TY  - BOOK
AU  - Sanford,John C.
AU  - Marks Ii,Robert J.
AU  - Behe,Michael J.
AU  - Dembski,William A.
AU  - Gordon,Bruce L.
TI  - Biological Information
SN  - 9789814508728
PY  - 2013///
CY  - Singapore
PB  - World Scientific Publishing Company
KW  - Electronic books
N1  - Intro -- Contents -- Title Page -- Acknowledgements -- General Introduction -- References and Notes -- Section One Information Theory &amp -- Biology: Introductory Comments Robert J. Marks II -- 1.1.1 Biological Information - What is It? Werner Gitt, Robert Compton and Jorge Fernandez -- Introduction -- Defining Subsets of Information -- Distinguishing Attributes of Information -- Code plus syntax -- Meaning -- Expected Action -- Intended Purpose -- The Definition of Universal Information -- The Nature of Universal Information -- Does Biological Life Contain Universal Information? -- Code plus Syntax -- Abstract Meaning -- The Expected Acti on -- The Intended Purpose -- UI Senders, Transmitters and Receivers -- The Existence, Validity and Significance of Universal Information -- Conclusion -- References -- 1.1.2 A General Theory of Information Cost Incurred by Successful Search William A. Dembski, Winston Ewert and Robert J. Marks II -- 1. The Search Matrix -- Example 1.1: Uniform random sampling with perfect knowledge -- Example 1.2: Uniform random sampling with zero knowledge -- Example 1.3: Uniform random sampling with partial knowledge -- Example 1.4: Smooth gradient fitness with single peak -- 2. General Targeted Search -- 3. Search Examples -- Example 3.1: Uniform random sampling with perfect knowledge and without replacement -- Example 3.2: Easter egg hunt -- Example 3.3: Competitive search -- Example 3.4: Tournament play -- Example 3.5: Populati on search -- 4. Information and Efficiency Measures -- 5. Liftings and Lowerings -- 6. Conservation of Information - The Uniform Case -- 7. Conservation of Information - The General Case -- 8. Regulating the Information Industry -- Acknowledgment -- References and Notes -- 1.1.3 Pragmatic Information John W. Oller, Jr. -- Introduction -- Ranking in Sign Systems; Tampering with the Sign Architecture -- Pragmatic Mapping -- The Vanishing Ratio of Meaningful to Random Strings -- The Logical Sequence for Discovering Meaning -- Conclusions -- Addendum -- Acknowledgments -- References -- 1.2.1 Limits of Chaos and Progress in Evolutionary Dynamics William F. Basener -- 1. Introduction -- 1.1 Goals and Perspective. -- 1.2 History and Applicati on of Topology and Dynamical Systems -- 1.3 General Questions in Evolutionary Models -- 2. Evolutionary Models and Dynamical Systems -- 2.1. Simple Populati on Models -- 2.2. Simple Mutati on-Selection Models -- 2.3. Population Models with Mutati on-Selection -- 3. Chaos and Recurrent Behavior -- 4. Conclusions -- References -- 1.2.2 Tierra: The Character of Adaptation Winston Ewert, William A. Dembski and Robert J. Marks II -- 1. Introduction -- 2. Description of Tierra -- 2.1 Programs -- 2.2 Ancestor -- 2.3 Parallel Tierra -- 2.4 Network Tierra -- 3. Looking for complexity -- 4. Examples -- 4.1 Parasite -- 4.2 Immunity -- 4.3 Hyper-parasites -- 4.4 Social behavior -- 4.5 Cheater -- 4.6 Shorter program -- 4.7 Loop unrolling -- 4.8 Parallel code -- 4.9 Recap -- 5. Summary -- Acknowledgments -- 6. Appendix: Tierra program comparisons -- 6.1 Ancestor and parasite -- 6.2 Immunity -- 6.3 Ancestor and hyper-parasite -- 6.4 Hyper-parasite and social program -- 6.5 Social program and cheater -- 6.6 Ancestor and short code -- 6.7 Loop unrolling -- 6.8 Parallel -- References -- 1.2.3 Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation George Monta�nez, Robert J. Marks II, Jorge Fernandez and John C. Sanford -- 1. Introduction -- 2. Method and Results -- 2.1 The Model -- 2.2 Analyses -- 2.2.1 First Level of Analysis: -- 2.2.2 Second Level of Analysis: -- 2.2.3 Third Level of Analysis: -- 2.2.4 Summary of Results: -- 3. Discussion; 3.1 Possible Objections -- 4. Conclusions -- References -- 1.3.1 Entropy, Evolution and Open Systems Granville Sewell -- 1. Compensation -- 2. The Equations of Entropy Change -- 3. A Tautology -- 4. The Common Sense Law of Physics -- 5. Conclusions -- 6. References -- 1.3.2 Information and Thermodynamics in Living Systems Andy C. McIntosh -- 1. Introduction -- 2. Biological information storage and retrieval - thermodynamic issues -- 2.1 Thermodynamics and isolated systems -- 2.2 Non isolated systems -- 2.2.1 Entropy deficiency -- 2.2.2 Open systems and machinery -- 2.3 Can negative entropy be harvested from somewhere else? -- 3. Free energy and Machines -- 3.1 Free energy -- 3.2 Machines and raised free energies -- 3.3 Thermodynamic law of non-isolated systems -- 3.4 Crystal formation -- 3.5 Bio polymer formation -- 4. A different paradigm: Thermodynamics constrained by functional information -- 4.1 A different paradigm: Information definitions -- 4.2 A different paradigm: principles of information and thermodynamics -- 4.2.1 Principles of information exchange -- 4.2.2 Principles of information interaction with energy and matter in biological systems -- 5. Conclusions -- Acknowledgement -- References -- Section Two Biological Information and Genetic Theory: Introductory Comments John C. Sanford -- 2.1 Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information Jonathan Wells -- 1. Introduction -- 2. Widespread Transcription Into RNAs That Are Probably Functional -- 3. Direct Evidence for Some Specific Functions of Non-Protein- Coding RNAs -- 4. Functions of Non-Protein-Coding DNA That Are Not Determined by Precise Nucleotide Sequences -- 4.1 The Length of DNA Sequences -- 4.2 Chromatin Organization -- 4.3 Chromosome Arrangement in the Nucleus -- 5. Conclusion: Multiple Levels of Biological Information -- Addendum; Acknowledgments -- References -- 2.2 Can Purifying Natural Selection Preserve Biological Information? Paul Gibson, John R. Baumgardner, Wesley H. Brewer and John C. Sanford -- Introduction -- Results -- Conditions allowing perfect purifying selection -- Effects of high mutati on rate and mutation-mutation interference -- Effects of environmental variance -- Effects of varying degrees of randomness within the selecti on process -- Effects of minimal levels of noise from multiple sources -- Effects of larger population size, more time, and more recombination -- Experiments using the latest estimate of human mutation rate and fitness effect distribution -- Discussion -- General Implications -- Robustness of Findings -- Potential Effects of Other Factors -- Conclusion -- Materials and Methods -- Acknowledgments -- References -- Appendix 1: Key parameter settings and their basis -- 2.3 Selection Threshold Severely Constrains Capture of Beneficial Mutations John C. Sanford, John R. Baumgardner and Wesley H. Brewer -- Introduction -- Results -- Conditions allowing optimal selection for beneficial mutations -- Effect of environmental variance -- Introduction of probability into the selection process -- Effect of high mutation rate and consequent selecti on interference among beneficial mutations -- Effect of extremely beneficial mutations -- Effect of adding deleterious mutations -- Effect of multiple sources of noise, at minimal levels -- Modest levels of noise with a larger population -- The effect of time on STd and STb values -- Discussion -- Can low-impact beneficial mutations contribute to genome building? -- Can high-impact beneficial mutations explain the origin of the genome? -- Can equal-but-opposite compensating mutations stop degeneration? -- Can high-impact compensating beneficial mutations stop degeneration?; Might beneficial mutations be common? -- Possible criticisms -- Concluding comments -- Methods -- Addendum - -- Acknowledgments -- References -- Appendix I: Key parameter settings and their justification: -- 2.4 Using Numerical Simulation to Test the "Mutation-Count" Hypothesis Wesley H. Brewer, John R. Baumgardner and John C. Sanford -- Introduction -- Methods -- Results -- Discussion -- Acknowledgements -- References -- 2.5 Can Synergistic Epistasis Halt Mutation Accumulation? Results from Numerical Simulation John R. Baumgardner, Wesley H. Brewer and John C. Sanford -- Introduction -- Methods -- Modeling general epistasis -- Modeling additive interactions -- Modeling multi plicative interactions -- Modeling synergistic epistasis -- Results -- Preliminaries -- Large SE effects and modest selection pressure -- Extreme SE effects and moderate selection pressure -- Extremely exaggerated SE effects and extreme selection pressure -- Discussion -- The importance of genic interactions -- The significance of SE -- Testing the limits of SE -- Modeling SE realistically -- Pros and cons of the SE hypothesis -- Conclusions -- References -- 2.6 Computational Evolution Experiments Reveal a Net Loss of Genetic Information Despite Selection Chase W. Nelson and John C. Sanford -- Introduction -- Mendel's Accountant -- Avida -- Selection threshold and genetic entropy -- Methods -- Experiments using Mendel's Accountant -- Experiments using Avida -- Results -- Experiments using Mendel's Accountant -- Experiments using Avida -- Discussion -- Selection threshold and genetic entropy -- High-impact beneficial mutations -- Distribution of mutational fitness effects -- Junk DNA -- Irreducible complexity and the waiting time to beneficial mutation -- Reductive evolution -- Conclusions -- Addendum -- Acknowledgments -- References; 2.7 Information Loss: Potential for Accelerating Natural Genetic Attenuation of RNA Viruses Wesley H. Brewer, Franzine D. Smith and John C. Sanford
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