skip to main content
10.1145/1464122.1464131acmotherconferencesArticle/Chapter ViewAbstractPublication PagesafipsConference Proceedingsconference-collections
research-article
Free Access

Simulation of biological cells by systems composed of string-processing finite automata

Published:21 April 1964Publication History

ABSTRACT

In the last few years enormous progress has been made in clarifying the operational mechanisms of living cells. It has been established beyond reasonable doubt that all aspects of cell activity are controlled by sequences of elementary genetic units. A comma-free triplet coding in the four-letter alphabet of DNA is transcribed on RNA and causes the formation of sequences of amino acids, which make up polypeptides and proteins. Various theories of transcription control for such systems are now under study. Recently, synthetic nucleic acid (RNA) chains have been fed into the cell machinery, thus demonstrating that protein synthesis can be controlled artificially. Numerous finer details of the problem could be mentioned (see Crick, Nirenberg, Rich, Waddington, and Anfinsen) but shall not be considered in this report.

References

  1. Anfinsen, C. B. In The Molecular Basis of Evolution. John Wiley Science Editions, New York, 1963. p. 115 et seq.Google ScholarGoogle Scholar
  2. Arbib, M. "Turing Machines, Finite Automata and Neural Nets." J. Assoc. Comp. Mach. 8 (4):467--475, 1961. Google ScholarGoogle ScholarDigital LibraryDigital Library
  3. Blum, H. F. "On the Origin and Evolution of Living Machines." Amer. Sci. 49:474--501, 1961.Google ScholarGoogle Scholar
  4. Burks, A. W. "Toward a Theory of Aumata Based on More Realistic Primitive Elements." Proc. IFIP Congress, Munich, Germany, 1962. North Holland Publishing Company, Amsterdam, 1963. pp. 379--385.Google ScholarGoogle Scholar
  5. Burks, A. W. "The Logic of Fixed and Growing Automata." In Proc. Int. Symp. Switching Theory. Part I. Harvard Univ. Press, Cambridge, Mass., 1959. pp. 147--188.Google ScholarGoogle Scholar
  6. Cannonito, F. B. "The Godel Incompleteness Theorem and Intelligent Machines." In Proc. AFIPS Spring Joint Comp. Conf., San Francisco, Calif. May 1962. pp. 71--77. Google ScholarGoogle ScholarDigital LibraryDigital Library
  7. Chance, B., et al. "Metabolic Control Mechanisms. Part V. Solution for the Equations Representing Interaction Between Glycolysis and Respiration in Ascites Tumor Cells." J. Biol. Chem. 235:2425--2439, 1960.Google ScholarGoogle Scholar
  8. Coffin, R. W., H. E. Goheen, and W. R. Stahl. "Simulation of a Turing Machine on a Digital Computer." Proc. AFIPS Western Joint Computer Conference, Las Vegas, Nev., November 1963. Google ScholarGoogle ScholarDigital LibraryDigital Library
  9. Crick, F. H. C. "On the Genetic Code." Science 139(3554):461--464, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  10. Davis, M. D. Computability and Unsolvability. McGraw-Hill, New York, 1958.Google ScholarGoogle Scholar
  11. Eden, M. "A Probabilistic Model of Morphogenesis." In Symposium on Information Theory in Biology. H. P. Yockey, R. L. Platsman, H. Quastler, eds. Pergamon Press, New York, 1958. pp. 359--370.Google ScholarGoogle Scholar
  12. Frank, G. M. "Self-Regulation of Cellular Processes." In Biological Cybernetics. N. M. Sisakayan and A. I. Berg, eds. Acad. Sci. USSR, Moscow, 1962. (In Russian). Available as JPRS 19637. pp. 40--55.Google ScholarGoogle Scholar
  13. Garfinkel, D. "Computer Simulation of Steady-State Glutamate Metabolism in Rat Brain." J. Theoret. Biol. 3:412--422, 1962.Google ScholarGoogle ScholarCross RefCross Ref
  14. Gill, A. "State-Identification Experiments in Finite Automata." Information and Control. 4:132--154, 1961.Google ScholarGoogle ScholarCross RefCross Ref
  15. Ginsburg, S. "On the Length of the Smallest Uniform Experiment Which Distinguishes the Terminal States of a Machine." J. Assoc. Comp. Mach. 5:266--280, 1958. Google ScholarGoogle ScholarDigital LibraryDigital Library
  16. Glushkov, V. M. "Abstract Theory of Automata." Uspekhi Mat. Nauk, 16(5):3--62, 1961. (In Russian).Google ScholarGoogle Scholar
  17. Hennie, F. C. "Iterative Arrays of Logical Circuits." MIT Press Research Monographs, Cambridge, Mass. John Wiley, New York, 1961.Google ScholarGoogle Scholar
  18. Hommes, F. A., and F. W. Zilliken. "Induction of Cell Differentiation: III. A Quantitative Approach in the Analysis of Induction." Bull. Math. Biophys. 24:71--80, 1962.Google ScholarGoogle ScholarCross RefCross Ref
  19. Isaacs, A., H. G. Klemperer, and G. Hitchcock. "Studies on the Mechanism of Action of Interferon." Virology 13:191--199, 1961.Google ScholarGoogle ScholarCross RefCross Ref
  20. Jacob, F., and J. Monod. "Genetic Regulatory Mechanisms in the Synthesis of Protein." J. Molec. Biol. 3:318--356, 1961.Google ScholarGoogle ScholarCross RefCross Ref
  21. Labouesse, B., B. H. Havsteen, and G. P. Hess. "Conformational Changes in Enzyme Catalysis." Proc. Nat. Acad. Sci. 48(12):2137--2145, 1962.Google ScholarGoogle ScholarCross RefCross Ref
  22. Lofgren, L. "Kinematic and Tesselation Models of Self-Repair." In Biological Prototypes and Synthetic Systems. E. E. Bernard and M. R. Kare, eds. Plenum Press, New York, 1962.Google ScholarGoogle Scholar
  23. Lyapunov, A. A. "Some Questions on the Teaching of Automata." In Principles of the Design of Self-Learning Systems. Kiev, USSR. Available as JPRS 18181, 1963. pp. 180--185.Google ScholarGoogle Scholar
  24. Markov, A. A. "The Theory of Algorithms." Amer. Math. Soc. Translation Ser. 2. 15:1--14, 1960.Google ScholarGoogle Scholar
  25. McCulloch, W. S., and W. Pitts. "A Logical Calculus of the Ideas Imminânt in Nervous Activity." Bull. Math. Biophys. 5:115--133, 1943.Google ScholarGoogle ScholarCross RefCross Ref
  26. McNaughton, R. "The Theory of Autommata---A Survey". Adv. in Computers. 2:379--421, Academic Press, New York, 1961.Google ScholarGoogle Scholar
  27. Medvedev, Zh. A. "Errors in the Reproduction of Nucleic Acids and Proteins, and Their Biological Significance." Problems Kibernetikii No. 9. A. A. Lyapunov, ed. Gos. Izd. Fiz-Mat. Lit., Moscow, 1963, pp. 241--264. (In Russian).Google ScholarGoogle Scholar
  28. Monod, J., J. P. Changeux, and F. Jacob. "Allosteric Proteins and Cellular Control Systems." J. Molec. Biol. 6:306--329, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  29. Moore, E. F. "Machine Models of Self-Reporduction." In Mathematical Problems in the Biological Sciences. Sympos. No. 14 of Amer. Math. Soc., Providence, R.I., 1961. pp. 17--33.Google ScholarGoogle Scholar
  30. Myhill, J. "Linear Bounded Automata." WADD Tech. Note 60--165. Wright Air Development Division, Wright Patterson Air Force Base, Ohio, 1960.Google ScholarGoogle Scholar
  31. Nirenberg, N. W. "The Genetic Code, Part II." Sci. Amer. 208(3):80--94, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  32. Pardee, A. B. "Biochemistry: Sterile or Virgin for Mathematicians." In Mathematical Problems in the Biological Sciences. Sympos. No. 14 of Amer. Math. Soc., Providence, R.I., 1961. pp. 69--82.Google ScholarGoogle Scholar
  33. Pask, G. "The Simulation of Learning and Decision-Making Behavior." In Aspects of the Theory of Artificial Intelligence. C. A. Muses, ed. Plenum Press, New York, 1962. pp. 165--210.Google ScholarGoogle Scholar
  34. Pasynskiy, A. G. "Some Problems of Biochemical Cybernetics." Vest. Acad. Nauk USSR. 32:25--31, 1962. (In Russian).Google ScholarGoogle Scholar
  35. Pattee, H. H. "On the Origin of Macromolecular Sequences." Biophys. J. 1 (8):683--710, 1961.Google ScholarGoogle ScholarCross RefCross Ref
  36. Rabin, M. O., and D. Scott. "Finite Automata and Their Decision Problems." IBM J. Res. and Develop. 5:114--125, 1959.Google ScholarGoogle ScholarDigital LibraryDigital Library
  37. Rashevsky, N. "Mathematical Foundations of General Biology." Ann. N.Y. Acad. Sci. 96:1105--1116, 1962.Google ScholarGoogle Scholar
  38. Rice, W. E., and R. M. Bock. "The Problem of Sequence Determination in Transfer RNA." J. Theoret. Biol. 4(3):260--267, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  39. Rich, A. "The Transfer of Information Between the Nucleic Acids." In Synthesis of Molecular and Cellular Structures. D. Rudnick, ed. Ronald Press, Inc., New York, 1961. pp. 3--11.Google ScholarGoogle Scholar
  40. Rosen, R. "Digital Computers and the Problems of Cellular Regulation." Report read at 1963 Denver Conference of the Association for Computing Machinery, August 27--30, 1963.Google ScholarGoogle Scholar
  41. Schutzenberger, M. P. "On the Definition of a Family of Automata." Inform. and Control. 4:245--270, 1961.Google ScholarGoogle ScholarCross RefCross Ref
  42. Sorkin, Yu. I. "Algorithmic Solvability of the Problem of Isomorphism of Automata." Doklady Nauk USSR. 137(4):804--806, 1961. (In Russian).Google ScholarGoogle Scholar
  43. Stahl, W. R. "Solvable and Unsolvable Problems for an Algorithmic Model of a Cell." (Submitted for publication).Google ScholarGoogle Scholar
  44. Stahl, W. R., R. W. Coffin, and H. E. Goheen. "The Turing Machine as a Research Tool for Algorithmic Simulation." (Submitted for publication).Google ScholarGoogle Scholar
  45. Stahl, W. R., and H. E. Goheen. "Molecular Algorithms." J. Theoret. Biol. 5:266--287, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  46. Stahl, W. R., M. C. Waters, and R. W. Coffin. "Pattern Recognition Algorithms Implemented as Turing Programs." (Submitted for publication).Google ScholarGoogle Scholar
  47. Sugita, M. "Functional Analysis of Chemical Systems in Vivo Using a Logical Circuit Equivalent. II. The Idea of a Molecular Automaton." J. Theoret. Biol. 4(2):179--192, 1963.Google ScholarGoogle ScholarCross RefCross Ref
  48. Tsetlin, M. L. "On the Behavior of Finite Automata in Random Media." Avtomat. i Telemekh. 22:1345--1354, 1961. (In Russian).Google ScholarGoogle Scholar
  49. Trachtenbrot, B. A. "Algorithms and the Machine Solution of Problems." (In Russian). Available under the title Algorithms and Automatic Computing Machines. D. C. Heath and Co., Boston, Mass., 1963.Google ScholarGoogle Scholar
  50. Turing, A. M. "On Computable Numbers, with an Application to the Entscheidungs-problem." Proc. London Math. Soc. Ser. 2. 42:23--265, 1937.Google ScholarGoogle Scholar
  51. Turing, A. M. "The Chemical Basis of Morphogenesis". Phil. Trans. Royal Soc., Ser. B. 237:37--72, 1954.Google ScholarGoogle Scholar
  52. Turing, A. M. "Solvable and Unsolvable Problems." Science News (London). 31:7--23, 1954.Google ScholarGoogle Scholar
  53. Turing, A. M. "Can a Machine Think?" Reprinted in The World of Mathematics. J. R. Newman, ed. Simon and Schuster, New York, 1956. pp. 2099--2123.Google ScholarGoogle Scholar
  54. Ulam, S. "On Some Mathematical Problems Connected with Patterns of Growth of Figures." In Mathematical Problems in the Biological Sciences. Sympos. No. 14 of the Amer. Math. Soc., Providence, R.I., 1961. pp. 215--224.Google ScholarGoogle Scholar
  55. von Neumann, J. "The General and Logical Theory of Automata." In Cerebral Mechanisms and Behavior. L. A. Jeffress, ed. John Wiley, New York, 1951. pp. 1--41.Google ScholarGoogle Scholar
  56. von Neumann, J. In The Computer and the Brain. Yale University Press, New Haven, Conn., 1958. pp. 69--73. Google ScholarGoogle ScholarDigital LibraryDigital Library
  57. Waddington, C. H. In New Patterns in Genetics and Development. Columbia University Press, New York, 1962.Google ScholarGoogle ScholarCross RefCross Ref
  58. Wang, H. "A Variant to Turing's Theory of Computing Machines." J. Assoc. Comp. Mach. 4(1):63--92, 1961. Google ScholarGoogle ScholarDigital LibraryDigital Library
  59. Yovits, M. C., and S. Cameron. Self-Organizing Systems. Pergamon Press, New York, 1960.Google ScholarGoogle Scholar
  1. Simulation of biological cells by systems composed of string-processing finite automata

    Recommendations

    Comments

    Login options

    Check if you have access through your login credentials or your institution to get full access on this article.

    Sign in
    • Published in

      cover image ACM Other conferences
      AFIPS '64 (Spring): Proceedings of the April 21-23, 1964, spring joint computer conference
      April 1964
      636 pages
      ISBN:9781450378901
      DOI:10.1145/1464122

      Copyright © 1964 ACM

      Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

      Publisher

      Association for Computing Machinery

      New York, NY, United States

      Publication History

      • Published: 21 April 1964

      Permissions

      Request permissions about this article.

      Request Permissions

      Check for updates

      Qualifiers

      • research-article

    PDF Format

    View or Download as a PDF file.

    PDF

    eReader

    View online with eReader.

    eReader