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An Outline of Informational Genetics

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An Outline of Informational Genetics Cover

 

Synopses & Reviews

Publisher Comments:

Heredity performs literal communication of immensely long genomes through immensely long time intervals. Genomes nevertheless incur sporadic errors referred to as mutations which have significant and often dramatic effects, after a time interval as short as a human life. How can faithfulness at a very large timescale and unfaithfulness at a very short one be conciliated? The engineering problem of literal communication has been completely solved during the second half of the XX-th century. Originating in 1948 from Claude Shannon's seminal work, information theory provided means to measure information quantities and proved that communication is possible through an unreliable channel (by means left unspecified) up to a sharp limit referred to as its capacity, beyond which communication becomes impossible. The quest for engineering means of reliable communication, named error-correcting codes, did not succeed in closely approaching capacity until 1993 when Claude Berrou and Alain Glavieux invented turbocodes. By now, the electronic devices which invaded our daily lives (e.g., CD, DVD, mobile phone, digital television) could not work without highly efficient error-correcting codes. Reliable communication through unreliable channels up to the limit of what is theoretically possible has become a practical reality: an outstanding achievement, however little publicized. As an engineering problem that nature solved aeons ago, heredity is relevant to information theory. The capacity of DNA is easily shown to vanish exponentially fast, which entails that error-correcting codes must be used to regenerate genomes so as to faithfully transmit the hereditary message. Moreover, assuming that such codes exist explains basic and conspicuous features of the living world, e.g., the existence of discrete species and their hierarchical taxonomy, the necessity of successive generations and even the trend of evolution towards increasingly complex beings. Providing geneticists with an introduction to information theory and error-correcting codes as necessary tools of hereditary communication is the primary goal of this book. Some biological consequences of their use are also discussed, and guesses about hypothesized genomic codes are presented. Another goal is prompting communication engineers to get interested in genetics and biology, thereby broadening their horizon far beyond the technological field, and learning from the most outstanding engineer: Nature.

Table of Contents: Foreword / Introduction / A Brief Overview of Molecular Genetics / An Overview of Information Theory / More on Molecular Genetics / More on Information Theory / An Outline of Error-Correcting Codes / DNA is an Ephemeral Memory / A Toy Living World / Subsidiary Hypothesis, Nested System / Soft Codes / Biological Reality Conforms to the Hypotheses / Identification of Genomic Codes / Conclusion and Perspectives

Table of Contents

An informal overview — Genetics and communication engineering — Seeing heredity as a communication process — Regeneration versus replication — A brief overview of molecular genetics — DNA structure and replication — DNA directs the construction of a phenotype — From DNA to protein, and from a genome to a phenotype — Genomes are very long — An overview of information theory — Shannon's paradigm — Quantitative measurement of information — Coding processes — A brief introduction to error-correcting codes — Variant of Shannon's paradigm intended to genetics — Computing an upper bound of DNA capacity — Facts of genetics and information theory — More on molecular genetics — Molecular memories : DNA and RNA — Place and function of DNA in the cell — Genome and phenotype — DNA recombination and crossing over — More on information theory — Alphabet, sources, and entropy — About source coding — About channel coding — Short introduction to algorithmic information theory — Information and its relationship to semantics — An outline of error-correcting codes --Communicating a message through a channel — Repetition as a means of error correction — Encoding a full message — Error-correcting codes within information theory — Convolutional codes — Turbocodes — Historical outlook — Necessity of genomic error correcting codes and its consequences — DNA is an ephemeral memory — Probability of symbol erasure or substitution — Capacity computations — Estimating the error frequency before correction — Paradoxically, a permanent memory is ephemeral — A toy living world — A simple model — Computing statistical quantities — The initial memory content is progressively forgotten — Introducing natural selection in the toy living world — Example of a toy living world using a very simple code — Evolution in the toy living world : phyletic graphs — Subsidiary hypothesis, nested system — Description of a nested system — Rate and length of component codes — Distances in the nested system — Consequences of the subsidiary hypothesis — Soft codes — Introducing codes defined by a set of constraints — Genomic error-correcting codes as "soft codes" — Biological soft codes form nested systems — Further comments about genomic soft codes — Is a eukaryotic gene a systematic codeword? — Biological reality conforms to the hypotheses — Genomes are very redundant — Living beings belong to discrete species — Necessity of successive regenerations — Saltationism in evolution — Trend of evolution towards complexity — Evolution is contingent — Relationship between genomes and phenotypes — Identification of genomic codes — Necessity of identifying genomic codes — Identifying error-correction means — Genome distinction and conservation — Difficulties with sexual reproduction — Conclusion and perspectives.

Product Details

ISBN:
9781122915205
Publisher:
Morgan & Claypool Publishers
Subject:
main_subject
Author:
Battail, Gerard
Subject:
all_subjects
Publication Date:
20081115
Binding:
ELECTRONIC
Language:
English
Pages:
187

Related Subjects

Computers and Internet » Computers Reference » Bioinformatics
Computers and Internet » Computers Reference » General
Engineering » Communications » Information Theory
Engineering » Communications » Telephony
Reference » Science Reference » Technology
Science and Mathematics » Biology » Molecular

An Outline of Informational Genetics
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Product details 187 pages Morgan & Claypool - English 9781122915205 Reviews:
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