Skip to main content

The Evolutionary Unfolding of Complexity

  • Conference paper
Evolution as Computation

Part of the book series: Natural Computing Series ((NCS))

Abstract

We analyze the population dynamics of a broad class of fitness functions that exhibit epochal evolution—a dynamical behavior, commonly observed in both natural and artificial evolutionary processes, in which long periods of stasis in an evolving population are punctuated by sudden bursts of change. Our approach—statistical dynamics—combines methods from both statistical mechanics and dynamical systems theory in a way that offers an alternative to current “landscape” models of evolutionary optimization. We describe the population dynamics on the macroscopic level of fitness classes or phenotype subbasins, while averaging out the genotypic variation that is consistent with a macroscopic state. Metastability in epochal evolution occurs solely at the macroscopic level of the fitness distribution. While a balance between selection and mutation maintains a quasistationary distribution of fitness, individuals diffuse randomly through selectively neutral subbasins in genotype space. Sudden innovations occur when, through this diffusion, a genotypic portal is discovered that connects to a new subbasin of higher fitness genotypes. In this way, we identify evolutionary innovations with the unfolding and stabilization of a new dimension in the macroscopic state space. The architectural view of subbasins and portals in genotype space clarifies how frozen accidents and the resulting phenotypic constraints guide the evolution to higher complexity.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. C. Adami. Self-organized criticality in living systems. Phys. Lett A, 203:29–32, 1995.

    Article  Google Scholar 

  2. L. M. Adleman. Molecular computation of solutions to combinatorial problems. Science, 266:1021–1024, 1994.

    Article  Google Scholar 

  3. L. Altenberg. Genome growth and the evolution of the genotype-phenotype map. In W. Banzhaf and F. H. Eeckman, editors. Evolution and Biocomputation. Computational Models of Evolution, Monterey, California, July 1992, pages 205–259, Springer-Verlag, Berlin, 1995.

    Google Scholar 

  4. T. Bäck. Evolutionary algorithms in theory and practice: Evolution strategies, evolutionary programming, genetic algorithms. Oxford University Press, New York, 1996.

    MATH  Google Scholar 

  5. L. Barnett. Tangled webs: Evolutionary dynamics on fitness landscapes with neutrality. Master’s thesis. School of Cognitive Sciences, University of East Sussex, Brighton, 1997. http://www.cogs.susx.ac.uk/lab/adapt/nnbib.html.

    Google Scholar 

  6. R. K. Belew and L. B. Booker, editors. Proceedings of the Fourth International Conference on Genetic Algorithms. Morgan Kaufmann, San Mateo, CA, 1991.

    Google Scholar 

  7. J. J. Binney, N. J. Dowrick, A. J. Fisher, and M. E. J. Newman. The Theory of Critical Phenomena: An Introduction to the Renormalization Group. Oxford Science Publications, 1992.

    MATH  Google Scholar 

  8. L. Chambers, editor. Practical Handbook of Genetic Algorithms. CRC Press, Boca Raton, 1995.

    Book  Google Scholar 

  9. J. Chen, E. Antipov, B. Lemieux, W. Cedeno, and D. H. Wood. In vitro selection for a OneMax DNA evolutionary computation. In E. Winfree and D. K. Gilford, editors, DNA Based Computers V. American Mathematical Society, Providence, RI, 2000.

    Google Scholar 

  10. J. P. Crutchfield and M. Mitchell. The evolution of emergent computation. Proc. Natl Acad. Sci. U.S.A., 92:10742–10746, 1995.

    Article  MATH  Google Scholar 

  11. L. D. Davis, editor. The Handbook of Genetic Algorithms. Van Nostrand Reinhold, 1991.

    Google Scholar 

  12. B. Derrida and L. Peliti. Evolution in a flat fitness landscape. Bull. Math. Bio., 53(3):355–382, 1991.

    MATH  Google Scholar 

  13. M. Eigen. Self-organization of matter and the evolution of biological macromolecules. Naturwissenschaften, 58:465–523, 1971.

    Article  Google Scholar 

  14. M. Eigen, J. McCaskill, and P. Schuster. The molecular quasispecies. Adv. Chem. Phys., 75:149–263, 1989.

    Article  Google Scholar 

  15. S. F. Elena, V. S. Cooper, and R. E. Lenski. Punctuated evolution caused by selection of rare beneficial mutations. Science, 272:1802–1804, 1996.

    Article  Google Scholar 

  16. L. Eshelman, editor. Proceedings of the Sixth International Conference on Genetic Algorithms. Morgan Kaufmann, San Mateo, CA, 1995.

    Google Scholar 

  17. W. J. Ewens. Mathematical Population Genetics, volume 9 of Biomathematics. Springer-Verlag, Berlin, 1979.

    Google Scholar 

  18. W. Fontana and P. Schuster. Continuity in evolution: On the nature of transitions. Science, 280:1451–5, 1998.

    Article  Google Scholar 

  19. W. Fontana, P. F. Stadler, E. G. Bornberg-Bauer, T. Griesmacher, I. L. Hofacker, M. Tacker, P. Tarazona, E. D. Weinberger, and P. Schuster. RNA folding and combinatory landscapes. Phys. Rev. E, 47:2083–2099, 1992.

    Article  Google Scholar 

  20. S. Forrest, editor. Proceedings of the Fifth International Conference on Genetic Algorithms. Morgan Kaufmann, San Mateo, CA, 1993.

    Google Scholar 

  21. C. V. Forst, C. Reidys, and J. Weber. Evolutionary dynamics and optimizations: Neutral networks as model landscapes for RNA secondary-structure folding landscape. In F. Moran, A. Moreno, J. Merelo, and P. Chacon, editors. Advances in Artificial Life, volume 929 of Lecture Notes in Artificial Intelligence. Springer-Verlag, Berlin, 1995.

    Google Scholar 

  22. D. E. Goldberg. Genetic Algorithms in Search, Optimization, and Machine Learning. Addison-Wesley, Reading, MA, 1989.

    MATH  Google Scholar 

  23. S. J. Gould and N. Eldredge. Punctuated equilibria: The tempo and mode of evolution reconsidered. Paleobiology, 3:115–251, 1977.

    Google Scholar 

  24. D. L. Hartl and A. G. Clark. Principles of population genetics, 2nd edition. Sinauer Associates, 1989.

    Google Scholar 

  25. R. Haygood. The structure of Royal Road fitness epochs. Evolutionary Computation, submitted, 1997. ftp://ftp.itd.ucdavis.edu/pub/people/rch/StrucRoyRdFitEp.ps.gz.

    Google Scholar 

  26. M. Huynen. Exploring phenotype space through neutral evolution. J. of Mol. Evol, 43:165–169, 1996.

    Article  Google Scholar 

  27. M. Huynen, P. F. Stadler, and W. Fontana. Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl Acad. Sci. USA, 93:397–401, 1996.

    Article  Google Scholar 

  28. S. A. Kauffman and S. Levin. Towards a general theory of adaptive walks in rugged fitness landscapes. J. Theor. Bio., 128:11–45, 1987.

    Article  MathSciNet  Google Scholar 

  29. M. Kimura. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, 1983.

    Book  Google Scholar 

  30. J. R. Koza. Genetic Programming: On the Programming of Computers by Means of Natural Selection. MIT Press, Cambridge, MA, 1992.

    MATH  Google Scholar 

  31. L. F. Landweber and L. Kari. Universal molecular computation in ciliates. In L. F. Landweber, E. Winfree, editors. Evolution as Computation, this volume.

    Google Scholar 

  32. C. A. Macken and A. S. Perelson. Protein evolution in rugged fitness landscapes. Proc. Nat. Acad. Sci. USA, 86:6191-6195, 1989.

    Article  MathSciNet  Google Scholar 

  33. M. Mitchell. An Introduction to Genetic Algorithms. MIT Press, Cambridge, MA, 1996.

    Google Scholar 

  34. M. Mitcheh, J. P. Crutchfield, and P. T. Hraber. Evolving cellular automata to perform computations: Mechanisms and impediments. Physica D, 75:361–391, 1994.

    Article  Google Scholar 

  35. M. Newman and R. Engelhardt. Effect of neutral selection on the evolution of molecular species. Proc. R. Soc. London B., 256:1333–1338, 1998.

    Article  Google Scholar 

  36. A. E. Nix and M. D. Vose. Modeling genetic algorithms with Markov chains. Ann. Math. Art. Intel., 5, 1991.

    Google Scholar 

  37. A. Prügel-Bennett. Modelling evolving populations. J. Theor. Bio., 185:81–95, 1997.

    Article  Google Scholar 

  38. A. Prügel-Bennett and J. L. Shapiro. Analysis of genetic algorithms using statistical mechanics. Phys. Rev. Lett, 72(9): 1305–1309, 1994.

    Article  Google Scholar 

  39. M. Rattray and J. L. Shapiro. The dynamics of a genetic algorithm for a simple learning problem. J. Phys. A, 29(23):7451–7473, 1996.

    Article  MathSciNet  MATH  Google Scholar 

  40. L. E. Reichl. A Modern Course in Statistical Physics. University of Texas, Austin, 1980.

    Google Scholar 

  41. C. M. Reidys, C. V. Forst, and P. K. Schuster. Replication and mutation on neutral networks. Bull. Math. Biol, 63(1):57–94, 2001.

    Article  Google Scholar 

  42. R. F Streater. Statistical Dynamics: A Stochastic Approach to Nonequilibrium Thermodynamics. Imperial College Press, London, 1995.

    Book  MATH  Google Scholar 

  43. E. van Nimwegen and J. P. Crutchfield. Optimizing epochal evolutionary search: Population-size dependent theory. Machine Learning, 45(1):77–114, 2001.

    Article  MATH  Google Scholar 

  44. E. van Nimwegen and J. P. Crutchfield. Optimizing epochal evolutionary search: Population-size independent theory. Computer Methods in Applied Mechanics and Engineering, 186:171–194, 2000. Special issue on Evolutionary and Genetic Algorithms in Computational Mechanics and Engineering, D. Goldberg and K. Deb, editors.

    Article  MATH  Google Scholar 

  45. E. van Nimwegen, J. P. Crutchfield, and M. Mitchell. Finite populations induce metastability in evolutionary search. Phys. Lett. A, 229:144–150, 1997.

    Article  MathSciNet  MATH  Google Scholar 

  46. E. van Nimwegen, J. P. Crutchfield, and M. Mitchell. Statistical dynamics of the Royal Road genetic algorithm. Theoretical Computer Science, 229:41–102, 1999. Special issue on Evolutionary Computation, A. Eiben and G. Rudolph, editors.

    Article  MathSciNet  MATH  Google Scholar 

  47. M. D. Vose. Modeling simple genetic algorithms. In L. D. Whitley, editor. Foundations of Genetic Algorithms 2, Morgan Kauffman, San Mateo, CA, 1993.

    Google Scholar 

  48. M. D. Vose and G. E. Liepins. Punctuated equilibria in genetic search. Complex Systems, 5:31–44, 1991.

    MathSciNet  MATH  Google Scholar 

  49. J. Weber. Dynamics of Neutral Evolution. A case study on RNA secondary structures. PhD thesis, Biologisch-Pharmazeutische Fakultät der Friedrich Schiller-Universität Jena, 1996. http://www.tbi.univie.ac.at/papers/PhD_theses.html.

  50. S. Wright. Character change, speciation, and the higher taxa. Evolution, 36:427–43, 1982.

    Article  Google Scholar 

  51. J. M. Yeomans. Statistical Mechanics of Phase Transitions. Clarendon Press, Oxford, 1992.

    Google Scholar 

Download references

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2002 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Crutchfield, J.P., van Nimwegen, E. (2002). The Evolutionary Unfolding of Complexity. In: Landweber, L.F., Winfree, E. (eds) Evolution as Computation. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55606-7_4

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-55606-7_4

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-63081-1

  • Online ISBN: 978-3-642-55606-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics