| Foreword | 6 |
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| Carving Nature at its Joints? | 6 |
| Contents | 9 |
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| Contributors | 11 |
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| Introduction | 12 |
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| 1.1 Molecular Biology Meets Evolutionary Biology: Challenges to Post- Mayrian Biology | 12 |
| 1.2 Elaborating Key Concepts | 18 |
| 1.3 Detailed Contents of this Book | 22 |
| Articulating Different Modes of Explanation: The Present Boundary in Biological Research | 25 |
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| 2.1 Introduction | 25 |
| 2.2 Molecular Explanatory Models | 26 |
| 2.3 Putting These Models Side by Side or Opposing Them is a Dead- End | 28 |
| 2.4 The Difficulty of Interlinking Different Explanations | 32 |
| 2.5 A Paradoxical Conclusion | 34 |
| Compromising Positions: The Minding of Matter | 37 |
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| 3.1 TheWord | 37 |
| 3.2 | 38 |
| Four Themes | 38 |
| 3.3 Serving Two Masters: Minding Matter | 46 |
| 3.4 Conclusion | 53 |
| Abstractions, Idealizations, and Evolutionary Biology | 56 |
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| 4.1 Introduction | 56 |
| 4.2 Idealization and Abstraction | 56 |
| 4.3 Successes and Pitfalls | 60 |
| 4.4 The Informational Gene | 62 |
| The Adequacy of Model Systems for Evo-Devo: Modeling the Formation of Organisms/ Modeling the Formation of Society | 65 |
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| 5.1 Introduction | 65 |
| 5.2 New Model Systems for Evo-Devo | 68 |
| 5.3 Model Systems and the Assumptions of Developmental and Evolutionary Biology | 74 |
| Niche Construction in Evolution, Ecosystems and Developmental Biology | 77 |
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| 6.1 Introduction | 77 |
| 6.2 Niche Construction | 78 |
| 6.3 Earthworms | 82 |
| 6.4 Other Examples | 83 |
| 6.5 The Limitations of the Standard Theory | 84 |
| 6.6 Extended Evolutionary Theory | 87 |
| 6.7 Modelling Niche Construction | 88 |
| 6.8 The Implications of Niche Construction for Ecology | 89 |
| 6.9 A Simple Model of an Ecosystem | 90 |
| 6.10 Ecosystems and Evolution Without Niche Construction | 92 |
| 6.11 Ecosystems and Evolution with Niche Construction | 93 |
| 6.12 EMGAs | 95 |
| 6.13 Integrating Ecology and Evolution | 95 |
| 6.14 Niche Construction and Developmental Biology | 96 |
| 6.15 Gene Networks in Development and Ecosystems | 98 |
| Novelty, Plasticity and Niche Construction: The Influence of Phenotypic Variation on Evolution | 100 |
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| 7.1 Where Does Novelty Come From? A Hypothesis | 100 |
| 7.2 Biased Variation and Evolution | 102 |
| 7.3 Phenotypic Plasticity and its Significance | 104 |
| 7.4 The Organism-Environment Developmental Loop | 110 |
| The Evolution of Complexity | 117 |
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| 8.1 The Arrow of Complexity Hypothesis | 118 |
| 8.2 Replaying the Tape of Life | 119 |
| 8.3 Complexity Growth by Passive Diffusion | 121 |
| 8.4 The Evolution of Complexity in Artificial Life Models | 123 |
| 8.5 Objections and Replies | 128 |
| 8.6 Conclusions | 136 |
| Self-Organization, Self-Assembly, and the Origin of Life | 137 |
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| 9.1 Introduction | 137 |
| 9.2 The Origin of Life in Four Acts | 139 |
| 9.3 The Gospel of Inevitability | 141 |
| Self-Organization and Complexity in Evolutionary Theory, or, in this Life the Bread Always Falls Jammy Side Down | 147 |
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| 10.1 What is Life? | 148 |
| 10.2 Organization | 150 |
| 10.3 Is Natural Selection All-Powerful? | 152 |
| 10.4 Constraints | 154 |
| 10.5 Order for free | 157 |
| 10.6 Conclusion | 160 |
| References | 161 |
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| Index | 176 |