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
