Morphogenesis (eBook)

Morphogenesis 2
Preface 5
Contents 7
About the Authors 15
Chapter1 Introduction 18
Annick Lesne and Paul Bourgine 18
1.1 Fundamental Issues 18
1.1.1 The Notion of Shape 18
1.1.2 Some Paths to Explore the World of Shapes 19
1.1.3 Shapes and Their Causes 20
1.1.4 Modelling Morphogenesis 20
1.2 Morpho-Genesis 21
1.2.1 Shape-Generating Mechanisms 21
1.2.2 Equilibrium, Out-of-Equilibrium andFar-from-Equilibrium Shapes 21
1.2.3 Irreversibility 22
1.2.4 Self-Assembly and Self-Organisation 22
1.3 Instabilities, Phase Transitions and Symmetry Breaking 23
1.3.1 Phase Transitions, Bifurcations and Instabilities 23
1.3.2 Symmetry Breaking 24
1.3.3 Emergence 24
1.3.4 Fractal Shapes 25
1.4 Inanimate or Living Shapes 26
1.4.1 Some Questions 26
1.4.2 Are Living Shapes Special? 27
1.4.3 Functional Shapes 27
1.4.4 Genetic Programme, Self-Organisation and Epigenomics 28
1.4.5 The Robustness and Variability of Living Shapes 29
1.5 Book Overview 29
References 30
Chapter2 Ferrofluids: A Model System of Self-Organised Equilibrium 31
Jean-Claude Bacri and Florence Elias 31
2.1 Introduction: Situation with Regard to the Other Chapters 31
2.2 Physical Systems in Self-Organised Equilibrium 31
2.2.1 Examples of Self-Organised Physical Systems 32
2.2.2 The Origin of Order 35
2.2.3 The Bond Number 37
2.2.4 Domain Size and Choice of Pattern 37
2.2.5 Summary 38
2.3 Morphologies in Ferrofluids 38
2.3.1 Ferrofluids: A Model System for Studying Structures 38
2.3.2 Stripes and Bubbles, Foams and Rings in Ferrofluids 42
2.3.3 The Influence of History: Initial Conditions and Conditions of Formation 44
2.3.4 The Source of Patterns: Instabilities 47
2.4 Conclusion 53
References 54
Chapter3 Hierarchical Fracture Networks 56
Steffen Bohn 56
3.1 Introduction 56
3.2 The Formation of Hierarchical Fracture Networks 57
3.3 The Fracture Network as a Hierarchical Division of Space 59
3.4 A Characteristic Scale 60
3.5 Conclusion 62
Chapter4 Liquid Crystals and Morphogenesis 64
Yves Bouligand 64
4.1 Shells and Series of Arches 64
4.2 Helicoidal Plywood 66
4.3 Cholesteric Liquid Crystals and Stabilised Analogues 68
4.4 Specificity and Diversity of Liquid Crystals 69
4.4.1 Mesogenic Molecules 70
4.4.2 Structure of Liquid Crystals 71
4.4.3 Phase Transitions 72
4.5 Liquid Crystals and Stabilised Analogues in Biology: A Widespread Phenomenon 73
4.5.1 Muscles 73
4.5.2 Myelinic Figures and Fluid Cell Membranes 74
4.5.3 Stabilised Membranes 75
4.5.4 Nematic and Cholesteric Analogues 75
4.5.5 The Limits of a Widespread Phenomenon 75
4.6 Liquid Crystalline Self-Assemblies 76
4.7 Curvature and Structure 77
4.7.1 Diversity of Curvatures in Liquid Crystals and Their Analogues 77
4.7.2 Geometry of the Different Curvatures 79
4.7.3 Elastic Coefficients and Spontaneous Curvatures 83
4.8 Lyotropic Systems and Cell Fluidity 84
4.9 Liquids with Parallel Surfaces and the Geometrical Origin of Forms 87
4.9.1 Caps and Saddles: Elliptic or Hyperbolic Surfaces 88
4.9.2 Dupin Cyclides in Liquid Crystals 89
4.10 Germs and Textures of Liquid Crystals: Their Biological Analogues 92
4.11 Topological Nature of Liquid Crystalline Textures 96
4.11.1 Möbius Strips 96
4.11.2 Pairs of Interlocking Rings 97
4.12 Liquid Crystals and Mechanical Clock Movements 99
References 99
Chapter5 Biological Self-Organisation by Way of the Dynamics of Reactive Processes 102
James Tabony 102
5.1 Self-Organisation by Dynamic Processes in Physical Systems 105
5.2 Self-Organisation in Colonies of Living Organisms 107
5.3 Self-Organisation by Reaction and Diffusion: Stripes in a Test-Tube 108
5.4 Microtubule Self-Organisation 112
References 118
Chapter6 Dunes, the Collective Behaviour of Wind and Sand, or: Are Dunes Living Beings? 121
Stéphane Douady and Pascal Hersen 121
6.1 Discovery 121
6.2 The Wind Drives the Sand … Which Steals the Wind's Forceas It Flies 121
6.3 The Minimal Dune 122
6.4 The Wind Runs Over the Dune … and Pushes It Along 123
6.5 Does the Wind Flow Make the Dune? 123
6.6 Understanding the Barchan Shape 125
6.7 The Paradox of Corridors … or the Problem of Dunes Among Themselves 128
6.8 The Wind is Never Constant 128
6.9 Dunes are Not Isolated 129
6.10 The Grain of Sand, the Dune and the Corridor of Dunes …What About the Individual, the Flows and the Form? 130
References 132
Chapter7 Morphodynamics of Secretory Endomembranes 133
François Képès 133
7.1 Some Preliminary Reminders 133
7.2 Introduction 134
7.2.1 Cell Membrane and Translocation 134
7.2.2 Eukaryotic Secretory Pathway 135
7.2.3 Other Eukaryotic Compartments 137
7.2.4 Cytoplasm, Cytoskeleton and Compartmentalisation 137
7.3 Morphodynamics of Membranes 137
7.3.1 Biological Membranes 137
7.3.2 Segregation 138
7.3.3 Fission 140
7.3.4 Fusion 145
7.4 Functional Models 147
7.5 Conclusions 150
7.5.1 Themes 150
7.5.2 Evolutionary Perspectives 150
7.5.3 Questions 151
7.5.4 Prospects 152
References 152
Chapter8 From Epigenomic to Morphogenetic Emergence 156
Caroline Smet-Nocca, Andràs Paldi, and Arndt Benecke 156
8.1 Genetic Inheritance, Regulation of Gene Expression, and Chromatin Dynamics 158
8.1.1 Gene Transcription and the Regulation of Gene Expression 158
8.1.2 Genomic Structure and its Impact on Transcriptional Regulation 159
8.2 Epigenetic Mechanisms, Epigenetic Inheritance and Cell Differentiation 162
8.2.1 DNA Methylation: Epigenetic Marker of Transcriptional Repression 162
8.2.2 Structural and Functional Organisation of Chromatin: Spatio-Temporal Regulation 165
8.3 The Link Between Epigenetic Information and the Regulation of Gene Expression 171
8.3.1 The Link Between DNA Repair and Transcription 171
8.3.2 CBP/p300, HATs Involved in Cell Growth, Differentiation and Development 173
8.3.3 Epigenetics and Oncogenesis 174
8.4 Morphogenomics 176
References 179
Chapter9 Animal Morphogenesis 180
Nadine Peyriéras 180
9.1 The Acquisition of Cell Diversity 182
9.1.1 Heterogeneity of the Egg: What Is Determined from the Moment of Fertilisation? 183
9.1.2 The Interaction Between Cells and Their Environment and the ``Inside-Outside'' Hypothesis 184
9.2 The Anatomical Tradition of Embryology, Identification of Symmetry Breaking and Characterisation of Morphogenetic Fields 184
9.2.1 Symmetry-Breaking in Early Embryogenesis 185
9.2.2 Formation of Boundaries and Compartments During Organogenesis 188
9.3 The ``Bottom-Up'' Approach of Developmental Biology 189
9.3.1 Dynamics of Molecular and Genetic Interactions in the Formation of Patterns 191
9.3.2 The Concept of Morphogen and Pattern Generation Through the Threshold Effect 192
9.3.3 The Formation of Somites in Vertebrates: A Model of Coupled Oscillators 194
9.4 The Reconstruction of Cell Morphodynamics and the Revival of the Anatomical Tradition of Embryology 197
9.4.1 Cell Movements and Deformations in Morphogenesis 197
9.4.2 Cell Adhesion and Biomechanical Constraints in the Embryo 198
9.4.3 The Tensegrity Model 198
References 200
Chapter10 Phyllotaxis, or How Plants Do Maths When they Grow 202
Stéphane Douady 202
10.1 Discovery 202
10.2 Why? 203
10.3 How? 205
10.4 Van Iterson's Tree … Pruned! 207
10.5 Dynamics 209
10.6 Conclusion 210
References 211
Chapter11 The Logic of Forms in the Light of Developmental Biology and Palaeontology 212
Didier Marchand 212
11.1 Introduction 212
11.2 Palaeontology and Time 213
11.3 From the Cell to the Multicellular Organism: An Ever More Complex Game of ``Lego'' 214
11.4 The Major Body Plans: In the Early Cambrian, Quite Everything Was Already in Place 215
11.5 The Phylum of Vertebrates: A Fine Example of Peramorphosis 217
11.6 The Anomalies of Development: An Opening Towards New Morphologies 218
11.7 The Brain as the Last Space of Freedom 220
11.8 Conclusion 221
References 222
Chapter12 Forms Emerging from Collective Motion 223
Hugues Chaté and Guillaume Grégoire 223
12.1 Introduction 223
12.2 Towards a Minimal Model 225
12.2.1 The Ingredients 225
12.2.2 Formalisation 226
12.2.3 The Results of Vicsek et al. 228
12.3 Forms in the Absence of Cohesion 230
12.3.1 Moving in Self-Organised Groups 230
12.3.2 Microscopic Trajectories and Forms 231
12.4 When Cohesion Is Present: Droplets in Motion 232
12.4.1 Phase Diagrams and Form of Droplets 232
12.4.2 Cohesion Broken During the Onset of Motion 233
12.5 Back to Nature 234
References 235
Chapter13 Systems of Cities and Levels of Organisation 236
Denise Pumain 236
13.1 Three Levels of Observation of the Urban Fact 237
13.1.1 Emergent Properties at the City Level 237
13.1.2 The Structure of the System of Cities 239
13.2 A Functional Interpretation of the Hierarchical Ordering 242
13.2.1 Daily Life in the City 243
13.2.2 The Functions of the System of Cities 244
13.3 The Interactions that Construct the Levels 246
13.3.1 The Constituent Interactions of City Forms 248
13.3.2 The Constituent Interactions of Systems of Cities 250
13.4 Complex Systems Models for Urban Morphogenesis 253
13.4.1 Cities as Spatial Objects 254
13.4.2 Cities and Fractal Objects 255
13.4.3 From Support Space to Relational and Conforming Space 256
References 257
Chapter14 Levels of Organisation and Morphogenesis from the Perspective of D'Arcy Thompson 261
Yves Bouligand 261
14.1 Games of Construction 262
14.1.1 Chemical Syntheses and Biosyntheses 262
14.1.2 Supramolecular Assemblies and their Lattices 264
14.1.3 Molecular and Supramolecular Models 266
14.2 Water Games 266
14.2.1 Hydrostatic Forms 267
14.2.2 Hydrodynamic Figures 268
14.2.3 Morphological Adaptations to the Hydrodynamics of the Environment 269
14.3 The Fragile Architectures of Diffusion 270
14.3.1 Hydrostatic Diffusion 270
14.3.2 Hydrodynamic Diffusion 271
14.4 Stabilisation and Reorganisation of Forms 272
14.5 The Problem of Strong Local Curvature and New Prospects 273
14.6 Particular and General Morphogenetic Theories 275
14.6.1 The Direct or Indirect Role of the Genome in Morphogenesis 275
14.6.2 Symmetry Breaking and Differentiation 277
14.6.3 New Prospects in Morphogenesis and the Concept of Viability 280
References 281
Chapter15 The Morphogenetic Models of René Thom 283
Jean Petitot 283
15.1 General Content of the Model 283
15.2 Morphodynamics and Structural Stability 285
15.3 The Theory of Dynamical Systems 286
15.4 The Theory of Singularities and ``Elementary'' Morphogenetic Models 289
15.5 The Principles of Morphodynamic Models 290
15.6 The Models of Morphogenesis 291
References 291
Chapter16 Morphogenesis, Structural Stability and Epigenetic Landscape 292
Sara Franceschelli 292
16.1 The Correspondence 292
16.2 Delbrück's Model 295
16.3 Structural Stability and Morphogenetic Field 296
16.4 Epigenetic Landscape: A Mental Picture, a Metaphor …of What? 297
16.5 Interpretations 301
References 301
Chapter17 Morphological and Mutational Analysis: Tools for the Study of Morphogenesis 303
Jean-Pierre Aubin and Annick Lesne 303
17.1 Objectives 303
17.2 Motivations 305
17.2.1 Problems of Co-Viability 305
17.2.2 Biological Morphogenesis 307
17.2.3 Image Processing 308
17.2.4 Shape Optimisation 308
17.2.5 Dynamic Economics 308
17.2.6 Front Propagation 309
17.2.7 Visual Robotics 309
17.2.8 Interval Analysis 309
17.3 The Genesis of Morphological Analysis 309
17.4 From Shape Optimisation to Set-Valued Analysis 310
17.5 Velocities of Tubes as Mutations 314
17.6 Mutational Analysis 314
17.7 Morphological Equations 316
17.8 Embryogenesis of the Zebrafish 319
References 320
Chapter18 Computer Morphogenesis 323
Jean-Louis Giavitto and Antoine Spicher 323
18.1 Explaining Living Matter by Understanding Development 323
18.1.1 The Animal-Machine 323
18.1.2 From Self-Reproduction to Development 325
18.1.3 Development as a Dynamical System 326
18.1.4 What Formalism for Dynamical Systems with Dynamical Structure? 329
18.2 Rewriting Systems 331
18.2.1 Introduction 331
18.2.2 Rewriting Systems and the Simulation of Dynamical Systems 333
18.3 Multiset Rewriting and Chemical Modelling 334
18.3.1 Some Examples of Application 336
18.3.2 Paun Systems and Compartmentalisation 337
18.3.3 In Parenthesis: The Application to Parallel Programming 339
18.4 Lindenmayer Systems and the Growth of Linear Structures 340
18.4.1 Growth of a Filamentous Structure 340
18.4.2 Development of a Branching Structure 342
18.5 Beyond Linear Structures: Calculating a Form in Order to Understand It 343
18.5.1 Simulation and Explanation 343
18.5.2 Giving Form to a Population of Autonomous Agents 344
References 345
Index 348