Mutation, Randomness, and Evolution

Cover
Mutation, Randomness and Evolution
Copyright
Acknowledgments
Contents
List of figures
List of tables and boxes
	Tables
	Boxes
Chapter 1: Introduction: a curious disconnect
	1.1 Mutational origination as an evolutionary cause
	1.2 What this book is about
	1.3 Who this book is for
	1.4 How the argument unfolds
	1.5 Synopsis
Chapter 2: Ordinary randomness
	2.1 Introduction
	2.2 Lacking in foresight
	2.3 Uniformity or lack of pattern
	2.4 Stochastic or probabilistic
	2.5 Indeterminate
	2.6 Subjectively unpredictable
	2.7 Spontaneous
	2.8 Independent (part 1)
	2.9 Independent (part 2)
	2.10 Synopsis
Chapter 3: Practical Randomness
	3.1 Introduction
	3.2 What good is a randomness assumption?
	3.3 Uniformity
	3.4 Independence
	3.5 Predictability
	3.6 The random null hypothesis
	3.7 Beyond randomness: the principle of indifference
	3.8 Synopsis
Chapter 4: Evolutionary Randomness
	4.1 Introduction
	4.2 Rejection of pervasively directed mutations
	4.3 Rejection of Lamarckism
	4.4 Independence from adaptation or evolution
	4.5 Independence from fitness effects
	4.6 Exceptions and possible exceptions to independence
	4.7 Conditional independence and related ideas
	4.8 Mutation and altered development
	4.9 Synopsis
Chapter 5: Mutational mechanisms and evolvability
	5.1 Introduction
	5.2 What a specially evolved mutation system looks like
	5.3 Specialized systems of germline mutation in microbes
		5.3.1 Multiple-inversion systems (shufflons)
		5.3.2 Diversity-generating retroelements
		5.3.3 CRISPR-Cas and piRNAs
		5.3.4 Multiple cassette donation
		5.3.5 Phase variation
		5.3.6 Mating-type switching
	5.4 Formulating plausible scenarios
	5.5 Challenges and opportunities
	5.6 Conditional independence and specialized mutation systems
	5.7 Evolvability
	5.8 Synopsis
Chapter 6: Randomness as Irrelevance
	6.1 Introduction
	6.2 Arguments from analogy and metaphysics
		6.2.1 The “raw materials” metaphor
		6.2.2 Creativity
		6.2.3 Levels and types of causes
	6.3 Direct empirical arguments
	6.4 Mechanistic arguments
		6.4.1 Creativity arguments
		6.4.2 Directionality: the “opposing forces” argument
		6.4.3 Initiative and rate: the “gene pool” arguments
	6.5 The methodological argument
	6.6 The explanatory argument
		6.6.1 Darwin’s architect
		6.6.2 Later arguments
	6.7 Synopsis
Chapter 7: The problem of variation
	7.1 Introduction
	7.2 The power of the morphotron
	7.3 Source laws and consequence laws
	7.4 The Mendelian challenge
	7.5 The contemporary challenge
		7.5.1 The G matrix as predictor
		7.5.2 The challenge to gradualism
		7.5.3 The new genetics of adaptation
		7.5.4 Evo-devo
		7.5.5 Molecular evolution: the case of codon usage bias
		7.5.6 The genomic challenge to adaptationism
	7.6 Synopsis
Chapter 8: Climbing Mount Probable
	8.1 Introduction
	8.2 Climbing Mount Probable
	8.3 One-step adaptive walks under mutation bias
	8.4 Extended adaptive walks under mutation bias
	8.5 Protein adaptation under mutation bias
	8.6 Origin-fixation dynamics
	8.7 The sushi conveyor and the buffet
	8.8 Why the theory of forces fails
	8.9 The sources and forms of biases
	8.10 Understanding developmental biases as evolutionary causes
	8.11 An interpretation of structuralism
	8.12 Parallel evolution
	8.13 Conditioning on mutational effects
	8.14 Synopsis
Chapter 9: The revolt of the clay
	9.1 Introduction
	9.2 A predictive model of protein sequence evolution
	9.3 Mutation-biased adaptation in the lab
	9.4 CpG mutational hotspots and altitude adaptation
	9.5 Transition bias in natural parallelisms
	9.6 Preferences for regulatory or structural changes
	9.7 Developmental bias
	9.8 Evaluating the argument
		9.8.1 Cryptic fitness biases actually explain the data
		9.8.2 The connection to theory is thin
		9.8.3 Selection did all the hard work
		9.8.4 Mutation only affects the boring parts
	9.9 Synopsis
Chapter 10: Moving on
	10.1 Introduction
	10.2 Summary as historical narrative
	10.3 A synopsis of key points
	10.4 The objects and forms of explanations
	10.5 The importance of verbal theories of causation
	10.6 Discerning theories and traditions
	10.7 Synopsis
Appendix A: Mutation exemplars
	A.1 A replication error
	A.2 Error-prone repair of DNA damage
	A.3 A symbolic mutation process in a computer program
	A.4 Human-engineered mutations
Appendix B: Counting the universe of mutations
	B.1 Preliminaries
	B.2 A necessary simplification
	B.3 Point mutations
	B.4 De novo insertions
	B.5 Inversions, deletions, and tandem duplications
	B.6 Transpositions (translocations)
	B.7 Lateral gene transfers
	B.8 Compound events
	B.9 Summing up
	B.10 Recurrences
Appendix C: Randomness quotations
	C.1 Introduction
	C.2 List of quotations
Appendix D: Irrelevance quotations
	D.1 Introduction
	D.2 List of quotations
Bibliography
Index