On the Origins and Dynamics of Biodiversity: the Role of Chance (eBook)

Foreword 7
Acknowledgements 10
Summary 12
Contents 13
1 Questioning Chance 17
1.1 Introduction 17
1.2 Different Uses of the Word Chance in the Sciences 19
1.2.1 Chance in Quantum Mechanics and Mechanical Statistics 20
1.2.2 Chance for the Statistician 22
1.2.3 Chance for the Probability Theorist 23
1.2.4 Chance for the Numerical Analyst and the Computer Scientist 24
Box 1.1 Generating Pseudo-Random Numbers 25
1.2.5 Chance, Hazards, and Risks 26
1.2.6 Life Tested by the Vagaries of the Environment During Its Long History 27
2 Chance in Living Systems 30
2.1 Chance and Necessity 30
2.1.1 The Neutral Theory of Evolution: A Gentle Necessity 31
2.1.2 The Couple Chance-Necessity 32
2.1.3 Randomness and Evolution: The Necessity of Chance 33
2.1.4 From the Gene to the Ecosystem: Chance in the Different Organisational Levels of Living Systems 33
2.2 Known Genetic Diversification Mechanisms 34
2.2.1 Gene Diversification: The Randomness of One-Off Mutations 34
Reminder: 36
2.2.2 The Organisation and Plasticity of the Genome: The Vagaries of Piecewise Mutations 37
2.2.2.1 Prokaryotes 37
Box 2.1 The Mixing of the Genome Schematic Representation of the Principal, Known Mechanisms 38
2.2.2.2 Eukaryotes 39
2.2.2.3 The Particular Case of Gene Duplication 39
2.2.2.4 Epigenetics 40
2.2.2.5 Conclusion: The Diversity of Genome Modification Mechanisms 42
2.2.3 Reproduction and the Transmission of Genetic Information: Shuffling the Cards 42
2.2.3.1 Sexual Reproduction: The Production of Gametes 42
2.2.3.2 Sexual Reproduction: The Fertilisation and Fusion of Gametes 44
2.2.3.3 Other Methods of Reproduction 44
2.2.3.4 Horizontal and Vertical Transfers 44
2.3 The Cell and the Organism: A Limited Randomness 46
2.3.1 A Living Machine 46
2.3.2 Individual Homogeneity, the Diversity of Organisms 46
2.3.3 A Cooperative Structure 48
Box 2.2 Competition and Cooperation 48
2.3.4 A Limited, But Efficient Randomness: The Immune and Olfactory Systems 50
2.3.5 Using the Vagaries of the Environment 52
2.3.6 Organisms and Changes in the Environment 52
2.3.7 Random Behaviours 52
2.4 Lineages, Populations and Species: Chance Encounters, Couplings, and Disturbances 54
Box 2.3 Populations, Metapopulations, Species 54
Theoretical Diagram: Populations, Metapopulations and Species 55
2.5 The Main Sources of Biodiversity 57
2.6 Evolution and Its Theories: The Randomness of Genetic Modifications 58
2.7 Ecological Randomness: Live and Survive Together, Face Environmental Risks 61
Box 2.4 Competitive Exclusion 62
2.7.1 The Neutral Theory of Biodiversity 64
2.7.2 Spatial Distribution: Randomness and Necessity in the Environment 65
2.7.3 Evolutional Interpretation in the Face of Risks: Necessary Diversification and the no Less Necessary Random Distribution 66
2.7.3.1 Higher Plants and Their Spatial Distribution 66
Box 2.5 Co-evolution 68
Box 2.6 Frugivory and Seed Dissemination: The Use of Cecropia obtusa by the Bat, Artibeus jamaicensis 70
2.7.3.2 And for Animals: Which Distributions? 71
2.7.3.3 Micro-Organisms: At the Will of the Environment and of Others 72
2.7.3.4 Deterministic and Random Movement 72
2.7.4 The Dynamics of Biodiversity 74
2.7.5 Measuring Biodiversity 78
2.8 Randomness, Chaos and Complexity 81
2.8.1 From Chaos to Randomness 82
2.8.2 Intermittences 84
2.8.3 Two Types of Randomness, Two Complexities 84
2.9 Randomness and the Organisational Levels of Living Systems 86
Box 2.7 How do Living Systems Organise Themselves? 87
2.10 Conclusion 90
3 Lessons for Managing Living Systems 94
3.1 Organisms 94
3.2 Populations and Ecosystems 95
3.3 Biodiversity 96
3.4 Information and Genetic Heritage 97
3.5 Conserving Genetic Resources 97
3.6 Genetic Modification: Hybridisation and Selection 97
3.7 Genetic Manipulation: Gene Insertion 99
3.8 Cloning 100
3.9 Active Molecules of Biological Origin 101
3.10 Ecotoxicology 102
3.11 The Limits and Consequences of Mankinds Intervention on Living Systems 103
3.12 Bio-inspired and Bio-mimetic Technologies 104
4 The Contribution of Models and Modelling: Some Examples 105
4.1 Genetics and Calculating Probability: Elementary Laws and Evolution During the Genetic Constitution of a Population 106
4.1.1 The Mendelian Model 106
4.1.2 Genetic Evolution of an Autogamous Population 107
4.2 From Chaos to Randomness: Biological Roulettes An Example from the Discrete-Time Logistic Model 110
4.2.1 Discrete-Time Logistic Model 110
4.2.2 Analysis of the Simultaneous Dynamics of Two Populations 113
4.2.3 From the Erratic to the Regular: The Effect of Pairing 114
4.2.4 From Chaos to Randomness 115
4.3 The Continuous-Time Logistic Model and the Evolution of Biodiversity 117
4.4 Towards a General Schema for Modelling Living Systems and Their Diversities 124
5 Biodiversity and Ecological Theories 127
5.1 The Niche Theory 129
5.2 Niches and the Logistic Model 131
5.3 The Neutral Theory of Biodiversity 132
5.4 Can We Reconcile the Two Approaches? 134
5.5 A Set of Processes to Explain the Spatial Distribution of Individuals in Diversified Systems by Species 135
5.6 Chance at the Heart of Natural Ecosystems? 137
6 Chance and Evolution 140
6.1 Evolution But Its Very Simple 141
6.2 And Chance in All of That? 142
6.3 Biological Roulettes: Products and Engines of Evolution 146
6.4 Chance, Complexity and Biodiversity 147
6.5 Evolution and the Self-organisation of Living Systems and Others 150
7 Evaluating Biodiversity: The Example of French Guiana 152
7.1 A Large Diversity 152
7.2 Species Diversity and Its Evaluation: Data, Certainties and Uncertainties 153
7.2.1 The First Problem: Classification and Botanical Practices 154
7.2.2 The Second Problem: Field Access and the Field Itself 154
7.2.3 The Third Problem: Forestry and Ecological Data 155
7.2.4 Evaluation: A Draft Solution Using a Simple Model 157
7.2.5 Conclusion 159
7.3 Biodiversity on a Large, Physical Scale 159
7.4 Multi-scale and Multi-level Observations: From the Gene to the Ecosystem 159
7.5 A Very Favourable Terrain for Research on Biodiversity and its Dynamics 161
8 Conclusion 165
8.1 Living Things: Deterministic or Stochastic Machines? 165
8.2 Chance and Evolution 166
8.3 Chance is Everywhere in Biological Systems 167
8.4 Internal Processes Generating Random Events 167
8.5 Some Experiments and Much Observation 169
8.6 The Beginning of New Ways of Conducting Research? 171
Glossary 172
References 177
Further Reading 184
Index 186