Skip to main content

Evolution of Genetic Organization in Digital Organisms

  • Conference paper
Evolution as Computation

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

Abstract

We examine the evolution of expression patterns and the organization of genetic information in populations of self-replicating digital organisms. Seeding the experiments with a linearly expressed ancestor, we witness the development of complex, parallel secondary expression patterns. Using principles from information theory, we demonstrate an evolutionary pressure towards overlapping expressions causing variation (and hence further evolution) to sharply drop. Finally, we compare the overlapping sections of dominant genomes to those portions which are singly expressed and observe a significant difference in the entropy of their encoding.

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. Adami, C. (1995) Learning and complexity in genetic auto-adaptive systems, Physica D 80, 154.

    Google Scholar 

  2. Adami, C. (1998) Introduction to Artificial Life, Telos Springer-Verlag, New York.

    Book  MATH  Google Scholar 

  3. Adami, C., Collier, T.C., and Ofria, C. (1999) Robustness and evolvability of computer languages, to be published.

    Google Scholar 

  4. Basharin, G. P. (1959) On a statistical estimate of the entropy of a sequence of independent random variables. Theory Probability Appl. 4, 333.

    Article  MathSciNet  Google Scholar 

  5. Elena, S. F., Cooper, V. S., and Lenski, R. E. (1996) Punctuated evolution caused by selection of rare beneficial mutations. Science 272, 1802.

    Article  Google Scholar 

  6. Keese, P. and Gibbs, A. (1992) Origins of genes: “Big bang” or continuous creation? Proc. Natl. Acad. Sci. 89, 9489–9493.

    Article  Google Scholar 

  7. Miyata, T. and Yasunaga, T. (1978) Evolution of overlapping genes. Nature 272, 532.

    Article  Google Scholar 

  8. Mizokami, M., Orito, E., Ohba, K., Lau, J. Y. N., and Gojobori, T. (1997) Constrained evolution with respect to gene overlap of Hepatitis B virus, J. Mol. Evol. 44 (Suppl. 1), S83–S90.

    Article  Google Scholar 

  9. Normark, S., Bergström, S., Edlund, T., Grundström, T., Jaurin, B., Lindberg, F. P., and Olsson, O. (1983) Overlapping genes, Ann. Rev. Gen. 17, 499–525.

    Article  Google Scholar 

  10. Ofria, C., Brown, C. T., and Adami, C. (1998) Avida User’s Manual, in Introduction to Artificial Life, Telos Springer-Verlag, New York.

    Google Scholar 

  11. Ofria, C., Collier, T. C., Hsu, G., and Adami, C. (1999) Evolution of differentiated expression patterns in digital organisms, KRL preprint MAP-250 (February 1999).

    Google Scholar 

  12. Ray, T. S. (1992) An approach to the synthesis of life, in Proc. of Artificial Life II, C. G. Langton, C. Taylor, J. D. Farmer, and S. Rasmussen, Eds., Addison-Wesley, Redwood City, p. 371.

    Google Scholar 

  13. Ray, T. S. and Hart, J. (1998) Evolution of differentiated multi-threaded digital organisms, in Proc. of Artificial Life VI, C. Adami, R. K. Belew, H. Kitano, and C. E. Taylor, Eds., MIT Press, Cambridge, MA, p. 295.

    Google Scholar 

  14. Samuel, C. E. (1989) Polycistronic animal virus messenger RNAs, Prog. Nucleic Acids Res. Mol. Biol. 37, 127–153.

    Article  Google Scholar 

  15. Thearling, K. and Ray, T. S. (1994) Evolving multi-cellular artificial life, in Proc. of Artificial Life IV, R. A. Brooks and P. Maes, Eds., MIT Press, Cambridge, MA, p. 283.

    Google Scholar 

  16. Watson, J. D., Hopkins, N. H., Roberts, J. W., Steitz, J. A., and Weiner, A. M. (1987) Molecular Biology of the Gene, Fourth Edn., Benjamin Cummings, Menlo Park, CA, p. 457.

    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

Ofria, C., Adami, C. (2002). Evolution of Genetic Organization in Digital Organisms. 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_15

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-55606-7_15

  • 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