Evolutionary Biology

Abramson, G. (1997) Ecological model of extinctions Phys. Rev. E. 55, p 785 Abstract
Adami, C., Ofria, C., Collier, T. C. (2000) Evolution of Biological Complexity Proc. Nat. Acad. Sci (USA) 97 (2000) 4463.
Alvez, D., Fontanari, J.F., (1997) Error threshold in finite populations Preprint Abstract
Baatz, M., Wagner, G. P., (1996) Adaptive inertia caused by hidden pleiotropic effects. Theor. Popul. Biol.Postscript
Bak, P., Paczuski, M., (1996) Mass Extinctions vs Uniformitarianism in Biological Evolution. in Physics of Biological Systems Lecture Notes in Physics, Springer-Verlag. Abstract.
Balkenius, C. (1994) Biological Learning and Artificial Intelligence Cognitive Science Department, Lund University
Bedau, M. A., (1999) Quantifying the Extent and Intensity of Adaptive Evolution. In A. Wu, ed., Proceedings of 1999 Genetic and Evolutionary Computation Conference Workshop Program (pp. 34-37).
Bedau, M. A., Joshi, S., Lillie, B., (1999) Visualizing Waves of Evolutionary Activity of Alleles. In A. Wu, ed., Proceedings of 1999 Genetic and Evolutionary Computation Conference Workshop Program (pp. 96-98).
Bedau, M. A., Bahm, A. (1994) Bifurcation Structure in Diversity Dynamics. In R. Brooks and P. Maes, eds., Artificial Life IV: Proceedings of the Fourth International Workshop on the Synthesis and Simulation of Living Systems, Cambridge, MA: Bradford Books/MIT Press, pp. 258-268.
Bedau, M. A., Packard, N. H., (1992) Measurement of Evolutionary Activity, Teleology, and Life. In C. Langton, C. Taylor , D. Farmer, and S. Rasmussen, eds., Artificial Life II, Santa Fe Institute Studies in the Sciences of Complexity, Vol. X, Redwood City, CA: Addison-Wesley, pp. 431-461.
Bedau, M. A., Snyder, E., Packard, N.H., (1998) A Classification of Long-Term Evolutionary Dynamics. In Artificial Life VI; C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., MIT Press (1998), pp. 228-237.
Bedau, M. A., Snyder, E., Brown, T., Packard, N. H. (1998) A Comparison of Evolutionary Activity in Artificial Evolving Systems and in the Biosphere Santa Fe Institute Working Paper 98-03-024
Bedau, M. A., Brown, C. T., (1999) Visualizing Evolutionary Activity of Genotypes Artificial Life 5: 17-35.
Bedau, M. A., Seymour, R., (1994) Adaptation of Mutation Rates in a Simple Model of Evolution. In Russel J. Stonier and Xing Huo Yu, eds., Complex Systems; Mechanism of Adaptation, Amsterdam: IOS Press, pp. 37-44.
Bedau, M. A., (1994) Evolution of Sensorimotor Functionality. Perception and Action, Geneva, 1994.
Bignone, F. A., Livi, R., Propato, M., (1997) Symbolic and Global Dynamics in Coupled Genetic Networks: Evolution of Artificial Cell Populations at the Edge of and within Chaotic Transient BehaviourFourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Bornholdt, S., Sneppen, K. (2000) Robustness as an Evolutionary Principle submitted to Proc R. Soc. London B.
Bornholdt, S., Sneppen, K. (1998) Neutral Mutations and Punctuated Equilibrium in Evolving Genetic Networks Phys. Rev. Lett. 81 (1998) 236-239.
Bullock, S., (1997) An Exploration of Signalling Behaviour by both Analytic and Simulation Means for both Discrete and Continuous Models Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Bullock, S., Cliff, D. (1996) Modelling biases and biasing models: the role of 'hidden preferences' in the artificial co-evolution of symmetrical signals. Cognitive Science Research Paper 414 School of Cognitive and Computing Sciences, University of Sussex
Caldarelli, G., Higgs, P.G., McKane, A.J., (1998) Modelling coevolution in multispecies communities Preprint. Abstract
Cliff, D., Miller, G. (1995) Tracking the Red Queen: Measurements of Adaptive Progress in Co-evolutionary Simulations In F. Moran, A. Moreno, J.J Merelo and P Cachon (eds.) Advances in Artificial Life: Proceedings of the Third European Conference on Artificial Life (ECAL95).
Coker, P., Winter C., (1997) NSex Reproduction in Dynamic Environments Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Collins, R. J. (1992) Studies in Artificial Evolution. PhD Dissertation, Dept. of Computer Science, UCLA. Part 1, Part 2, Part3.Abstract
Collins, R. J. , Jefferson, D. R. (1991) The Evolution of Sexual Selection and Female Choice First European Conference on Artificial Life. The MIT Press/Bradford Books Abstract.
Di Paolo, E. A. (1999) A little more than kind and less than kin: the unwarranted use of kin selection in spatial models of communication. In Advances in Artificial life Proc. ECAL'99, Lausanne, Switzerland. eds. D. Floreano, J-D. Nicoud, and F. Mondada, (eds.). LNAI 1674 Springer-Verlag. pp 504 - 513
Di Paolo, E. A. (2000) Ecological symmetry breaking can favour the evolution of altruism in an action-response game. Journal of Theoretical Biology, 203, 135-152.
Di Paolo, E. (1996), A Computational Model of Speciation in Non-Uniform Environments Without Physical Barriers. Cognitive Science Research Paper 412, School of Cognitive and Computing Sciences, University of Sussex.
Ficici, Sevan G., Pollack, Jordan B. (2000). Effects of Finite Populations on Evolutionary Stable Strategies. Proceedings of the 2000 Genetic and Evolutionary Computation Conference, L. Darrell Whitley (ed.), Morgan-Kaufmann
Fletcher, J., Bedau, M. A., Zwick, M. (1998) Effect of Environmental Structure on Evolutionary Adaptation. In Proceedings of Artificial Life VI, Los Angeles, June 26-29, 1998; C. Adami, R. Belew, H. Kitano, and C. Taylor, eds., MIT Press (1998), pp. 189-198.
Fontana, W., (1996) On organization, in The future of science has begun: Approaches to Artificial Life and Artificial Intelligence. Nicola Dioguardi (ed.), Fundazione Carlo Erba.
Fontana, W., Buss, L.W. (1996) The barrier of objects: from dynamical systems to bounded organizations. In: J. Casti and A. Karlqvist, [eds.], Boundaries and Barriers. Addison-Wesley, Reading, MA.
Fontana, W., Buss, L.W.(1994) "The arrival of the fittest": towards a theory of biological organization.Bull. Math. Biol. 56:1-64.
Fontana, W., Wagner, G., Buss, L.W. (1994) Beyond digital naturalism. Artificial Life 1:211-227. [Reprinted in: C. Langton [ed.] (1995) in Artificial Life: An Overview. MIT Press.
Fontana, W., Buss, L.W.(1992) What would be conserved 'if the tape were run twice.' Proc. Nat. Acad. Sci., USA, 91:757-761. [Reprinted in: G. Cowan, D. Pines, and D. Melzer [eds.] (1994) Pages 223-244 in Complexity: Metaphors, Models and Reality. Addison-Wesley, Redwood City, CA.]
Forst, C.V., (1997) Molecular Evolution of Catalysis Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Gitchoff, P., Wagner,G.P., Recombination induced hypergraphs: a new approach to mutation-recombination isomorphism.Complexity. In press. Postscript
Green, D.G., (1993) Emergent Behavior in Biological Systems in Complex Systems - From Biology to Computation (Green D.G. and Bossomaier, T.J. ed.) pp 24-35 IOS Press, Amsterdam
Harvey, I. Bossomaier, T., (1997) Time Out of Joint: Attractors in Asynchronous Random Boolean Networks Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Harvey, I (1996) The Microbial Genetic Algorithm, submitted as a Letter to Evolutionary Computation.
Hemelrijk, C.K., (1997) Cooperation Without Genes, Games Or Cognition Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Hightower, R., Forrest, S., Perelson, A., (1996) The Evolution of Emergent Organization in Immune System Gene Libraries. In M. Mithchell, R. Belew (eds.) Adaptive Individuals in Evolving Populations: Models and Algorithms, Addison-Wesley.
Hightower, R., Forrest, S., Perelson, A., (1995) The Baldwin effect in the immune system: learning by somatic hypermutation. In L.J. Eshelman (ed.) Proceedings of the 5th Intl. Conference on Genetic Algorithms, Morgan Kaufmann, San Francisco, CA. pp. 184-192
Hoffmeyer, J., (1995) Biosemiotics: Towards a new Synthesis in Biology?. Presented at the ISHPSSB Conference in Leuven, Belgium, July 1995.
Huynen, M., (1995) Exploring Phenotype space through Neutral Evolution. Santa Fe Institute Working Paper 95-10-100. Abstract
Kalmykov, V.L. (1997) The Abstract Theory of Evolution of the Living in Proceedings of AISB 1997 Workshop on Evolutionary Computing, 7th - 8th April 1997, Organisers: D. Corne and J. Shapiro, The University of Manchester, pp. 25-30.
Kaneko, K., (1998) Diversity, Stability, Recursivity, and Rule Generation in Biological System: Intra-inter Dynamics Approach Int.J. Mod. Phes. B .Abstract
Kopp, S., Reidys, C. M., Schuster, P. (1997) Insights into Evolution of RNAStructures Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
McMullin, B., Varela, F. (1997) Rediscovering Computational Autopoiesis Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
McMullin, B., (1995) Replicators Don't. 3rd European Conference on Artificial Life, Granada, Spain, June 1995.
McMullin, B., (1992) Essays on Darwinism. 3: Genic and Organismic Selection School of Electronic Engineering, Dublin City University, Technical Report bmcm9203, May 1992. Abstract
McMullin, B., (1992) Essays on Darwinism. 2: Organismic Darwinism School of Electronic Engineering, Dublin City University, Technical Report bmcm9202, April 1992. Abstract
McMullin, B., (1992) Essays on Darwinism. 1: Ontological Foundations School of Electronic Engineering, Dublin City University, Technical Report bmcm9201, March 1992. Abstract
Miller, G. E., (1994) Artificial life as theoretical biology: how to do real science with computer simulation Cognitive Science Research Paper 378 School of Cognitive and Computing Sciences, University of Sussex
Miller, G. E., Cliff, D.,Co-Evolution of Pursuit and Evasion I: Biological and Game-Theoretic Foundations Cognitive Science Research Paper 311 School of Cognitive and Computing Sciences, University of Sussex
Newman, M. E. J. (1999) Simple models of evolution and extinction To appear as an invited article in Computing in Science and Engineering
Newman, M. E. J. , Fraser, S.M., Sneppen, K., Tozier, W. A. (1997) Comment on "Self-organized criticality in living systems" by C. Adami Phys. Lett. A 228, 202 (1997).
Newman M.E.J., Palmer, R. G. (1999) Models of Extinction: A Review SFI Working Paper 99-08-061
Nomuya, T. (1997) An Attempt for Description of QuasiAutopoietic Systems Using MetabolismRepair Systems Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press
Ofria, C., Adami, C., Collier, T. C. , Hsu, G.K., (1999) Evolution of differentiated expression patterns in digital organisms "Advances in Artificial Life", 5th European Conference ECAL'99, D. Floreano et al, eds. (1999).
Ofria, C., Adami, C., (1999) Evolution of genetic organization in digital organisms Proc. of DIMACS workshop on "Evolution as Computation", Jan. 11-12, Princeton, NJ. L. Landweber and E. Winfree, eds. (Springer, 1999)
Parsons, R., Forrest, S., Burks, C., (1996) Genetic Operators in the Immune System for the DNA Fragment-assembly Problem. Machine Learning.
Perelson, A. Hightower, R., Forrest, S., (1995) Evolution (and learning) of v-region genes. Research in Immunology.
Rechtsteiner, A., Bedau, M.A. (1999) A Generic Model for Quantitative Comparison of Genotypic Evolutionary Activity. In D. Floreano, J.-D. Nicoud, F. Mondada, eds., Fifth European Conference on Artificial Life (pp. 109-118). Heidelberg: Springer-Verlag.
Rechtsteiner, A., Bedau, M.A. (1999) A Generic Model for Measuring Excess Evolutionary Activity. In Banzhaf, W., Daida, J., Eiben, A. E., Garzon, M. H., Honavar, V., Jakiela, M., & Smith, R. E. (eds.), GECCO-99: Proceedings of the Genetic and Evolutionary Computation Conference, July 13-17, 1999, Orlando, Florida, Vol. 2 (pp. 1366-1373). San Francisco, CA: Morgan Kaufmann.
Roberts, B.W., Newman, M.E.J. (1995) A Model for Evolution and Extinction. Report No. CU-MSC-8-95-4, Cornell University.Abstract
Savage, M, Askenazi, M. (1998) Arborscapes: A Swarm-Based Multi-agent Ecological Disturbance Model Santa Fe Institute Working Paper 98-06-056. Abstract
Schmitz, O.J., Booth, G. (1996) Modeling food web complexity: the consequence of individual-based spatially explicit behavioral ecology on trophic interactions. Evolutionary Ecology.
Sharov, A.A., (1992) Biosemiotics: Functional-Evolutionary approach to the Analysis of the Sense of Information. T.A. Sebeok and J. Umiker-Sebeok (eds.). Biosemiotics. The Semiotic Web 1991, Mouton de Gruyter, New York, pp 345-373.
Sibani, P., Pedersen, A., (1999) Evolution dynamics in terraced NK landscapes Europhysics Lett. 48, 346-352 (1999)
Standish, R. K. (2000) An Ecolab Perspective on the Bedau Evolutionary Statistics Artificial Life VII, Portland, OR, USA.
van Nimwegen, E., Crutchfield J.P., (1999) Metastable Evolutionary Dynamics: Crossing Fitness Barriers or Escaping via Neutral Paths? adap-org/9907002
Wagner, G.P. (1996) Apparent stabilizing selection and the maintenance of neutral genetic variation Genetics 143:617-619. Postscript
Wagner, G.P., Altenberg, L. (1995) Complex adaptations and the evolution of evolvability. Evolution. Postscript
Wagner, G.P. (1995) Adaptation and the modular design of organisms. In: F. Morán, A. Morán, J.J. Merelo, and P. Chacón [eds.], Advances in Artificial Life. Springer Verlag, Berlin, pp 317-328. Postscript
Wagner, G.P. (1995) Homologues, natural kinds and the evolution of modularity. American Zoologist.Postscript
Watson, R.A., Reil, T., Pollack, J.B, (2000) Mutualism, Parasitism and Evolutionary Adaptation, ALife 7, Bedau, M. (ed.), MIT Press
Watson, R.A. and Pollack, J.B. (1999). How Symbiosis Can Guide Evolution. Fifth European Conference on Artificial Life. Dario Floreano, Jean-Daniel Nicoud, Francesco Mondada, eds. Springer, 1999.
Weller, K., (1997) Optimization Criteria for Design of Serial Transfer Evolution Experiments Fourth European Conference on Artificial Life, Phil Husbands and Inman Harvey (editors), MIT Press

Compiled by Ezequiel A. Di Paolo (c) 2000.
Suggestions, comments? Please, contact me.

ezequiel@sussex.ac.uk

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