Biological Information : New Perspectives - Proceedings Of The Symposium.
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Other Authors: | , , , |
Format: | eBook |
Language: | English |
Published: |
Singapore :
World Scientific Publishing Company,
2013.
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Edition: | 1st ed. |
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Online Access: | Click to View |
Table of Contents:
- Intro
- Contents
- Title Page
- Acknowledgements
- General Introduction
- References and Notes
- Section One Information Theory &
- 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 MontanĚez, 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.