Towards Understanding the Origin of Genetic Languages

Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from viruses and bacteria to human beings. Advances in genetics and experience in designing computers have taken us to a stage where we can understand the optimisation principles at the root of this system, from the availability of basic building blocks to the execution of tasks. The languages of DNA and proteins are argued to be the optimal solutions to the information processing tasks they carry out. The analysis also suggests simpler predecessors to these languages, and provides fascinating clues about their origin. Obviously, a comprehensive unraveling of the puzzle of life would have a lot to say about what we may design or convert ourselves into.

[1]  Graham Rawlinson,et al.  The Significance of Letter Position in Word Recognition , 2007, IEEE Aerospace and Electronic Systems Magazine.

[2]  R Giegé,et al.  An operational RNA code for amino acids and possible relationship to genetic code. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Apoorva Patel OPTIMAL DATABASE SEARCH: WAVES AND CATALYSIS , 2004 .

[4]  Apoorva D. Patel,et al.  The Triplet Genetic Code had a Doublet Predecessor , 2004, Journal of theoretical biology.

[5]  Future Computation , 2005, Computational Thinking.

[6]  Apoorva Patel Testing quantum dynamics in genetic information processing , 2008, Journal of Genetics.

[7]  F. Collins,et al.  Principles of Biochemistry , 1937, The Indian Medical Gazette.

[8]  E. Schrödinger,et al.  What is life? : the physical aspect of the living cell , 1946 .

[9]  P. Schimmel,et al.  Aminoacyl-tRNA synthetases: potential markers of genetic code development. , 2001, Trends in biochemical sciences.

[10]  Apoorva Patel,et al.  Mathematical Physics and Life , 2002, quant-ph/0202022.

[11]  Apoorva Patel Quantum algorithms and the genetic code , 2001 .

[12]  H. Gutfreund,et al.  Proteins: structures and molecular properties (second edition): T.E. Creighton, Freeman; New York, 1992; x + 507 pages; £22.95. ISBN 0-7167-7030-X , 1993 .

[13]  I. Stamatescu,et al.  Decoherence and the Appearance of a Classical World in Quantum Theory , 1996 .

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

[15]  S. Cusack,et al.  Class I tyrosyl‐tRNA synthetase has a class II mode of cognate tRNA recognition , 2002, The EMBO journal.

[16]  King Vidor,et al.  War and peace = 戦争と平和 , 1865 .

[17]  R. Alicki,et al.  Decoherence and the Appearance of a Classical World in Quantum Theory , 2004 .

[18]  W. P. Russ,et al.  Natural-like function in artificial WW domains , 2005, Nature.

[19]  R. Knight,et al.  Origins of the genetic code: the escaped triplet theory. , 2005, Annual review of biochemistry.

[20]  Apoorva Patel,et al.  Carbon — the first frontier of information processing , 2001, Journal of Biosciences.

[21]  B. Ganem RNA world , 1987, Nature.

[22]  Lov K. Grover A fast quantum mechanical algorithm for database search , 1996, STOC '96.

[23]  ORIGINS OF THE GENETIC CODE: The Escaped , 2005 .

[24]  P. Taylor,et al.  Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA. , 2002, Molecular cell.

[25]  D. A. Harris,et al.  Principles of Biochemistry (2nd edn) , 1993 .

[26]  Sang Joon Kim,et al.  A Mathematical Theory of Communication , 2006 .

[27]  Yoshikazu Nakamura Molecular Mimicry Between Protein and tRNA , 2001, Journal of Molecular Evolution.

[28]  F. Crick Codon--anticodon pairing: the wobble hypothesis. , 1966, Journal of molecular biology.

[29]  F. H. C. CRICK,et al.  Origin of the Genetic Code , 1967, Nature.

[30]  W. P. Russ,et al.  Evolutionary information for specifying a protein fold , 2005, Nature.

[31]  P. Campbell Principles of biochemistry second edition: by A L Lehninger, D L Nelson and M M Cox. pp 1013. Worth, New York. 1993. £30 , 1993 .

[32]  Gary J. Olsen,et al.  Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process , 2000, Microbiology and Molecular Biology Reviews.

[33]  M. Bretscher Origins of the Genetic Code , 1967, Nature.

[34]  L. Mosyak,et al.  The crystal structure of phenylalanyl-tRNA synthetase from thermus thermophilus complexed with cognate tRNAPhe. , 1997, Structure.

[35]  S. Rodin,et al.  Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. , 2006, DNA and cell biology.

[36]  S. Bagby,et al.  Evolution of the Genetic Triplet Code via Two Types of Doublet Codons , 2005, Journal of Molecular Evolution.

[37]  T. Creighton Proteins: Structures and Molecular Properties , 1986 .