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1 How Should Living Systems Be Studied? |
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1 | (36) |
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1 | (2) |
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1.2 A Half Century of Molecular Biology |
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3 | (4) |
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1.3 The Reemergence of Diversity and the Enumerative "-ome" Doctrine |
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7 | (3) |
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1.4 Diversity and Dependence on Environmental Circumstances |
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10 | (3) |
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1.5 Systems of Strongly Interacting Elements |
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13 | (2) |
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1.6 Are Living Organisms "Computing Machines"? |
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15 | (3) |
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1.7 Problems with the "Program" Point of View |
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18 | (2) |
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1.8 The Problem of Stability |
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20 | (2) |
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1.9 Systems Evolving Amongst Fluctuations |
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22 | (2) |
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24 | (3) |
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1.11 How the Parts Composing the Whole Are Determined by the Whole |
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27 | (1) |
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1.12 Universal Properties That Cannot Be Traced Back to Molecules |
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28 | (3) |
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1.13 Transcending Enumeration |
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31 | (6) |
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1.13.1 The Absolute Limitation of Enumeration |
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32 | (1) |
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1.13.2 Standard for Enumeration |
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32 | (1) |
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1.13.3 The Essence of Life Does Not Lie in Combinatorial Complexity |
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32 | (1) |
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1.13.4 The Importance of Fluctuations |
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33 | (1) |
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1.13.5 The Essential Difficulty Involved in Constructing That Precisely Describe Biological Phenomena |
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34 | (1) |
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1.13.6 The Lack of Reliable Fundamental Equations |
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34 | (1) |
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1.13.7 A Description of Phenomena is Not Equivalent to an Understanding |
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35 | (1) |
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1.13.8 The Necessity for a New Framework |
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35 | (2) |
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37 | (10) |
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2.1 The Understanding Obtained Through Construction |
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37 | (2) |
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2.2 The "Way" of Construction |
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39 | (1) |
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2.3 Examples of Studies in Constructive Biology |
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40 | (4) |
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2.4 On the Mode of Understanding |
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44 | (3) |
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2.4.1 Remark: Synthetic Biology |
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45 | (1) |
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2.4.2 Remark: Artificial Life |
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46 | (1) |
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3 Basic Concepts in Dynamical Systems |
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47 | (34) |
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3.1 Basic Picture in Dynamical Systems |
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47 | (10) |
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3.1.1 Representation of a Cell Ensemble by the Distribution of Points in the State Space |
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50 | (7) |
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3.2 The Role of Fluctuations |
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57 | (6) |
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3.2.1 Fluctuations and Stability |
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57 | (2) |
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3.2.2 The Relation Between Response and Fluctuations the Fluctuation-Response Relation |
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59 | (3) |
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3.2.3 Fluctuations Are Not due Entirely to Noise from the Environment But Result also from Internal Dynamics and Depend on the Internal State |
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62 | (1) |
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63 | (3) |
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3.4 Representation of "Softness" |
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66 | (5) |
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3.5 Coupled Dynamical Systems for the Study of Cell System |
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71 | (3) |
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74 | (7) |
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3.6.1 Relevance to Biological System |
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77 | (2) |
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3.6.2 Experimental Method in Studying Itinerancy |
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79 | (2) |
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4 Origin of Bioinformation |
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81 | (30) |
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4.1 Question to Be Addressed |
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81 | (8) |
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4.2 Logic: Minority Control Hypothesis |
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89 | (2) |
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91 | (3) |
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94 | (3) |
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4.5 Minority-Controlled State |
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97 | (3) |
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4.5.1 Preservation of Minority Molecule |
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97 | (1) |
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4.5.2 Control of the Growth Speed |
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97 | (1) |
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4.5.3 Control of Chemical Composition by the Minority Molecule |
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98 | (1) |
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99 | (1) |
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100 | (5) |
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105 | (6) |
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4.7.1 Heredity from a Kinetic Viewpoint |
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105 | (2) |
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4.7.2 Accessibility to MCS |
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107 | (1) |
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108 | (3) |
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5 Origin of a Cell with Recursive Growth |
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111 | (24) |
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5.1 Question to Be Addressed |
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111 | (1) |
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112 | (2) |
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114 | (4) |
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5.3.1 Modeling Strategy for the Chemical Reaction Networks |
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114 | (3) |
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117 | (1) |
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118 | (9) |
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5.4.1 Dependence of Phases on the Basic Parameters |
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120 | (2) |
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5.4.2 Maintenance of Recursive Production |
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122 | (3) |
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125 | (1) |
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125 | (2) |
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127 | (5) |
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5.5.1 Replicating Liposome |
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127 | (1) |
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5.5.2 Protein Synthesis within a Liposome |
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128 | (3) |
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5.5.3 For the Synthesis of Artificial Replicating Cell |
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131 | (1) |
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132 | (3) |
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6 Universal Statistics of a Cell with Recursive Growth |
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135 | (24) |
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6.1 Question to Be Addressed |
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135 | (2) |
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137 | (2) |
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139 | (1) |
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140 | (8) |
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6.4.1 Log-Normal Distribution |
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145 | (3) |
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148 | (4) |
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6.5.1 Confirmation of Zipf's Law |
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148 | (2) |
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6.5.2 Confirmation of Laws on Fluctuations |
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150 | (2) |
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152 | (7) |
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6.6.1 Cluster Analysis of Gene Expression |
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152 | (1) |
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6.6.2 Remark on Universal Log-Normal Statistics |
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153 | (1) |
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6.6.3 Relationship Between Abundance Statistics and Network Topology |
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154 | (5) |
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7 Cell Differentiation and Development |
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159 | (34) |
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7.1 Question to Be Addressed: Stability of Development |
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159 | (8) |
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7.1.1 Kauffman's Gene Network Model |
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164 | (3) |
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7.2 Logic: Isologous Diversification |
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167 | (3) |
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170 | (4) |
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7.3.1 Internal Biochemical Reaction Network |
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171 | (1) |
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7.3.2 Interaction Among the Cells |
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171 | (2) |
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173 | (1) |
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7.3.4 Molecular Fluctuation |
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173 | (1) |
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174 | (1) |
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174 | (6) |
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7.4.1 Five Stages of Isologous Diversification |
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174 | (6) |
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7.5 Further Results on Robustness and Dynamics of Differentiation |
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180 | (4) |
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7.5.1 Robustness of Developmental Process |
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180 | (2) |
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7.5.2 Transplant Experiment and Cellular Memory |
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182 | (1) |
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7.5.3 Separation of Inherent Time Scales |
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183 | (1) |
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7.5.4 Relevance of Low-Concentration Chemical to the Initiation of Differentiation |
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183 | (1) |
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184 | (3) |
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7.6.1 Differentiation of E. coli Through Interaction |
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184 | (3) |
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7.6.2 Interaction-Dependent Tumor Genesis |
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187 | (1) |
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187 | (3) |
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7.7.1 Summary of the Result |
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187 | (1) |
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7.7.2 Robustness from Unstable Dynamics |
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188 | (1) |
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7.7.3 Relevance of Molecules with Very Low Concentration to Development |
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189 | (1) |
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189 | (1) |
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7.7.5 Control of Tumor Formation |
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189 | (1) |
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7.8 Appendix: An Example of Model Equation |
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190 | (3) |
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8 Irreversible Differentiation from Stem Cell and Robust Development |
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193 | (34) |
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8.1 Question to Be Addressed: Regulation for Differentiation of Stem Cell |
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193 | (5) |
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8.2 Logic: Chaotic Stem Cell |
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198 | (3) |
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8.2.1 Direction of Determination: Logic |
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200 | (1) |
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201 | (1) |
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202 | (16) |
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8.4.1 Hierarchical Differentiation |
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202 | (3) |
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8.4.2 Dual Coding of Cellular State: Discrete Types and Continuous Modulation of Each Type |
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205 | (1) |
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8.4.3 Regulation of Stochastic Differentiation |
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206 | (1) |
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8.4.4 Differentiation of Colony |
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207 | (2) |
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209 | (2) |
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211 | (5) |
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8.4.7 Universality of Differentiation |
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216 | (2) |
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218 | (4) |
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8.5.1 Constructive Experiment from Embryonic Stern Cell |
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218 | (1) |
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8.5.2 Differentiation from Callus of Plant |
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219 | (1) |
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8.5.3 Construction of "Stem-type Cell" from Bacteria |
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219 | (3) |
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222 | (5) |
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9 Pattern Formation and Origin of Positional Information |
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227 | (28) |
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9.1 Question to Be Addressed: Origin of Positional Information |
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227 | (5) |
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232 | (1) |
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232 | (1) |
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233 | (8) |
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9.4.1 Generation of Positional Information |
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235 | (3) |
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9.4.2 Complementary Relationship between Internal Cell State and Positional Information |
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238 | (1) |
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9.4.3 Regeneration Process |
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238 | (2) |
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9.4.4 Importance of the Ordering in Development |
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240 | (1) |
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241 | (2) |
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243 | (8) |
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243 | (1) |
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244 | (2) |
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9.6.3 Induction and Plasticity |
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246 | (1) |
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9.6.4 Transformation of State Differentiation into Spatial Pattern |
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246 | (1) |
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9.6.5 Destabilization of Intracellular State and Regain of Plasticity: An Interpretation of Gastrulation |
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247 | (1) |
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9.6.6 Origin of Individuality |
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248 | (3) |
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9.7 Appendix: Model for Recursive Growth of Multicellular Organism |
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251 | (4) |
| 10 Genetic Evolution with Phenotypic Fluctuations |
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255 | (26) |
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10.1 Question to Be Addressed |
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255 | (3) |
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258 | (5) |
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10.3 Model and Result of the Simulation |
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263 | (3) |
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266 | (5) |
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10.5 Relevance to Biology |
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271 | (10) |
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10.5.1 Phenotype–Genotype Relationship at the Fluctuation Level |
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271 | (4) |
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10.5.2 Confirmation of the Relationship by the Model Presented in Sect. 10.3 |
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275 | (2) |
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10.5.3 Biological Significance |
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277 | (4) |
| 11 Speciation as a Fixation of Phenotypic Differentiation |
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281 | (34) |
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11.1 Question to Be Addressed |
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281 | (5) |
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11.2 Logic: Interaction-Based Speciation |
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286 | (2) |
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288 | (2) |
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288 | (2) |
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290 | (4) |
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11.4.1 Process for Genetic Diversification |
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290 | (4) |
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11.5 Further Remarks on the Differentiation Scenario |
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294 | (10) |
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11.5.1 Condition for Genetic Diversification |
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294 | (2) |
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11.5.2 Coevolution of Differentiated Groups |
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296 | (1) |
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296 | (1) |
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11.5.4 Deterministic Nature of Evolutionary Process |
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297 | (1) |
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11.5.5 Speciation: Reproductive Isolation Under Sexual Recombination |
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297 | (1) |
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11.5.6 Evolution of Mating Preference˛ |
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298 | (3) |
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11.5.7 Formation of Allele—Allele Correlation |
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301 | (1) |
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11.5.8 Allopatric Speciation as a Result of Sympatric Speciation |
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302 | (2) |
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11.6 Constructive Experiment |
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304 | (4) |
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11.7 Relevance to Biology |
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308 | (7) |
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11.7.1 Tempo in the Evolution |
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308 | (1) |
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11.7.2 Decrease in the Phenotypic Plasticity |
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309 | (1) |
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11.7.3 Relevance of Developmental Plasticity to Speciation |
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309 | (1) |
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11.7.4 Unified Theory for Speciation in Sexual and Asexual (and Unicellular) Organisms |
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310 | (1) |
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11.7.5 Adaptive Radiation |
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311 | (1) |
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11.7.6 On the Interaction |
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311 | (1) |
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11.7.7 Allopatric Speciation |
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312 | (1) |
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312 | (1) |
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11.7.9 Reversing the Order |
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313 | (2) |
| 12 Conclusion |
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315 | (34) |
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315 | (7) |
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12.1.1 Isologous Diversification — General Tendency Toward Differentiation from Identical Units Through Interaction |
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316 | (1) |
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12.1.2 Dynamic Consolidation — a Process Through which Plastic Differentiation is Fixed at a Separate Level with the Aid of Dynamic Interference Among Processes |
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317 | (2) |
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12.1.3 Itinerancy — Long-Term Change of Several Quasi-Steady States with Self-Organized Transition Rules |
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319 | (1) |
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12.1.4 Minority Control — the Tendency for Replicators with Minority Populations to Control the Behavior of the System |
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320 | (1) |
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12.1.5 The Universal Properties of Reproductive Systems |
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321 | (1) |
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12.2 Machine Versus Life Revisited |
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322 | (2) |
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12.3 Fluctuations, Response, and Stability |
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324 | (7) |
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12.4 The "Law" of Decreasing Plasticity in a Closed System |
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331 | (1) |
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12.5 The Restoration of Plasticity in an "Open" System |
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332 | (4) |
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12.6 A Theoretical Approach to Plasticity Dynamics |
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336 | (5) |
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12.7 Developmental Phenomenology: Stability, Irreversibility, Operations, Equation of State |
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341 | (4) |
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12.8 Toward an Understanding of the Dynamics of Cognition and Human Society |
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345 | (4) |
| References |
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349 | (16) |
| Index |
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365 | |
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