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Bulletin of Mathematical Biology

, Volume 52, Issue 3, pp 335–348 | Cite as

The cellular computer DNA: Program or data

  • Henri Atlan
  • Moshe Koppel
Article

Abstract

The classical metaphor of the genetic program written in the DNA nucleotidic sequences is reconsidered. Recent works on algorithmic complexity and logical properties of computer programs and data are used to question the explanatory value of that metaphor. Structural properties of strings are looked for which would be necessary to apply to DNA sequences if the metaphor is to be taken literally. The notion of sophistication is used to quantify meaningful complexity and to distinguish it from classical computational complexity. In this context, the distinction between program and data becomes relevant and an alternative metaphor of DNA as data to a parallel computing network embedded in the global geometrical and biochemical structure of the cell is discussed. An intermediate picture of an evolving network emerges as the most likely where the output of the cellular computing network can produce, at a different time scale, changes in the structure of the network itself by means of changes in the DNA activity patterns.

Keywords

Genetic Program Metaphor Binary String Input String Cellular Machinery 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Literature

  1. Agur, Z. and M. Kerzberg. 1987. The emergence of phenotypic novelties through progressive genetic change.Am. Natur. 129, 862–875.CrossRefGoogle Scholar
  2. Atlan, H. 1987. Self-creation of meaning.Physica Scripta 36, 563–576.Google Scholar
  3. Atlan, H., E. Ben-Ezra, F. Fogelman-Soulie, D. Pellegrin and G. Weisbuch. 1986. Emergence of classification procedures in automata networks as a model for functional self-organization.J. theor. Biol. 120, 371–380.MathSciNetCrossRefGoogle Scholar
  4. Bennett, C. 1989. On the logical “depth” of sequences and their reducibilities to incompressible sequences, in press.Google Scholar
  5. Blattner, F. R. 1983. Biological frontiers.Science 222, 4625, 719–720.Google Scholar
  6. Campos-Ortega, J. A. 1985. Genetics of early neurogenesis inDrosophila Melanogaster.Trends Neurosci. 8, 245–250.CrossRefGoogle Scholar
  7. Chaitin, G. J. 1975. A theory of program size formally identical to information theory.JACM 22, 329–340.zbMATHMathSciNetCrossRefGoogle Scholar
  8. Chaitin, G. J. 1979. Towards a mathematical definition of life. InThe Maximum Entropy Formalism, R. Levine and M. Tribus (Eds), pp. 479–500. Cambridge, MA: MIT Press.Google Scholar
  9. Cover, T. 1985. Kolmogoroff complexity, data compressing and inference. InThe Impact of Processing Techniques on Communications, Skwyrzynski (Ed.). The Hague. Martinus Nijhoff.Google Scholar
  10. deDuve, C. 1988. The second genetic code.Nature 333, 117.CrossRefGoogle Scholar
  11. Gehring, W. J. 1985. The molecular basis of development.Scient. Am. 140, 153–162.Google Scholar
  12. Goodwin, B. C. 1985. What are the causes of morphogenesis?Bio Essays 3, 32–36.Google Scholar
  13. Goodwin, B. C. 1988. Morphogenesis and heredity. InEvolutionary Processes and Metaphors, M.-W. Ho and S. W. Fox (Eds), pp. 145–162. New York: Wiley.Google Scholar
  14. Holliday, R. 1987. The inheritance of epigenetic defects.Science 238, 163–170.Google Scholar
  15. Hou, Y. M. and P. Schimmel. 1988. A simple structural feature is a major determinant of the identity of a transfer-RNA.Nature 333, 140.CrossRefGoogle Scholar
  16. Jacob, F. 1970.La Logique de Vivant. Paris: Gallimard.Google Scholar
  17. Kaufman, S. 1969. Metabolic stability and epigenesis in randomly constructed genetic nets.J. theor. Biol. 22, 427–467.MathSciNetGoogle Scholar
  18. Kolmogoroff, A. N. 1965. Three approaches to the quantitative definition of information.Prob. Inform. Transmission 1, 1–7.Google Scholar
  19. Koppel, M. 1987. Structure. InThe Universal Turing Machine: A Half-Century Survey, R. Herken (Ed.), pp. 435–452. Oxford University Press.Google Scholar
  20. Koppel, M. and H. Atlan. 1989. Program-length complexity, sophistication and induction.Inform. Sci., in press.Google Scholar
  21. Lwoff, A. 1962.Biological Order. Cambridge, MA: MIT Press.Google Scholar
  22. Milgram, M. and H. Atlan. 1983. Probabilistic automata as a model for epigenesis of cellular networks.J. theor. Biol. 103, 523–547.MathSciNetCrossRefGoogle Scholar
  23. National Research Council Report. 1988.Mapping and Sequencing the Human Genome. Washington, DC: National Academy Press.Google Scholar
  24. Philipson, L. and J. Tooze. 1987. The human genome project.Biofutur 58, 94–101.Google Scholar
  25. Pittendrigh, C. S. 1858. Adaptation, natural selection and behavior. InBehavior and Evolution. A. Roe and G. G. Simpson (Eds), pp. 390–416. Yale University Press.Google Scholar
  26. Rumelhart, D. E., J. L. McClelland (PDP Research Group). 1986.Parallel Distributed Processing, Vol. 1. Cambridge, MA: MIT Press.Google Scholar
  27. Shannon, C. 1948. A mathematical theory of communication.Bell. Systems J. 27, 379–423; 623–656.MathSciNetGoogle Scholar
  28. Subtelny, S. and I. R. Konigsberg. 1979.Determinants of Spatial Organization. New York: Academic Press.Google Scholar
  29. Thomas, R. 1973. Boolean formalization of genetic control circuits.J. theor. Biol. 42, 563–585.CrossRefGoogle Scholar
  30. Turing, A. M. 1936. On computable numbers, with an application for the Entscheidungsproblem.Proc. Lond. math. Soc. 42, 230–265.zbMATHGoogle Scholar
  31. Wada, A. 1987. Automated high-speed DNA sequencing.Nature 325, 771–772.CrossRefGoogle Scholar
  32. Weisbuch, G. 1985. Modelling natural systems with networks of automata: the search for generic behaviors. InDynamical Systems and Cellular Automata, J. Demongeot, E. Goles and M. Tchuente (Eds), pp. 293–304. New York: Academic Press.Google Scholar

Copyright information

© Society for Mathematical Biology 1990

Authors and Affiliations

  • Henri Atlan
    • 1
  • Moshe Koppel
    • 2
  1. 1.Dept of BiophysicsHadassah Medical CenterJerusalemIsrael
  2. 2.Dept of MathematicsBar-Ilan UniversityRamat GanIsrael

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