| I. Limits to Knowledge: An Introduction |
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Limits to Our Knowledge of Evolution |
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3 | (1) |
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3 | (11) |
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14 | (3) |
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17 | (3) |
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20 | (2) |
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22 | (2) |
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24 | (4) |
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28 | (7) |
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Limits to Knowledge in Population Genetics |
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35 | (3) |
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A Classification of Limits to Knowledge in Population Genetics |
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37 | (1) |
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The Analysis of Gene Genealogies |
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38 | (4) |
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Inferences Based on Coalescence Theory |
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40 | (1) |
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41 | (1) |
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Adaptive Evolution in Complex Biological Systems |
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42 | (6) |
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Chalcone Synthase Genes in Morning Glory |
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43 | (1) |
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Gene Duplication and Divergence in Evolution |
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44 | (3) |
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Interlocus Gene Conversion-Recombination |
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47 | (1) |
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Genetics and Population Biology of White Flower Color Phenotypes in Morning Glory |
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47 | (1) |
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48 | (2) |
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50 | (21) |
| II. The Philosophy of Biology, Paradigms, and Paradigm Shifts |
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Laws, History, and the Nature of Biological Understanding |
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71 | (2) |
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Avoiding Paradigm-Based Limits to Knowledge of Evolution |
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73 | (2) |
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Paradigms and Worldviews in Biology |
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75 | (1) |
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The Amechanistic Paradigm in Evolutionary Study |
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76 | (3) |
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Crisis in the Amechanistic Evolutionary Paradigm |
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79 | (2) |
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Intellectual Confinement by the Amechanistic Paradigm |
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79 | (1) |
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Evidence for Paradigm Crisis |
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80 | (1) |
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Adaptation, Not Adaptationism: Avoiding Another Limiting Paradigm |
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81 | (3) |
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Are There Philosophical Limits to Knowledge of Evolution? |
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84 | (2) |
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Prospects for Extending the Limits to Knowledge of Evolution |
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86 | (5) |
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Examples of the Feasibility of Reintegrating Evolutionary Studies |
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86 | (2) |
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Conflict or Synergism? The Continued Utility of Subdisciplines |
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88 | (1) |
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``Complexity Problems'' in Adaptive Studies and Strategy to Address Them |
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88 | (2) |
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Broad Evolutionary Time Scales |
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90 | (1) |
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The Possible Generality of Evolutionary Study |
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91 | (1) |
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91 | (1) |
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92 | (5) |
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Anticipating Scientific Revolutions in Evolutionary Genetics |
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97 | (1) |
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Questions Clear and Questions Not |
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98 | (2) |
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Scientific Revolutions and How We Do Not See Them |
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100 | (2) |
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Scientific Revolutions in Progress |
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102 | (7) |
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Rejecting the Neutral Model |
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103 | (1) |
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The Rediscovery of the Hill-Robertson Effect |
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103 | (2) |
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The Seeds of a Revolution |
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105 | (4) |
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109 | (1) |
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110 | (7) |
| III. Limits to Historical Inference and Prediction |
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Inferring Ancestral Character States |
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117 | (2) |
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119 | (3) |
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119 | (1) |
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120 | (1) |
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121 | (1) |
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122 | (1) |
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122 | (7) |
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122 | (2) |
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Star Phylogeny with Clock |
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124 | (2) |
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Star Phylogeny with No Clock |
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126 | (3) |
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129 | (5) |
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131 | (3) |
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134 | (1) |
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134 | (1) |
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The Problem of Inferring Selection and Evolutionary History from Molecular Data |
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135 | (2) |
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Why Is Evolution So Difficult to Study Experimentally? |
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137 | (1) |
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Recapturing Evolutionary History |
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138 | (1) |
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Are There Significant New Insights to Be Gained in Population Genetics? |
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139 | (1) |
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The Problem of Weak or Recent Selection |
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140 | (1) |
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How Do We Increase the Signal? |
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141 | (1) |
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Issues of Linkage Disequilibrium |
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142 | (1) |
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Will the Ability Technically to Obtain Large Sample Sizes Extend the Limits of What We Can Rigorously Distinguish? |
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143 | (1) |
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144 | (1) |
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145 | (6) |
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Evolutionary Genetics of Primate Color Vision: Recent Progress and Potential Limits to Knowledge |
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151 | (2) |
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Color Vision Systems in Primates |
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153 | (2) |
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Critical Amino Acid Residues for Spectral Tuning |
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155 | (6) |
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Frequent Gene Conversion between X-Linked Opsin Alleles or Genes |
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161 | (4) |
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Origins of Color Vision Systems in Higher Primates |
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165 | (6) |
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171 | (2) |
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173 | (2) |
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175 | (4) |
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The Limits to Knowledge in Conservation Genetics: The Value of Effective Population Size |
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179 | (2) |
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The Parameters of Genetic Planning |
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181 | (2) |
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Measuring Effective Population Size |
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183 | (2) |
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Population Fragmentation---The Island Model |
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185 | (2) |
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Population Fragmentation---The Interdemic Model |
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187 | (1) |
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188 | (2) |
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190 | (2) |
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192 | (3) |
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What Is the Structure of Human Populations? |
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195 | (1) |
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Human Disease Gene Mapping |
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196 | (2) |
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198 | (1) |
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Hierarchical Model of Human Evolution |
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199 | (2) |
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201 | (1) |
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202 | (3) |
| IV. Quantitative Genetics and the Prediction of Phenotype from Genotype |
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Limits to Prediction of Phenotypes from Knowledge of Genotypes |
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205 | (3) |
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208 | (1) |
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Multiplicity of Small Effects |
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209 | (1) |
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210 | (2) |
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Simpson's Paradox: Complex Systems Viewed from the Margins |
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212 | (2) |
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The NK Model Viewed at the Margins |
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214 | (2) |
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N-Locus Diploid Epistasis Viewed from the Margins |
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216 | (4) |
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Genotype x Environment Interaction |
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220 | (1) |
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221 | (1) |
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222 | (3) |
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The Limits to Knowledge in Quantitative Genetics |
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225 | (1) |
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Phenotypes versus Genetic Values |
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226 | (1) |
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The Nature of Quantitative Variation |
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227 | (2) |
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The Meaning of Quantitative Variation |
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229 | (3) |
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Population Genetics and Population Dynamics |
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232 | (1) |
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Issues Concerning Outbreeding Depression and Species Incompatibilities |
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233 | (1) |
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234 | (1) |
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235 | (4) |
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Genetics of Species Differentiation: What Is Unknown and What Will Be Unknowable? |
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Musings about Generality in Biology |
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239 | (2) |
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Haldane's Rule and the Peril of Overgeneralization |
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241 | (2) |
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Species Differentiation and the Uncertainty in Extrapolation from Population Genetic Variation |
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243 | (4) |
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247 | (1) |
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247 | (2) |
| Conclusions |
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249 | (2) |
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| Index |
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251 | |