The Hierarchical Genome
gordonr at cc.UManitoba.CA
Wed Mar 18 13:16:17 EST 1998
I've convinced World Scientific to offer a prepublication price for my
book, The Hierarchical Genome, especially for all the people who have
helped me out with reprints, reading sections, and comments. After 9
years it's finally done! There's a lot of discussion of zebrafish
in the book.
Gordon, R. (1998). The Hierarchical Genome and Differentiation Waves:
Novel Unification of Development, Genetics and Evolution (sent to press
Feb. 25, 1998, publication planned for Sept., 1998). Singapore: World
Scientific, about 1500p., list US$108, prepublication orders 15% lower =
Foreword: Pieter D. Nieuwkoop/Natalie K. Bjoerklund
Flip Animation of the Ectoderm Contraction Wave
Chapter 1: Introduction
1.01 Consider a Spherical Cow
1.02 The Epigenetic Problem
1.03 Wholeness and the Symmetry of the Early Embryo
1.04 Wholeness through the Ruse of Organicism
1.05 The Grip of Vitalism
1.06 The Rise and Fall of Physics in Embryology
1.07 Can We Restore the Physics of the Youth of Embryology?
1.08 Avoiding the Spatial Component of Embryogenesis
1.09 Wholeness, the Environment, and Symmetry Breaking
1.10 Wholeness through Surface Tension
1.11 Nonmaterial Physics as the Entelechy of Vitalism
1.12 Towards a New Physics of Embryos
1.13 New Tools of the Trade
1.14 Are We Headed for Reductionism?
1.15 Chemical or Mechanochemical Instabilities?
1.16 Critique of the Theory of Self-Organizing Systems
1.17 Protein Folding as a Deluding Paradigm
1.18 A Word on Language
1.19 The Embryology/Psychology Merry-go-round (Carrousel)
1.20 The Cosmic Context
Chapter 2: Neural Induction and the Organizer
2.01 A Moment of Discovery
2.02 Origins of the Idea of Induction
2.03 Preformationism versus Epigenesis: To Be or To Become? That
is the Question
2.04 The Hunting of the Snark (The Inducer Molecule)
2.05 A Cornucopia of Inducers
2.06 The Snark Was a Boojum
2.07 Limb Induction: A Parallel Case?
2.08 Mesoderm and Other Inductions
2.09 Regional Induction
2.10 The Cell State Splitter
2.11 Meet the Axolotl
2.12 A History of Sexism in Science Whodunit: Hilde Mangold or
Chapter 3: Theory of the Cell State Splitter
3.02 How to Stop a Wave on a Sphere
3.03 How the Ectoderm Contraction Wave Actually Stops: the Lens
3.04 Internal Pressure May Synchronize Preparation of the Cell
3.05 The Right Place, at the Right Time, into the Right Kinds
3.06 The Intracellular Mechanics of the Cell State Splitter
3.07 Force Generating and Load Bearing Cytoskeletal Components:
3.08 Force Generating and Load Bearing Cytoskeletal Components:
3.09 Force Generating and Load Bearing Cytoskeletal Components:
Intermediate filaments (IF)
3.10 Combinations of Cytoskeletal Components
Chapter 4: Development and Genetics
4.01 The General Cell State Splitter
4.02 Differentiation Trees
4.03 Genetics and Differentiation Trees
4.04 A New Definition of 'Tissue'
4.05 The Relationship Between Cells and Tissues in Regulating
4.06 The Relationship Between Cells and Tissues in Mosaic
Chapter 5: Development and Evolution
5.01 Evolution of Cell State and Tissue Splitting
5.02 The Secondary Importance of Embryonic Induction
5.03 Dedifferentiation and Redifferentiation
5.04 The Selfish Differentiation Tree
5.05 The Ciliate Origin of Multicellular Organisms
Chapter 6: Macroevolution
6.01 Redefining Microevolution and Macroevolution
6.02 Possible DNA Mechanisms for Macroevolutionary Change of
6.03 Differentiation Trees in Punctuated Equilibrium
6.04 The Grand Sweep of Evolution
6.05 Neutralist Theory
6.06 A Universe Aware of Itself: Differentiation Waves and the
Chapter 7: The Biogenetic Law
7.01 'Ontogeny Recapitulates Phylogeny' Revisited via
7.02 Organisms with Two Differentiation Trees
7.03 Winding up Evolution
Chapter 8: The Homeobox
8.01 Why Insects and Vertebrates Share Homeobox Domains
8.02 The Development of Bilateral Asymmetry
8.03 Facets of Embryogenesis
Chapter 9: A Cornucopia of Differentiation Waves
9.01 Activation Wave
9.02 Cleavage Waves
9.03 The Compaction Wave
9.04 Mitotic Waves
9.05 Quantal Mitoses and a Model for Limb Morphogenesis
9.06 Head and Tail Duplications
9.07 First Sitings of the Differentiation Waves of the Axolotl
9.08 Differentiation Waves of the Neural Plate
9.09 A Possible Pair of Differentiation Waves in the Later
9.10 Neural Crest
9.11 Differentiation Waves in Plant Meristems
9.12 Differentiation Waves in Fly and Fish Eyes
9.13 Single Cell versus Multiple Cell Differentiation Waves
9.14 Repetitive Waves
9.15 Drosophila Bristles: A Wave/Mechanical Reinterpretation
9.16 The American Shorthair Tabby Domestic Cat and Pigment
9.17 Butterfly Eye Spots
9.18 The Milk Line
9.19 Waves in Assorted Tissues
9.20 Waves on Anuran Embryos
9.21 Hints of Other Differentiation Waves, Especially Somites
9.22 Uninvited Waves
9.23 Are Others' Waves Our Waves?
9.24 Are Differentiation Waves Merely Epiphenomena?
9.25 Mutant Waves
9.26 Wave Parallels between Mosaic and Regulating Organisms
9.27 Launching Domains May Have Specific Electrical, Mechanical
and Molecular Properties
Chapter 10: Conclusion
10.01 The Logic of Evolution
10.02 Is Evolution Progressive?
10.03 Were We Inevitable?
10.04 The Living Ghost of Orthogenesis
10.05 On Purpose and Progress
10.06 The Beads-on-a-String 'New Synthesis'
10.07 Gene Duplication as the Essence of Macroevolution
10.08 The Blessings of Ever Increasing Dimensionality
10.09 The Fractal Tree of Life
10.10 The Novel Unification of Development, Genetics and
10.11 Exploring the Higher Order Structure of the Genome
10.12 How to Find a GEM (Gene Expression Map)
10.13 A Clockwork Universe Within: Nuclear Tensegrity Mechanics
(Wurfels) as a Foundation for the Nuclear State Splitter
10.14 The Top Ten Questions
10.15 Paradigms for Developmental Biology
10.16 A New Curriculum for Biologists
Appendices (reprints of 8 related papers)
References (about 6900)
Glossary and Abbreviations
Surname and Subject Index
Chapters 4-8 consist of 272 propositions and their justifications. Here
are some highlights:
P014: the genetic program for development is the differentiation tree,
which consists of alternations between genetic and mechanical events.
P020: the epigenetic landscape for an organism is its differentiation
P035: positional information does not exist.
P053: the sex of an individual is determined by triggering of an
expansion or a contraction differentiation wave, corresponding to female
and male (or vice versa).
P060: cytoplasmic determinants may not exist.
P079: organisms whose differentiation trees evolve into differentiation
webs cease to radiate.
P095: the success of nuclear transplantation between two differentiated
cells is inversely dependent on the differences between their
P103: cancer may involve differentiation and/or dedifferentiation waves.
P109: the differentiation tree is a logical, rather than physical,
organization of the DNA.
P123: multicellular organisms are descended from ciliates via
P137: the hopeful monster can be reconsidered, if we distinguish the
'hopeful genotype' from the 'hopeful phenotype'.
P141: multigene families are created in the course of duplication of
branches of the differentiation tree.
P150: a gene in a differentiation cascade will be activated as a subtree
the differentiation tree. It will be expressed as a subgraph of the
P161: large topological changes in a differentiation tree may account
P166: 'developmental homeostasis' ('canalization') does not exist, and
does not form a basis for stasis.
P167: embryonic regulation does not exist.
P170: differentiation trees may allow us to 'compute' at least mosaic
organisms, and their developmental constraints.
P171: evolution has had four major stages, namely quasispecies
single celled species, species with limited cell type differentiation,
species with continuing differentiation.
P198: evolution of the central nervous system is primarily a matter of
growth via bifurcation of its portion of the differentiation tree.
P202: learning is primarily a matter of extension of the differentiation
tree beyond its inherited components.
P203: instinct is genetic assimilation of an extension of the
differentiation tree corresponding to a learned behavior.
P209: the differentiation tree is in effect the Bauplan of an organism.
P239: defragmentation of the genome would permit a new bout of
P240: artificial life should be based on differentiation trees.
P242: gradients of morphogens are irrelevant to differentiation.
P245: gene expression boundaries are determined by the trajectories of
differentiation waves. P262: the homeobox 'code' and regional
differentiation can be explained in terms of consecutive differentiation
waves with nested, overlapping
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World Scientific Publishing Co.
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World Scientific Publishing
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E-mail: tmarshall at wspc.com (Tonya Marshall)
They accept any major credit card except Discover. Also you could send a
check made payable to World Scientific Publishing Co.
Dr. Richard Gordon, Department of Radiology
University of Manitoba, Health Sciences Centre
820 Sherbrook Street, Winnipeg, MB R3A 1R9 Canada
Phone: (204) 789-3828, Fax: (204) 787-2080, Home: (204) 589-0411
E-mail: GordonR at cc.UManitoba.ca
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