Mutation, randomness, and evolution / Arlin Stoltzfus.

Format:

Book

Author/Creator:

Stoltzfus, Arlin, author.

Contributor:

UPSO (University Press Scholarship Online)

Language:

English

Subjects (All):

Mutation (Biology).

Evolution (Biology).

Physical Description:

1 online resource : illustrations

polychrome

Edition:

First edition.

Place of Publication:

Oxford ; New York, NY : Oxford University Press, 2021.

[Place of publication not identified] : [publisher not identified], [2021]

System Details:

text file

Contents:

1 Introduction: a curious disconnect p. 1

1.1 Mutational origination as an evolutionary cause p. 1

1.4 How the argument unfolds p. 11

2 Ordinary randomness p. 15

2.2 Lacking in foresight p. 16

2.3 Uniformity or lack of pattern p. 16

2.4 Stochastic or probabilistic p. 20

2.5 Indeterminate p. 21

2.6 Subjectively unpredictable p. 22

2.7 Spontaneous p. 24

2.8 Independent (part 1) p. 28

2.9 Independent (part 2) p. 30

3 Practical randomness p. 35

3.2 What good is a randomness assumption? p. 35

3.3 Uniformity p. 39

3.4 Independence p. 40

3.5 Predictability p. 41

3.6 The random null hypothesis p. 43

3.7 Beyond randomness: the principle of indifference p. 44

4 Evolutionary randomness p. 47

4.2 Rejection of pervasively directed mutations p. 47

4.3 Rejection of Lamarckism p. 48

4.4 Independence from adaptation or evolution p. 52

4.5 Independence from fitness effects p. 53

4.6 Exceptions and possible exceptions to independence p. 56

4.7 Conditional independence and related ideas p. 60

4.8 Mutation and altered development p. 63

5 Mutational mechanisms and evolvability p. 67

5.2 What a specially evolved mutation system looks like p. 68

5.3 Specialized systems of germline mutation in microbes p. 70

5.3.1 Multiple-inversion systems (shufflons) p. 70

5.3.2 Diversity-generating retroelements p. 71

5.3.3 CRISPR-Cas and piRNAs p. 71

5.3.4 Multiple cassette donation p. 74

5.3.5 Phase variation p. 75

5.3.6 Mating-type switching p. 76

5.4 Formulating plausible scenarios p. 77

5.5 Challenges and opportunities p. 82

5.6 Conditional independence and specialized mutation systems p. 85

5.7 Evolvability p. 86

6 Randomness as irrelevance p. 93

6.2 Arguments from analogy and metaphysics p. 94

6.2.1 The "raw materials" metaphor p. 94

6.2.2 Creativity p. 95

6.2.3 Levels and types of causes p. 96

6.3 Direct empirical arguments p. 98

6.4 Mechanistic arguments p. 100

6.4.1 Creativity arguments p. 100

6.4.2 Directionality: the "opposing forces" argument p. 100

6.4.3 Initiative and rate: the "gene pool" arguments p. 102

6.5 The methodological argument p. 103

6.6 The explanatory argument p. 105

6.6.1 Darwin's architect p. 106

6.6.2 Later arguments p. 107

7 The problem of variation p. 111

7.2 The power of the morphotron p. 112

7.3 Source laws and consequence laws p. 113

7.4 The Mendelian challenge p. 116

7.5 The contemporary challenge p. 118

7.5.1 The G matrix as predictor p. 119

7.5.2 The challenge to gradualism p. 120

7.5.3 The new genetics of adaptation p. 122

7.5.4 Evo-devo p. 124

7.5.5 Molecular evolution: the case of codon usage bias p. 126

7.5.6 The genomic challenge to adaptationism p. 130

8 Climbing Mount Probable p. 135

8.2 Climbing Mount Probable p. 136

8.3 One-step adaptive walks under mutation bias p. 137

8.4 Extended adaptive walks under mutation bias p. 140

8.5 Protein adaptation under mutation bias p. 143

8.6 Origin-fixation dynamics p. 145

8.7 The sushi conveyor and the buffet p. 146

8.8 Why the theory of forces fails p. 149

8.9 The sources and forms of biases p. 152

8.10 Understanding developmental biases as evolutionary causes p. 155

8.11 An interpretation of structuralism p. 157

8.12 Parallel evolution p. 159

8.13 Conditioning on mutational effects p. 161

9 The revolt of the clay p. 165

9.2 A predictive model of protein sequence evolution p. 166

9.3 Mutation-biased adaptation in the lab p. 169

9.4 CpG mutational hotspots and altitude adaptation p. 176

9.5 Transition bias in natural parallelisms p. 177

9.6 Preferences for regulatory or structural changes p. 183

9.7 Developmental bias p. 186

9.8 Evaluating the argument p. 188

9.8.1 Cryptic fitness biases actually explain the data p. 188

9.8.2 The connection to theory is thin p. 189

9.8.3 Selection did all the hard work p. 191

9.8.4 Mutation only affects the boring parts p. 192

10.2 Summary as historical narrative p. 197

10.3 A synopsis of key points p. 201

10.4 The objects and forms of explanations p. 203

10.5 The importance of verbal theories of causation p. 206

10.6 Discerning theories and traditions p. 210.

Notes:

Includes bibliographical references and index.

Electronic reproduction. Oxford Available via World Wide Web.

Description based on online resource; title from PDF title page (Oxford Scholarship Online, viewed on August 13, 2021).

Other Format:

Print version: Stoltzfus, Arlin. Mutation, randomness, and evolution.

ISBN:

9780191880063

019188006X

9780192582966

0192582968

Publisher Number:

99988388187

Access Restriction:

Restricted for use by site license.