Self-replication, evolvability and asynchronicity in stochastic worlds

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3777 LNCS, Issue , 2005, Pages 126-169

  Nehaniv, Chrystopher L ^a  

^a UNIVERSITY OF HERTFORDSHIRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATA THEORY; COMPUTATIONAL METHODS; COMPUTER NETWORKS; LIVING SYSTEMS STUDIES; PARALLEL PROCESSING SYSTEMS;

ARTIFICIAL LIVING SYSTEMS; ASYNCHRONICITY; EVOLVABILITY; GENETIC REGULATORY NETWORKS (DGRN); SELF-REPLICATION;

RANDOM PROCESSES;

EID: 33646719696     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11571155_13     Document Type: Conference Paper

References (107)

1. BioSystems 69, 2-3. Special issue on Evolvability, C. L. Nehaniv (ed.) (2003).
2. ADAMI, C., OFRIA, C., AND COLLIER, T. C. Evolution of biological complexity. Proc. Natl. Acad. Sci. U.S.A. 97 (2000), 4463-4468.
3. ALISSANDRAKIS, A., NEHANIV, C. L., AND DAUTENHAHN, K. Synchrony and perception in robotic imitation across embodiments. In Proc. IEEE International Symposium on Computational Intelligence in Robotics and Automation (CIRA'03) (2003), pp. 923-930.
4. ALISSANDRAKIS, A., NEHANIV, C. L., AND DAUTENHAHN, K. Towards robot cultures? - learning to imitate in a robotic arm test-bed with dissimilarly embodied agents. Interaction Studies 5, 1 (2004), 3-44.
5. ALTENBERG, L. The evolution of evolvability in genetic programming. In Advances in Genetic Programming, K. E. Kinnear, Ed. MIT Press, 1994, pp. 47-74.
6. ARTHUR, W. The Origin of Animal Body Plans: A Study in Evolutionary Developmental Biology, 1st paperback edition ed. Cambridge, 2000.
7. BANZHAF, W. Artificial regulatory networks and genetic programming. In Genetic Programming - Theory and Applications. Kluwer, 2003, pp. 43-61.
8. BERNERS-LEE, T. Evolvability. In 7th International WWW Conference, Brisbane, Australia (15 April 1998). keynote address: slides on-line at http://www.w3.org/Talks/1998/0415-Evolvability/.
9. BONNER, J. T. The Evolution of Complexity, by Means of Natural Selection. Princeton University Press, 1988.
10. BURKS, A. W. Essays on Cellular Automata. University of Illinois Press, Urbana, Illinois, 1970.
11. BUSS, L. W. The Evolution of Individuality. Princeton University Press, 1987.
12. BYL, J. Self-reproduction in small cellular automata. Physica D 34 (1989), 295-299.
13. CODD, E. F. Cellular Automata. Academic Press, New York, 1968.
14. CONRAD, M. The geometry of evolution. BioSystems 24, 2 (1990), 61-81.
15. CRUTCHFIELD, J. P. Observing complexity and the complexity of observation. In Inside versus Outside, H. Atmanspacher, Ed. Springer, Berlin, 1993, pp. 235-272.
16. DARWIN, C. The Origin of Species by Means of Natural Selection, 1st ed. John Murray, London, 1859.
17. DARWIN, C., AND WALLACE, A. On the tendency of species to form varieties; and on the perpetuation of varieties and species by natural means of selection. Journal of the Proceedings of the Linnean Society, Zoology 3 (20 August 1858), 45-62.
18. DAVIDSON, E. H. Genomic Regulatory Systems: Development and Evolution. Academic Press, 2001.
19. DAWKINS, R. The Selfish Gene. Oxford, 1976.
20. DAWKINS, R. The evolution of evolvability. In Artificial Life, C. Langton, Ed. Addison Wesley, 1989.
21. DÖMÖSI, P., AND NEHANIV, C. L. Algebraic Theory of Finite Automata Networks: An Introduction (SIAM Monographs on Discrete Mathematics and Applications, Vol. 11). Society for Industrial and Applied Mathematics, Philadelphia, 2005.
22. EDMUNDSON, A. C. A Fuller Explanation: The Synergistic Geometry of R. Buckminster Fuller. Birkhäuser, 1987.
23. EGRI-NAGY, A., AND NEHANIV, C. L. Evolvability of the genotype-phenotype relation in populations of self-replicating digital organisms in a tierra-like system. In Proc. European Conference on Artificial Life (ECAL'03), September 14-17, 2003 Dortmund, Germany (2003), vol. Springer Lecture Notes in Artificial Intelligence Vol. 2801, pp. 2380-247.
24. FOGEL, L. J., OWEN, A. J., AND WALSH, M. J. Artificial Intelligence Through Simulated Evolution. John Wiley, 1966.
25. GOGUEN, J. Requirements engineering as the reconciliation of technical and social issues. In Requirements Engineering: Social and Technical Issues, M. Jirotka and J. Goguen, Eds. Academic Press, 1994, pp. 165-199.
26. GOGUEN, J. Formality and informality in requirements engineering. In Proceedings, Fourth International Conference on Requirements Engineering (April 1996), IEEE Computer Society, pp. 102-108.
27. HOLLAND, J. Adaptation in Natural and Artificial Systems. MIT Press, 1975.
28. KIMURA, M. The neutral theory of molecular evolution. Cambridge Univ. Press, 1983.
29. KIRSCHNER, M., AND GERHART, J. Evolvability. Proc. Natl. Acad. Sci. USA 95 (1998), 8420-8427.
30. KOZA, J. R. Evolution of subsumption. In Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, 1992, ch. 13.
31. KOZA, J. R. Genetic Programming II: The Next Generation. MIT Press, 1994.
32. LAING, R. Automaton models of reproduction by self-inspection. Journal of Theoretical Biology 66 (1977), 437-456.
33. LANGTON, C. G. Self-reproduction in cellular automata. Physica D 10 (1984), 135-144.
34. LANGTON, C. G. Studying artificial life with cellular automata. Physica D 22 (1986), 120-149.
35. LEHMAN, M. M. The role and impact of assumptions in software development, maintenance and evolution. In IEEE International Workshop on Software Evolvability (2005), IEEE Computer Society Press, p. (in press).
36. LEYSER, O., AND DAY, S. Mechanisms in Plant Development. Blackwell, 2003.
37. LOHN, J. D. Self-replicating systems in cellular space models. In Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution. Vol. 26 in Lectures on Mathematics in the Life Sciences (Providence, Rhode Island, 1999), C. L. Nehaniv, Ed., American Mathematical Society, pp. 11-30.
38. LOHN, J. D., AND REGGIA, J. A. Automatic discovery of self replicating structures in cellular automata. IEEE Transactions on Evolutionary Computation 1, 3 (1997), 165-178.
39. LYNCH, M., AND KATJU, V. The altered evolutionary trajectories of gene duplicates. Trends in Genetics 11 (2004), 544-549.
40. MACIAS, N. J., AND DURBECK, L. J. K. Adaptive methods for growing electronic circuits on an imperfect synthetic matrix. BioSystems 73 (2004), 173-204.
41. MANGE, D., SANCHEZ, E., STAUFFER, A., TEMPESTI, G., MARCHAL, P., AND PIGUET, C. Embryonics: A new methodology for designing field-programmable gate arrays with self-repair and self-replicating properties. In Readings in Hardware/Software Co-Design, G. D. Micheli, R. Ernst, and W. Wolf, Eds. Morgan Kaufmann, San Francisco, 2002, pp. 643-655.
42. MARGULIS, L. Symbiosis in Cell Evolution. W. H. Freeman & Co., 1981.
43. MARGULIS, L., AND SAGAN, D. Acquiring Genomes; A Theory of the Origins of Species. Basic Books, 2002. Foreword by Ernst Mayr.
44. MAYNARD SMITH, J. A darwinian view of symbiosis. In Symbiosis as a Source of Evolutionary Innovation, L. Margulis and R. Fester, Eds. MIT Press, 1991, pp. 26-39.
45. MAYNARD SMITH, J., AND SZATHMÁRY, E. The Major Transitions in Evolution. W. H. Freeman, 1995.
46. MICHOD, R. E. Eros and Evolution: A Natural Philosophy of Sex. Addison-Wesley, 1995.
47. MICHOD, R. E. Darwinian Dynamics: Evolutionary Transitions in Fitness and Individuality. Princeton, 1999.
48. MICHOD, R. E., AND ROZE, D. Cooperation and conflict in the evolution of individuality. III. transitions in the unit of fitness. In Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution. Vol. 26 in Lectures on Mathematics in the Life Sciences (Providence, Rhode Island, 1999), American Mathematical Society, pp. 47-91.
49. MOORE, E. F. Machine models of self-reproduction. In Proceedings of the Fourteenth Symposium on Applied Mathematics (1962, (Reprinted in A. W. Burks (ed.), 1968)), American Mathematical Society, pp. 17-33.
50. MORITA, K., AND IMAI, K. A simple self-reproducing cellular automaton with shape-encoding mechanism. In Artificial Life V (1997), C. G. Langten and K. Shimohara, Eds., MIT Press, pp. 489-496.
51. NAKAMURA, K. Asynchronous cellular automata and their computational ability. Systems, Computers, Controls 5, 5 (1974), 58-66. translated from Japanese, Denshi Tsushin Gakkai Ronbunshi, 57-D, No. 10, pp. 573-580, October 1974.
52. NEHANIV, C. L. Evolvability in biology, artifacts, and software systems. In Proceedings of the Evolvability Workshop at the the Seventh International Conference on the Simulation and Synthesis of Living Systems (Artificial Life 7) 1-2 August 2000, Reed College, Portland, Oregon, USA (2000). On-line at: http://homepages.feis.herts.ac.uk/nehaniv/a17ev/.
53. NEHANIV, C. L. Evolution in asynchronous cellular automata. In Artificial Life VIII: Proc. 8th Intl. Conf. on Artificial Life (2002), R. K. Standish, M. A. Bedau, and H. A. Abbass, Eds., MIT Press, pp. 65-73.
54. NEHANIV, C. L. Internal constraints and ecology in evolution: A case study in tierra. In Proceedings of the Fifth German Workshop on Artificial Life (GWAL V) (2002), pp. 243-252.
55. NEHANIV, C. L. Self-reproduction in asynchronous cellular automata. In Proc. 2002 NASA/DoD Conference on Evolvable Hardware (15-18 July 2002 - Alexandria, Virginia) (2002), IEEE Computer Society Press, pp. 201-209.
56. NEHANIV, C. L. Asynchronous automata networks can emulate any synchronous automata network. International Journal of Algebra & Computation 14, 5 & 6 (2004), 719-739. Presented at International Workshop on Semigroups, Automata, and Formal Languages (June 2002 - Crema, Italy).
57. NEHANIV, C. L. The algebra of time. In Proc. National Conf. of the Japan Society for Industrial and Applied Mathematics (September 1993), pp. 127-128.
58. NEHANIV, C. L., AND DAUTENHAHN, K. Self-replication and reproduction: Considerations and obstacles for rigorous definitions. In Proceedings of the Third German Workshop on Artificial Life (GWAL III) (1998), pp. 283-290.
59. NEHANIV, C. L., AND DAUTENHAHN, K. Artificial Life Fundamentals: The Simulation and Synthesis of Living Systems. Springer Verlag, in prep.
60. NEHANIV, C. L., AND RHODES, J. L. On the manner in which biological complexity may grow. Lectures on Mathematics in the Life Sciences 26 (1999), 93-102.
61. NEHANIV, C. L., AND RHODES, J. L. Axioms for biological complexity and mathematically rigorous measures of computational capacity: Applications to evolution of computation in cells. In Proc. Computation in Cells: An EPSRC Emergent Computing Workshop (17-18 April 2000) (2000), H. Bolouri and R. Paton, Eds., University of Hertfordshire, U.K., pp. 71-76.
62. NEHANIV, C. L., AND RHODES, J. L. The evolution and understanding of biological complexity from an algebraic perspective. Artificial Life 6, 1 (2000), 45-67.
63. OHNO, S. Evolution by Gene Duplication. Springer Verlag, 1970.
64. ORGEL, L. E. Molecular replication. Nature 358 (1992), 203-209.
65. PARNAS, D. On the criteria to be used in decomposing systems into modules. Communications of the Association for Computing Machinery 15, 2 (1972), 1052-1058.
66. PEPPER, J. W. The evolution of evolvability in genetic linkage patterns. BioSystems 69(2-3). Special issue on Evolvability, C. L. Nehaniv (ed.) (2003), 115-126.
67. QUICK, T., NEHANIV, C. L., DAUTENHAHN, K., AND ROBERTS, G. Evolving embodied genetic regulatory network-driven control systems. In Proc. European Conference on Artificial Life (ECAL'03), Springer LNAI Vol. 2801 (2003), pp. 266-277.
68. RASMUSSEN, S., CHEN, L., DEAMER, D., KRAKAUER, D., PACKARD, N., STADLER, P., AND BEDAU, M. Transitions from nonliving to living matter. Science 303 (2004), 963-965.
69. RAY, T. S. An approach to the synthesis of life. In Artificial Life II, F. Jones, Ed. Addison-Wesley, 1991, pp. 371-408.
70. RECHENBERG, I. Evolutionsstrategie - Optimierung technischer Systeme nach Prinzipien der biologischen Evolution. Frommann-Holzboog, 1973.
71. REGGIA, J. A., ARMENTROUT, S., CHOU, H. H., AND PENG, Y. Simple systems that exhibit self-directed replication. Science 259 (1993), 1282-1288.
72. RENDELL, L., AND WHITEHEAD, H. Culture in whales and dolphins. Behavioral and Brain Sciences 24, 2 (2001), 309-382.
73. RIDLEY, M. Evolution, 2nd ed. Blackwell Science, 1996.
74. SAPP, J. Evolution by Association. Oxford, 1994.
75. SAYAMA, H. Constructing Evolutionary Systems on a Simple Deterministic Cellular Automata Space. PhD thesis, Department of Information Science, Grad uate School of Science, University of Tokyo, December 1998.
76. SAYAMA, H. Introduction of structural dissolution into langton's self-reproducing loop. In Artificial Life VI: Proceedings of the Sixth International Conference on Artificial Life (1998), C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor, Eds., MIT Press, pp. 114-122. On-line material at: http://necsi.org/postdocs/sayama/sdsr/.
77. SAYAMA, H. A new structurally dissolvable self-reproducing loop evolving in a simple cellular automata space. Artificial Life 5, 4 (1999), 343-365.
78. SCHILSTRA, M., AND BOLOURl, H. Logical modelling of developmental genetic regulatory networks with netbuilder. In 2nd Int. Conf. Systems Biology (ICSB 2001). Omnipress, 2001.
79. SCHILSTRA, M., AND NEHANIV, C. L. The logic of genetic regulation, submitted.
80. SCHWEFEL, H.-P. Numerische Optimierung von Computer-Modellen mittels der Evolutionsstrategie. Birkhäuser, 1977.
81. SIGMUND, K. Games of Life. Penguin, 1995.
82. SIPPER, M. The artificial self-replication page, http://www.cs.bgu.ac.il/ ~sipper/selfrep/.
83. SOMMERVILLE, I. Software Engineering, 5th ed. Addison-Wesley, 1996.
84. SZATHMÁRY, E. Chemes, genes, memes: A classification of replicators. In Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity, and Digital Evolution. volume=26, in Lectures on Mathematics in the Life Sciences (Providence, Rhode Island, 1999), C. L. Nehaniv, Ed., American Mathematical Society, pp. 1-10.
85. SZOSTAK, J., BARTEL, D., AND LUISI, P. Synthesizing life. Nature 409 (2001), 383-390.
86. TEMPESTI, G. A new self-reproducing cellular automaton capable of construction and computation. In ECAL'95: Third European Conference on Artificial Life (1995), vol. Lecture Notes in Computer Science 929, pp. 555-563.
87. TOFFOLI, T. Integration of phase-difference relations in asynchronous sequential networks. In Automata, Languages, and Programming (Fifth Colloquium, Udine, July 1978), Lecture Notes in Computer Science 62 (1978), G. Ausiello and C. Bohm, Eds., Springer Verlag, pp. 457-463.
88. TOFFOLI, T., AND MARGOLUS, N. Cellular Automata Machines. MIT Press, 1987.
89. TYRRELL, A. M., SANCHEZ, E., FLOREANO, D., TEMPESTI, G., MANGE, D., MORENO, J. M., ROSENBERG, J., AND VILLA, A. E. P. Poetic tissue: An integrated architecture for bio-inspired hardware. In Evolvable Systems: From Biology to Hardware, 5th International Conference, ICES 2003, Trondheim, Norway, March 17-20, 2003, Lecture Notes in Computer Science, Vol. 2606 (2003), Springer Verlag, pp. 129-140.
90. VAN BELLE, T., AND ACKLEY, D. H. Code factoring and the evolution of evolvability. In GECCO 2002: Proceedings of the Genetic and Evolutionary Computation Conference (2002), Morgan Kaufmann, pp. 1383-1390.
91. VAN BELLE, T., AND ACKLEY, D. H. Uniform subtree mutation. In Proc. EuroGP-2002, the 5th European Conference on Genetic Programming (2002), pp. 152-161.
92. VAN NIMWEGEN, E., CRUTCHFIELD, J. P., AND HUYNEN, M. Neutral evolution of mutational robustness. Proc. Natl. Acad. Sci. U.S.A. 96 (1999), 9716-9720.
93. VAN NIMWEGEN, E., CRUTCHFIELD, J. P., AND MITCHELL, M. Statistical dynamics of the royal road genetic algorithm. Theoretical Computer Science 229, Special Issue on Evolutionary Computation, A. E. Eiben and G. Rudolph (eds.) (1999).
94. VARELA, F. J. Principles of biological autonomy. orth Holland, 1979.
95. VARELA, F. J., MATURANA, H. R., AND URIBE, R. Autopoiesis: The organization of living systems. BioSystems 5, 4 (1974), 187-196.
96. VARSHAVSKY, V. System time and system timing. In Algebraic Engineering, C. L. Nehaniv and M. Ito, Eds. World Scientific Press, 1999, pp. 38-57.
97. VITÁNYI, P. M. B. Sexually reproducing cellular automata. Mathematical Biosciences 18 (1973), 23-54.
98. VON NEUMANN, J. Probabilistic logics and the synthesis of reliable organisms from unreliable components. In Automata Studies (Annals of Mathematics Studies, Number 34), C. E. Shannon and J. McCarthy, Eds. Princeton, 1956, pp. 43-98.
99. VON NEUMANN, J. Theory of Self-Reproducing Automata. Edited and completed by A. W. Burks. University of Illinois Press, 1966.
100. WAGNER, G. P., Ed. The Character Concept in Evolutionary Biology. Academic Press, 2001.
101. WAGNER, G. P., AND ALTENBERG, L. Complex adaptations and the evolution of evolvability. Evolution 50, 3 (1996), 967-976.
102. WATSON, J. D., AND CRICK, F. H. C. Molecular structure of nucleic acids. Nature 171 (1953), 737-738.
103. WERNICK, P., AND LEHMAN, M. M. Software process white box modelling for feast/1. Journal of Systems and Software 46, 2-3 (1999), 193-201.
104. WEST-EBERHARD, M. Developmental Plasticity and Evolution. Oxford University Press, 2003.
105. WHITEN, A., GOODALL, J., MCGREW, W. C., NISHIDA, T., REYNOLDS, V., SUGIYAMA, Y., TUTIN, C. E. G., WRANGHAM, R. W., AND BOESCH, C. Culture in chimpanzees. Nature 399 (1999), 682-685.
106. WOLPERT, L. The Triumph of the Embryo. Oxford University Press, 1991.
107. WRIGHT, S. The role of mutation, inbreeding, crossbreeding, and selection in evolution. Proceedings of the Sixth International Congress on Genetics 1 (1932), 356-366.