The Hierarchical Genome, Table of Contents

Richard Gordon gordonr at cc.UManitoba.CA
Mon Mar 22 08:55:17 EST 1999


Dear Colleagues,
Mark Farmer suggested I send this to the whole protist list, since it might
not otherwise come to your attention. I've written a book on
differentiation and evolution that, among other things, revives the 1800s
hypothesis that ciliates are homologous with whole multicellular organisms.
See Section 5.05 below. I've included below Propositions 113-127 that deal
with this possibility.
Yours, -Dick Gordon

Gordon, R. (1999). The Hierarchical Genome and Differentiation Waves: Novel
Unification of Development, Genetics and Evolution (publication planned for
April, 1999). Singapore: World Scientific and London: Imperial College
Press, 2 vols., about 1835p., 6943 references, list US$108 or GBP 74,
prepublication orders 15% lower. For students and people in developing
countries, there are ongoing discounts of 20% and 25%, respectively, even
after publication. Order form:
http://www.wspc.com.sg/books/lifesci/2755.html

CONTENTS

Foreword   vii
  Figure 1. Pieter D. Nieuwkoop with Richard Gordon...  viii
  Figure 2. Pieter D. Nieuwkoop with Natalie K. Björklund...  xii
Preface   xiii
Flip Animation of the Ectoderm Contraction Wave  xxi
Proposition Page Numbers  lviii

1.00  Introduction  1
1.01  Consider a Spherical Cow  1
  Figure 3. A scanning electron micrograph (SEM) of a fertilized human
egg...  3
1.02  The Epigenetic Problem  7
1.03  Wholeness and the Symmetry of the Early Embryo  10
1.04  Wholeness through the Ruse of Organicism  12
1.05  The Grip of Vitalism  16
1.06  The Rise and Fall of Physics in Embryology  20
1.07  Can We Restore the Physics of the Youth of Embryology?  24
1.08  Avoiding the Spatial Component of Embryogenesis  26
1.09  Wholeness, the Environment, and Symmetry Breaking  30
1.10  Wholeness through Surface Tension  34
1.11  Nonmaterial Physics as the Entelechy of Vitalism  36
1.12  Towards a New Physics of Embryos  38
1.13  New Tools of the Trade  40
1.14  Are We Headed for Reductionism?  46
1.15  Chemical or Mechanochemical Instabilities?  49
1.16  Critique of the Theory of Self-Organizing Systems  53
1.17  Protein Folding as a Deluding Paradigm  56
1.18  A Word on Language  59
1.19  The Embryology/Psychology Merry-go-round (Carrousel)  64
1.20  The Cosmic Context  66

2.00  Neural Induction and the Organizer  69
2.01  A Moment of Discovery  69
  Figure 4. The stages of embryonic development of a urodele salamander...  70
2.02  Origins of the Idea of Induction  71
2.03  Preformationism versus Epigenesis: To Be or To Become?
  That is the Question  75
2.04  The Hunting of the Snark (The Inducer Molecule)  80
2.05  A Cornucopia of Inducers  83
2.06  The Snark Was a Boojum  88
2.07  Limb Induction: A Parallel Case?  93
2.08  Mesoderm and Other Inductions  95
2.09  Regional Induction  99
2.10  The Cell State Splitter  101
2.11  Meet the Axolotl  105
  Table 1: Timing of early stages of the axolotl embryo...  106
2.12  A History of Sexism in Science Whodunit: Hilde Mangold
  or Hans Spemann?  112

3.00  Theory of the Cell State Splitter  120
3.01  Overview  120
  Figure 5. Classical model of differentiation...  121
  Figure 6. Alternative classical model for differentiation  122
  Figure 7. Our new view of differentiation...  122
  Figure 8. State of determination...  123
  Figure 9. Determination tree...  125
   Figure 10. A differentiation tree...  126
3.02  How to Stop a Wave on a Sphere  128
  Figure 11. The contraction wave... in the simple 'shell' model....  129
  Figure 12. The spherical ectoderm of a urodele embryo... in the 'shell'
model...  129
  Figure 13. In the 'shell' model... when... a full hemisphere...  130
3.03  How the Ectoderm Contraction Wave Actually Stops:
  the Lens Model  133
3.04  Internal Pressure May Synchronize Preparation of the Cell
  State Splitters  136
3.05  The Right Place, at the Right Time, into the Right Kinds  139
3.06  The Intracellular Mechanics of the Cell State Splitter Yields
Ectodermal Differentiation  140
  Figure 14. A pressure P inside an embryo...  147
3.07  Force Generating and Load Bearing Cytoskeletal Components:
Microtubules (MT)  149
3.08  Force Generating and Load Bearing Cytoskeletal Components:
Microfilaments (MF)  152
3.09  Force Generating and Load Bearing Cytoskeletal Components:
Intermediate filaments (IF)  155
3.10  Combinations of Cytoskeletal Components  158

4.00  Development and Genetics  164
4.01  The General Cell State Splitter (Propositions 1-9)  164
4.02  Differentiation Trees (Propositions 10-20)  183
  Figure 15. A few simple differentiation trees...  184
  Figure 16. Terminology for parts of a differentiation tree...  189
  Figure 17. When the cell state splitter mechanically resolves...  208
  Figure 18. Smooth propagation of a contraction differentiation wave...  214
  Figure 19. Propagation of a 'bull's-eye' wave...  214
  Figure 20. Propagation of a spacing pattern wave...  215
  Figure 21. The epigenetic landscape...  217
4.03  Genetics and Differentiation Trees (Propositions 21-29)  221
4.04  A New Definition of 'Tissue' (Propositions 30-39)  241
  Table 2: Positional information and induction vs differentiation waves...
252
4.05  The Relationship Between Cells and Tissues in Regulating
  Embryos (Propositions 40-54)  263
4.06  The Relationship Between Cells and Tissues in Mosaic
  Embryos (Propositions 55-66)  301
  Figure 22. Four dimensional geometry of the development of a mosaic
organism...  313
  Figure 23. Four dimensional geometry of the development of a regulating
  organism...  314
5.00  Development and Evolution  354
5.01  Evolution of Cell State and Tissue Splitting (Propositions 67-73)  354
  Figure 24. DNA basis for a differentiation tree branch duplication...  361
  Figure 25. State of the DNA after a duplication...  362
  Figure 26. Coevolution of DNA after a duplication...  363
5.02  The Secondary Importance of Embryonic Induction
  (Propositions 74-92)  368
  Figure 27. Hierarchical differentiation cascade...  374
  Figure 28. Differentiation cascade as a web...  375
  Figure 29. Induction is secondary...  376
  Figure 30. Unbreakable inductions...  378
5.03  Dedifferentiation and Redifferentiation (Propositions 93-107)  412
  Figure 31. Two models for transdifferentiation...  414
5.04  The Selfish Differentiation Tree (Propositions 108-112)  436
5.05  The Ciliate Origin of Multicellular Organisms
  (Propositions 113-127)  447
447	Proposition 113: ciliates pattern their surfaces via cortical waves.
453	Proposition 114: the cortical waves of ciliates may involve changes
in protein expression, which may also be changes in cortical gene
expression.
458	Proposition 115: centrosomes may be symbiotic organelles.
464	Proposition 116: maternal determinants may be related to centrosomes.
467	Proposition 117: bacterial colonies capable of pattern formation
are homologous to the cortex of multicellular organisms.
472	Proposition 118: coordinated beating of cilia (metachronic waves)
in ciliates and in multicellular organisms are homologous, perhaps evolving
from surface colonies of primitive spirochetes.
476	Proposition 119: phenomena such as twinning and regeneration appear
to have a universal cortical basis.
478	Proposition 120: there is an evolutionary continuity in the cortex
as the seat of differentiation waves.
480	Proposition 121: during eukaryotic evolution, cortical
differentiation via differentiation waves preceded cellular differentiation.
482	Proposition 122: cortical inheritance and differentiation waves
preceded nuclear inheritance in the origin of eukaryotes.
483	Proposition 123: multicellular organisms are descended from
ciliates via recellularization of their cortical bacterial symbionts.
493	Proposition 124: control of the nuclear genome by differentiation
waves came relatively late in evolution.
497	Proposition 125: some of the Ediacaran organisms were ciliates.
498	Proposition 126: gastrulation started with the ciliates.
501	Proposition 127: the physics of the cortex may be the key to
morphogenesis.

6.00  Macroevolution  505
6.01  Redefining Microevolution and Macroevolution
  (Propositions 128-133)  505
  Figure 32. Nematode macroevolution...  509
  Figure 33. How to delete a middle subtree of a differentiation tree...  518
  Figure 34. Simplification of a differentiation tree by fusion...  519
6.02  Possible DNA Mechanisms for Macroevolutionary Change of
Differentiation Trees (Propositions 134-157)  520
  Figure 35. Reducing developmental time discrepancies...  528
  Figure 36 Genes per cascade vs number of kinds of cells...  550
  Table 3: Estimated numbers of genes per differentiation cascade...  551
  Table 4: Isochore correlations...  552
  Figure 37. A differentiation tree showing a terminal branch and a
subtree...  557
6.03  Differentiation Trees in Punctuated Equilibrium
  (Propositions 158-170)  573
  Figure 38. The lineage tree of the nematode...  606
6.04  The Grand Sweep of Evolution (Propositions 171-194)  609
  Figure 39. Bonner's Law...  629
  Figure 40. Computer simulation of a... phylogenetic tree...  633
  Figure 41. Evolution of brain size in mammals...  642
6.05  Neutralist Theory (Propositions 195-197)  658
6.06  A Universe Aware of Itself: Differentiation Waves and the Brain
(Propositions 198-205)  668

7.00  The Biogenetic Law  701
7.01  'Ontogeny Recapitulates Phylogeny' Revisited via
  Differentiation Trees (Propositions 206-218)  701
  Figure 42. Differentiation tree of a common ancestor...  708
  Figure 43. Differentiation tree of an archetype...  709
  Figure 44. Heterotropy...  720
  Figure 45. Heterochrony and differentiation trees...  725
7.02  Organisms with Two Differentiation Trees
  (Propositions 219-229)  726
  Figure 46. In continuing differentiation metamorphosis...  733
  Figure 47. In pulsatile metamorphosis...  733
  Figure 48. In single tissue metamorphosis...  734
  Figure 49. In dedifferentiation metamorphosis...  735
  Figure 50. Deferred metamorphosis  736
7.03 Winding up Evolution (Propositions 230-240)  747

8.00  The Homeobox  764
8.01  Why Insects and Vertebrates Share Homeobox Domains
  (Propositions 241-250)  764
  Figure 51. The Drosophila morphogenetic furrow...  794
  Figure 52. a) Variogram analysis...  795
8.02 The Development of Bilateral Asymmetry (Propositions 251-258)  803
  Figure 53. Microtubule/wave colored symmetry...  818
  Figure 54. Bilaterally symmetric shear couples...  823
  Figure 55. Torque applied to a cell on the left side...  824
  Figure 56. Torque applied to a cell on the right side...  824
8.03 Facets of Embryogenesis (Propositions 259-272)  830

9.00  A Cornucopia of Differentiation Waves  865
9.01  Activation Wave  865
9.02  Cleavage Waves  867
9.03  The Compaction Wave  874
9.04  Mitotic Waves  875
9.05  Quantal Mitoses and a Model for Limb Morphogenesis  881
9.06  Head and Tail Duplications  884
9.07  First Sitings of the Differentiation Waves of the Axolotl  893
9.08  Differentiation Waves of the Neural Plate  895
9.09  A Possible Pair of Differentiation Waves in the Later Epidermis  898
9.10  Neural Crest  901
9.11  Differentiation Waves in Plant Meristems  902
9.12  Differentiation Waves in Fly and Fish Eyes  908
9.13  Single Cell versus Multiple Cell Differentiation Waves  914
9.14  Repetitive Waves  917
9.15  Drosophila  Bristles: A Wave/Mechanical Reinterpretation  920
9.16  The American Shorthair Tabby Domestic Cat and Pigment
  Patterns  925
9.17  Butterfly Eye Spots  928
9.18  The Milk Line  936
9.19  Waves in Assorted Tissues  938
9.20  Waves on Anuran Embryos  943
  Figure 57. A nearly sagittal section of a Stage 10 1/2 axolotl embryo...  951
  Figure 58. Enlargement of one wave profile of the ectoderm contraction
wave...  952
9.21  Hints of Other Differentiation Waves  953
9.22  Uninvited Waves  956
  Figure 59. First observations of what may be waves on explants of axolotl
  ectoderm...  963
9.23  Are Others' Waves Our Waves?  967
  Table 5: Classes of calcium waves...  977
9.24  Are Differentiation Waves Merely Epiphenomena?  980
9.25  Mutant Waves  984
9.26  Wave Parallels between Mosaic and Regulating Organisms  988
9.27  Launching Domains May Have Specific Electrical, Mechanical
  and Molecular Properties  990

10.00  Conclusion  993
10.01  The Logic of Evolution  993
10.02  Is Evolution Progressive?  995
10.03  Were We Inevitable?  1002
10.04  The Living Ghost of Orthogenesis  1012
10.05  On Purpose and Progress  1017
10.06  The Beads-on-a-String 'New Synthesis'  1022
10.07  Gene Duplication as the Essence of Macroevolution  1026
10.08  The Blessings of Ever Increasing Dimensionality  1030
  Figure 60. Differentiation tree space...  1030
10.09  The Fractal Tree of Life  1035
  Figure 61. Darwin's schematic tree of life...  1038
  Figure 62. A tissue lineage tree...  1040
10.10  The Novel Unification of Development, Genetics and
  Evolution  1042
10.11  Exploring the Higher Order Structure of the Genome  1047
10.12  How to Find a GEM  1055
10.13  A Clockwork Universe Within: Nuclear Tensegrity Mechanics (Wurfels)
as a Foundation for the Nuclear State Splitter  1058
  Figure 63. Wurfel model for chromosomes...  1062
10.14  The Top Ten Questions  1070
10.15  Paradigms for Developmental Biology  1078
10.16  A New Curriculum for Biologists  1083

Appendix I   1085
Gordon, R. & G.W. Brodland (1987). The cytoskeletal mechanics  of brain
morphogenesis: cell state splitters cause primary neural  induction. Cell
Biophysics 11,  177-238.


Appendix II   1147
Brodland, G. W., R. Gordon, M. J. Scott, N. K. Björklund, K. B. Luchka,
C. C. Martin, C. Matuga, M. Globus, S. Vethamany-Globus & D. Shu (1994).
Furrowing surface contraction wave coincident with primary neural induction
in amphibian embryos. J. Morph.  219 (2), 131-142.

Appendix III   1159
Pursued by the Differentiation Wave

Appendix IV   1168
Björklund, N. K. & R. Gordon (1993b). Nuclear state splitting: a working
model for the mechanochemical coupling of differentiation waves to master
genes  (with an Addendum). Russian J. Dev. Biol. 24 (2), 79-95.

Appendix V   1185
Gordon, R., N. K. Björklund & P. D. Nieuwkoop (1994). Dialogue on embryonic
induction and differentiation waves. Int. Rev. Cytol. 150, 373-420.

Appendix VI   1233
Björklund, N.K. & R. Gordon (1994). 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. Computers & Chemistry  18 (3), 333-345.

Appendix VII   1246
Gordon, R. & N.K. Björklund (1996). How to observe surface contraction
waves on axolotls. Int. J. Dev. Biol.  40 (4), 913-914.

Appendix VIII   1248
Gordon, R. (1992d). Physicist to biologist: A first order phase transition.
Bulletin of the Canadian Society for Theoretical Biology  (10), 4-5.


Index of Propositions   1252
References   1266
Glossary and Abbreviations  1584
Citation and Subject Index   1643
Permissions and Note Added in Proof

Dr. Richard Gordon, Radiology, U. Manitoba, HSC, 820 Sherbrook Street,
Winnipeg R3A 1R9 Canada, Phone: (204) 789-3828, fax: (204)
787-2080/forthcoming book: The Hierarchical Genome & Differentiation Waves:
Novel Unification of Development, Genetics & Evolution:
http://www.wspc.com.sg/books/lifesci/2755.html



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