Biological Information

New Perspectives

Proceedings of the Symposium

Cornell University, USA, 31 May – 3 June 2011

edited by: Robert J Marks II (Baylor University, USA) edited by: Michael J Behe (Lehigh University, USA) edited by: William A Dembski (Discovery Institute, USA) edited by: Bruce L Gordon (Houston Baptist University, USA) edited by: John C Sanford (Cornell University, USA)

In the spring of 2011, a diverse group of scientists gathered at Cornell University to discuss their research into the nature and origin of biological information. This symposium brought together experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. This volume presents new research by those invited to speak at the conference.

The contributors to this volume use their wide-ranging expertise in the area of biological information to bring fresh insights into the many explanatory difficulties associated with biological information. These authors raise major challenges to the conventional scientific wisdom, which attempts to explain all biological information exclusively in terms of the standard mutation/selection paradigm.

Several clear themes emerged from these research papers: 1) Information is indispensable to our understanding of what life is; 2) Biological information is more than the material structures that embody it; 3) Conventional chemical and evolutionary mechanisms seem insufficient to fully explain the labyrinth of information that is life. By exploring new perspectives on biological information, this volume seeks to expand, encourage, and enrich research into the nature and origin of biological information.

Sample Chapter(s)
General Introduction (74 KB)
Biological Information — What is It? (266 KB)


Contents:
  • Session One — Information Theory & Biology: Introductory Comments (Robert J Marks II):
    • Biological Information — What is It? (Werner Gitt, Robert Compton and Jorge Fernandez)
    • A General Theory of Information Cost Incurred by Successful Search (William A Dembski, Winston Ewert and Robert J Marks II)
    • Pragmatic Information (John W Oller, Jr)
    • Limits of Chaos and Progress in Evolutionary Dynamics (William F Basener)
    • Tierra: The Character of Adaptation (Winston Ewert, William A Dembski and Robert J Marks II)
    • Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation (George Montañez, Robert J Marks II, Jorge Fernandez and John C Sanford)
    • Entropy, Evolution and Open Systems (Granville Sewell)
    • Information and Thermodynamics in Living Systems (Andy C McIntosh)
  • Session Two — Biological Information and Genetic Theory: Introductory Comments (John C Sanford):
    • Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information (Jonathan Wells)
    • Can Purifying Natural Selection Preserve Biological Information? (Paul Gibson, John R Baumgardner, Wesley H Brewer and John C Sanford)
    • Selection Threshold Severely Constrains Capture of Beneficial Mutations (John C Sanford, John R Baumgardner and Wesley H Brewer)
    • Using Numerical Simulation to Test the “Mutation-Count” Hypothesis (Wesley H Brewer, John R Baumgardner and John C Sanford)
    • Can Synergistic Epistasis Halt Mutation Accumulation? Results from Numerical Simulation (John R Baumgardner, Wesley H Brewer and John C Sanford)
    • Computational Evolution Experiments Reveal a Net Loss of Genetic Information Despite Selection (Chase W Nelson and John C Sanford)
    • Information Loss: Potential for Accelerating Natural Genetic Attenuation of RNA Viruses (Wesley H Brewer, Franzine D Smith and John C Sanford)
    • DNA.EXE: A Sequence Comparison between the Human Genome and Computer Code (Josiah Seaman)
    • Biocybernetics and Biosemiosis (Donald Johnson)
  • Session Three — Theoretical Molecular Biology: Introductory Comments (Michael J Behe):
    • An Ode to the Code: Evidence for Fine-Tuning in the Standard Codon Table (Jed C Macosko and Amanda M Smelser)
    • A New Model of Intracellular Communication Based on Coherent, High-Frequency Vibrations in Biomolecules (L Dent)
    • Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations (Michael J Behe)
    • The Membrane Code: A Carrier of Essential Biological Information That is Not Specified by DNA and is Inherited Apart from It (Jonathan Wells)
    • Explaining Metabolic Innovation: Neo-Darwinism Versus Design (Douglas D Axe and Ann K Gauger)
  • Session Four — Biological Information and Self-Organizational Complexity Theory: Introductory Comments (Bruce L Gordon):
    • Evolution Beyond Entailing Law: The Roles of Embodied Information and Self Organization (Stuart Kauffman)
    • Towards a General Biology: Emergence of Life and Information from the Perspective of Complex Systems Dynamics (Bruce H Weber)

Readership: Academics, researchers, postgraduates and advanced undergraduates in bioinformatics. Biologists, mathematicians/statisticians, physicists and computer scientists.

i
FRONT MATTER
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DOI: 10.1142/9789814508728_fmatter
Abstract | PDF (200 KB) | pdf Cache
  • Section one: Information Theory & Biology: Introductory Comments
  • 1
    Information Theory & Biology: Introductory Comments
    DOI: 10.1142/9789814508728_others01
    Abstract | PDF (154 KB)   | pdf Cache
    11
    Biological Information — What is It?
    , ,
    DOI: 10.1142/9789814508728_0001
    Abstract | PDF (266 KB)   | pdf Cache
    26
    A General Theory of Information Cost Incurred by Successful Search
    , ,
    DOI: 10.1142/9789814508728_0002
    Abstract | PDF (525 KB)   | pdf Cache
    64
    Pragmatic Information
    DOI: 10.1142/9789814508728_0003
    Abstract | PDF (314 KB)   | pdf Cache
    87
    Limits of Chaos and Progress in Evolutionary Dynamics
    DOI: 10.1142/9789814508728_0004
    Abstract | PDF (1166 KB)   | pdf Cache
    105
    Tierra: The Character of Adaptation
    , ,
    DOI: 10.1142/9789814508728_0005
    Abstract | PDF (553 KB)   | pdf Cache
    139
    Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation
    , , ,
    DOI: 10.1142/9789814508728_0006
    Abstract | PDF (537 KB)   | pdf Cache
    168
    Entropy, Evolution and Open Systems
    DOI: 10.1142/9789814508728_0007
    Abstract | PDF (100 KB)  | pdf Cache
    179
    Information and Thermodynamics in Living Systems
    DOI: 10.1142/9789814508728_0008
    Abstract | PDF (2255 KB)   | pdf Cache
  • Section Two: Biological Information and Genetic Theory: Introductory Comments
  • 203
    Biological Information and Genetic Theory: Introductory Comments
    DOI: 10.1142/9789814508728_others02
    Abstract | PDF (78 KB)   | pdf Cache
    210
    Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information
    DOI: 10.1142/9789814508728_0009
    Abstract | PDF (171 KB)   | pdf Cache
    232
    Can Purifying Natural Selection Preserve Biological Information?
    , , ,
    DOI: 10.1142/9789814508728_0010
    Abstract | PDF (1600 KB)   | pdf Cache
    264
    Selection Threshold Severely Constrains Capture of Beneficial Mutations
    , ,
    DOI: 10.1142/9789814508728_0011
    Abstract | PDF (1088 KB)   | pdf Cache
    298
    Using Numerical Simulation to Test the “Mutation-Count” Hypothesis
    , ,
    DOI: 10.1142/9789814508728_0012
    Abstract | PDF (325 KB)   | pdf Cache
    312
    Can Synergistic Epistasis Halt Mutation Accumulation? Results from Numerical Simulation
    , ,
    DOI: 10.1142/9789814508728_0013
    Abstract | PDF (343 KB)   | pdf Cache
    338
    Computational Evolution Experiments Reveal a Net Loss of Genetic Information Despite Selection
    ,
    DOI: 10.1142/9789814508728_0014
    Abstract | PDF (401 KB)   | pdf Cache
    369
    Information Loss: Potential for Accelerating Natural Genetic Attenuation of RNA Viruses
    , ,
    DOI: 10.1142/9789814508728_0015
    Abstract | PDF (222 KB)   | pdf Cache
    385
    DNA.EXE: A Sequence Comparison between the Human Genome and Computer Code
    DOI: 10.1142/9789814508728_0016
    Abstract | PDF (3904 KB)   | pdf Cache
    402
    Biocybernetics and Biosemiosis
    DOI: 10.1142/9789814508728_0017
    Abstract | PDF (176 KB)   | pdf Cache
  • Section Three: Theoretical Molecular Biology: Introductory Comments
  • 415
    Theoretical Molecular Biology: Introductory Comments
    DOI: 10.1142/9789814508728_others03
    Abstract | PDF (46 KB)   | pdf Cache
    418
    An Ode to the Code: Evidence for Fine-Tuning in the Standard Codon Table
    ,
    DOI: 10.1142/9789814508728_0018
    Abstract | PDF (1526 KB)   | pdf Cache
    435
    A New Model of Intracellular Communication Based on Coherent, High-Frequency Vibrations in Biomolecules
    DOI: 10.1142/9789814508728_0019
    Abstract | PDF (223 KB)   | pdf Cache
    450
    Getting There First: An Evolutionary Rate Advantage for Adaptive Loss-of-Function Mutations
    DOI: 10.1142/9789814508728_0020
    Abstract | PDF (422 KB)   | pdf Cache
    474
    The Membrane Code: A Carrier of Essential Biological Information That Is Not Specified by DNA and Is Inherited Apart from It
    DOI: 10.1142/9789814508728_0021
    Abstract | PDF (120 KB)   | pdf Cache
    489
    Explaining Metabolic Innovation: Neo-Darwinism versus Design
    ,
    DOI: 10.1142/9789814508728_0022
    Abstract | PDF (1176 KB)   | pdf Cache
  • Section Four: Biological Information and Self-Organizational Complexity Theory: Introductory Comments
  • 509
    Biological Information and Self-Organizational Complexity Theory: Introductory Comments
    DOI: 10.1142/9789814508728_others04
    Abstract | PDF (52 KB)   | pdf Cache
    513
    Evolution Beyond Entailing Law: The Roles of Embodied Information and Self Organization
    DOI: 10.1142/9789814508728_0023
    Abstract | PDF (136 KB)   | pdf Cache
    533
    Towards a General Biology: Emergence of Life and Information from the Perspective of Complex Systems Dynamics
    DOI: 10.1142/9789814508728_0024
    Abstract | PDF (165 KB)   | pdf Cache
    561
    BACK MATTER
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    DOI: 10.1142/9789814508728_bmatter
    Abstract | PDF (40 KB)   | pdf Cache