Degenerate neutrality creates evolvable fitness landscapes

Whitacre, Dr James M and Bender, Dr Axel (2009) Degenerate neutrality creates evolvable fitness landscapes. [Conference Paper] (In Press)

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Understanding how systems can be designed to be evolvable is fundamental to research in optimization, evolution, and complex systems science. Many researchers have thus recognized the importance of evolvability, i.e. the ability to find new variants of higher fitness, in the fields of biological evolution and evolutionary computation. Recent studies by Ciliberti et al (Proc. Nat. Acad. Sci., 2007) and Wagner (Proc. R. Soc. B., 2008) propose a potentially important link between the robustness and the evolvability of a system. In particular, it has been suggested that robustness may actually lead to the emergence of evolvability. Here we study two design principles, redundancy and degeneracy, for achieving robustness and we show that they have a dramatically different impact on the evolvability of the system. In particular, purely redundant systems are found to have very little evolvability while systems with degeneracy, i.e. distributed robustness, can be orders of magnitude more evolvable. These results offer insights into the general principles for achieving evolvability and may prove to be an important step forward in the pursuit of evolvable representations in evolutionary computation.

Item Type:Conference Paper
Keywords:degeneracy, evolutionary computation, evolvability, neutral networks, optimization, redundancy, robustness
Subjects:Computer Science > Complexity Theory
Biology > Theoretical Biology
Biology > Evolution
Computer Science > Artificial Intelligence
ID Code:6576
Deposited By:Whitacre, Dr James M
Deposited On:06 Jul 2009 10:43
Last Modified:11 Mar 2011 08:57

References in Article

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[1] M. Aldana, E. Balleza, S. Kauffman, and O. Resendiz, "Robustness and evolvability in genetic regulatory networks," J. Theor. Biol., vol. 245, pp. 433-448, 2007.

[2] S. Ciliberti, O. C. Martin, and A. Wagner, "Innovation and robustness in complex regulatory gene networks," Proc. Natl. Acad. Sci. USA, vol. 104, p. 13591, 2007.

[3] S. A. Kauffman, "Requirements for evolvability in complex systems: orderly components and frozen dynamics," Physica D, vol. 42, pp. 135–152, 1990.

[4] M. Kirschner and J. Gerhart, "Evolvability," Proc. Natl. Acad. Sci. USA, vol. 95, pp. 8420-8427, 1998.

[5] A. Wagner, "Robustness and evolvability: a paradox resolved," Proc. R. Soc. Lond., Ser. B: Biol. Sci., vol. 275, pp. 91-100, 2008.

[6] J. Reisinger, K. O. Stanley, and R. Miikkulainen, "Towards an empirical measure of evolvability," GECCO, pp. 257-264, 2005.

[7] T. Smith, A. Philippides, P. Husbands, and M. O'Shea, "Neutrality and ruggedness in robot landscapes," in Congress on Evolutionary Computation, 2002, pp. 1348-1353.

[8] V. K. Vassilev and J. F. Miller, "The Advantages of Landscape Neutrality in Digital Circuit Evolution," in Evolvable systems: from biology to hardware Berlin: Springer, 2000.

[9] T. Yu and J. F. Miller, "Neutrality and the Evolvability of Boolean Function Landscape," in Proceedings of the 4th European Conference on Genetic Programming, 2001, pp. 204-217.

[10] A. Wagner, "Neutralism and selectionism: a network-based reconciliation," Nature Reviews Genetics, 2008.

[11] G. P. Wagner and L. Altenberg, "Complex adaptations and the evolution of evolvability," Evolution, vol. 50, pp. 967-976, 1996.

[12] J. M. Whitacre, "Adaptation and Self-Organization in Evolutionary Algorithms," Thesis: University of New South Wales, 2007, p. 283.

[13] P. J. Bentley, "Fractal Proteins," Genetic Programming and Evolvable Machines, vol. 5, pp. 71-101, 2004.

[14] C. Ferreira, "Gene Expression Programming: A New Adaptive Algorithm for Solving Problems," Complex Systems, vol. 13, pp. 87-129, 2001.

[15] R. E. Keller and W. Banzhaf, "Genetic programming using genotype-phenotype mapping from linear genomes into linear phenotypes," Genetic Programming, pp. 116–122, 1996.

[16] J. D. Knowles and R. A. Watson, "On the Utility of Redundant Encodings in Mutation-Based Evolutionary Search," Lecture Notes in Computer Science, pp. 88-98, 2003.

[17] S. Kumar and P. Bentley, On Growth, Form and Computers: Academic Press, 2003.

[18] J. Miller and P. Thomson, "Beyond the complexity ceiling: Evolution, emergence and regeneration," in GECCO, 2004.

[19] J. F. Miller, "Evolving a Self-Repairing, Self-Regulating, French Flag Organism," Lecture Notes in Computer Science, pp. 129-139, 2004.

[20] F. Rothlauf and D. E. Goldberg, "Redundant Representations in Evolutionary Computation," Evolutionary Computation, vol. 11, pp. 381-415, 2003.

[21] F. Rothlauf, Representations for Genetic And Evolutionary Algorithms. Heidelburg: Springer Verlag, 2006.

[22] M. J. West-Eberhard, "Evolution in the light of developmental and cell biology, and vice versa," Proc. Natl. Acad. Sci. USA, vol. 95, pp. 8417-8419, 1998.

[23] S. A. Newman and G. B. Mueller, "Epigenetic mechanisms of character origination," Journal of Experimental Zoology, vol. 288, pp. 304-317, 2000.

[24] A. L. Hughes, "Leading Edge of the Neutral Theory of Molecular Evolution," Ann. N. Y. Acad. Sci., vol. 1133, pp. 162-179, 2008.

[25] T. Ohta, "Near-neutrality in evolution of genes and gene regulation," Proc. Natl. Acad. Sci. USA, vol. 99, pp. 16134-16137, 2002.

[26] P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker, "From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures," Proc. R. Soc. Lond., Ser. B: Biol. Sci., vol. 255, pp. 279-284, 1994.

[27] E. van Nimwegen and J. P. Crutchfield, "Metastable evolutionary dynamics: Crossing fitness barriers or escaping via neutral paths?," Bulletin of Mathematical Biology, vol. 62, pp. 799-848, 2000.

[28] E. van Nimwegen, J. P. Crutchfield, and M. Huynen, "Neutral evolution of mutational robustness," Proc. Natl. Acad. Sci. USA, vol. 96, pp. 9716-9720, 1999.

[29] J. Visser, J. Hermisson, G. P. Wagner, L. A. Meyers, H. Bagheri-Chaichian, J. L. Blanchard, L. Chao, J. M. Cheverud, S. F. Elena, and W. Fontana, "Perspective: Evolution and Detection of Genetic Robustness," Evolution, vol. 57, pp. 1959-1972, 2003.

[30] W. Banzhaf, "Genotype-Phenotype-Mapping and Neutral Variation-A Case Study in Genetic Programming," Lecture Notes in Computer Science, pp. 322-322, 1994.

[31] M. Kimura, "Solution of a Process of Random Genetic Drift with a Continuous Model," Proc. Natl. Acad. Sci. USA, vol. 41, pp. 144-150, 1955.

[32] G. M. Edelman and J. A. Gally, "Degeneracy and complexity in biological systems," Proc. Natl. Acad. Sci. USA, p. 231499798, 2001.

[33] A. Wagner, "Distributed robustness versus redundancy as causes of mutational robustness," Bioessays, vol. 27, pp. 176-188, 2005.

[34] A. Wagner, "Robustness against mutations in genetic networks of yeast," Nat. Genet., vol. 24, pp. 355-362, 2000.

[35] H. A. Simon, A Behavioral Model of Rational Choice. Santa Monica: Rand Corp, 1953.

[36] M. Ebner, M. Shackleton, and R. Shipman, "How neutral networks influence evolvability," Complexity, vol. 7, pp. 19-33, 2001.


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