Predictive Methods for Genomics and Evolution

Preface xi
Acknowledgments xiii
Acronyms xv

1 What Is Biology? 1
1.1 DNA: Nature, Role, and Function 3
1.2 Hybridization Affinity 19
1.3 Summary 30

2 Genomes to Phenotypes, Environments, and Genomes 37
2.1 Phenotype Determination: The Conventional View 37
2.2 Environments and Autopoiesis 45
2.3 Phenotype Determination: An Alternative View 47
2.4 Summary 52

3 Species Definitions and Their Limitations 57
3.1 The Importance of the Concept of Species 57
3.2 Current Species Definitions 62
3.3 What Exactly Is a "Species"? 69
3.4 A Deeper Definition of "Species" 73
3.5 Summary 84

4 Speciation and Evolution 89
4.1 Darwinian Evolution 89
4.2 Neo-Darwinian Evolution: The Modern Synthesis 94
4.3 Speciation Processes 97
4.4 Summary 108

5 From Genomes to Evolution 113
5.1 From Genotypes to Phenotypes: Evolutionary Scale 114
5.2 Is the Course of Evolution Predictable at the Macroscale? 120
5.3 Is the Course of Evolution Predictable at the Lineage Scale? 125
5.4 Summary 134

6 Conventional Phylogenetics and Systematics 139
6.1 DNA: The Thin Thread of Life 140
6.2 Distance Methods versus Parsimony Analysis 146
6.3 Probabilistic Methods and Evolutionary Models 149
6.4 Case Study in Molecular Taxonomy: COI 155
6.5 Summary 165

7 New Approaches to Phylogenetics 173
7.1 Phylogenetic Trees 173
7.2 Phylogenetic Tree Assessment 177
7.3 Phylogenetic Hypotheses Based on Deep DNA Structure 178
7.4 Summary 180

8 About the Origin of Life 185
8.1 Theories of the Origin of Life on Earth: From Creationism to Panspermia 185
8.2 Complex Systems: A Holistic Approach 188
8.3 A Case Study: Polytene Chromosomes in Black Flies 195
8.4 Summary 210

9 Toward an Analytical Biology 217
9.1 What Is Data Science (DS)? 218
9.2 What Is Machine Learning (ML)? 224
9.3 Causality vs. Correlation 226
9.4 What Is Artificial Intelligence (AI)? 228
9.5 The Natural Intelligence of DNA and Biological Organisms 229
9.6 Summary 231

10 Appendices 235
10.1 Genotypes 235
10.2 Standard Biological Taxonomies 235
10.3 Divergence in Black Flies 238
10.4 Software 244

Bibliography 244
Index 245