The Hierarchical Genome and Differentiation Waves

The following sections are included:

• FOREWORD

• PREFACE

• FLIP ANIMATION OF THE ECTODERM CONTRACTION WAVE

• PROPOSITION PAGE NUMBERS

• CONTENTS

The following sections are included:

• Consider a Spherical Cow

• The Epigenetic Problem

• Wholeness and the Symmetry of the Early Embryo

• Wholeness through the Ruse of Organicism

• The Grip of Vitalism

• The Rise and Fall of Physics in Embryology

• Can We Restore the Physics of the Youth of Embryology?

• Avoiding the Spatial Component of Embryogenesis

• Wholeness, the Environment, and Symmetry Breaking

• Wholeness through Surface Tension

• Nonmaterial Physics as the Entelechy of Vitalism

• Towards a New Physics of Embryos

• New Tools of the Trade

• Are We Headed for Reductionism?

• Chemical or Mechanochemical Instabilities?

• Critique of the Theory of Self-Organizing Systems

• Protein Folding as a Deluding Paradigm

• A Word on Language

• The Embryology/Psychology Merry-go-round (Carrousel)

• The Cosmic Context

The following sections are included:

• A Moment of Discovery

• Origins of the Idea of Induction

• Preformationism versus Epigenesis: To Be or To Become? That is the Question

• The Hunting of the Snark (The Inducer Molecule)

• A Cornucopia of Inducers

• The Snark Was a Boojum

• Limb Induction: A Parallel Case?

• Mesoderm and Other Inductions

• Regional Induction

• The Cell State Splitter

• Meet the Axolotl

• A History of Sexism in Science Whodunit: Hilde Mangold or Hans Spemann?

The following sections are included:

• Overview

• How to Stop a Wave on a Sphere

• How the Ectoderm Contraction Wave Actually Stops: the Lens Model

• Internal Pressure May Synchronize Preparation of the Cell State Splitters

• The Right Place, at the Right Time, into the Right Kinds

• The Intracellular Mechanics of the Cell State Splitter Yields Ectodermal Differentiation

• Force Generating and Load Bearing Cytoskeletal Components: Microtubules (MT)

• Force Generating and Load Bearing Cytoskeletal Components: Microfilaments (MF)

• Force Generating and Load Bearing Cytoskeletal Components: Intermediate Filaments (IF)

• Combinations of Cytoskeletal Components

The following sections are included:

• The General Cell State Splitter

• Differentiation Trees

• Genetics and Differentiation Trees

• A New Definition of 'Tissue'

• The Relationship between Cells and Tissues in Regulating Embryos

• The Relationship between Cells and Tissues in Mosaic Embryos

The following sections are included:

• Evolution of Cell State and Tissue Splitting

• The Secondary Importance of Embryonic Induction

• Dedifferentiation and Redifferentiation

• The Selfish Differentiation Tree

• The Ciliate Origin of Multicellular Organisms

The following sections are included:

• Redefining Microevolution and Macroevolution

• Possible DNA Mechanisms for Macroevolutionary Change of Differentiation Trees

• Differentiation Trees in Punctuated Equilibrium

• The Grand Sweep of Evolution

• Neutralist Theory
  • Quantitative Traits
  • Definition of Species
  • Differences between Specialized and Generalized Species
  • Advantages of Sex

• A Universe Aware of Itself: Differentiation Waves and the Brain

The following sections are included:

• 'Ontogeny Recapitulates Phylogeny' Revisited via Differentiation Trees

• Organisms with Two Differentiation Trees

• Winding Up Evolution

The following sections are included:

• Why Insects and Vertebrates Share Homeobox Domains

• The Development of Bilateral Asymmetry

• Facets of Embryogenesis

The following sections are included:

• Activation Wave

• Cleavage Waves

• The Compaction Wave

• Mitotic Waves

• Quantal Mitoses and a Model for Limb Morphogenesis

• Head and Tail Duplications

• First Sitings of the Differentiation Waves of the Axolotl

• Differentiation Waves of the Neural Plate

• A Possible Pair of Differentiation Waves in the Later Epidermis

• Neural Crest

• Differentiation Waves in Plant Meristems

• Differentiation Waves in Fly and Fish Eyes

• Single Cell versus Multiple Cell Differentiation Waves

• Repetitive Waves

• Drosophila Bristles: A Wave/Mechanical Reinterpretation

• The American Shorthair Tabby Domestic Cat and Pigment Patterns

• Butterfly Eye Spots

• The Milk Line

• Waves in Assorted Tissues

• Waves on Anuran Embryos

• Hints of Other Differentiation Waves

• Uninvited Waves

• Are Others' Waves Our Waves?

• Are Differentiation Waves Merely Epiphenomena?

• Mutant Waves

• Wave Parallels between Mosaic and Regulating Organisms

• Launching Domains May Have Specific Electrical, Mechanical and Molecular Properties

The following sections are included:

• The Logic of Evolution

• Is Evolution Progressive?

• Were We Inevitable?

• The Living Ghost of Orthogenesis

• On Purpose and Progress

• The Beads-on-a-String 'New Synthesis'

• Gene Duplication as the Essence of Macroevolution

• The Blessings of Ever Increasing Dimensionality

• The Fractal Tree of Life

• The Novel Unification of Development, Genetics and Evolution

• Exploring the Higher Order Structure of the Genome

• How to Find a GEM

• A Clockwork Universe Within: Nuclear Tensegrity Mechanics (Wurfels) as a Foundation for the Nuclear State Splitter

• The Top Ten Questions

• Paradigms for Developmental Biology

• A New Curriculum for Biologists

The following sections are included:

• Appendix I: The Cytoskeletal Mechanics of Brain Morphogenesis: Cell State Splitters Cause Primary Neural Induction

• Appendix II: Furrowing Surface Contraction Wave Coincident With Primary Neural Induction in Amphibian Embryos

• Appendix III: Pursued by the Differentiation Wave

• Appendix IV: NUCLEAR STATE SPLITTING: A WORKING MODEL FOR THE MECHANOCHEMICAL COUPLING OF DIFFERENTIATION WAVES TO MASTER GENES

• Appendix V: Dialogue on Embryonic Induction and Differentiation Waves

• Appendix VI: SURFACE CONTRACTION AND EXPANSION WAVES CORRELATED WITH DIFFERENTIATION IN AXOLOTL EMBRYOS—I. PROLEGOMENON AND DIFFERENTIATION DURING INVAGINATION THROUGH THE BLASTOPORE, AS SHOWN BY THE FATE MAP

• Appendix VII: How to observe surface contraction waves on axolotl embryos

• Appendix VIII: Physicist to Biologist: A First Order Transition

• INDEX OF PROPOSITIONS

• REFERENCES

• GLOSSARY AND ABBREVIATIONS

• CITATION AND SUBJECT INDEX

• PERMISSIONS AND NOTE ADDED IN PROOF