Physical Theory in Biology

The following sections are included:

• Preface

• Table of Contents

• The Contributors

• Introduction

The following sections are included:

• 1 Nature of Emergence in Physics and Biology

• 2 Emergence Classes

• 3 Tangled Wave Functions and Separability in Quantum Mechanics

• 4 Does Irreducible Emergence Occur in Biology?

• References

The following sections are included:

• 1 The Chapels of San Carlo

• 2 The Romance of Reduction

• 3 Layered Webs

• 4 Vector Field Hierarchies and the Dirac Manifold

• 5 The Signs of Synthesis

• 6 The Limits of Expression

• 7 Conclusions

• Acknowledgments

• References

The following sections are included:

• 1 Introduction

• 2 Measures of Complexity

• 3 Origins of Complexity

• 4 Characteristics of Complexity

• 5 Reducing Complexity
  • 5.1 Averaging
  • 5.2 Fields and Symmetries

• 6 A Pluralistic Approach to Complexity
  • 6.1 Viewpoints, Descriptions, and the Observer
  • 6. 2 Natural Descriptions
    • 6. 2.1 A biological system: Drosophila development
    • 6.2.2 A formal-logic system: Primitives and the grue-bleen problem
  • 6. 3 Formal Systems
  • 6.4 Reductionism and the Dynamics Versus Computation Problem

• 7 Conclusion

• Acknowledgements

• References

The following sections are included:

• 1 Introduction

• 2 Machines and Grammars
  • 2.1 Turing Machines and the Halting Problem
  • 2.2 Formal Grammars and the Chomsky Hierarchy

• 3 Symbolic Dynamics
  • 3.1 Topological and Metric Entropies, Set Dimensions
  • 3.2 Generating Partitions

• 4 Computation in Dynamical Systems
  • 4.1 ε-Machines and Statistical Complexity
    • 4.1.1 ε-Machines for the logistic map
  • 4.2 Cellular Automata and Computation at the Edge of Chaos
  • 4.3 Sulis Machines: the Organism in Its World

• 5 More Questions

• Acknowledgements

• References

The following sections are included:

• 1 Introduction

• 2 Morphogenetic Fields

• 3 Biology of Tetrahymena
  • 3.1 Cytogeometry
  • 3.2 Tetrahymena Doublets
  • 3.3 Left-Handed Cells
  • 3.4 Regulation Pathways

• 4 The Tetrahymena Field Model
  • 4.1 Solutions
  • 4.2 Pathways

• 5 Biology of Salamander Limb Regeneration
  • 5.1 Limb Graft Experiments
    • 5.1.1 Ordinary limb regeneration
    • 5.1.2 Contralateral and ipsilateral grafts
    • 5.1.3 The proximo-distal shift graft

• 6 An Interpretive Look at the Limb Graft Experiments
  • 6.1 The Pattern Specification Field
  • 6.2 The Intercalary Region
  • 6.3 Contralateral versus Ipsilateral Blastema Grafts

• 7 The Regeneration Field Model
  • 7.1 Solutions
    • 7.1.1 The contralateral graft
    • 7.1.2 The ipsilateral graft

• Acknowledgments

• References

The following sections are included:

• 1 Introduction

• 2 Morphogenesis, Surfaces and Fields

• 3 The Application of Surface Field Theory to Gastrulation

• 4 Toward a Theory of Form

• 5 Concluding Remarks

• References

The following sections are included:

• 1 Introduction

• 2 Developmental Fields

• 3 Morphogenesis

• 4 Modeling Morphogenesis

• 5 Morphogenetic Dynamics

• 6 Morphogenetic Attractors

• References

The following sections are included:

• 1 Introduction

• 2 A Description of the Model

• 3 Geometry, Speculation and Genes

• 4 A Promising Molecular Mechanism for the Morphogen

• Acknowledgements

• References

• Appendix. The Cylindrical Flat Worm

The following sections are included:

• 1 The Problem of Living Organization

• 2 The Coherence of Energy Transfer in Metabolism
  • 2.1 Coupled Energy Transfer
  • 2.2 Enzymes — Flexi-Molecular Energy Machines
  • 2.3 The Solid-State Cell
  • 2.4 Coherence and Metabolic Regulation

• 3 Coherent Excitations and Nonequilibrium Phase Transitions
  • 3.1 Coherent Excitations and Biological Rhythms
  • 3.2 The Fröhlich State and Sensitivity to Weak Electromagnetic Fields

• 4 Coherent Photons in Living Organisms

• 5 The Coherence of Organisms

• 6 The Coherence of the Morphogenetic Field

• 7 Weak Magnetic Fields Perturb Body Pattern

• 8 Cooperative Emission of Coherent Light

• 9 Global Birefringent Patterns Suggestive of Coherent Phase Ordering of Liquid Crystals

• 10 Conclusion

• 11 Epilogue

• References

The following sections are included:

• 1 Introduction

• 2 Nested Order in Tetrahymena

• 3 Reversals of Handedness and Developmental Fields in Tetrahymena

• 4 Genic Mutations Affecting Global Patterning in Tetrahymena

• 5 Homology or Analogy?

• Acknowledgements

• References

The following sections are included:

• 1 Introduction

• 2 Molecular Interactions in a Lamellar Lipid System

• 3 The Hamiltonian and Mean Field Theory

• 4 The Density of States

• 5 The Packing Problem

• 6 Results and Discussion

• Acknowledgement

• References

The following sections are included:

• 1 Introduction

• 2 Memory Models and Statistical Mechanics

• 3 The Hopfield model

• 4 The Hopfield Model, "Spin" Systems and Statistical Mechanics

• 5 The Multiple Interaction Model

• 6 Numerical Analysis of MI(3)
  • 6.1 Stability and MI(3) Storage Capacity
  • 6.2 Memory Retrievability

• 7 Mean Field Theory of the MI Model
  • 7.1 Retrieval State Solutions
  • 7.2 Symmetric Solutions

• 8 Discussion

• References

The following sections are included:

• 1 Introduction

• 2 Neurobiological Considerations
  • 2.1 Overview
  • 2.2 Functional Anatomy
  • 2.3 Nested Distributed Systems

• 3 Hierarchical Cluster Model
  • 3.1 Architecture
  • 3.2 Dynamic Form
  • 3.3 Assertions of the HCM
  • 3.4 Limitations of the HCM

• 4 Multilevel Memory Properties
  • 4.1 Model Implementation
  • 4.2 Mathematical Formulation
    • 4.2.1 Spatial features
    • 4.2.2 Temporal features
    • 4.2.3 Computational energy
  • 4.3 Simulations
    • 4.3.1 Overview
    • 4.3.2 Method
  • 4.4 Results
    • 4.4.1 τ = 0 conditions
    • 4.4.2 τ ≠ 0 conditions

• 5 Learning and Development
  • 5.1 Outline
  • 5.2 Perspectives on Learning
  • 5.3 Learning by Selection in the HCM
    • 5.3.1 Memory stabilization
    • 5.3.2 Numerical simulation

• 6 Perturbation and Disease
  • 6.1 Neuropathology as System Perturbation
  • 6.2 The HCM and Illness
  • 6.3 Alzheimer's Disease
  • 6.4 Hierarchical Memory Loss

• 7 Integrative Neural Modeling
  • 7.1 Perspectives
  • 7.2 Complex Systems
  • 7.3 Neural Computation
  • 7.4 Applications to Technology and Neuroscience

• 8 Concluding Remarks

• Acknowledgements

• References

The following sections are included:

• 1 Introduction

• 2 The Hopfield Model

• 3 A Two Category Switching Model

• 4 The Challenge of Pogonomyrmez barbatus

• 5 Eight Category Model

• 6 Modified Category Switching Model

• 7 Discussion

• 8 Extended Applications

• References

The following sections are included:

• 1 Statistical Analysis of Nucleotide Sequences

• 2 Reconstruction of the Evolutionary Tree

• 3 Maximum Information Principle- A Formulation on Molecular Evolution

• 4 A Model of Molecular Evolution

• 5 Further Discussions on Molecular Evolution of Nucleic Acid Sequences

• 6 Future Perspectives

• References

The following sections are included:

• 1 Introduction

• 2 Codon Space

• 3 Competitive Learners in Codon Space

• 4 What They Saw

• 5 The Tetrahedral Representation and the Primordial Code

• References

• Appendix. Learning Codon Space by Inter-Neuron Competition

The following sections are included:

• 1 Introduction

• 2 Modules As the Structural and Functional Basis of Biological Hierarchies

• 3 Biological Bureaucracies Coordinate Modular Development

• 4 Bureaucracies Influence Morphogenesis by Influencing Cell Behavior

• 5 Mutant Phenotypes Suggest Developmental Genetic Strategies

• 6 The Evolution of Development- A Bureaucratic Shuffle?

• References

The following sections are included:

• 1 Introduction

• 2 Dynamics and Evolution
  • B.l Stability of Equilibria
  • B.2 Dynamic Stability and the ESS Conditions
  • B.3 The Dynamics of Mixed Strategies
  • B.4 Sex Games

• 3 Superparasitism in Parasitic Wasps: An Application of Game Theory

• 4 Summary and Conclusions

• References

• Appendix. Evolutionary Game Theory: A Physicist's Primer
  • A.l Payoffs and Strategies
  • A.2 Mixed Strategies
  • A.3 Other Types of Games
  • A.4 Evolutionary Games
    • A.4.1 The Hawk-Dove game
    • A.4.2 Evolutionarily Stable Strategies

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The following sections are included:

• Index