References

1

Adami, Chris. Unpublished. Learning and complexity in genetic auto-adaptive systems. Caltech preprint: MAP - 164, One of the Marmal Aid Preprint Series In Theoretical Nuclear Physics, October 1993. Adami has used the input-output facilities of the new Tierra languages to feed data to creatures, and select for responses that result from simple computations, not contained in the seed genome. Contact: chris@almach.caltech.edu

2

Anonymous. 1988. Worm invasion. Science 11-11-88: 885.

3

Barton-Davis, Paul. Unpublished. Independent implementation of the Tierra system, contact: pauld@cs.washington.edu.

4

Beaudry, Amber A., and Gerald F. Joyce. 1992. Directed evolution of an RNA enzyme. Science 257: 635-641.

5

Bell, Graham. 1982. The masterpiece of nature: the evolution and genetics of sexuality. Berkeley: University of California Press.

6

Benner, Steven A., Andrew D. Ellington, and Andreas Tauer. 1989. Modern metabolism as a palimpsest of the RNA world. Proc. Natl. Acad. Sci. U.S.A. 86: 7054-7058.

7

Brooks, Rodney. Unpublished. Brooks has created his own Tierra-like system, which he calls Sierra. In his implementation, each machine instruction consists of an opcode and an operand. Successive instructions overlap, such that the operand of one instruction is interpreted as the opcode of the next instruction. Contact: brooks@ai.mit.edu

8

Burstyn, Harold L. 1990. RTM and the worm that ate internet. Harvard Magazine 92(5): 23-28.

9

Buss, Leo W. 1987. The evolution of individuality. Princeton, NJ: Princeton University Press. Pp. 203.

10

Cairn-Smith, A. G. 1985. Seven clues to the origin of life. Cambridge: Cambridge University Press.

11

Carroll, L. 1865. Through the Looking-Glass. London: MacMillan.

12

Chao, Lin, Christopher Vargas, Brian B. Spear, and Edward C. Cox. 1983. Transposable elements as mutator genes in evolution. Nature 303: 633-635.

13

Charlesworth, B. 1976. Recombination modification in a fluctuating environment, Genetics 83: 181-195.

14

Darwin, Charles. 1859. On the origin of species by means of natural selection or the preservation of favored races in the struggle for life. London: Murray.

15

Davidge, Robert. 1992. Processors as organisms. CSRP 250. School of Cognitive and Computing Sciences, University of Sussex. Presented at the ALife III conference. Contact: robertd@cogs.susx.ac.uk

16

Davidge, Robert. 1993. Looping as a means to survival: playing Russian roulette in a harsh environment. In: Self organization and life: from simple rules to global complexity, proceedings of the second European conference on artificial life. Contact: robertd@cogs.susx.ac.uk

17

Davidson, Eric H., and Roy J. Britten. 1979. Regulation of gene expression: Possible role of repetitive sequences. Science 204: 1052-1059.

18

Dayhoff, Judith. 1990. Neural network architectures. New York: Van Nostrand Reinhold. Pp. 259.

19

DeAngelis, D., and L. Gross [eds]. 1992. Individual based models and approaches in ecology. New York: Chapman and Hill.

20

de Groot, Marc. Unpublished. Primordial soup, a Tierra-like system that has the additional ability to spawn self-reproducing organisms from a sterile soup. Contact: marc@kg6kf.ampr.org, marc@toad.com, marc@remarque.berkeley.edu

21

Doolittle, W. Ford, and Carmen Sapienza. 1980. Selfish genes, the phenotype paradigm and genome evolution. Nature 284: 601-603.

22

Eigen, Manfred. 1993. Viral quasispecies. Scientific American 269(1): 32-39. July 1993.

23

Farmer, J. D. & Belin, A. Artificial life: the coming evolution. Proceedings in celebration of Murray Gell-Mann's 60th Birthday. Cambridge: University Press. (Reprinted in Artificial Life II. Pp. 815-840.)

24

Feferman, Linda. 1992. Simple rules... complex behavior [video]. Santa Fe, NM: Santa Fe Institute. Contact: fef@santafe.edu,

25

Feng, Qing, Tae Kyo Park, and Julius Rebek. 1992. Crossover reactions between synthetic replicators yield active and inactive recombinants. Science 256: 1179-1180.

26

Ghiselin, Michael. 1974. The economy of nature and the evolution of sex. Berkeley: University of California Press.

27

Goldberg, D. E. 1989. Genetic algorithms in search, optimization, and machine learning. Reading, MA: Addison-Wesley.

28

Gould, Steven J. 1989. Wonderful life. W. W. Norton & Company, Inc. Pp. 347.

29

Gray, James. Unpublished. Natural selection of computer programs. This may have been the first Tierra-like system, but evolving real programs on a real rather than a virtual machine, and predating Tierra itself: ``I have attempted to develop ways to get computer programs to function like biological systems subject to natural selection.... I don't think my systems are models in the usual sense. The programs have really competed for resources, reproduced, run, and `died'. The resources consisted primarily of access to the CPU and partition space.... On a PDP11 I could have a population of programs running simultaneously.'' Contact: Gray.James_L+@northport.va.gov

30

Green, Melvin M. 1988. Mobile DNA elements and spontaneous gene mutation. In M. E. Lambert, J. F. McDonald, I. B. Weinstein [eds.]: Eukaryotic transposable elements as mutagenic agents. Pp. 41-50. Banbury Report 30, Cold Spring Harbor Laboratory.

31

Halvorson, Herlyn O., and Albert Monroy. 1985. The origin and evolution of sex. New York: A. R. Liss.

32

Hapgood, Fred. 1979. Why males exist: an inquiry into the evolution of sex. New York: William Morrow.

33

Hertz, John, Anders Krogh, and Richard G. Palmer. 1991. Introduction to the theory of neural computation. Addison-Wesley Publishing Co. Pp. 327.

34

Hogeweg, P. 1989. Mirror beyond mirror: puddles of life. In: Langton, C. [ed], Artificial Life, Santa Fe Institute Studies in the Sciences of Complexity, vol. VI, 297-316. Redwood City, CA: Addison-Wesley.

35

Holland, John Henry. 1975. Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control, and artificial intelligence (Univ. of Michigan Press, Ann Arbor).

36

Hong, J. I., Feng, Q., Rotello, V. & Rebek, J. 1992. Competition, cooperation, and mutation: improving a synthetic replicator by light irradiation. Science 255: 848-850.

37

Huston, Michael. 1979. A general hypothesis of species diversity, American Naturalist 113: 81-101.

38

Huston, Michael. 1992. Biological diversity and human resources. Impact of science on society 166: 121-130.

39

Huston, Michael. 1993. Biological diversity: the coexistence of species on changing landscapes. Cambridge University Press.

40

Huston, M., DeAngelis, D., and Post, W. 1988. New computer models unify ecological theory. Bioscience 38(10): 682-691.

41

Jelinek, Warren R., and Carl W. Schmid. 1982. Repetitive sequences in eukaryotic DNA and their expression. Annual Reviews of Biochemistry 51: 813-844.

42

Joyce, Gerald F. 1992. Directed molecular evolution. Scientific American, December 1992: 90-97.

43

Kampis, George. 1993. Coevolution in the computer: the necessity and use of distributed code systems. Printed in the ECAL93 proceedings, Brussels. Contact: gk@cfnext.physchem.chemie.uni-tuebingen.de

44

Kampis, George. 1993. Life-like computing beyond the machine metaphor. In: R. Paton [ed]: Computing with biological metaphors, London: Chapman and Hall. Contact: gk@cfnext.physchem.chemie.uni-tuebingen.de

45

Kauffman, Stuart A. 1993. The origins of order, self-organization and selection in evolution. Oxford University Press. Pp. 709.

46

Kerem, Bat-sheva, Johanna M. Rommens, Janet A. Buchanan, Danuta Markiewicz, Tara K. Cox, Aravinda Chakravarti, Manuel Buchwald, and Lap-Chee Tsui. 1989. Identification of the cystic fibrosis gene: genetic analysis. Science 245: 1073-1080.

47

Koza, John R. 1992. Genetic programming, on the programming of computers by means of natural selection. Cambridge, MA: MIT Press.

48

Langton, C. G. 1986. Studying artificial life with cellular automata. Physica 22D: 120-149.

49

Levy, Steven. 1992. Artificial Life, the quest for a new creation. Pantheon Books, New York. Pp. 390.

50

Levy, Steven. 1992. A-Life Nightmare. Whole Earth Review #76, Fall 1992, p. 22.

51

Litherland, J. 1993. Open-ended evolution in a computerised ecosystem. A Masters of Science dissertation in the Department of Computer Science, Brunel University. Contact: david.martland@brunel.ac.uk

52

Mac Arthur, Robert H., and Edward O. Wilson. 1967. The theory of island biogeography. Princeton University Press. Pp. 203.

53

Maley, Carlo C. 1993. A model of early evolution in two dimensions. Masters of Science thesis, Zoology, New College, Oxford University. Contact: cmaley@oxford.ac.uk

54

Manousek, Wolfgang. 1992. Spontane Komplexitaetsentstehung --- TIERRA, ein Simulator fuer biologische Evolotion. Diplomarbeit, Universitaet Bonn, Germany, Oktober 1992. Contact: Kurt Stueber, stueber@vax.mpiz-koeln.mpg.d400.de

55

Margulis, Lynn, and Dorion Sagan. 1986. Origin of sex. New Haven: Yale University Press.

56

Marx, Jean L. 1989. The cystic fibrosis gene is found. Science 245: 923-925.

57

Maynard Smith, J. 1971. What use is sex?, J. Theoret. Biol. 30: 319-335.

58

Maynard Smith, J. 1992. Byte-sized evolution. Nature 355: 772-773.

59

Maynard Smith, J, Christopher G. Dowson, and Brian G. Spratt. 1991. Localized sex in bacteria. Nature 349: 29-31.

60

Mead, Carver. 1993. Analog VLSI and neural systems. Addison-Wesley Publishing Co. Pp. 371.

61

Michod, Richard E., and Bruce R. Levin. 1988. The evolution of sex: an examination of current ideas. Sunderland, MA: Sinauer Associates.

62

Moravec, Hans. 1988. Mind Children: the future of robot and human intelligence. Cambridge, MA: Harvard University Press.

63

Moravec, Hans. 1989. Human culture: a genetic takeover underway. In: Langton, C. [ed], Artificial Life, Santa Fe Institute Studies in the Sciences of Complexity, vol. VI, 167-199. Redwood City, CA: Addison-Wesley.

64

Moravec, Hans. 1993. Pigs in cyberspace. Extropy #10, Winter/Spring, 1993.

65

Morris, S. Conway. 1989. Burgess shale faunas and the Cambrian explosion. Science 246: 339-346.

66

Nowick, J., Feng, Q., Tijivikua, T., Ballester, P. & Rebek, J. 1991. Journal of the American Chemical Society 113: 8831-8839.

67

Orgel, L. E., and F. H. C. Crick. 1980. Selfish DNA: the ultimate parasite. Nature 284: 604-607.

68

Rasmussen, Steen, Carsten Knudsen, Rasmus Feldberg, and Morten Hindsholm. 1990. The coreworld: emergence and evolution of cooperative structures in a computational chemistry. Physica D 42: 111-134.

69

Rasmussen, S., C. Knudsen, and R. Feldberg. 1991. Dynamics of programmable matter. In: Langton, C., C. Taylor, J. D. Farmer, & S. Rasmussen [eds], Artificial Life II, Santa Fe Institute Studies in the Sciences of Complexity, vol. X, 211-254. Redwood City, CA: Addison-Wesley.

70

Ray, T. S. 1979. Slow-motion world of plant `behavior' visible in rainforest. Smithsonian 9(12): 121-30.

71

Ray, T. S. 1991. An approach to the synthesis of life. In: Langton, C., C. Taylor, J. D. Farmer, & S. Rasmussen [eds], Artificial Life II, Santa Fe Institute Studies in the Sciences of Complexity, vol. X, 371-408. Redwood City, CA: Addison-Wesley.

72

Ray, T. S. 1991. Population dynamics of digital organisms. In: Langton, C. G. [ed.], Artificial Life II Video Proceedings. Redwood City, CA: Addison Wesley.

73

Ray, T. S. 1991. Is it alive, or is it GA? In: Belew, R. K., and L. B. Booker [eds.], Proceedings of the 1991 International Conference on Genetic Algorithms, 527-534. San Mateo, CA: Morgan Kaufmann.

74

Ray, T. S. 1991. Evolution and optimization of digital organisms. In: Billingsley K. R., E. Derohanes, H. Brown, III [eds.], Scientific Excellence in Supercomputing: The IBM 1990 Contest Prize Papers, Athens, GA, 30602: The Baldwin Press, The University of Georgia.

75

Ray, T. S. 1992. Foraging behaviour in tropical herbaceous climbers (Araceae). Journal of Ecology. 80: 189-203.

76

Ray, T. S. 1992. Tierra.doc. Documentation for the Tierra Simulator V4.0, 9-9-92. Newark, DE: Virtual Life. The full source code and documentation for the Tierra program is available by anonymous ftp at: tierra.slhs.udel.edu [128.175.41.34] and life.slhs.udel.edu [128.175.41.33], or by contacting the author.

77

Ray, T. S. 1994. Evolution and complexity. In: Cowan, George A., David Pines and David Metzger [eds.], Complexity: Metaphors, Models, and Reality, Pp. 161-173. Addison-Wesley Publishing Co.

78

Ray, T. S. 1994. Evolution, complexity, entropy, and artificial reality. Physica D. 75: 239-263

79

Rommens, Johanna M., Michael C. Iannuzzi, Bat-sheva Kerem, Mitchell L. Drumm, Georg Melmer, Michhael Dean, Richard Rozmahel, Jeffery L. Cole, Dara Kennedy, Noriko Hidaka, Martha Zsiga, Manuel Buchwald, John R. Riordan, Lap-Chee Tsui, Francis S. Collins. 1989. Identification of the cystic fibrosis gene: chromosome walking and jumping. Science 245: 1059-1065.

80

Riordan, John R., Johanna M. Rommens, Bat-sheva Kerem, Noa Alon, Richard Rozmahel, Zbyszko Grzelczak, Julian Zielenski, Si Lok, Natasa Plavsic, Jia-Ling Chou, Mitchell L. Drumm, Michael C. Lannuzzi, Francis S Collins, Lap-Chee Tsui. 1989. Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA. Science 245: 1066-1073.

81

Skipper, Jakob. 1992. The computer zoo -- evolution in a box. In: Francisco J. Varela and Paul Bourgine [eds.], Toward a practice of autonomous systems, proceedings of the first European conference on Artificial Life. MIT Press, Cambridge, MA. Pp. 355-364. Contact: Jakob.Skipper@copenhagen.ncr.com

82

Sober, E. 1984. The nature of selection. MIT Press, Cambridge, MA.

83

Spafford, Eugene H. 1989. The internet worm program: an analysis. Computer Communication Review 19(1): 17-57. Also issued as Purdue CS technical report TR-CSD-823. Contact: spaf@purdue.edu

84

Spafford, Eugene H. 1989. The internet worm: crisis and aftermath. CACM 32(6): 678-687. Contact: spaf@purdue.edu

85

Stanley, Steven M. 1973. An ecological theory for the sudden origin of multicellular life in the late precambrian, Proc. Nat. Acad. Sci. 70: 1486-1489.

86

Stearns, Steven C. 1987. The evolution of sex and its consequences. Boston: Birkhäuser Verlag.

87

Strickberger, Monroe W. 1985. Genetics. Macmillan Publishing Co. New York.

88

Strong, D. R. and T. S. Ray. 1975. Host tree location behavior of a tropical vine ( Monstera gigantea) by skototropism. Science, 190: 804-06.

89

Surkan, Al. Unpublished. Self-balancing of dynamic population sectors that consume energy. Department of computer science, UNL. ``Tierra-like systems are being explored for their potential applications in solving the problem of predicting the dynamics of consumption of a single energy carrying natural resource''. Contact: surkan@cse.unl.edu

90

Syvanen, Michael. 1984. The evolutionary implications of mobile genetic elements. Ann. Rev. Genet. 18: 271-293.

91

Tackett, Walter, and Jean-Luc Gaudiot. 1993. Adaptation of self-replicating digital organisms. Proceedings of the International Joint Conference on Neural Networks, Nov. 1993, Beijing, China. IEEE Press. Contact: tackett@ipld01.hac.com, tackett@priam.usc.edu

92

Taylor, Charles E., David R. Jefferson, Scott R. Turner, and Seth R. Goldman. 1989. RAM: artificial life for the exploration of complex biological systems. In: Langton, C. [ed], Artificial Life, Santa Fe Institute Studies in the Sciences of Complexity, vol. VI, 275-295. Redwood City, CA: Addison-Wesley.

93

Thomas, C. A. 1971. The genetic organization of chromosomes. Ann. Rev. Genet. 5: 237-256.

94

Todd, Peter M. 1993. Artificial death. Proceedings of the Second European Conference on Artificial Life (ECAL93), Vol. 2, Pp. 1048-1059. Brussels, Belgium: Universite Libre de Bruxelles. Contact: ptodd@spo.rowland.org

95

Van Valen, L. 1973. A new evolutionary law. Evolutionary Theory 1: 1-30.

96

Williams, George C. 1975. Sex and evolution. Princeton: Princeton University Press.