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

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.

[1]  J. Changeux,et al.  Allosteric proteins and cellular control systems. , 1963, Journal of molecular biology.

[2]  R. Bock,et al.  The problem of sequence determination in transfer RNA. , 1963, Journal of theoretical biology.

[3]  Blum Hf On the origin and evolution of living machines. , 1961 .

[4]  K. Hirschhorn,et al.  New Patterns in Genetics and Development , 1963 .

[5]  M. Nirenberg The genetic code. II. , 1963, Scientific American.

[6]  Lars Löfgren,et al.  Kinematic and Tessellation Models Of Self-Repair , 1962 .

[7]  A. M. Turing,et al.  Solvable and Unsolvable Problems , 1954 .

[8]  V. Glushkov THE ABSTRACT THEORY OF AUTOMATA , 1961 .

[9]  Christian B. Antinsen,et al.  The Molecular Basis of Evolution , 1960 .

[10]  Arthur Gill,et al.  Sate-Identification Experiments in Finite Automata , 1961, Inf. Control..

[11]  N RASHEVSKY Mathematical foundations of general biology. , 1962, Annals of the New York Academy of Sciences.

[12]  H. Pattee On the origin of macromolecular sequences. , 1961, Biophysical Journal.

[13]  Hao Wang,et al.  A Variant to Turing's Theory of Computing Machines , 1957, JACM.

[14]  David Garfinkel,et al.  Computer simulation of steady-state glutamate metabolism in rat brain , 1962 .

[15]  Frank B. Cannonito The Gödel incompleteness theorem and intelligent machines , 1962, AIEE-IRE '62 (Spring).

[16]  C. H. Waddington,et al.  New patterns in genetics and development , 1964 .

[17]  Seymour Ginsburg,et al.  On the Length of the Smallest Uniform Experiment which Distinguishes the Terminal States of a Machine , 1958, JACM.

[18]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[19]  M. L. Tsetlin On the Behavior of Finite Automata in Random Media , 1961 .

[20]  Edmond P. Odescalchi Can a Machine Think , 1958 .

[21]  C. Anfinsen The Molecular Basis of Evolution , 1959, The Yale Journal of Biology and Medicine.

[22]  Michael A. Arbib Turing Machines, Finite Automata and Neural Nets , 1961, JACM.

[23]  M Sugita,et al.  Functional analysis of chemical systems in vivo using a logical circuit equivalent. II. The idea of a molecular automation. , 1963, Journal of theoretical biology.

[24]  John von Neumann,et al.  The Computer and the Brain , 1960 .

[25]  B. Hess,et al.  Metabolic control mechanisms. 5. A solution for the equations representing interaction between glycolysis and respiration in ascites tumor cells. , 1960, The Journal of biological chemistry.

[26]  H. Klemperer,et al.  Studies on the mechanism of action of interferon. , 1961, Virology.

[27]  E. F. Moore Machine Models of Self-Reproduction , 1962 .

[28]  H. Blum On the origin and evolution of living machines. , 1961, American scientist.

[29]  F. Hommes,et al.  Induction of cell differentiation: III. A quantitative approach in the analysis of induction , 1962 .

[30]  A. Turing On Computable Numbers, with an Application to the Entscheidungsproblem. , 1937 .

[31]  Arthur W. Burks,et al.  Toward a Theory of Automata Based on more Realistic Primitive Elements , 1962, IFIP Congress.

[32]  W R Stahl,et al.  Molecular algorithms. , 1963, Journal of theoretical biology.

[33]  J. Monod,et al.  Genetic regulatory mechanisms in the synthesis of proteins. , 1961, Journal of molecular biology.

[34]  Dana S. Scott,et al.  Finite Automata and Their Decision Problems , 1959, IBM J. Res. Dev..

[35]  Gordon Pask,et al.  The Simulation of Learning and Decision-Making Behavior , 1962 .

[36]  J. Mullen Iterative arrays of logical circuits , 1962 .

[37]  S. Baron,et al.  STUDIES ON THE MECHANISM OF ACTION OF INTERFERON. , 1963, Virology.

[38]  Marcel Paul Schützenberger,et al.  On the Definition of a Family of Automata , 1961, Inf. Control..

[39]  Richard Bellman,et al.  Mathematical Problems in the Biological Sciences , 1962 .

[40]  Martin D. Davis,et al.  Computability and Unsolvability , 1959, McGraw-Hill Series in Information Processing and Computers.

[41]  Robert W. Coffin,et al.  Simulation of a Turing machine on a digital computer , 1963, AFIPS '63 (Fall).