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E-raamat: Mutation, Randomness, and Evolution

4.50/5 (8 hinnangut Goodreads-ist)
(Research Biologist, National Institute of Standards and Technology, Gaithersburg, Maryland, USA)
  • Formaat: PDF+DRM
  • Ilmumisaeg: 22-Apr-2021
  • Kirjastus: Oxford University Press
  • Keel: eng
  • ISBN-13: 9780192582966
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Mutation, Randomness, and EvolutionSuurem pilt
  • Formaat: PDF+DRM
  • Ilmumisaeg: 22-Apr-2021
  • Kirjastus: Oxford University Press
  • Keel: eng
  • ISBN-13: 9780192582966
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What does it mean to say that mutation is random? How does mutation influence evolution? Are mutations merely the raw material for selection to shape adaptations?

The author draws on a detailed knowledge of mutational mechanisms to argue that the randomness doctrine is best understood, not as a fact-based conclusion, but as the premise of a neo-Darwinian research program focused on selection. The successes of this research program created a blind spot - in mathematical models and verbal theories of causation - that has stymied efforts to re-think the role of variation. However, recent theoretical and empirical work shows that mutational biases can and do influence the course of evolution, including adaptive evolution, through a first come, first served mechanism.

This thought-provoking book cuts through the conceptual tangle at the intersection of mutation, randomness, and evolution, offering a fresh, far-reaching, and testable view of the role of variation as a dispositional evolutionary factor. The arguments will be accessible to philosophers and historians with a serious interest in evolution, as well as to researchers and advanced students of evolution focused on molecules, microbes, evo-devo, and population genetics.

Arvustused

An insightful and comprehensive critique of neo Darwinian narratives about the role of mutation in evolution, proposing a view that embraces the capacity for mutation bias to influence the course of evolution. Potentially polarizing and thoroughly thought-provoking, Stoltzfus's volume makes a substantial contribution to evolutionary theory and discourse. * The Quarterly Review of Biology *

List of figures xi
List of tables and boxes xiii
1 Introduction: a curious disconnect 1(14)
1.1 Mutational origination as an evolutionary cause
1(4)
1.2 What this book is about
5(4)
1.3 Who this book is for
9(2)
1.4 How the argument unfolds
11(2)
1.5 Synopsis
13(2)
2 Ordinary randomness 15(20)
2.1 Introduction
15(1)
2.2 Lacking in foresight
16(1)
2.3 Uniformity or lack of pattern
16(4)
2.4 Stochastic or probabilistic
20(1)
2.5 Indeterminate
21(1)
2.6 Subjectively unpredictable
22(2)
2.7 Spontaneous
24(4)
2.8 Independent (part 1)
28(2)
2.9 Independent (part 2)
30(3)
2.10 Synopsis
33(2)
3 Practical randomness 35(12)
3.1 Introduction
35(1)
3.2 What good is a randomness assumption?
35(4)
3.3 Uniformity
39(1)
3.4 Independence
40(1)
3.5 Predictability
41(2)
3.6 The random null hypothesis
43(1)
3.7 Beyond randomness: the principle of indifference
44(1)
3.8 Synopsis
45(2)
4 Evolutionary randomness 47(20)
4.1 Introduction
47(1)
4.2 Rejection of pervasively directed mutations
47(1)
4.3 Rejection of Lamarckism
48(4)
4.4 Independence from adaptation or evolution
52(1)
4.5 Independence from fitness effects
53(3)
4.6 Exceptions and possible exceptions to independence
56(4)
4.7 Conditional independence and related ideas
60(3)
4.8 Mutation and altered development
63(1)
4.9 Synopsis
64(3)
5 Mutational mechanisms and evolvability 67(26)
5.1 Introduction
67(1)
5.2 What a specially evolved mutation system looks like
68(2)
5.3 Specialized systems of germline mutation in microbes
70(7)
5.3.1 Multiple-inversion systems (shufflons)
70(1)
5.3.2 Diversity-generating retroelements
71(1)
5.3.3 CRISPR-Cas and piRNAs
71(3)
5.3.4 Multiple cassette donation
74(1)
5.3.5 Phase variation
75(1)
5.3.6 Mating-type switching
76(1)
5.4 Formulating plausible scenarios
77(5)
5.5 Challenges and opportunities
82(3)
5.6 Conditional independence and specialized mutation systems
85(1)
5.7 Evolvability
86(3)
5.8 Synopsis
89(4)
6 Randomness as irrelevance 93(18)
6.1 Introduction
93(1)
6.2 Arguments from analogy and metaphysics
94(4)
6.2.1 The "raw materials" metaphor
94(1)
6.2.2 Creativity
95(1)
6.2.3 Levels and types of causes
96(2)
6.3 Direct empirical arguments
98(2)
6.4 Mechanistic arguments
100(3)
6.4.1 Creativity arguments
100(1)
6.4.2 Directionality: the "opposing forces" argument
100(2)
6.4.3 Initiative and rate: the "gene pool" arguments
102(1)
6.5 The methodological argument
103(2)
6.6 The explanatory argument
105(2)
6.6.1 Darwin's architect
106(1)
6.6.2 Later arguments
107(1)
6.7 Synopsis
107(4)
7 The problem of variation 111(24)
7.1 Introduction
111(1)
7.2 The power of the morphotron
112(1)
7.3 Source laws and consequence laws
113(3)
7.4 The Mendelian challenge
116(2)
7.5 The contemporary challenge
118(14)
7.5.1 The G matrix as predictor
119(1)
7.5.2 The challenge to gradualism
120(2)
7.5.3 The new genetics of adaptation
122(2)
7.5.4 Evo-devo
124(2)
7.5.5 Molecular evolution: the case of codon usage bias
126(4)
7.5.6 The genomic challenge to adaptationism
130(2)
7.6 Synopsis
132(3)
8 Climbing Mount Probable 135(30)
8.1 Introduction
135(1)
8.2 Climbing Mount Probable
136(1)
8.3 One-step adaptive walks under mutation bias
137(3)
8.4 Extended adaptive walks under mutation bias
140(3)
8.5 Protein adaptation under mutation bias
143(2)
8.6 Origin-fixation dynamics
145(1)
8.7 The sushi conveyor and the buffet
146(3)
8.8 Why the theory of forces fails
149(3)
8.9 The sources and forms of biases
152(3)
8.10 Understanding developmental biases as evolutionary causes
155(2)
8.11 An interpretation of structuralism
157(2)
8.12 Parallel evolution
159(2)
8.13 Conditioning on mutational effects
161(1)
8.14 Synopsis
162(3)
9 The revolt of the clay 165(32)
9.1 Introduction
165(1)
9.2 A predictive model of protein sequence evolution
166(3)
9.3 Mutation-biased adaptation in the lab
169(7)
9.4 CpG mutational hotspots and altitude adaptation
176(1)
9.5 Transition bias in natural parallelisms
177(6)
9.6 Preferences for regulatory or structural changes
183(3)
9.7 Developmental bias
186(2)
9.8 Evaluating the argument
188(6)
9.8.1 Cryptic fitness biases actually explain the data
188(1)
9.8.2 The connection to theory is thin
189(2)
9.8.3 Selection did all the hard work
191(1)
9.8.4 Mutation only affects the boring parts
192(2)
9.9 Synopsis
194(3)
10 Moving on 197(20)
10.1 Introduction
197(1)
10.2 Summary as historical narrative
197(4)
10.3 A synopsis of key points
201(2)
10.4 The objects and forms of explanations
203(3)
10.5 The importance of verbal theories of causation
206(4)
10.6 Discerning theories and traditions
210(4)
10.7 Synopsis
214(3)
Appendix A: Mutation exemplars 217(6)
A.1 A replication error
217(1)
A.2 Error-prone repair of DNA damage
218(2)
A.3 A symbolic mutation process in a computer program
220(1)
A.4 Human-engineered mutations
221(2)
Appendix B: Counting the universe of mutations 223(8)
B.1 Preliminaries
223(1)
B.2 A necessary simplification
224(1)
B.3 Point mutations
224(1)
B.4 De novo insertions
225(1)
B.5 Inversions, deletions, and tandem duplications
226(1)
B.6 Transpositions (translocations)
226(1)
B.7 Lateral gene transfers
227(1)
B.8 Compound events
228(1)
B.9 Summing up
228(1)
B.10 Recurrences
229(2)
Appendix C: Randomness quotations 231(6)
C.1 Introduction
231(1)
C.2 List of quotations
232(5)
Appendix D: Irrelevance quotations 237(6)
D.1 Introduction
237(1)
D.2 List of quotations
237(6)
Bibliography 243(24)
Index 267
Arlin Stoltzfus is a Fellow of the Institute for Bioscience and Biotechnology Research, and a Research Biologist at the National Institute of Standards and Technology in Gaithersburg, Maryland, USA . He is an evolutionary biologist who uses computer-based approaches to study evolution at the molecular level. His primary interest has been to develop and evaluate theories about evolutionary factors other than natural selection. He and his coworkers proposed the theory of Constructive Neutral Evolution, and showed theoretically that biases in the introduction of variation may impose biases on evolution without requiring neutrality.
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