Expanding the Grammar of Biology

The Symmetry Principle used to be the only generalization known for Chargaff’s second parity rule. In this chapter, we present the conceptual theoretical framework used to discover four new higher order parity rules.

[1]  Michel Eduardo Beleza Yamagishi,et al.  Chargaff's "Grammar of Biology": New Fractal-like Rules , 2011, ArXiv.

[2]  E. Chargaff.  Structure and function of nucleic acids as cell constituents. , 1951, Federation proceedings.

[3]  A. M. Turing,et al.  Computing Machinery and Intelligence , 1950, The Philosophy of Artificial Intelligence.

[4]  D. Forsdyke,et al.  Deviations from Chargaff's second parity rule correlate with direction of transcription. , 1999, Journal of theoretical biology.

[5]  E. Chargaff.  Preface to a Grammar of Biology , 1971 .

[6]  Robert M. Waterhouse,et al.  Genomic insights into the Ixodes scapularis tick vector of Lyme disease , 2016, Nature Communications.

[7]  V. V. Zinoviev,et al.  Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases. , 2004, Nucleic acids research.

[8]  M. Yamagishi,et al.  Nucleotide Frequencies in Human Genome and Fibonacci Numbers , 2006, Bulletin of mathematical biology.

[9]  V. Prabhu.  Symmetry observations in long nucleotide sequences. , 1993, Nucleic acids research.

[10]  Maclyn McCarty,et al.  STUDIES ON THE CHEMICAL NATURE OF THE SUBSTANCE INDUCING TRANSFORMATION OF PNEUMOCOCCAL TYPES , 1944, The Journal of experimental medicine.

[11]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[12]  Morris Kline,et al.  Mathematics for the Nonmathematician , 1985 .

[13]  Hong-Da Chen,et al.  Inverse Symmetry in Complete Genomes and Whole-Genome Inverse Duplication , 2009, PloS one.

[14]  Donald R. Forsdyke,et al.  Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations , 2004, Applied bioinformatics.

[15]  Bernard J. F. Lonergan.  Insight: A Study of Human Understanding , 1970 .

[16]  E. Chargaff.  Heraclitean Fire: Sketches from a Life Before Nature , 1978 .

[17]  Simone Wannemaker,et al.  The Double Helix A Personal Account Of The Discovery Of The Structure Of Dna , 2016 .

[18]  Jordi Vallverdú,et al.  Can machines talk? Comparison of Eliza with modern dialogue systems , 2016, Comput. Hum. Behav..

[19]  F. Crick,et al.  Molecular structure of nucleic acids , 2004, JAMA.

[20]  Pierre Baldi,et al.  Why are complementary DNA strands symmetric? , 2002, Bioinform..

[21]  A. Jamie Cuticchia,et al.  Compositional symmetries in complete genomes , 2001, Bioinform..

[22]  Jennifer A. Doudna,et al.  Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.

[23]  D. Forsdyke,et al.  Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species , 1995, Journal of Molecular Evolution.

[24]  E. Chargaff,et al.  Seapration of B. subtilis DNA into complementary strands. II. Template functions and composition as determined by transcription with RNA polymerase. , 1968, Proceedings of the National Academy of Sciences of the United States of America.

[25]  David Mitchell,et al.  A test of Chargaff's second rule. , 2006, Biochemical and biophysical research communications.

[26]  E. Chargaff.  Chemical specificity of nucleic acids and mechanism of their enzymatic degradation , 1950, Experientia.

[27]  E. Chargaff.  How Genetics Got a Chemical Education , 1979, Annals of the New York Academy of Sciences.