {Holland, J.H. and Holyoak, K.J. and Nisbett, R.E. and Thagard, P.R.}, title = {Induction: Processes of Inference, Learning, and Discovery}, publisher = {MIT Press}, address = {Cambridge}, year = 1986, key = {refs-general,adaptation,genetic-algorithms}, note = { {\it ~\\ Classifier systems and genetic algorithms viewed within the larger context of induction in general.} } } @article{HoiLe77, author = {Hoi, L.}, title = {On Machines as Living Things}, journal = {Acta Cybernetica}, volume = 3, number = 4, year = 1977, key = {CA,automata-theory,automata-biol}, note = { {\it ~\\ Description of a cellular-automaton-like system in which the individual ``cells'' can move around like molecules in a fluid (c.f. the paper by Lugowski in these proceedings).} } } @phdthesis{Hollstien71, author = {Hollstien, R.B.}, title = {Artificial Genetic Adaptation in Computer Control Systems}, school = {The University of Michigan}, year = 1971, key = {genetic-algorithms}, note = { {\it ~\\ } } } @book{Hopcroft79, author = {Hopcroft, J.E. and Ullman, J.D.}, title = {Introduction to Automata Theory, Languages, and Computation}, publisher = {Addison-Wesley}, address = {Menlo Park}, year = 1979, key = {automata-theory,refs-general}, note = { {\it ~\\ The classic text book on the formal theory of computation.} } } @article{Hopfield82, author = {Hopfield, J.J.}, title = {Neural networks and physical systems with emergent collective computational abilities}, journal = {Proc. Nat. Acad. Sci.}, volume = 79, pages = {2554-2558}, year = 1982, key = {refs-bottomup,neural-nets,ai-connect,parallel}, note = { {\it ~\\ A proposal for a distributed system supporting emergent computation.} } } @book{Huberman88, editor = {Huberman, B.}, title = {The Ecology of Computation}, publisher = {Elsevier}, address = {New York}, year = 1988, key = {models-computer,refs-bottomup,eco-compute,parallel}, note = { {\it ~\\ A collection of papers on distributed computations viewed as ``ecosystems'' of interacting computational agents.} } } @book{Iyengar84, author = {Iyengar, S.S.}, title = {Computer Modeling of Complex Biological Systems}, publisher = {CRC Press}, address = {Boca Raton}, year = 1984, key = {models-computer}, note = { {\it ~\\ Methods for programming primarily mathematical models of biological systems.} } } @incollection{Jacobs72, author = {Jacobs, W.}, title = {How a Bug's Mind Works}, booktitle = {Cybernetics, Artificial Intelligence, and Ecology}, editor = {Robinson, H.W. and Knight, D.E.}, publisher = {Spartan Books}, year = 1972, key = {cybernetics}, note = { {\it ~\\ Describes the structure and behavior of PERCY, a simulated bug capable of learning. Emphasis is on adaptation in {\it simple} behavior generators (c.f. the articles by Coderre and Travers in these proceedings).} } } @article{Jacobson58, author = {Jacobson, H. J.}, title = {On Models of Reproduction}, journal = {American Scientist}, volume = 46, number = 3, pages = {255-284}, year = {September 1958}, key = {self-rep}, note = { {\it ~\\ Description of a self-reproducing train set!} } } @book{Jean84, author = {Jean, R.V.}, title = {Mathematical Approach to Pattern and Form in Plant Growth}, publisher = {John Wiley \& Sons}, address = {New York}, year = 1984, key = {models-math,plants,pattern-formation,development}, note = { {\it ~\\ } } } @article{Joyce84, author = {Joyce, G.F. and Tschirgi, R.D.}, title = {Automata Simulation of the Selection Process}, journal = {BioSystems}, volume = 17, pages = {65-72}, year = 1984, key = {models-computer,adaptation}, note = { {\it ~\\ } } } @article{Kampis87, author = {Kampis, G. and Csanyi, V.}, title = {Replication in Abstract and Natural Systems}, journal = {BioSystems}, volume = 20, pages = {143-152}, year = 1987, key = {self-rep}, note = { {\it ~\\ Argues against validity of automaton models of self-reproduction.} } } @article{Karplus86, author = {Karplus, M. and McMammon, J.A.}, title = {The Dynamics of Proteins}, journal = {Scientific American}, volume = 254, number = 4, pages = {42-51}, year = {April, 1986}, key = {models-computer,models-graphics}, note = { {\it ~\\ Computer simulation of the dynamic structure of proteins.} } } @article{Kauffman69, author = {Kauffman, S.A.}, title = {Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets}, journal = {J. Theor. Biol.}, volume = 22, pages = {437-467}, year = 1969, key = {dynamics,theory-biol}, note = { {\it ~\\ Analysis of the dynamics of random, complex networks of Boolean automata. Such nets have come to be referred to under the general title of ``The Kauffman Model,'' and constitute an active area of research, e.g., \cite{Derrida86a,Derrida86b,Weisbuch86}.} } } @article{Kauffman84, author = {Kauffman, S.A.}, title = {Emergent Properties in Random Complex Automata}, journal = {Physica D}, volume = 10, publisher = {North-Holland}, address = {Amsterdam}, year = 1984, key = {dynamics,theory-biol}, note = { {\it ~\\ Reviews the surprisingly ordered dynamics of randomly assembled Boolean networks of automata, and discusses the emergence of powerful subautomata called ``forcing-structures,'' which come to dominate the dynamics.} } } @article{Kauffman86a, author = {Kauffman, S.A.}, title = {Autocatalytic Sets of Proteins}, journal = {J. Theor. Biol.}, volume = 119, pages = {1-24}, year = 1986, key = {origins,autocat-net,theory-biol}, note = { {\it ~\\ Discussion of the possibilities for the emergence of autocatalytic sets of proteins and their relevance to the origin of life.} } } @article{Kauffman86b, author = {Kauffman, S.A. and Smith, R.G.}, title = {Adaptive Automata based on Darwinian Selection}, journal = {Physica D}, volume = 22, pages = {68-82}, year = 1986, key = {automata-theory,adaptation,evolution}, note = { {\it ~\\ Discussion of issues plus results of experimental selection for automata whose dynamical attractors match a predetermined target pattern.} } } @article{Kauffman87a, author = {Kauffman, S.A.}, title = {Developmental Logic and its Evolution}, journal = {BioEssays}, volume = 6, number = 2, pages = {82-87}, year = 1987, key = {dynamics,evolution,origins}, note = { {\it ~\\ The emergence of small, stable attractors in random, complex boolean networks as models of cell-types and the selective evolution of those cell-types.} } } @article{Kauffman87b, author = {Kauffman, S.A. and Levin, S.}, title = {Towards a General Theory of Adaptive Walks on Rugged Landscapes}, journal = {J. Theor. Biol.}, volume = 128, pages = {11-45}, year = 1987, note = { {\it ~\\ Combinatorial optimization, whether in biological evolution or in the synaptic-weight-space of neural-net models, confronts a rugged fitness landscape. This article takes a step towards studying the statistical structure of such landscapes.} } } @book{Kauffman89, author = {Kauffman, S.A.}, title = {Origins of Order: Self-Organization and Selection in Evolution}, publisher = {Oxford University Press}, address = {Oxford}, year = {1989 - in press}, note = { {\it ~\\ Discusses the balance struck between self-organized properties in complex systems and natural selection, with implications for evolution. Topics include: fitness landscapes, evolution of catalytic activities, origin of life, dynamics of genetic regulatory-networks, and morphogenesis.} } } @article{Kemeny55, author = {Kemeny, J. G.}, title = {Man Viewed as a Machine}, journal = {Scientific American}, volume = 192, number = 4, year = {April 1955}, key = {refs-general,man-machine}, note = { {\it ~\\ } } } @book{Kohonen77, author = {Kohonen, T.}, title = {Associative Memory}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1977, key = {ai-connect,computers-parallel}, note = { {\it ~\\ } } } @article{Kolata84, author = {Kolata, G.}, title = {Esoteric Math has Practical Result}, journal = {Science}, volume = 225, pages = {494-495}, year = 1984, key = {models-math.models-graphics,plants}, note = { {\it ~\\ Generation of the detailed structure of leaves and other natural objects by means of a fixed-point algorithm.} } } @article{Kornfield81, author = {Kornfield, W.A. and Hewitt, C.}, title = {The Scientific Community Metaphor}, journal = {IEEE Transactions on Systems, Man, and Cybernetics}, volume = {SMC-11}, pages = {24-33}, year = 1981, key = {refs-bottomup,eco-compute}, note = { {\it ~\\ Analysis of the problem solving capabilities of scientific communities and discussion of a parallel, distributed programming methodology that incorporates these capabilities.} } } @techreport{Laing69, author = {Laing, R.}, title = {Formalisms for Living Systems (Part {I)}}, institution = {University of Michigan}, number = {T.R. no. 08226-8-T}, year = 1969, key = {automata-theory,automata-biol}, note = { {\it ~\\ Discussion and comparison of several different modeling strategies for living systems based on formal computational systems.} } } @techreport{Laing70, author = {Laing, R.}, title = {Asexual and Sexual Reproduction Expressed in the von Neumann Cellular System (Formalisms for Living Systems (Part {I}) Sections 9.2 - 9.5)}, institution = {University of Michigan}, year = 1970, key = {automata-selfrepro,automata-biol}, note = { {\it ~\\ An extension to the preceeding paper introducing the capacity for sexual reproduction to the von Neumann model.} } } @article{Laing71, author = {Laing, R.}, title = {Formalisms for Biology: A Hierarchy of Developmental Processes}, journal = {Intern. J. Neuroscience}, volume = 2, pages = {219-232}, year = 1971, key = {automata-biol}, note = { {\it ~\\ Demonstration of the applicability of formal grammar theory and automata theory to the modeling of biological development.} } } @article{Laing72, author = {Laing, R.}, title = {Artificial Organisms and Autonomous Cell Rules}, journal = {Journal of Cybernetics}, volume = 2, number = 1, pages = {38-49}, year = 1972, key = {automata-biol}, note = { {\it ~\\ A formal system for modeling features of biological development.} } } @article{Laing73, author = {Laing, R.}, title = {The Capabilities of Some Species of Artificial Organisms}, journal = {Journal of Cybernetics}, volume = 3, number = 2, pages = {16-25}, year = 1973, key = {automata-biol}, note = { {\it ~\\ Description of behavioral potential of artificial organisms composed of freely interacting elementary components enclosed in an expandeble envelope.} } } @inproceedings{Laing75a, author = {Laing, R.}, title = {Artificial Molecular Machines: A Rapproachment Between Kinematic and Tessellation Automata}, booktitle = {Proceedings of the International Symposium on Uniformly Structured Automata and Logic}, address = {Tokyo}, year = {August 1975}, key = {automata-selfrepro,automata-biol}, note = { {\it ~\\ Artificial molecules consisting of chains of Wang program statements are demonstrated to be computation-universal and are shown to be capable of constructing copies of themselves and each other.} } } @article{Laing75b, author = {Laing, R.}, title = {Some Alternative Reproduction Strategies in Artificial Molecular Machines}, journal = {J. Theor. Biol.}, volume = 54, pages = {63-84}, year = 1975, key = {automata-selfrepro}, note = { {\it ~\\ A more accessible version of the {\it Artificial Molecular Machines} paper.} } } @article{Laing76, author = {Laing, R.}, title = {Automaton Introspection}, journal = {Journal of Computer and System Sciences}, volume = 13, pages = {172-183}, year = 1976, key = {automata-biol,automata-selfrepro}, note = { {\it ~\\ Discussion of the manner in which an automaton can determine its own structure.} } } @article{Laing77, author = {Laing, R.}, title = {Automaton Models of Reproduction by Self-Inspection}, journal = {J. Theor. Biol.}, volume = 66, pages = {437-456}, year = 1977, key = {automata-selfrepro}, note = { {\it ~\\ Introduces a self-reproducing automaton which can reproduce without a description of itself. Rather, the machine generates its own description by self-inspection. Unlike von Neumann's system, this system will support Lamarckian inheritance.} } } @article{Laing79, author = {Laing, R.}, title = {Machines as Organisms: An Exploration of the Relevance of Recent Results}, journal = {BioSystems}, volume = 11, year = 1979, key = {automata-biol}, note = { {\it ~\\ A good overview of Laing's work on artificial organisms, with commentaries and his responses.} } } @incollection{Laing82, author = {Laing, R.}, title = {Replicating Systems Concepts: Self-Replicating Lunar Factory and Demonstration}, booktitle = {Advanced Automation for Space Missions}, editor = {Freitas, R. and Gilbreath, W.P.}, publisher = {NASA Conf. Pub. 2255}, pages = {189-335}, year = 1982, key = {automata-selfrepro,applications}, note = { {\it ~\\ A detailed report commissioned by NASA on the feasability of constructing self-replicating lunar factories.} } } @article{Langton84, author = {Langton, C.G.}, title = {Self-Reproduction in Cellular Automata}, journal = {Physica D}, volume = 10, number = {1-2}, pages = {135-144}, year = 1984, key = {automata-selfrepro,CA}, note = { {\it ~\\ Details of a simple self-reproducing CA configuration.} } } @article{Langton86, author = {Langton, C.G.}, title = {Studying Artificial Life with Cellular Automata}, journal = {Physica D}, volume = 22, pages = {120-149}, year = 1986, key = {models-computer,CA,automata-selfrepro}, note = { {\it ~\\ A preliminary investigation of the potential of CA for supporting life.} } } @article{Langton87, author = {Langton, C.G.}, title = {Virtual State Machines in Cellular Automata}, journal = {Complex Systems}, volume = 1, pages = {257-271}, year = 1987, key = {CA}, note = { {\it ~\\ Discussion of the importance of propagating structures in CA. Contains example of a Turing machine implemented on the model of protein synthesis using propagating structures.} } } @article{Langton88a, author = {Langton, C.G. and Kelley, K.}, title = {Toward Artificial Life}, journal = {Whole Earth Review}, volume = 58, pages = {74-79}, year = 1988, key = {reviews}, note = { {\it ~\\ Review of the first Artificial Life workshop at Los Alamos. Includes pictures and descriptions of many of the presentations.} } } @book{Leduc11, author = {Leduc, Stephane}, title = {The Mechanism of Life}, publisher = {Rebman}, address = {London}, year = 1911, key = {alt-mat,synthetic-biol}, note = { {\it ~\\ A controversial work on biogenesis. For a review, see the article by Zeleny {\it et al} in these proceedings.} } } @incollection{LeeCY63, author = {Lee, C.Y.}, title = {A Turing Machine Which Prints its own Code Script}, booktitle = {Mathematical Theory of Automata}, publisher = {Polytechnic Press}, pages = {155-164}, year = 1963, key = {automata-selfrepro,automata-theory}, note = { {\it ~\\ } } } @book{Lehninger82, author = {Lehninger, A.L.}, title = {Principles of Biochemistry}, publisher = {Worth}, address = {New York}, year = 1982, key = {refs-general}, note = { {\it ~\\ A classic textbook. The introduction defines biology as the attempt to uncover ``the molecular logic of the living state''.} } } @article{Letvin59, author = {Letvin, J.Y. and Maturana, H.R. and McCulloch, W.S. and Pitts, W.H.}, title = {What the Frog's Eye Tells the Frog's Brain}, journal = {Proc. I.R.E.}, volume = 47, pages = {1940ff}, year = 1959, key = {cybernetics,brain-model,neuro-biol}, note = { {\it ~\\ Classic paper identifying functional groups of neurons which act as feature detectors.} } } @article{Lindenmayer68, author = {Lindenmayer, A.}, title = {Mathematical Models for Cellular Interactions in Development, {I \& II}}, journal = {Journal of Theoretical Biology}, volume = 18, pages = {280-315}, year = 1968, key = {L-systems,development}, note = { {\it ~\\ Lindenmayer's original articles on L-Systems.} } } @article{Lindenmayer71, author = {Lindenmayer, A.}, title = {Developmental Systems without Cellular Interactions: Their Languages and Grammars}, journal = {J. Theor. Biol.}, volume = 30, pages = {455-484}, year = 1971, key = {L-systems,development}, note = { {\it ~\\ Description of {\it context-free} L-systems.} } } @proceedings{Lindenmayer76, editor = {Lindenmayer, A. and Rozenberg, G.}, title = {Automata, Languages, Development}, publisher = {North-Holland}, address = {Amsterdam}, year = 1976, key = {L-systems,development,automata-theory}, note = { {\it ~\\ Early collection of papers on L-Systems.} } } @incollection{Lindenmayer77, author = {Lindenmayer, A.}, title = {Theories and Observations of Developmental Biology}, booktitle = {Foundational Problems in Special Sciences}, editor = {Butts, R.E. and Hintikka, J.}, publisher = {D. Reidel}, pages = {103-118}, year = 1977, note = { {\it ~\\ On the role of mathematical theories in biology.} } } @incollection{Lindenmayer82, author = {Lindenmayer, A.}, title = {Developmental Algorithms: {Lineage} versus Interactive Control Mechanisms}, booktitle = {Developmental Order: Its Origin and Regulation}, editor = {Subtelny, S. and Green, P.B.}, publisher = {A.R. Liss}, address = {New York}, pages = {219-245}, year = 1982, key = {L-systems,development}, note = { {\it ~\\ Discussion of {\it context-free} vs. {\it context-sensitive} developmental controls.} } } @article{Lindsay68, author = {Lindsay, R.K.}, title = {Artificial Evolution of Intelligence}, journal = {Contemporary Psychology}, volume = 13, number = 3, pages = {113-116}, year = 1968, key = {evolution-model,ai-history}, note = { {\it ~\\ A critical review of \cite{Fogel66} including an interesting discussion of the problem.} } } @incollection{Lofgren62, author = {Lofgren, L.}, title = {Kinematic and Tesselation Models of Self-Repair}, booktitle = {Biological Prototypes and Synthetic Systems}, volume = 1, editor = {Bernard, E.E. and Kare, M.R.}, publisher = {Plenum}, year = 1962, key = {automata-selfrepro,automata-biol}, note = { {\it ~\\ Formal analysis of self-repairing automata.} } } @article{Lodish79, author = {Lodish, H.F. and Rothman, J.E.}, title = {The Assembly of Cell Membranes}, journal = {Scientific American}, volume = 240, number = 1, pages = {38-53}, year = {January 1979}, key = {bio-behavior,coop-behave}, note = { {\it ~\\ Details of low-level self-assembly of cell membranes.} } } @article{Lovelock72, author = {Lovelock, J.E.}, title = {Gaia as Seen Through the Atmosphere}, journal = {Atmosphere and Environment}, volume = 6, pages = {579-580}, year = 1972, key = {life-other,life-general,ecosystems}, note = { {\it ~\\ } } } @book{Lovelock79, author = {Lovelock, J.E.}, title = {Gaia: A New Look at Life on Earth}, publisher = {Oxford University Press}, address = {Oxford}, year = 1979, key = {refs-general,life-other,life-general,ecosystems}, note = { {\it ~\\ Presentation of the theory that the Earth itself must be seen as a living organism.} } } @article{Lovelock83, author = {Lovelock, J.E.}, title = {{Daisy World:} {A} Cybernetic Proof of the {Gaia} Hypothesis}, journal = {The CoEvolution Quarterly}, volume = 38, pages = {66-72}, year = 1983, key = {models-computer,life-other,cybernetics,ecosystems}, note = { {\it ~\\ } } } @book{Lumsden81, author = {Lumsden, C.J. and Wilson, E.O.}, title = {Genes, Mind, and Culture: The Coevolutionary Process.}, publisher = {Harvard University Press}, address = {Cambridge}, year = 1981, key = {soc-bio,evolution-culture,evolution}, note = { {\it ~\\ Sociobiology extended to human culture. See \cite{WilsonEO75}.} } } @book{MacDonald83, author = {MacDonald, N.}, title = {Trees and Networks in Biological Models}, publisher = {John Wiley}, address = {Chichester}, year = 1983, key = {refs-general}, note = { {\it ~\\ Mathematical properties of trees and networks and applications to biology. Includes two chapters on L-systems.} } } @phdthesis{MacLaren78, author = {MacLaren, L.}, title = {A Production System Architecture based on Biological Examples}, school = {University of Washington}, year = 1978, key = {models-computer}, note = { {\it ~\\ } } } @article{Mallove80, author = {Mallove, E.F. and Forward, R.L. and Paprotny, Z. and Lehmann, J.}, title = {Interstellar Travel and Communication: A Bibliography}, journal = {J Brit. Interplanetary Soc.}, volume = 33, pages = {201-248}, year = 1980, note = { {\it ~\\ A compilation of over 2500 references on the topic of interstellar transportation and communication, broken down into categories including: origin of extra-solarlife, exotic biochemistries, alien life morphologies, possible alien artifacts, the ``zoo'' hypothesis(!), and so forth.} } } @book{Mandlebrot78, author = {Mandelbrot, B.}, title = {Fractals: Form, Chance, and Dimension}, publisher = {W.H. Freeman}, address = {New York}, year = 1978, key = {refs-general,fractals}, note = { {\it ~\\ This and the following book detail in elegant form the manner in which extremely complex structures can emerge from relatively simple recursive rules. } } } @book{Mandelbrot83, author = {Mandelbrot, B.}, title = {The Fractal Geometry of Nature}, publisher = {W.H. Freeman}, address = {New York}, year = 1983, key = {refs-general,fractals}, note = { {\it ~\\ } } } @article{Margolus84, author = {Margolus, N.}, title = {Physics-Like Models of Computation}, journal = {Physica D}, volume = 10, pages = {81-95}, year = 1984, key = {CA,models-physics,computers-parallel}, note = { {\it ~\\ Discussion of reversible cellular automata illustrated by an implementation of Fredkin's Billiard-Ball model of computation.} } } @book{Margulis70, author = {Margulis, L.}, title = {Origin of Eucaryotic Cells}, publisher = {Yale University Press}, address = {New Haven}, year = 1970, key = {refs-general,evolution}, note = { {\it ~\\ Presents the thesis that eukaryotic cells are the result of the development of a symbiotic relationship between early prokaryotic cells.} } } @book{Margulis81, author = {Margulis, L.}, title = {Symbosis in Cell Evolution}, publisher = {W.H. Freeman}, address = {San Francisco}, year = 1981, key = {evolution}, note = { {\it ~\\ Further evidence for the symbiosis theory presented in \cite{Margulis70}.} } } @book{Margulis8X, author = {Margulis, L. and Sagan, D.}, title = {Microcosmos}, publisher = {??}, address = {??}, year = {198X}, note = { {\it ~\\ } } } @book{Marquand68, author = {Marquand, J.}, title = {Life: its Nature, Origins, and Distribution ({C.S.P.} no. 17)}, publisher = {Oliver and Boyd}, address = {Edinburgh}, year = 1968, key = {origins,life-general}, note = { {\it ~\\ } } } @article{Martinez79, author = {Martinez, H.M.}, title = {An Automaton Analogue of Unicellularity}, journal = {BioSystems}, volume = 11, pages = {133-162}, year = 1979, key = {evolution-model,automata-biol}, note = { {\it ~\\ An attempt to formalize the evolution of cellular organization.} } } @article{Matela85, author = {Matela, R.J. and Ransom, R.}, title = {A Topological Model of Cell Division: Structure of the Computer Program}, journal = {BioSystems}, volume = 18, pages = {65-78}, year = 1985, key = {models-computer,automata-biol}, note = { {\it ~\\ } } } @article{Maturana75, author = {Maturana, H.R.}, title = {The Organization of the Living}, journal = {Int. J. Man-Mach. Stud.}, volume = 7, pages = {313ff}, year = 1975, key = {autopoiesis,life-org}, note = { {\it ~\\ An early exposition of {\em Autopoiesis}: a theory of ``self-propagating'' structures.} } } @article{May76, author = {May, R.M.}, title = {Simple Mathematical Models with Very Complicated Dynamics}, journal = {Nature}, volume = {261}, pages = {459ff}, year = 1976, key = {refs-general,dynamics-ecology,dynamics,chaos}, note = { {\it ~\\ Excellent early review of simple chaotic dynamical systems with consequences for ecological modeling. Reprinted in \cite{BaiLin84}.} } } @book{Maynard-Smith75, author = {Maynard Smith, J.}, title = {The Theory of Evolution - $3^{rd}$ edition}, publisher = {Penguin}, address = {New York}, year = 1975, note = { {\it ~\\ A classic.} } } @book{Maynard-Smith82, author = {Maynard Smith, J.}, title = {Evolution and the Theory of Games}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1982, note = { {\it ~\\ Application of von Neumann's theory of games to the modeling of evolution. Another classic.} } } @book{Maynard-Smith86, author = {Maynard Smith, J.}, title = {The Problems of Biology}, publisher = {Oxford University Press}, address = {Oxford}, year = 1986, note = { {\it ~\\ Excellent lay introduction to the fundamental problems of biology.} } } @article{McCulloch43, author = {McCulloch, W.S. and Pitts, W.}, title = {A Logical Calculus of the Idea Immanent in Nervous Activity}, journal = {Bulletin of Mathematical Biophysics}, volume = 5, pages = {115-133}, year = 1943, key = {neural-nets,ai-history,ai-connect}, note = { {\it ~\\ The original paper on McCulloch-Pitts neurons.} } } @book{Meinhardt82, author = {Meinhardt, H.}, title = {Models of Biological Pattern Formation}, publisher = {Academic Press}, address = {New York}, year = 1982, key = {pattern-formation}, note = { {\it ~\\ } } } @book{MillerJG78, author = {Miller, J.G.}, title = {Living Systems}, publisher = {McGraw Hill}, address = {New York}, year = 1978, key = {refs-general}, note = { {\it ~\\ A detailed, system-theoretic approach to life.} } } @book{MillerSM74, author = {Miller, S.M. and Orgel, L.E.}, title = {The Origins of Life on Earth}, publisher = {Prentice-Hall}, address = {Englewood Cliffs, NJ}, year = 1974, key = {origins}, note = { {\it ~\\ Theory of the origin of life based on the results of the classic Miller/Urey/Orgel experiments on the pre-biotic synthesis of organic compounds.} } } @book{Minsky67, author = {Minsky, M.}, title = {Computation, Finite and Infinite Machines}, publisher = {Prentice-Hall}, address = {Englewood, CA}, year = 1967, key = {automata-theory,automata-biol}, note = { {\it ~\\ An introduction to automata theory written at a time when the emulation of natural systems was still a guiding principle.} } } @book{Minsky69, author = {Minsky, M. and Papert, S.}, title = {Perceptrons: An Introduction to Computational Geometry}, publisher = {MIT Press}, address = {Cambridge}, year = 1969, key = {models-computer,ai-history,ai-connect}, note = { {\it ~\\ A treatise on the capabilities and limitations of one class of perceptron models. This book is widely - but unfairly - considered responsible for halting early AI research on connectionist/neural-net models of intelligence.} } } @book{Minsky86, author = {Minsky, M.}, title = {The Society of Mind}, publisher = {Simon and Schuster}, address = {New York}, year = 1986, key = {refs-bottomup,ai,ai-philos,eco-compute}, note = { {\it ~\\ A loosley-coupled theory of intelligence based on the model of a distributed society of interacting ``experts''.} } } @book{Monod71, author = {Monod, J.}, title = {Chance and Necessity}, publisher = {Alfred A. Knopf}, address = {New York}, year = 1971, key = {refs-general}, note = { {\it ~\\ A classic monograph on ``necessary'' {\em vs.} ``accidental'' features of living organisms.} } } @article{Moore56, author = {Moore, E.F.}, title = {Artificial Living Plants}, journal = {Scientific American}, volume = 195, number = 4, pages = {118-125}, year = {October 1956}, key = {automata-biol,alt-mat,applications,plants}, note = { {\it ~\\ Proposal for a species of self-reproducing machines which would mine and refine raw materials to construct offspring, and which would then be harvested for the materials from which they constructed themselves.} } } @article{Moore64a, author = {Moore, E.F.}, title = {Mathematics in the Biological Sciences}, journal = {Scientific American}, volume = 211, number = 3, pages = {148-164}, year = {September 1964}, note = { {\it ~\\ Moore predicts that the most significant applications of mathematics in the biological sciences will stem from the analysis of problems in the theory of computing machines.} } } @incollection{Moore64b, author = {Moore, E.F.}, title = {The Firing Squad Synchronization Problem}, booktitle = {Sequential Machines - Selected Papers}, editor = {Moore, E.F.}, publisher = {Addison-Wesley}, pages = {213-214}, year = 1964, key = {automata-theory,refs-bottomup,self-org}, note = { {\it ~\\ This is a classic problem in distributed control: how to get a line of locally-communicating agents to all do something at the same time, using only local message passing.} } } @incollection{Moore70, author = {Moore, E.F.}, title = {Machine Models of Self-Reproduction}, booktitle = {Essays on Cellular Automata}, editor = {Burks, A.W.}, publisher = {University of Illinois Press}, pages = {187-203}, year = 1970, key = {CA,automata-theory,automata-selfrepro}, note = { {\it ~\\ Moore's proof of the existence of ``Garden of Eden'' configurations in cellular automata: configurations which cannot occur under the action of a specific CA rule. Moore also provides a way around Rosen's paradox \cite{Rosen59}.} } } @book{Moravec88, author = {Moravec, H.}, title = {Mind Children: The Future of Robot and Human Intelligence}, publisher = {Harvard University Press}, address = {Cambridge}, year = 1988, key = {ai-robotics,ai-philos,applications,soc-impact,ethics-rights,alt-mats}, note = { {\it ~\\ A wide ranging treatise on the past, present, and future capabilities of robots by the director of Carnegie-Mellon's Robotics Institute. Moravec predicts that robots will replace the human race within the next century!} } } @article{Morowitz59, author = {Morowitz, H.J.}, title = {A Model of Reproduction}, journal = {American Scientist}, volume = 47, number = 2, pages = {261-263}, year = 1959, key = {self-rep}, note = { {\it ~\\ A simple extension to Jacobson's self-reproducing train set \cite{Jacobson58}.} } } @techreport{Mortimer70, author = {Mortimer, J.A.}, title = {A Cellular Model for Mammalian Cerebeller Cortex}, institution = {The University of Michigan}, number = {LCG-107}, year = 1970, key = {CA,brain-model,neuro-biol}, note = { {\it ~\\ ``An automata-theoretic model of mammalian cortex is developed to investigate the role of the four principle neuronal populations in determining the spatio-temporal response of the cortex to natural and electrical inputs''.} } } @article{Mosqueira83, author = {Mosqueira, F. G.}, title = {A Simple Competition Model Involving Selection}, journal = {Bull. Math. Biol.}, volume = 45, number = 1, pages = {51-67}, year = 1983, key = {evolution-model}, note = { {\it ~\\ } } } @incollection{Myhill70, author = {Myhill, J.}, title = {The Abstract Theory of Self-Reproduction}, booktitle = {Essays on Cellular Automata}, editor = {Burks, A.W.}, publisher = {University of Illinois Press}, pages = {206-218}, year = 1970, key = {automata-selfrepro}, note = { {\it ~\\ } } } @inproceedings{Nakano78, author = {Nakano, K.}, title = {Models of Self-Repairing Systems}, booktitle = {Proceedings of the $4^{th}$ International Joint Conference on Pattern Recognition, held in Kyoto, Japan, 1978}, publisher = {Kyoto University}, address = {Kyoto, Japan}, pages = {374-378}, year = 1978, key = {automata-selfrepro,automata-biol}, note = { {\it ~\\ A cellular model in which a perturbed pattern of cells returns to the original pattern.} } } @incollection{Newell63, author = {Newell, A. and Simon, H.A.}, title = {{GPS:} {A} Program that Simulates Human Thought}, booktitle = {Computers and Thought}, editor = {Feigenbaum, E.A. and Feldman, J.}, publisher = {McGraw-Hill}, address = {New York}, year = 1963, key = {ai-history,ai}, note = { {\it ~\\ Probably the most influential paper establishing the ``physical symbol system'' computational paradigm as the underlying model of intelligence used by AI.} } } @article{Newell80, author = {Newell, A.}, title = {Physical Symbol Systems}, journal = {Cognitive Science}, volume = 4, pages = {135-183}, year = 1980, key = {ai,ai-history}, note = { {\it ~\\ A more recent presentation of the physical symbol system hypothesis. For the opposite view, see \cite{Hofstadter82}.} } } @book{NicolisG77, author = {Nicolis, G. and Prigogine, I.}, title = {Self-Organization in Nonequilibrium Systems}, publisher = {John Wiley \& Sons}, address = {New York}, year = 1977, key = {dynamics,self-org}, note = { {\it ~\\ Classic treatise on the dynamics of dissipative systems.} } } @book{NicolisJS86, author = {Nicolis, J.S.}, title = {Dynamics of Hierarchical Systems}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1986, key = {dynamics,self-org}, note = { {\it ~\\ Aproaches to studying the dynamics and structures of hierarchical systems composed of many interacting parts.} } } @article{Niesert87, author = {Niesert, U.}, title = {How Many Genes to Start With? A Computer Simulation about the Origin of Life}, journal = {Origins of Life}, volume = 17, pages = {155-169}, year = 1987, key = {origins,models-computer}, note = { {\it ~\\ } } } @article{Nijhout81, author = {Nijhout, H. F.}, title = {The Color Patterns of Butterflies and Moths}, journal = {Scientific American}, volume = 245, number = 5, year = {November 1981}, key = {refs-bottomup,pattern-formation,self-org}, note = { {\it ~\\ Description of the way in which the wide variety of complex wing patterns of butterflies and moths emerge from the actions of a few simple rules.} } } @article{Niklas86, author = {Niklas, K.J.}, title = {Computer-Simulated Plant Evolution}, journal = {Scientific American}, volume = 254, number = 3, pages = {78-86}, year = {March 1986}, key = {evolution-model,computer-model,plants}, note = { {\it ~\\ A model which traces the fossil record of the evolution of plant structure.} } } @book{Oparin38, author = {Oparin, A.I.}, title = {The Origin of Life}, publisher = {Macmillan}, address = {New York}, year = 1938, key = {origins}, note = { {\it ~\\ Oparin's coacervate hypothesis on the origin of life. $2^{nd}$ edition published by Dover in 1967.} } } @article{Oppenheimer86, author = {Oppenheimer, P.}, title = {Real Time Design and Animation of Fractal Plants and Trees}, journal = {Computer Graphics}, volume = 20, number = 4, year = {August 1986}, key = {fractals,models-graphics,plants}, note = { {\it ~\\ } } } @book{Orgel73, author = {Orgel, L.E.}, title = {The Origins of Life: Molecules and Natural Selection}, publisher = {Wiley}, address = {New York}, year = 1973, key = {origins}, note = { {\it ~\\ } } } @article{Ostrand71, author = {Ostrand, T.J.}, title = {Pattern Reproduction in Tesselation Automata of Arbitrary Dimension}, journal = {Journal of Computer and System Sciences}, volume = 5, number = 6, year = 1971, key = {automata-selfrepro,pattern-formation}, note = { {\it ~\\ } } } @article{Pabo86, author = {Pabo, C.O. and Suchanek, E.G.}, title = {Computer-Aided Model-Building Strategies for Protein Design}, journal = {Biochemistry}, volume = 25, pages = {5987-5991}, year = 1986, key = {applications}, note = { {\it ~\\ } } } @book{Pagels88, author = {Pagels, H.R.}, title = {The Dreams of Reason: The Computer and the Rise of the Sciences of Complexity}, publisher = {Simon and Schuster}, address = {New York}, year = 1988, key = {refs-general,complex}, note = { {\it ~\\ An excellent book reviewing the emerging synthesis of nonlinear science and bottom-up computational approaches in the study of complex systems.} } } @book{Palmer85, author = {Palmer, E.M.}, title = {Graphical Evolution}, publisher = {John-Wiley \& Sons}, address = {New York}, year = 1985, key = {refs-general}, note = { {\it ~\\ An introduction to the theory of random graphs - an important tool in modeling networks of interactions.} } } @book{Papert80, author = {Papert, S.}, title = {Mindstorms: Children, Computers, and Powerful Ideas}, publisher = {Basic Books}, address = {New York}, year = 1980, key = {ai,applications,education}, note = { {\it ~\\ Papert's description of his LOGO language and its applications in children's education.} } } @article{Partridge80a, author = {Partridge, B.L.}, title = {The Effect of School Size on the Structure and Dynamics of Minnow Schools}, journal = {Anim. Behav.}, volume = 28, pages = {68-77}, year = 1980, key = {schooling}, note = { {\it ~\\ } } } @article{Partridge80b, author = {Partridge, B.L. and Pitcher, T. and Cullen, J.M. and Wilson, J.}, title = {The Three-Dimensional Structure of Fish Schools}, journal = {Behavioral Ecology and Sociobiology}, volume = 6, pages = {277-288}, year = 1980, key = {schooling}, note = { {\it ~\\ } } } @article{Partridge84, author = {Partridge, D. and Lopez, P.D. and Johnston, V.S.}, title = {Computer Programs as Theories in Biology}, journal = {J. Theor. Biol.}, volume = 108, pages = {539-564}, year = 1984, key = {theory-biol}, note = { {\it ~\\ Discussion of the notion that a program itself constitutes a theory of the system whose behavior it emulates. The inadequecy of traditional programming languages for this role are identified, a more adequate methodology is proposed, and examples of its use are presented.} } } @proceedings{Pattee66, editor = {Pattee, H. H. and Edelsack, E.A. and Fein, L. and Callahan, A.B.}, title = {Natural Automata and Useful Simulations}, publisher = {Macmillan}, address = {London}, year = 1966, key = {models-computer,automata-biol}, note = { {\it ~\\ Proceedings of the Symposium on Fundamental Biological Models, held at the Stanford Biophysics Laboratory, June 17, 1965. This symposium was dedicated to ``the process of modeling itself as an instrument for gaining understanding of the behavior of living matter''.} } } @incollection{Pattee85, author = {Pattee, H.H.}, title = {Universal Principles of Measurement and Language Function in Evolving Systems.}, booktitle = {Complexity, Language, and Life: Mathematical Approaches}, editor = {Casti, J. and Karlqvist, A.}, publisher = {Springer-Verlag}, address = {Berlin}, pages = {168-281}, year = 1985, note = { {\it ~\\ } } } @incollection{Pattee88, author = {Pattee, H.H.}, title = {Instabilities and Information in Biological Self-Organization}, booktitle = {Self-Organizing Systems: The Emergence of Order}, editor = {Yates, F.E.}, publisher = {Plenum}, address = {New York}, year = 1988, key = {self-org}, note = { {\it ~\\ } } } @book{Peacocke83, author = {Peacocke, A. R.}, title = {An Introduction to the Physical Chemistry of Biological Organization}, publisher = {Clarendon Press}, address = {Oxford}, year = 1983, key = {refs-general,life-org}, note = { {\it ~\\ Excellent introduction to the thermodynamics of living systems. Contains an extensive bibliography on biological organization.} } } @article{Penrose58a, author = {Penrose, L.S. and Penrose, R.}, title = {A Self-Reproducing Analogue}, journal = {Nature}, volume = 179, year = 1957, key = {self-rep,history}, note = { {\it ~\\ Penrose's first self-reproduction model, which is really more like crystal growth.} } } @article{Penrose58b, author = {Penrose, L.S.}, title = {Mechanics of Self-Reproduction}, journal = {Ann. Human Genetics}, volume = 23, pages = {59-72}, year = 1958, key = {self-rep,history}, note = { {\it ~\\ } } } @article{Penrose59a, author = {Penrose, L.S.}, title = {Self-Reproducing Machines}, journal = {Scientific American}, volume = 200, number = 6, pages = {105-113}, year = {June 1959}, key = {self-rep,history}, note = { {\it ~\\ Self-reproducing machines constructed out of simple mechanical blocks which can hook onto one another to form chains.} } } @article{Penrose59b, author = {Penrose, L.S.}, title = {Automatic Mechanical Self-Reproduction}, journal = {New Biology}, volume = 28, pages = {92-117}, year = 1959, key = {self-rep,history}, note = { {\it ~\\ } } } @article{Penrose60, author = {Penrose, L.S.}, title = {Developments in the Theory of Self-Replication}, journal = {New Biology}, volume = 31, pages = {57-66}, year = 1960, key = {self-rep,history}, note = { {\it ~\\ } } } @article{Pickover87a, author = {Pickover, C.}, title = {Biomorphs: {Computer} Displays of Biological Forms Generated from Mathematical Feedback Loops}, journal = {Computer Graphics Forum}, volume = 5, number = 4, pages = {313-316}, year = 1987, key = {models-graphics}, note = { {\it ~\\ A computer graphics algorithm is used to create complicated forms resembling invertebrate organisms.} } } @article{Pickover87b, author = {Pickover, C.}, title = {Mathematics and {Beauty} {IV:} {}Computer Graphics and Wild Monopodial Tendril Plant Growth}, journal = {Computer Graphics World}, volume = 10, number = 7, pages = {143-145}, year = 1987, key = {models-graphics}, note = { {\it ~\\ Algorithms for the artistic rendering of plant and coral-like forms are described.} } } @article{Pitcher73, author = {Pitcher, T.J.}, title = {The Three Dimensional Structure of Schools in the Minnow}, journal = {Anim. Behav.}, volume = 21, pages = {673-686}, year = 1973, key = {schooling}, note = { {\it ~\\ } } } @phdthesis{Plum72, author = {Plum, T.}, title = {Simulations of a Cell-Assembly Model}, school = {The University of Michigan}, year = 1972, key = {models-computer}, note = { {\it ~\\ A simulation based on Hebb's cell-assembly model, in which clusters of neurons perform computational tasks in the absence of any global controller.} } } @article{Pollard65, author = {Pollard, E.C.}, title = {The Fine Structure of the Bacterial Cell and the Possibility of its Artificial Synthesis}, journal = {American Scientist}, volume = 53, year = 1965, note = { {\it ~\\ } } } @article{Pontecorvo58, author = {Pontecorvo, G.}, title = {Self-Reproduction and All That}, journal = {Symposium of the Society for Experimental Biology}, volume = 12, pages = {1-5}, year = 1958, key = {self-rep}, note = { {\it ~\\ } } } @book{Poundstone85, author = {Poundstone, W.}, title = {The Recursive Universe}, publisher = {William Morrow}, address = {New York}, year = 1985, key = {CA-LIFE,refs-general,refs-bottomup}, note = { {\it ~\\ Review of discoveries made in Conway's game of LIFE, interspersed with speculations on its implications for understanding the universe.} } } @book{Preston84, author = {Preston, K. and Duff, M.J.B.}, title = {Modern Cellular Automata Theory and Applications}, publisher = {Plenum Press}, address = {New York}, year = 1984, key = {CA,CA-LIFE}, note = { {\it ~\\ A good book on CA's, with applications primarily in the domain of image processing. Some discussion of LIFE-like CA rules, e.g. in hexagonal lattices.} } } @article{Priese76, author = {Priese, L.}, title = {On a Simple Combinatorial Structure Sufficient for Nontrivial Self-Reproduction}, journal = {J. Cybern.}, volume = 6, number = {1-2}, pages = {101-137}, year = 1976, key = {self-rep}, note = { {\it ~\\ Self-reproduction in a reversible system.} } } @incollection{Quillian68, author = {Quillian, M.R.}, title = {Semantic Memory}, booktitle = {Semantic Information Processing}, editor = {Minsky, M.}, publisher = {MIT Press}, address = {Cambridge}, pages = {227-270}, year = 1968, key = {ai}, note = { {\it ~\\ An early discussion of {\em semantic networks} - dynamic distributed knowledge representation networks.} } } @book{Ransom81, author = {Ransom, R.}, title = {Computers and Embryos: Models in Developmental Biology}, publisher = {John Wiley}, address = {Chichester}, year = 1981, key = {models-computer,development}, note = { {\it ~\\ } } } @article{Rastetter83, author = {Rastetter, W.H.}, title = {Enzyme Engineering}, journal = {Appl. Biochem. and Biotech.}, volume = 8, pages = {423-436}, year = 1983, key = {wetware}, note = { {\it ~\\ Recombinant DNA technology makes possible the production of modified protein catalysts.} } } @article{Reed67, author = {Reed, J.}, title = {Simulation of Biological Evolution and Machine Learning}, journal = {J. Theoret. Biol.}, volume = 17, pages = {319-342}, year = 1967, key = {evolution-model}, note = { {\it ~\\ An early attempt to apply evolution to machine learning in the context of a card-game.} } } @article{Reeke88, author = {Reeke, G. and Edelman, G.}, title = {Real Brains and Artificial Intelligence}, journal = {Daedalus}, volume = 117, pages = {143-174}, year = 1988, key = {ai,neuro-biol,brain-model}, note = { {\it ~\\ Critique of traditional AI and a description of Edelman's Neuronal Group Selection hypothesis \cite{Edelman87}.} } } @book{Reichardt78, author = {Reichardt, J.}, title = {Robots: Fact, Fiction, and Prediction}, publisher = {Penguin Books}, address = {London}, year = 1978, key = {automata-history,robotics}, note = { {\it ~\\ Contains a detailed timeline of the historical roots of automata and robots.} } } @article{Reynolds87, author = {Reynolds, C.W.}, title = {Flocks, Herds, and Schools: A Distributed Behavioral Model}, journal = {Computer Graphics: {\em Proceedings of SIGGRAPH `87}}, volume = 21, number = 4, pages = {25-34}, year = {July 1987}, key = {models-graphics,refs-bottomup,schooling}, note = { {\it ~\\ Description of Reynold's bottom-up system for the study of flocking behavior.} } } @article{Rizki85, author = {Rizki, M.M. and Conrad, M.}, title = {{EVOLVE III}: A Discrete Events Model of an Evolutionary Ecosystem}, journal = {BioSystems}, volume = 18, pages = {121-133}, year = 1985, key = {evolution-model,ecosystem}, note = { {\it ~\\ A continuation in the series of artificial ecosystem models initiated by Conrad (see \cite{Conrad70a}).} } } @article{Rizki86, author = {Rizki, M.M. and Conrad, M.}, title = {Computing the Theory of Evolution}, journal = {Physica D}, volume = 22, pages = {83-99}, year = 1986, key = {evolution-model}, note = { {\it ~\\ A discrete event simulation of an evolving artificial ecosystem. In this model, the fitness of an `organism' is an emergent property of the ecosystem.} } } @article{Rosen59, author = {Rosen, R.}, title = {On a Logical Paradox Implicit in the Notion of a Self-reproducing Automaton}, journal = {Bull. Math. Biophysics}, volume = 21, pages = {387-394}, year = 1959, key = {self-rep,automata-theory}, note = { {\it ~\\ A paradox based on a logical ``Catch-22.'' For responses see \cite{Guttman66,Moore70}.} } } @article{Rosen66, author = {Rosen, R.}, title = {A Note on Replication in {(M,R)} Systems}, journal = {Bulletin of Mathematical Biophysics}, volume = 28, pages = {149-151}, year = 1966, key = {self-rep}, note = { {\it ~\\ } } } @book{Rosen72, editor = {Rosen, R.}, title = {Foundations of Mathematical Biology}, publisher = {Academic Press}, address = {New York}, year = {1972-73}, key = {refs-general}, note = { {\it ~\\ An edited collection in three volumes: I) Subcellular Systems, II) Cellular Systems, and III) Supercellular Systems.} } } @phdthesis{Rosenberg67, author = {Rosenberg, R.}, title = {Simulation of Genetic Populations with Biochemical Properties}, school = {University of Michigan}, year = 1967, key = {evolution-model,autom-biol}, note = { {\it ~\\ An early study of adaptation in which the adaptation takes place in the enzymatic control over a set of artificial chemical interactions. This system exhibits a genuine genotype/phenotype distinction.} } } @book{Rosenblatt62, author = {Rosenblatt, F.}, title = {Principles of Neurodynamics: Perceptrons and the Theory of Brain Mechanisms}, publisher = {Spartan Books}, address = {Washington}, year = 1962, key = {ai-history,ai-connect}, note = { {\it ~\\ Early work on what would now be referred to as a ``connectionist'' model.} } } @incollection{Rothstein79a, author = {Rothstein, J.}, title = {Generalized Entropy, Boundary Conditions, and Biology}, booktitle = {The Maximum Entropy Formalism}, editor = {Levine, R.D. and Tribus, M.}, publisher = {MIT Press}, address = {Cambridge}, pages = {423-468}, year = 1979, key = {theory-bio}, note = { {\it ~\\ Argues that novel features in living systems are a consequence of complexity - rather than specifically of biology - and that other complex systems should exhibit similar novel features.} } } @article{Rothstein79b, author = {Rothstein, J.}, title = {Generalized Life}, journal = {Cosmic Search}, volume = 1, pages = {35-37,44-46}, year = 1979, key = {theory-bio,life-general}, note = { {\it ~\\ Organisms viewed as self-replicating, computer-controlled heat engines able to play survival games.} } } @article{Rothstein82, author = {Rothstein, J.}, title = {Physics of Selective Systems: Computation and Biology}, journal = {Int. J. Theor. Physics}, volume = 21, number = {3-4}, pages = {327-350}, year = 1982, key = {theory-bio}, note = { {\it ~\\ ``The statistical thermodynamics of systems displaying selective behavior is used to discuss some important ultimate physical limitations of computers and biological systems''.} } } @inproceedings{Rothstein85, author = {Rothstein, J.}, title = {On the Scientific Validity and Utility of the Living Earth Concept and its Further Generalization}, booktitle = {Proceedings of the symposium: Is the Earth a Living Organism? University of Massachusetts, Amherst, August 1-6 1985}, organzation = {National Audubon Society Expedition Institute}, address = {Northeast Audubon Center, Sharon, Connecticut, 06069}, year = 1985, key = {life-other,ecosystem}, note = { {\it ~\\ A critical look at the Gaia (``Earth as living organism'') hypothesis \cite{Lovelock79}.} } } @article{Royal81, author = {The Royal Society}, title = {Theories of Biological Pattern Formation}, journal = {Philosophical Transactions of the Royal Society of London}, volume = {B295}, pages = {425ff}, year = 1981, key = {pattern-formation,self-org}, note = { {\it ~\\ } } } @book{Rozenberg74, author = {Rozenberg, G. and Salomaa, A.}, title = {L-Systems: Lecture Notes in Computer Science no. 15}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1974, key = {L-systems}, note = { {\it ~\\ } } } @book{Rozenberg86, author = {Rozenberg, G. and Salomaa, A.}, title = {The Book of L}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1986, key = {L-systems}, note = { {\it ~\\ Collection of papers on L-systems.} } } @article{Rozonoer79a, author = {Rozonoer, L.I. and Sedykh, E.I.}, title = {Evolution Mechanisms of Self-Reproducing Systems {I}}, journal = {Automation and Remote Control}, volume = 40, number = 2, pages = {243-251}, year = 1979, key = {evolution-model,self-rep}, note = { {\it ~\\ This and the following two articles treat evolution in a system consisting of a large number of self-reproducing entities.} } } @article{Rozonoer79b, author = {Rozonoer, L.I. and Sedykh, E.I.}, title = {Evolution Mechanisms of Self-Reproducing Systems {II}}, journal = {Automation and Remote Control}, volume = 40, number = 3, pages = {419-429}, year = 1979, key = {evolution-model,self-rep}, note = { {\it ~\\ } } } @article{Rozonoer79c, author = {Rozonoer, L.I. and Sedykh, E.I.}, title = {Evolution Mechanisms of Self-Reproducing Systems {III}}, journal = {Automation and Remote Control}, volume = 40, number = 5, pages = {741-749}, year = 1979, key = {evolution-model,self-rep}, note = { {\it ~\\ } } } @misc{SaganC, author = {Sagan, C.}, title = {Life}, howpublished = {Encyclopedia Britannica, {\it $15^{th}$ ed.} Macropaedia, Vol. 10}, key = {refs-general,life-defs}, note = { {\it ~\\ A very nice article on definitions of life.} } } @article{Samuel59, author = {Samuel, A.L.}, title = {Some Studies in Machine Learning using the Game of Checkers}, journal = {IBM J. Res. Dev.}, volume = 3, pages = {210-229}, year = 1959, key = {ai-history,adaptation,genetic-algorithms}, note = { {\it ~\\ Samuel's original paper on machine learning using adaptation.} } } @article{Samuel67, author = {Samuel, A.L.}, title = {Some Studies in Machine Learning using the Game of Checkers {II} - Recent Progress}, journal = {IBM J. Res. Dev.}, volume = 11, pages = {601-617}, year = 1967, key = {ai-history,adaptation,genetic-algorithms}, note = { {\it ~\\ } } } @book{Sampson76, author = {Sampson, J.R.}, title = {Adaptive Information Processing}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1976, key = {adaptation,nodels-computer,applications}, note = { {\it ~\\ A collection of topics which constituted a one-semester undergraduate course on adaptive information processing. Topics include the formal theory of automata, biological information processing, and artificial intelligence.} } } @book{Sampson84, author = {Sampson, J.R.}, title = {Biological Information Processing: Current Theory and Computer Simulation}, publisher = {Wiley \& Sons}, address = {New York}, year = 1984, key = {refs-general,models-computer}, note = { {\it ~\\ A book which grew out of - and updates - Sampson's previous book \cite{Sampson76}.} } } @book{Savageau76, author = {Savageau, M.A.}, title = {Biochemical Systems Analysis}, publisher = {Addison-Wesley}, address = {Reading, MA}, year = 1976, key = {models-math}, note = { {\it ~\\ Methods for the analysis of catalyzed reaction networks.} } } @article{Schrandt60, author = {Schrandt, R.G. and Ulam, S.M.}, title = {On Patterns of Growth of Figures in Two Dimensions}, journal = {Notices of the American Mathematical Society}, volume = 7, pages = {642ff}, year = 1960, key = {pattern-formation,CA,automata-history}, note = { {\it ~\\ Early studies of pattern development in cellular automata, including competitions between two kinds of patterns. Reprinted in \cite{Burks70}.} } } @book{Schrodinger44, author = {Schr\"{o}dinger, E.}, title = {What is Life?}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1944, key = {refs-general,life-defs}, note = { {\it ~\\ A classic treatise on the nature of life.} } } @article{Schuster86, author = {Schuster, P.}, title = {Dynamics of Molecular Evolution}, journal = {Physica D}, volume = 22, pages = {100-119}, year = 1986, key = {dynamics,evolution,theory-biol}, note = { {\it ~\\ } } } @techreport{Schwartz83, author = {Schwartz, J.T.}, title = {A Taxonomic Table of Parallel Computers, Based on 55 Designs}, institution = {Courant Institute, New York University}, year = 1983, key = {computers-parallel}, note = { {\it ~\\ An excellent comparison of a wide variety of actual and proposed parallel architectures.} } } @book{Scott86, author = {Scott, A.}, title = {The Creation of Life: Past, Future, Alien}, publisher = {Blackwell}, address = {Oxford}, year = 1986, key = {origins,alt-mat,applications,life-extra}, note = { {\it ~\\ Popular review of theories of the origin of life, together with an examination of the possibilities for the creation of novel forms of life.} } } @article{Searle80, author = {Searle, J.}, title = {Minds, Brains, and Programs}, journal = {Behavioral \& Brain Sciences}, volume = 3, pages = {417-458}, year = 1980, key = {ai-critic,ai-philos}, note = { {\it ~\\ The classic ``Chineese room'' argument against AI programs being considered ``intelligent''.} } } @book{SegelLA80, editor = {Segel, L.A.}, title = {Mathematical Models in Molecular and Cellular Biology}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1980, key = {models-math}, note = { {\it ~\\ } } } @book{SegelLA84, author = {Segel, L.A.}, title = {Modeling Dynamic Phenomena in Molecular and Cellular Biology}, publisher = {Cambridge University Press}, address = {Cambridge}, year = 1984, key = {models-math,models-computer}, note = { {\it ~\\ A general approach to the mathematical modeling of dynamic biological phenomena. Emphasizes role of computers in modeling.} } } @book{Shannon49, author = {Shannon, C.E. and Weaver, W.}, title = {A Mathematical Theory of Communication}, publisher = {University of Illinois Press}, address = {Urbana, Illinois}, year = 1949, key = {refs-general}, note = { {\it ~\\ The classic introduction to Shannon's information theory, which generalizes Boltzman's measure of thermodynamic entropy $S$. Shannon's entropy measure $H$ is used by many researchers attempting to quantify the notion of biological organization, e.g., see \cite{Gatlin72}.} } } @incollection{Shannon56a, author = {Shannon, C.E.}, title = {A Universal Turing Machine with Two Internal States}, booktitle = {Automata Studies}, editor = {Shannon, C.E. and McCarthy, J.}, publisher = {Princeton University Press}, address = {Princeton}, year = 1956, key = {automata-theory}, note = { {\it ~\\ A proof that a Universal Turing Machine can be constructed using only two internal states.} } } @book{Shannon56b, author = {Shannon, C.E. and McCarthy, J.}, title = {Automata Studies}, publisher = {Princeton University Press}, address = {Princeton}, year = 1956, key = {automata-theory,history,ai-history}, note = { {\it ~\\ An early collection of papers on automata theory including articles by many of the early pioneers in the application of automata theory to the study of natural systems: Shannon, von Neumann, Ashby, Minsky, Moore, McCarthy, Kleene, and others.} } } @book{Shapiro86, author = {Shapiro, R.}, title = {Origins: A Skeptic's Guide to the Creation of Life on Earth}, publisher = {Summit Books}, address = {New York}, year = 1986, key = {origins}, note = { {\it ~\\ A very readable survey of theories of the origin of life together with analysis and criticism.} } } @article{Shaw62, author = {Shaw, E.}, title = {The Schooling of Fishes}, journal = {Scientific American}, volume = {206}, pages = {128-138}, year = {June 1962}, key = {schooling}, note = { {\it ~\\ Study of the development of schooling behavior in young fish.} } } @book{Shklovskii66, author = {Shklovskii, I. and Sagan, C.}, title = {Intelligent Life in the Universe}, publisher = {Holden-Day}, address = {San Francisco}, year = 1966, key = {refs-general,origins,life-extra}, note = { {\it ~\\ The case for life elsewhere in the universe.} } } @article{Shoch82, author = {Shoch, J.F. and Hupp, J.A.}, title = {Computing Practices: The `Worm' Programs - Early Experience with a Distributed Computation}, journal = {Comm. ACM}, volume = 25, number = 3, pages = {172-180}, year = 1982, key = {computers-parallel}, note = { {\it ~\\ } } } @book{Simons83, author = {Simons, G.}, title = {Are Computers Alive? Evolution and New Life Forms}, publisher = {Birkhauser}, address = {Boston}, year = 1983, key = {refs-general}, note = { {\it ~\\ A must read. See the following description.} } } @book{Simons85, author = {Simons, G.}, title = {The Biology of Computer Life}, publisher = {Birkhauser}, address = {Boston}, year = 1985, note = { {\it ~\\ These two books by Simons discuss the computer's potential for exercising free will and feeling emotions. Although the emphasis is more on traditional AI and computational methodologies, everything discussed in these books is central to the study of Artificial Life.} } } @book{Simon69, author = {Simon, Herbert A.}, title = {The Sciences of the Artificial}, publisher = {M.I.T. Press}, address = {Boston}, year = 1969, key = {refs-general}, note = { {\it ~\\ An excellent monograph on the nature of complexity and the study of artificial systems.} } } @article{Skarda87, author = {Skarda, C.A. and Freeman, W.J.}, title = {How Brains Make Chaos in Order to Make Sense of the World}, journal = {Behavioral and Brain Sciences}, volume = 10, pages = {161-195}, year = 1987, key = {brain-model,neuro-biol,chaos,ai-connect}, note = { {\it ~\\ } } } @inproceedings{SmithA68, author = {Smith III, A.R.}, title = {Simple Computation-Universal Cellular Spaces and Self-Reproduction}, booktitle = {Ninth Annual Symposium on Switching and Automata Theory}, publisher = {IEEE}, pages = {269-277}, year = 1968, key = {CA,automata-theory,automata-selfrepro}, note = { {\it ~\\ } } } @article{SmithA71, author = {Smith III, A.R.}, title = {Simple Computation-Universal Cellular Spaces}, journal = {JACM}, volume = 18, number = 3, pages = {339-353}, year = 1971, key = {CA,automata-theory}, note = { {\it ~\\ Proof that 1D cellular automata are capable of supporting universal computation.} } } @incollection{SmithA76, author = {Smith III, A.R.}, title = {Introduction to and Survey of Polyautomata Theory}, booktitle = {Automata, Languages, Development}, editor = {Lindenmayer, A. and Rozenberg, G.}, publisher = {North-Holland}, pages = {405-422}, year = 1976, key = {CA,automata-theory}, note = { {\it ~\\ A good survey of work on cellular-automaton-like systems up to 1975.} } } @article{SmithA84a, author = {Smith III, A.R.}, title = {Plants, Fractals, and Formal Languages}, journal = {Computer Graphics}, volume = 18, number = 3, year = 1984, key = {fractals,models-graphics,plants,automata-theory}, note = { {\it ~\\ Applications of formal grammars for generating graphic fractals - ``graftals''- in the modeling of plants.} } } @techreport{SmithA84b, author = {Smith III, A. R.}, title = {Graftal Formalism Notes}, institution = {Computer Graphics Department, Lucasfilm Ltd.}, number = 114, year = 1984, key = {fractals,models-graphics,plants,automata-theory}, note = { {\it ~\\ Formal results in Smith's ``graftal'' system.} } } @phdthesis{Smith80, author = {Smith, S.F.}, title = {A Learning System Based on Genetic Adaptive Algorithms}, school = {University of Pittsburgh}, year = 1980, key = {genetic-algorithms}, note = { {\it ~\\ } } } @article{Spiegelman67, author = {Spiegelman, S.}, title = {An {\em in-vitro} Analysis of a Replicating Molecule}, journal = {American Scientist}, volume = 55, pages = {3-68}, year = 1967, key = {wetware}, note = { {\it ~\\ Description of ``Spiegelman's Monster''.} } } @article{Stahl63, author = {Stahl, W.R. and Goheen, H.E.}, title = {Molecular Algorithms}, journal = {Journal of Theoretical Biology}, volume = 5, pages = {266-287}, year = 1963, key = {automata-biol,automata-theory,models-computer}, note = { {\it ~\\ ``Turing Machines are used to model `algorithmic enzymes' which transform biochemicals represented as letter strings.'' Several dozen enzymes collected into a primitive ``cell'' exhibit a kind of ``logical homeostasis''.} } } @inproceedings{Stahl64, author = {Stahl, W.R. and Coffin, R.W. and Goheen, H.E.}, title = {Simulation of Biological Cells by Systems Composed of String-Processing Finite Automata}, booktitle = {AFIPS Conference Proceedings Vol 25 - 1964 Spring Joint Computer Conference}, pages = {89-102}, year = 1964, key = {automata-biol,automata-theory,models-computer}, note = { {\it ~\\ Strings representing DNA, RNA, proteins and other biochemicals are processed by ``algorithmic enzymes''.} } } @article{Stahl65a, author = {Stahl, W.R.}, title = {Algorithmically Unsolvable Problems for a Cell Automaton}, journal = {J. Theoret. Biol.}, volume = 8, pages = {371-394}, year = 1965, key = {automata-biol,automata-theory,theory-biol}, note = { {\it ~\\ A Turing-Machine-based simulation of a cell is presented and it is demonstrated that if the cell were to attempt hereditary adaptation it would be faced with certain unsolvable problems.} } } @incollection{Stahl65b, author = {Stahl, W.R.}, title = {Self-Reproducing Automata}, booktitle = {Perspectives in Biology and Medicine}, volume = {VIII}, publisher = {University of Chicago Press}, year = 1965, key = {automata-selfrepro,automata-theory}, note = { {\it ~\\ Overview of self-reproducing automata and discussion of his automata-based simulation of cellular self-reproduction.} } } @article{Stahl67, author = {Stahl, W. R.}, title = {A Computer Model of Cellular Self-Reproduction}, journal = {J. Theoret. Biol.}, volume = 14, pages = {187-205}, year = 1967, key = {automata-selfrepro,automata-theory}, note = { {\it ~\\ A Turing-Machine-based simulation of a cell with 46 genes which is capable of repeated self-reproduction and differentiation.} } } @book{Stanley86, editor = {Stanley, H.E. and Ostrowsky, N.}, title = {On Growth and Form}, publisher = {Martinus Nijhoff Publishers}, address = {Boston}, year = 1986, note = { {\it ~\\ Proceedings of a summer school held in Corsica, France in 1985 on the wide variety of complicated forms and patterns that emerge in systems whose fundamental components are essentially engaged in random walks.} } } @book{Stevens74, author = {Stevens, P.S.}, title = {Patterns in Nature}, publisher = {Little, Brown and Co.}, address = {Boston}, year = 1974, note = { {\it ~\\ } } } @article{Sutton81, author = {Sutton, R.S. and Barto, A.G.}, title = {Toward a Modern Theory of Adaptive Networks: Expectation and Prediction}, journal = {Psychological Review}, volume = 88, pages = {135-170}, year = 1981, key = {adaptation}, note = { {\it ~\\ } } } @inproceedings{Thatcher63, author = {Thatcher, J.}, title = {The Construction of a Self-Describing Turing Machine}, booktitle = {Proceedings of the Symposium on Mathematical Theory of Automata, New York, April 1962}, publisher = {Polytechnic Press}, address = {New York}, year = 1963, key = {automata-biol,automata-selfrepro}, note = { {\it ~\\ } } } @incollection{Thatcher70a, author = {Thatcher, J.}, title = {Self-Describing Turing Machines and Self-Reproducing Cellular Automata}, booktitle = {Essays on Cellular Automata}, editor = {A.W. Burks}, publisher = {University of Illinois Press}, pages = {103-131}, year = 1970, key = {automata-biol,automata-selfrepro,CA}, note = { {\it ~\\ } } } @incollection{Thatcher70b, author = {Thatcher, J.}, title = {Universality in the von {Neumann} Cellular Model}, booktitle = {Essays on Cellular Automata}, editor = {A.W. Burks}, publisher = {University of Illinois Press}, pages = {132-186}, year = 1970, key = {automata-theory,automata-selfrepro,automata-history}, note = { {\it ~\\ } } } @book{Thom75, author = {Thom, R.}, title = {Structural Stability and Morphogenesis}, publisher = {W.A. Benjamin}, address = {Reading, Mass.}, year = 1975, key = {dynamics,models-math,chaos}, note = { {\it ~\\ The presentation of ``Catastrophe Theory'' by its inventor.} } } @book{Thomas74, author = {Thomas, L.}, title = {The Lives of a Cell}, publisher = {Viking}, address = {New York}, year = 1974, key = {refs-general}, note = { {\it ~\\ Philosophical, poetic, thought-provoking essays on biology.} } } @book{Thompson42, author = {Thompson, d'Arcy. W.}, title = {Growth and Form}, publisher = {Macmillan}, address = {New York}, year = 1942, key = {refs-general}, note = { {\it ~\\ Influential text on morphogenesis. Shows how structural changes during development can be modeled as mapping transformations.} } } @article{Thompson85, author = {Thompson, R.L. and Goel, N.S.}, title = {A Simulation of T4 Bacteriophage Assembly and Operation}, journal = {BioSystems}, volume = 18, pages = {23-45}, year = 1985, key = {self-org,self-assembly,models-computer,coop-behave}, note = { {\it ~\\ } } } @article{Thompson88, author = {Thompson, R.L. and Goel, N.S.}, title = {Movable Finite Automata (MFA) Models for Biological Systems {I}: Bacteriophage Assembly and Operation}, journal = {J. Theor. Biol.}, volume = {In press}, year = 1988, key = {self-org,self-assembly,models-computer,coop-behave}, note = { {\it ~\\ See also \cite{Goel88b} as well as Goel and Thompsons' contribution to these proceedings.} } } @phdthesis{Toffoli77, author = {Toffoli, T.}, title = {Cellular Automata Mechanics}, school = {The University of Michigan}, year = 1977, key = {automata-theory,CA}, note = { {\it ~\\ Toffoli's demonstration of reversible universal computation.} } } @incollection{Toffoli80, author = {Toffoli, T.}, title = {Reversible Computing}, booktitle = {Automata, Languages, and Programming}, editor = {De Bakker and Van Leeuwen}, publisher = {Springer-Verlag}, pages = {632-644}, year = 1980, key = {automata-theory,CA}, note = { {\it ~\\ } } } @article{Toffoli84a, author = {Toffoli, T.}, title = {{CAM6:} A high-Performance Cellular-Automaton Machine}, journal = {Physica D}, volume = 10, year = 1984, key = {CA,automata-theory,computers-parallel,models-physics,models-gaphics}, note = { {\it ~\\ Description of the architecture of a hardware CA machine.} } } @article{Toffoli84b, author = {Toffoli, T.}, title = {Cellular Automata as an alternative to (rather than an approximation of) differential equations in modeling physics}, journal = {Physica D}, volume = 10, year = 1984, key = {refs-general,CA,models-physics,models}, note = { {\it ~\\ An insightful discussion of the reasons for and against modeling physical systems with differential equations.} } } @book{Toffoli87, author = {Toffoli, T. and Margolus, N.}, title = {Cellular Automata Machines}, publisher = {MIT Press}, address = {Cambridge}, year = 1987, key = {CA,automata-theory,computers-parallel,models-physics,models-gaphics}, note = { {\it ~\\ An excellent book on the application of cellular automata to modeling physical systems.} } } @article{Toombs67, author = {Toombs, R. and Barricelli, N.A.}, title = {Simulation of Biological Evolution and Machine Learning}, journal = {J. Theoret. Biol.}, volume = 17, pages = {319-342}, year = 1967, key = {evolution-model}, note = { {\it ~\\ } } } @article{Turing37a, author = {Turing, A.M.}, title = {On Computable Numbers, with an Application to the Entscheidungsproblem}, journal = {Proceedings of the London Mathematical Society}, volume = {Series 2}, number = 42, pages = {230-265}, year = {1936-1937}, key = {automata-theory,automata-history}, note = { {\it ~\\ Turing's famous demonstration of the formal limits on computation based on a proof that the {\em halting problem} is undecidable. Reprinted in \cite{Davis65}.} } } @article{Turing37b, author = {Turing, A.M.}, title = {A Correction}, journal = {Proceedings of the London Mathematical Society}, volume = {Series 2}, number = 43, pages = {544-546}, year = {1937}, key = {automata-theory,automata-history}, note = { {\it ~\\ A correction to the previous paper.} } } @article{Turing50, author = {Turing, A.M.}, title = {Can a Machine Think?}, journal = {Mind}, pages = {433-460}, year = {October 1950}, key = {ai,ai-history,man-machine}, note = { {\it ~\\ The paper in which Turing introduced the ``Turing test'' for machine intelligence. Reprinted in \cite{Feigenbaum63}.} } } @article{Turing52, author = {Turing, A.M.}, title = {The Chemical Basis of Morphogenesis}, journal = {Phil. Trans. Roy. Soc. of London}, volume = {Series B: Biological Sciences}, number = 237, pages = {37-72}, year = 1952, key = {models-math}, note = { {\it ~\\ A reaction-diffusion model for development.} } } @book{Tsypkin71, author = {Tsypkin, Y.Z.}, title = {Adaptation and Learning in Automatic Systems}, publisher = {Academic Press}, address = {New York}, year = 1971, key = {adaptation,applications}, note = { {\it ~\\ } } } @article{UlamSM62, author = {Ulam, S.M.}, title = {On some Mathematical Problems Connected with Patterns of Growth of Figures}, journal = {Proceedings of Symposia in Applied Mathematics}, volume = 14, pages = {215-224}, year = 1962, key = {automata-theory,pattern-formation,CA}, note = { {\it ~\\ An early study on pattern development in cellular automata by the man who suggested CA's to von Neumann. Reprinted in \cite{Burks70}.} } } @article{Ulmer83, author = {Ulmer, K.M.}, title = {Protein Engineering}, journal = {Science}, volume = 219, pages = {666-671}, year = 1983, key = {applications}, note = { {\it ~\\ } } } @article{Urey52, author = {Urey, H.C.}, title = {The Early Chemical History of the Earth and the Origin of Life}, journal = {Proc. Nat. Acad. Sci}, volume = 38, pages = {351ff}, year = 1958, key = {origins}, note = { {\it ~\\ Extensions to Oparin's coacervate hypothesis for the origin of life.} } } @article{Valdez80, author = {Valdez, F. and Freitas, R.}, title = {Comparison of Reproducing and Nonreproducing Starprobe strategies for Galactic Exploration}, journal = {J. British Interplanetary Soc.}, volume = 33, pages = {402-408}, year = 1980, key = {applications,self-repro}, note = { {\it ~\\ } } } @book{VanOver80, author = {Van Over, R.}, title = {Sun Songs: Creation Myths from Around the World}, publisher = {New American Library}, address = {New York}, year = 1980, key = {refs-general,origins}, note = { {\it ~\\ A very nice survey of creation myths.} } } @article{Varela74, author = {Varela, F.J. and Maturana, H.R. and Uribe, R.}, title = {Autopoiesis: The Organization of Living Systems}, journal = {BioSystems}, volume = 5, number = 4, pages = {187-196}, year = 1974, key = {autopoiesis,life-org}, note = { {\it ~\\ One of the first presentations of the concept of autopoiesis.} } } @book{Vartanian60, author = {Vartanian, A.}, title = {La Mettrie's L'Homme Machine: A Study in the Origins of an Idea}, publisher = {Princeton University Press}, address = {Princeton}, year = 1960, key = {man-machine,refs-general,history}, note = { {\it ~\\ The classic $18^{th}$ century treatise on man as machine. Translated into English with an introductory monograph and notes.} } } @article{Vichniac84, author = {Vichniac, G.Y.}, title = {Simulating Physics with Cellular Automata}, journal = {Physica D}, volume = 10, pages = {96-116}, year = 1984, key = {CA,models-physics}, note = { {\it ~\\ Bottom-up approach to modeling physical phenomena.} } } @article{Vitanyi73, author = {Vitayni, P.M.B.}, title = {Sexually Reproducing Cellular Automata}, journal = {Math. Biosci.}, volume = 18, pages = {23-54}, year = 1973, key = {CA,automata-selfrepro}, note = { {\it ~\\ } } } @techreport{vonNeumann45, author = {von Neumann, J.}, title = {First Draft of a Report on the EDVAC}, institution = {University of Pennsylvania}, year = 1945, key = {computers-history}, note = { {\it ~\\ The report that got von Neumann's name associated with the serial, stored-program, general purpose, digital architecture upon which 99.99\% of all computers today are based.} } } @incollection{vonNeumann51, author = {von Neumann, J.}, title = {The General and Logical Theory of Automata}, booktitle = {Cerebral Mechanisms in Behavior}, publisher = {Wiley}, address = {New York}, pages = {1-41}, year = 1941, key = {automata-theory}, note = { {\it ~\\ } } } @incollection{vonNuemann56, author = {von Neumann, J.}, title = {Probabilistic Logics and the Synthesis of Reliable Organisms from Unreliable Components}, booktitle = {Automata Studies}, editor = {Shannon, C. and McCarthy, J.}, publisher = {Princeton University Press}, address = {Princeton}, year = 1956, key = {automata-theory}, note = { {\it ~\\ } } } @book{vonNeumann58, author = {von Neumann, J.}, title = {The Computer and the Brain}, publisher = {Yale University Press}, address = {New Haven}, year = 1958, key = {brain-model,refs-general}, note = { {\it ~\\ A classic book comparing the architecture of computers with the architecture of the brain.} } } @book{vonNeumann66, author = {von Neumann, J.}, title = {Theory of Self-Reproducing Automata}, editor = {A.W. Burks}, publisher = {University of Illinois Press}, address = {Urbana}, year = 1966, key = {refs-general,CA,automata-theory,complex,automata-selfrepro}, note = { {\it ~\\ Von Neumann's work on self-reproducing automata, completed and edited after his death by Arthur Burks. Also includes transcripts of von Nuemann's 1949 University of Illinois lectures on the ``Theory and Organization of Complicated Automata''.} } } @techreport{vonTiesen80, author = {von Tiesenhausen, G. and Darbo, W.}, title = {Self-Replicating Systems - A Systems Engineering Approach}, institution = {NASA TM-78304}, year = 1980, key = {applications,self-rep}, note = { {\it ~\\ } } } @book{Waddington68, editor = {Waddington, C. H.}, title = {Towards a Theoretical Biology: Vols. 1-4}, publisher = {Edinburgh University Press}, address = {Edinburgh}, year = {1968, 1969, 1970, 1972}, key = {refs-general}, note = { {\it ~\\ A classic. Proceedings of an enlightened series of meetings organized by Waddington just as the ``dark-ages'' were setting in. These meetings were attended by many of the early pioneers in Artificial Life.} } } @article{Waksman69, author = {Waksman, A.}, title = {A Model of Replication}, journal = {JACM}, volume = 16, pages = {178-188}, year = 1969, key = {self-rep}, note = { {\it ~\\ } } } @article{WalterC69a, author = {Walter, C.}, title = {Stability of Controlled Biological Systems}, journal = {J. Theor. Biol.}, volume = 23, pages = {23-28}, year = 1969, note = { {\it ~\\ } } } @article{WalterC69b, author = {Walter, C.}, title = {The Absolute Stability of Certain Types of Controlled Biological Systems}, journal = {J. Theor. Biol.}, volume = 23, pages = {39-52}, year = 1969, note = { {\it ~\\ } } } @article{Walter50, author = {Walter, W.G.}, title = {An Imitation of Life}, journal = {Scientific American}, volume = 182, number = 5, pages = {42-45}, year = {May 1950}, key = {ai-history,history,ai-robotics,ai-philos}, note = { {\it ~\\ Reports experiments with two autonomous, electronic ``turtles'' - Elmer \& Elsie - equipped with various sensors and simple control circuitry which wander around their environment and interact with one another.} } } @article{Walter51, author = {Walter, W.G.}, title = {A Machine that Learns}, journal = {Scientific American}, volume = 185, number = 2, pages = {60-63}, year = {August 1951}, key = {ai-history,history,ai-robotics,ai-philos}, note = { {\it ~\\ Further experiments with Elmer \& Elsie.} } } @book{Watson87, author = {Watson, J.D. and Hopkins, N.H. and Roberts, J.W. and Steitz, J.A. and Weiner, A.M.}, title = {Molecular Biology of the Gene ($4^{th}$ Edition), Vols. I \& II}, publisher = {Benjamin/Cummings}, address = {Menlo Park}, year = 1987, key = {refs-general}, note = { {\it ~\\ The complete reference to current knowledge about the mechanisms of life. See also \cite{Alberts83}.} } } @phdthesis{Weinberg70a, author = {Weinberg, R.}, title = {Computer Simulation of a Living Cell}, school = {The University of Michigan}, year = 1970, key = {automata-biol,models-computer}, note = { {\it ~\\ Computer simulation of {\it Escherichia Coli}.} } } @techreport{Weinberg70b, author = {Weinberg, R.}, title = {Computer Simulation of a Primitive, Evolving Eco-System}, institution = {The University of Michigan}, number = {T.R. no. 03296-6-T}, year = 1970, key = {automata-biol,models-computer,ecosystem}, note = { {\it ~\\ Application of the genetic algorithm to simulated populations of bacteria. The 40 loci on the genetic instruction string are indexed in order to make use of the {\em inversion} operator.} } } @article{Weinberg71, author = {Weinberg, R. and Zeigler, B.P. and Laing, R.A.}, title = {Computer Simulation of a Living Cell: Metabolic Control System Experiments}, journal = {Journal of Cybernetics}, volume = 1, number = 2, pages = {34-48}, year = 1971, key = {automata-biol,models-computer}, note = { {\it ~\\ } } } @article{Weisbuch86, author = {Weisbuch, G.}, title = {Mini Review: Networks of Automata and Biological Organization}, journal = {J. Theoret. Biol.}, volume = 121, pages = {255-267}, year = 1986, key = {automata-theory,automata-biol,life-org}, note = { {\it ~\\ Argues that ``a conceptual breakthrough has been obtained by comparing the properties of organization of living systems to the dynamical properties of random or complex networks of automata''.} } } @article{West70, author = {West, M.W. and Ponnamperuma, C.}, title = {Bibliography on the Origin of Life}, journal = {Space Life Sci.}, volume = 2, pages = {225-295}, year = 1970, key = {refs-general,origins}, note = { {\it ~\\ A bibliography of some 1600 references to work on the origin of life. Supplement published in the same journal V. 3, pp 293-304 (1972).} } } @book{Whyte69, editor = {Whyte, L.L. and Wilson, A.G. and Wilson, D.}, title = {Hierarchical Structures}, publisher = {Elsevier}, address = {New York}, year = 1969, note = { {\it ~\\ } } } @book{Wiener48, author = {Wiener, N.}, title = {Cybernetics, or Control and Communication in the Animal and the Machine}, publisher = {John Wiley}, address = {New York}, year = 1948, key = {refs-general,cybernetics}, note = { {\it ~\\ Wiener's classic book on cybernetics. Second edition with additions published in 1961.} } } @incollection{Wigner61, author = {Wigner, E.P.}, title = {The Probability of the Existence of a Self-Reproducing Unit}, booktitle = {The Logic of Personal Knowledge}, publisher = {The Free Press}, pages = {231-248}, year = 1961, key = {self-rep}, note = { {\it ~\\ } } } @book{WilsonEO71, author = {Wilson, E.O.}, title = {The Insect Societies}, publisher = {Belknap/Harvard University Press}, address = {Cambridge}, year = 1971, key = {colony,coop-behave,refs-general}, note = { {\it ~\\ Social insects provide some of the most accessible natural examples of the manner in which complex behavior emerges from the collective behavior of relatively simple entities. This book provides a detailed overview of the social insects and includes an extensive bibliography.} } } @book{WilsonEO75, author = {Wilson, E.O.}, title = {Sociobiology: The New Synthesis}, publisher = {Belknap/Harvard University Press}, address = {Cambridge}, year = 1975, key = {soc-bio,refs-general}, note = { {\it ~\\ The classic treatise on the genetic determination of social behavior. Sociobiology has started an enormous controversy within the social sciences concerning the relative importance of {\em {\em nature (genetics)} vs. {\em nurture (culture)}} in the determination of behavior.} } } @article{WilsonEO85, author = {Wilson, E. O.}, title = {The Sociogenesis of Insect Colonies}, journal = {Science}, volume = 288, number = 4707, pages = {1489-1495}, year = 1985, key = {soc-bio,coop-behave,colony}, note = { {\it ~\\ Sociogenesis is `the process by which colony members undergo changes in caste, behavior, and physical location incident to colonial development'. Wilson argues that `some of the processes can also be usefully compared with morphogenesis at the levels of cells and tissues'.} } } @inproceedings{WilsonSW85, author = {Wilson, S.W.}, title = {Knowledge Growth in an Artificial Animal}, booktitle = {Proceedings of an International Conference on Genetic Algorithms and their Applications}, editor = {Grefenstette, J.J.}, organization = {Carnegie-Mellon University}, year = {July 24-26 1985}, key = {genetic-algorithms}, note = { {\it ~\\ } } } @book{Winfree80, author = {Winfree, A.T.}, title = {The Geometry of Biological Time}, publisher = {Springer-Verlag}, address = {Berlin}, year = 1980, key = {dynamics,chaos,models-math}, note = { {\it ~\\ Dynamics of biological oscillators.} } } @book{Winfree87, author = {Winfree, A. T.}, title = {When Time Breaks Down}, publisher = {Princeton University Press}, address = {Princeton}, year = 1987, key = {dynamics,chaos,models-math}, note = { {\it ~\\ Dysfunction in biological oscillators.} } } @article{Wolfram83, author = {Wolfram, S.}, title = {Stastical Mechanics of Cellular Automata}, journal = {Rev. Modern Physics}, volume = 55, pages = {601-644}, year = 1983, key = {CA,automata-theory,models-physics,refs-general,refs-bottomup,dynamics, complex,chaos}, note = { {\it ~\\ Important paper largely responsible for the resurgence of interest in cellular automata.} } } @article{Wolfram84a, author = {Wolfram, S.}, title = {Cellular Automata as Models of Complexity}, journal = {Nature}, volume = 311, number = 4, pages = {419-424}, year = 1984, key = {CA,complex,refs-general,refs-bottomup,dynamics,chaos,models-physics}, note = { {\it ~\\ A well written account of the manner in which complex dynamics can emerge from simple components.} } } @article{Wolfram84b, author = {Wolfram, S.}, title = {Universality and Complexity in Cellular Automata}, journal = {Physica D}, volume = 10, pages = {1-35}, year = 1984, key = {CA,automata-theory,models-physics,refs-general,refs-bottomup,dynamics, complex,chaos}, note = { {\it ~\\ Identifies four qualitative classes of CA dynamics.} } } @book{Wolfram86, editor = {Wolfram, S.}, title = {Theory and Applications of Cellular Automata}, publisher = {World Scientific}, address = {Singapore}, year = 1986, key = {CA,automata-theory,models-physics,refs-general,refs-bottomup,dynamics, complex,chaos}, note = { {\it ~\\ Collection of papers on CA's. Contains an extensive bibliography.} } } @incollection{Wolpert68, author = {Wolpert, L.}, title = {{The French Flag Problem: A} Contribution to the Discussion on Pattern Development and Recognition.}, booktitle = {Towards a Theoretical Biology, Vol. I}, editor = {C.H. Waddington}, publisher = {Edinburgh University Press}, pages = {125-133}, year = 1968, key = {pattern-formation}, note = { {\it ~\\ } } } @article{Wolpert78, author = {Wolpert, L.}, title = {Pattern Formation in Biological Development}, journal = {Scientific American}, volume = 239, number = 4, pages = {154-164}, year = {October 1978}, key = {pattern-formation}, note = { {\it ~\\ This and the preceding paper discuss of the manner in which the context in which cells find themselves affects their development.} } } @article{Wood80, author = {Wood, W.A.}, title = {Bacteriophage T4 Morphogenesis as a Model for Assembly of Subcellular Structure}, journal = {Quart. Rev. Biol.}, volume = 55, pages = {353-367}, year = 1980, key = {self-assembly,self-org}, note = { {\it ~\\ } } } @incollection{Woods75, author = {Woods, W.A.}, title = {What's in a Link?}, booktitle = {Representation and Understanding: Studies in Cognitive Science}, editor = {Bobrow, E.G. and Collins, A.M.}, publisher = {Academic Press}, pages = {35-82}, year = 1975, key = {ai,ai-history,ai-connect,network}, note = { {\it ~\\ Nice discussion of semantic networks.} } } @article{Zeigler70, author = {Zeigler, B.P. and Weinberg, R.}, title = {System Theoretic Analysis of Models: Computer Simulation of a Living Cell}, journal = {J. Theor. Biol.}, volume = 29, pages = {35-56}, year = 1970, key = {models-computer,automata-biol}, note = { {\it ~\\ Application of the concepts of homomorphism and aggregation to the modeling of a living cell: {\it Escherichia Coli}.} } } @book{Zeigler76, author = {Zeigler, B.P.}, title = {Theory of Modeling and Simulation}, publisher = {Wiley \& Sons}, address = {New York}, year = 1976, key = {models}, note = { {\it ~\\ Presents the ``Discrete Event'' modeling scheme.} } } @article{Zeleny77a, author = {Zeleny, M.}, title = {Self-Organization of Living Systems: A Formal Model of Autopoiesis}, journal = {Int. J. General Systems}, volume = 4, pages = {13-28}, year = 1977, key = {autopoiesis,models-computer}, note = { {\it ~\\ A formal computer implementation and extension of the original Varela-Maturana-Uribe model of ``autopoiesis'' - the theory of ``self-producing'' systems: i.e., systems whose high-level functions include the maintainence of the low-level organization which supports the high-level functions.} } } @inproceedings{Zeleny77b, author = {Zeleny, M.}, title = {Organization as an Organism}, booktitle = {Proceedings of the SGSR Annual Meeting, Denver Colo., 1977}, organization = {Society for General Systems Research, Washington, D.C.}, pages = {262-270}, year = 1977, key = {autopoiesis,life-org}, note = { {\it ~\\ Basic notion of social autopoiesis and an institutional example.} } } @article{Zeleny78, author = {Zeleny, M.}, title = {{APL-Autopoiesis:} Experiments in Self-Organization of Complexity}, journal = {Progress in Cybernetics and Systems Research}, volume = {III}, year = 1978, key = {autopoiesis,models-computer,self-org}, note = { {\it ~\\ } } } @book{Zeleny81a, editor = {Zeleny, M.}, title = {Autopoiesis: A Theory of Living Organization}, publisher = {Elsevier}, address = {New York}, year = 1981, key = {autopoiesis,life-org}, note = { {\it ~\\ A multi-author discussion of autopoiesis. A comprehensive summary of ``self-producing'' systems and their modeling.} } } @article{Zeleny81b, author = {Zeleny, M.}, title = {Autopoiesis Today}, journal = {Cybernetics Forum: {Special Issue devoted to Autopoiesis}}, volume = 10, number = {2/3}, pages = {3-6}, year = 1981, key = {autopoiesis,life-org}, note = { {\it ~\\ This volume - edited by Zeleny - contains reprints of classical papers on autopoiesis, including the works of Maturana, Varela, Uribe, and Zeleny. Also contains a comprehensive annotated bibliography.} } }