The Hierarchical Genome
gordonr at cc.UManitoba.CA
Fri Mar 27 18:40:18 EST 1998
Susan Duhon suggested I sent this to our whole urodeles list. Many of you
were involved one way or another in helping me through it.
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!
Yours, -Dick Gordon (gordonr at cc.umanitoba.ca)
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 or GBP 74, prepublication orders 15% lower =3D
Description: Over the past few decades numerous scientists have called for
a unification of the fields of embryo development, genetics, and evolution.
Each field has glaring holes in its ability to explain the fundamental
phenomena of life. In this book, the author shows how the phenomenon of
cell differentiation, considered in its temporal and spatial aspects during
embryogenesis, provides a starting point for a unified theory of
multicellular organisms (plants, fungi and animals), including their
evolution and genetics. This unification is based on the recent discovery
of differentiation waves by the author and his colleagues, described in the
appendices, and illustrated by a flip movie prepared by a medical artist.
To help the reader through the many fields covered, a glossary is included.
Readership: scientists interested in biology, and graduate students;
computer scientists (artificial life, computing embryos, fractal
morphogenesis & evolution), engineers (tensegrity, embryonics, active
media), microbiologists (bacteria, ciliates, yeast), evolutionists
(systematists, paleontologists, Baldwin effect, macroevolution, radiation,
punctuated equilibrium, hopeful monsters, population biology, ciliate
origin of multicellular organisms, haplontic/diplontic life cycles),
developmental biologists (all major mosaic and regulating systems,
including nematodes, Arabidopsis, Drosophila, zebrafish, Xenopus, chick,
mouse, urodeles, sea urchins, metamorphosis, short germ band insects,
polyembryonic wasps, sex determination), molecular developmental biologists
(homeobox genes, control hierarchies, compaction, gastrulation,
neurulation, limb formation, segmentation, regeneration, placodes,
bilateral asymmetry, morphogenetic furrow), geneticists (structure of whole
genomes, chromosomes in development and evolution, birth defects),
historians and philosophers of biology (vitalism, orthogenesis,
reductionism, neoDarwinism, progressive evolution), theoretical and
mathematical biologists, neurophysiologists and psychologists (incomplete
development of the brain, brain laterality, speech, sleep, learning,
instinct), physicists (biophysics of embryos), cell biologists
(cytoskeletal and nuclear mechanics, asymmetric cell division,
mechanochemical signaling pathways, transdifferentiation, calcium waves),
ecologists (fluctuating asymmetry, evolution of behavior, parallel
Foreword: Pieter D. Nieuwkoop/Natalie K. Bj=F6rklund
Flip Animation of the Ectoderm Contraction Wave, K. Jack Butler
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
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 Hans
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 Mod=
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 Yields
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 Embry=
4.06 The Relationship Between Cells and Tissues in Mosaic Embryos
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 Brai=
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 Epidermi=
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 Patterns
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
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 Evolution
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
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 tree.
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
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 recellulariza=
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 of
the differentiation tree. It will be expressed as a subgraph of the
P161: large topological changes in a differentiation tree may account for
P166: 'developmental homeostasis' ('canalization') does not exist, and so
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 evolution,
single celled species, species with limited cell type differentiation, and
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 radiation.
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
P262: the homeobox 'code' and regional differentiation can be explained in
terms of consecutive differentiation waves with nested, overlapping
Orders may be placed with:
Ms. Sook Cheng Lim, Assistant Director(Publishing)
World Scientific Publishing Co.
Block 1022 Hougang Avenue 1 #05-3520, Tai Seng Industrial Estate
Singapore 538890 , Republic of Singapore
Phone: 65-3825-663, Fax: 65-3825-919
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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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