Bourgine / LESNE / Lesne Morphogenesis

Origins of Patterns and Shapes
1. Auflage 2010
ISBN: 978-3-642-13174-5
Verlag: Springer
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 353 Seiten, eBook

What are the relations between the shape of a system of cities and that of fish school? Which events should happen in a cell in order that it participates to one of the finger of our hands? How to interpret the shape of a sand dune? This collective book written for the non-specialist addresses these questions and more generally, the fundamental issue of the emergence of forms and patterns in physical and living systems. It is a single book gathering the different aspects of morphogenesis and approaches developed in different disciplines on shape and pattern formation. Relying on the seminal works of D'Arcy Thompson, Alan Turing and René Thom, it confronts major examples like plant growth and shape, intra-cellular organization, evolution of living forms or motifs generated by crystals. A book essential to understand universal principles at work in the shapes and patterns surrounding us but also to avoid spurious analogies.

Zielgruppe

Research

Autoren/Hrsg.

Bourgine, Paul

Lesne, Annick

LESNE, Annick

Inhaltsverzeichnis

1;Morphogenesis;2
2;Preface;5
3;Contents;7
4;About the Authors;15
5;Chapter1 Introduction;18
5.1;Annick Lesne and Paul Bourgine;18
5.1.1;1.1 Fundamental Issues;18
5.1.1.1;1.1.1 The Notion of Shape;18
5.1.1.2;1.1.2 Some Paths to Explore the World of Shapes;19
5.1.1.3;1.1.3 Shapes and Their Causes;20
5.1.1.4;1.1.4 Modelling Morphogenesis;20
5.1.2;1.2 Morpho-Genesis;21
5.1.2.1;1.2.1 Shape-Generating Mechanisms;21
5.1.2.2;1.2.2 Equilibrium, Out-of-Equilibrium andFar-from-Equilibrium Shapes;21
5.1.2.3;1.2.3 Irreversibility;22
5.1.2.4;1.2.4 Self-Assembly and Self-Organisation;22
5.1.3;1.3 Instabilities, Phase Transitions and Symmetry Breaking;23
5.1.3.1;1.3.1 Phase Transitions, Bifurcations and Instabilities;23
5.1.3.2;1.3.2 Symmetry Breaking;24
5.1.3.3;1.3.3 Emergence;24
5.1.3.4;1.3.4 Fractal Shapes;25
5.1.4;1.4 Inanimate or Living Shapes;26
5.1.4.1;1.4.1 Some Questions;26
5.1.4.2;1.4.2 Are Living Shapes Special?;27
5.1.4.3;1.4.3 Functional Shapes;27
5.1.4.4;1.4.4 Genetic Programme, Self-Organisation and Epigenomics;28
5.1.4.5;1.4.5 The Robustness and Variability of Living Shapes;29
5.1.5;1.5 Book Overview;29
5.1.6;References;30
6;Chapter2 Ferrofluids: A Model System of Self-Organised Equilibrium;31
6.1;Jean-Claude Bacri and Florence Elias;31
6.1.1;2.1 Introduction: Situation with Regard to the Other Chapters;31
6.1.2;2.2 Physical Systems in Self-Organised Equilibrium;31
6.1.2.1;2.2.1 Examples of Self-Organised Physical Systems;32
6.1.2.2;2.2.2 The Origin of Order;35
6.1.2.3;2.2.3 The Bond Number;37
6.1.2.4;2.2.4 Domain Size and Choice of Pattern;37
6.1.2.5;2.2.5 Summary;38
6.1.3;2.3 Morphologies in Ferrofluids;38
6.1.3.1;2.3.1 Ferrofluids: A Model System for Studying Structures;38
6.1.3.2;2.3.2 Stripes and Bubbles, Foams and Rings in Ferrofluids;42
6.1.3.3;2.3.3 The Influence of History: Initial Conditions and Conditions of Formation;44
6.1.3.4;2.3.4 The Source of Patterns: Instabilities;47
6.1.4;2.4 Conclusion;53
6.1.5;References;54
7;Chapter3 Hierarchical Fracture Networks;56
7.1;Steffen Bohn;56
7.1.1;3.1 Introduction;56
7.1.2;3.2 The Formation of Hierarchical Fracture Networks;57
7.1.3;3.3 The Fracture Network as a Hierarchical Division of Space;59
7.1.4;3.4 A Characteristic Scale;60
7.1.5;3.5 Conclusion;62
8;Chapter4 Liquid Crystals and Morphogenesis;64
8.1;Yves Bouligand;64
8.1.1;4.1 Shells and Series of Arches;64
8.1.2;4.2 Helicoidal Plywood;66
8.1.3;4.3 Cholesteric Liquid Crystals and Stabilised Analogues;68
8.1.4;4.4 Specificity and Diversity of Liquid Crystals;69
8.1.4.1;4.4.1 Mesogenic Molecules;70
8.1.4.2;4.4.2 Structure of Liquid Crystals;71
8.1.4.3;4.4.3 Phase Transitions;72
8.1.5;4.5 Liquid Crystals and Stabilised Analogues in Biology: A Widespread Phenomenon;73
8.1.5.1;4.5.1 Muscles;73
8.1.5.2;4.5.2 Myelinic Figures and Fluid Cell Membranes;74
8.1.5.3;4.5.3 Stabilised Membranes;75
8.1.5.4;4.5.4 Nematic and Cholesteric Analogues;75
8.1.5.5;4.5.5 The Limits of a Widespread Phenomenon;75
8.1.6;4.6 Liquid Crystalline Self-Assemblies;76
8.1.7;4.7 Curvature and Structure;77
8.1.7.1;4.7.1 Diversity of Curvatures in Liquid Crystals and Their Analogues;77
8.1.7.2;4.7.2 Geometry of the Different Curvatures;79
8.1.7.3;4.7.3 Elastic Coefficients and Spontaneous Curvatures;83
8.1.8;4.8 Lyotropic Systems and Cell Fluidity;84
8.1.9;4.9 Liquids with Parallel Surfaces and the Geometrical Origin of Forms;87
8.1.9.1;4.9.1 Caps and Saddles: Elliptic or Hyperbolic Surfaces;88
8.1.9.2;4.9.2 Dupin Cyclides in Liquid Crystals;89
8.1.10;4.10 Germs and Textures of Liquid Crystals: Their Biological Analogues;92
8.1.11;4.11 Topological Nature of Liquid Crystalline Textures;96
8.1.11.1;4.11.1 Möbius Strips;96
8.1.11.2;4.11.2 Pairs of Interlocking Rings;97
8.1.12;4.12 Liquid Crystals and Mechanical Clock Movements;99
8.1.13;References;99
9;Chapter5 Biological Self-Organisation by Way of the Dynamics of Reactive Processes;102
9.1;James Tabony;102
9.1.1;5.1 Self-Organisation by Dynamic Processes in Physical Systems;105
9.1.2;5.2 Self-Organisation in Colonies of Living Organisms;107
9.1.3;5.3 Self-Organisation by Reaction and Diffusion: Stripes in a Test-Tube;108
9.1.4;5.4 Microtubule Self-Organisation;112
9.1.5;References;118
10;Chapter6 Dunes, the Collective Behaviour of Wind and Sand, or: Are Dunes Living Beings?;121
10.1;Stéphane Douady and Pascal Hersen;121
10.1.1;6.1 Discovery;121
10.1.2;6.2 The Wind Drives the Sand … Which Steals the Wind's Forceas It Flies;121
10.1.3;6.3 The Minimal Dune;122
10.1.4;6.4 The Wind Runs Over the Dune … and Pushes It Along;123
10.1.5;6.5 Does the Wind Flow Make the Dune?;123
10.1.6;6.6 Understanding the Barchan Shape;125
10.1.7;6.7 The Paradox of Corridors … or the Problem of Dunes Among Themselves;128
10.1.8;6.8 The Wind is Never Constant;128
10.1.9;6.9 Dunes are Not Isolated;129
10.1.10;6.10 The Grain of Sand, the Dune and the Corridor of Dunes …What About the Individual, the Flows and the Form?;130
10.1.11;References;132
11;Chapter7 Morphodynamics of Secretory Endomembranes;133
11.1;François Képès;133
11.1.1;7.1 Some Preliminary Reminders;133
11.1.2;7.2 Introduction;134
11.1.2.1;7.2.1 Cell Membrane and Translocation;134
11.1.2.2;7.2.2 Eukaryotic Secretory Pathway;135
11.1.2.3;7.2.3 Other Eukaryotic Compartments;137
11.1.2.4;7.2.4 Cytoplasm, Cytoskeleton and Compartmentalisation;137
11.1.3;7.3 Morphodynamics of Membranes;137
11.1.3.1;7.3.1 Biological Membranes;137
11.1.3.2;7.3.2 Segregation;138
11.1.3.3;7.3.3 Fission;140
11.1.3.4;7.3.4 Fusion;145
11.1.4;7.4 Functional Models;147
11.1.5;7.5 Conclusions;150
11.1.5.1;7.5.1 Themes;150
11.1.5.2;7.5.2 Evolutionary Perspectives;150
11.1.5.3;7.5.3 Questions;151
11.1.5.4;7.5.4 Prospects;152
11.1.6;References;152
12;Chapter8 From Epigenomic to Morphogenetic Emergence;156
12.1;Caroline Smet-Nocca, Andràs Paldi, and Arndt Benecke;156
12.1.1;8.1 Genetic Inheritance, Regulation of Gene Expression, and Chromatin Dynamics;158
12.1.1.1;8.1.1 Gene Transcription and the Regulation of Gene Expression;158
12.1.1.2;8.1.2 Genomic Structure and its Impact on Transcriptional Regulation;159
12.1.2;8.2 Epigenetic Mechanisms, Epigenetic Inheritance and Cell Differentiation;162
12.1.2.1;8.2.1 DNA Methylation: Epigenetic Marker of Transcriptional Repression;162
12.1.2.2;8.2.2 Structural and Functional Organisation of Chromatin: Spatio-Temporal Regulation;165
12.1.3;8.3 The Link Between Epigenetic Information and the Regulation of Gene Expression;171
12.1.3.1;8.3.1 The Link Between DNA Repair and Transcription;171
12.1.3.2;8.3.2 CBP/p300, HATs Involved in Cell Growth, Differentiation and Development;173
12.1.3.3;8.3.3 Epigenetics and Oncogenesis;174
12.1.4;8.4 Morphogenomics;176
12.1.5;References;179
13;Chapter9 Animal Morphogenesis;180
13.1;Nadine Peyriéras;180
13.1.1;9.1 The Acquisition of Cell Diversity;182
13.1.1.1;9.1.1 Heterogeneity of the Egg: What Is Determined from the Moment of Fertilisation?;183
13.1.1.2;9.1.2 The Interaction Between Cells and Their Environment and the ``Inside-Outside'' Hypothesis;184
13.1.2;9.2 The Anatomical Tradition of Embryology, Identification of Symmetry Breaking and Characterisation of Morphogenetic Fields;184
13.1.2.1;9.2.1 Symmetry-Breaking in Early Embryogenesis;185
13.1.2.2;9.2.2 Formation of Boundaries and Compartments During Organogenesis;188
13.1.3;9.3 The ``Bottom-Up'' Approach of Developmental Biology;189
13.1.3.1;9.3.1 Dynamics of Molecular and Genetic Interactions in the Formation of Patterns;191
13.1.3.2;9.3.2 The Concept of Morphogen and Pattern Generation Through the Threshold Effect;192
13.1.3.3;9.3.3 The Formation of Somites in Vertebrates: A Model of Coupled Oscillators;194
13.1.4;9.4 The Reconstruction of Cell Morphodynamics and the Revival of the Anatomical Tradition of Embryology;197
13.1.4.1;9.4.1 Cell Movements and Deformations in Morphogenesis;197
13.1.4.2;9.4.2 Cell Adhesion and Biomechanical Constraints in the Embryo;198
13.1.4.3;9.4.3 The Tensegrity Model;198
13.1.5;References;200
14;Chapter10 Phyllotaxis, or How Plants Do Maths When they Grow;202
14.1;Stéphane Douady;202
14.1.1;10.1 Discovery;202
14.1.2;10.2 Why?;203
14.1.3;10.3 How?;205
14.1.4;10.4 Van Iterson's Tree … Pruned!;207
14.1.5;10.5 Dynamics;209
14.1.6;10.6 Conclusion;210
14.1.7;References;211
15;Chapter11 The Logic of Forms in the Light of Developmental Biology and Palaeontology;212
15.1;Didier Marchand;212
15.1.1;11.1 Introduction;212
15.1.2;11.2 Palaeontology and Time;213
15.1.3;11.3 From the Cell to the Multicellular Organism: An Ever More Complex Game of ``Lego'';214
15.1.4;11.4 The Major Body Plans: In the Early Cambrian, Quite Everything Was Already in Place;215
15.1.5;11.5 The Phylum of Vertebrates: A Fine Example of Peramorphosis;217
15.1.6;11.6 The Anomalies of Development: An Opening Towards New Morphologies;218
15.1.7;11.7 The Brain as the Last Space of Freedom;220
15.1.8;11.8 Conclusion;221
15.1.9;References;222
16;Chapter12 Forms Emerging from Collective Motion;223
16.1;Hugues Chaté and Guillaume Grégoire;223
16.1.1;12.1 Introduction;223
16.1.2;12.2 Towards a Minimal Model;225
16.1.2.1;12.2.1 The Ingredients;225
16.1.2.2;12.2.2 Formalisation;226
16.1.2.3;12.2.3 The Results of Vicsek et al.;228
16.1.3;12.3 Forms in the Absence of Cohesion;230
16.1.3.1;12.3.1 Moving in Self-Organised Groups;230
16.1.3.2;12.3.2 Microscopic Trajectories and Forms;231
16.1.4;12.4 When Cohesion Is Present: Droplets in Motion;232
16.1.4.1;12.4.1 Phase Diagrams and Form of Droplets;232
16.1.4.2;12.4.2 Cohesion Broken During the Onset of Motion;233
16.1.5;12.5 Back to Nature;234
16.1.6;References;235
17;Chapter13 Systems of Cities and Levels of Organisation;236
17.1;Denise Pumain;236
17.1.1;13.1 Three Levels of Observation of the Urban Fact;237
17.1.1.1;13.1.1 Emergent Properties at the City Level;237
17.1.1.2;13.1.2 The Structure of the System of Cities;239
17.1.2;13.2 A Functional Interpretation of the Hierarchical Ordering;242
17.1.2.1;13.2.1 Daily Life in the City;243
17.1.2.2;13.2.2 The Functions of the System of Cities;244
17.1.3;13.3 The Interactions that Construct the Levels;246
17.1.3.1;13.3.1 The Constituent Interactions of City Forms;248
17.1.3.2;13.3.2 The Constituent Interactions of Systems of Cities;250
17.1.4;13.4 Complex Systems Models for Urban Morphogenesis;253
17.1.4.1;13.4.1 Cities as Spatial Objects;254
17.1.4.2;13.4.2 Cities and Fractal Objects;255
17.1.4.3;13.4.3 From Support Space to Relational and Conforming Space;256
17.1.5;References;257
18;Chapter14 Levels of Organisation and Morphogenesis from the Perspective of D'Arcy Thompson;261
18.1;Yves Bouligand;261
18.1.1;14.1 Games of Construction;262
18.1.1.1;14.1.1 Chemical Syntheses and Biosyntheses;262
18.1.1.2;14.1.2 Supramolecular Assemblies and their Lattices;264
18.1.1.3;14.1.3 Molecular and Supramolecular Models;266
18.1.2;14.2 Water Games;266
18.1.2.1;14.2.1 Hydrostatic Forms;267
18.1.2.2;14.2.2 Hydrodynamic Figures;268
18.1.2.3;14.2.3 Morphological Adaptations to the Hydrodynamics of the Environment;269
18.1.3;14.3 The Fragile Architectures of Diffusion;270
18.1.3.1;14.3.1 Hydrostatic Diffusion;270
18.1.3.2;14.3.2 Hydrodynamic Diffusion;271
18.1.4;14.4 Stabilisation and Reorganisation of Forms;272
18.1.5;14.5 The Problem of Strong Local Curvature and New Prospects;273
18.1.6;14.6 Particular and General Morphogenetic Theories;275
18.1.6.1;14.6.1 The Direct or Indirect Role of the Genome in Morphogenesis;275
18.1.6.2;14.6.2 Symmetry Breaking and Differentiation;277
18.1.6.3;14.6.3 New Prospects in Morphogenesis and the Concept of Viability;280
18.1.7;References;281
19;Chapter15 The Morphogenetic Models of René Thom;283
19.1;Jean Petitot;283
19.1.1;15.1 General Content of the Model;283
19.1.2;15.2 Morphodynamics and Structural Stability;285
19.1.3;15.3 The Theory of Dynamical Systems;286
19.1.4;15.4 The Theory of Singularities and ``Elementary'' Morphogenetic Models;289
19.1.5;15.5 The Principles of Morphodynamic Models;290
19.1.6;15.6 The Models of Morphogenesis;291
19.1.7;References;291
20;Chapter16 Morphogenesis, Structural Stability and Epigenetic Landscape;292
20.1;Sara Franceschelli;292
20.1.1;16.1 The Correspondence;292
20.1.2;16.2 Delbrück's Model;295
20.1.3;16.3 Structural Stability and Morphogenetic Field;296
20.1.4;16.4 Epigenetic Landscape: A Mental Picture, a Metaphor …of What?;297
20.1.5;16.5 Interpretations;301
20.1.6;References;301
21;Chapter17 Morphological and Mutational Analysis: Tools for the Study of Morphogenesis;303
21.1;Jean-Pierre Aubin and Annick Lesne;303
21.1.1;17.1 Objectives;303
21.1.2;17.2 Motivations;305
21.1.2.1;17.2.1 Problems of Co-Viability;305
21.1.2.2;17.2.2 Biological Morphogenesis;307
21.1.2.3;17.2.3 Image Processing;308
21.1.2.4;17.2.4 Shape Optimisation;308
21.1.2.5;17.2.5 Dynamic Economics;308
21.1.2.6;17.2.6 Front Propagation;309
21.1.2.7;17.2.7 Visual Robotics;309
21.1.2.8;17.2.8 Interval Analysis;309
21.1.3;17.3 The Genesis of Morphological Analysis;309
21.1.4;17.4 From Shape Optimisation to Set-Valued Analysis;310
21.1.5;17.5 Velocities of Tubes as Mutations;314
21.1.6;17.6 Mutational Analysis;314
21.1.7;17.7 Morphological Equations;316
21.1.8;17.8 Embryogenesis of the Zebrafish;319
21.1.9;References;320
22;Chapter18 Computer Morphogenesis;323
22.1;Jean-Louis Giavitto and Antoine Spicher;323
22.1.1;18.1 Explaining Living Matter by Understanding Development;323
22.1.1.1;18.1.1 The Animal-Machine;323
22.1.1.2;18.1.2 From Self-Reproduction to Development;325
22.1.1.3;18.1.3 Development as a Dynamical System;326
22.1.1.4;18.1.4 What Formalism for Dynamical Systems with Dynamical Structure?;329
22.1.2;18.2 Rewriting Systems;331
22.1.2.1;18.2.1 Introduction;331
22.1.2.2;18.2.2 Rewriting Systems and the Simulation of Dynamical Systems;333
22.1.3;18.3 Multiset Rewriting and Chemical Modelling;334
22.1.3.1;18.3.1 Some Examples of Application;336
22.1.3.2;18.3.2 Paun Systems and Compartmentalisation;337
22.1.3.3;18.3.3 In Parenthesis: The Application to Parallel Programming;339
22.1.4;18.4 Lindenmayer Systems and the Growth of Linear Structures;340
22.1.4.1;18.4.1 Growth of a Filamentous Structure;340
22.1.4.2;18.4.2 Development of a Branching Structure;342
22.1.5;18.5 Beyond Linear Structures: Calculating a Form in Order to Understand It;343
22.1.5.1;18.5.1 Simulation and Explanation;343
22.1.5.2;18.5.2 Giving Form to a Population of Autonomous Agents;344
22.1.6;References;345
23;Index;348

Introduction.- Self-organization at equilibrum. A model system: ferrofluids.- Hierarchical networks of fractures.- Liquid crystals and morphogenesis.- Biological self-organization by way of the dynamics of reactive processes.- Sand dunes.- Morphodynamics of secretory pathways.- From epigenomics to morphogenetic emergence.- Animal morphogenesis.- Phyllotaxy.- Logic of forms.- Forms emerging from collective motion.- Systems of cities and levels of organization.- Levels of organization and morphogenesis: the viewpoint of D'Arcy Thompson.- Morphogenetic models of René Thom.- Morphogenesis, structural stability and epigenetic landscape.- Morphological and mutational analysis: tools for morphogenesis study.- Morphogenesis in computer science.