Compositional evolution : the impact of sex, symbiosis, and modularity on the gradualist framework of evolution / Richard A. Watson.

Format:

Book

Author/Creator:

Watson, Richard A., 1968-

Series:

Vienna series in theoretical biology

The Vienna series in theoretical biology

Language:

English

Subjects (All):

Evolution (Biology)--Mathematical models.

Evolution (Biology).

Computational biology.

Evolutionary computation.

Physical Description:

xvi, 324 pages : illustrations ; 24 cm.

Place of Publication:

Cambridge, Mass. : MIT Press, [2006]

Summary:

No biological concept has had greater impact on the way we view ourselves and the world around us than the theory of evolution by natural selection. Darwin's masterful contribution was to provide an algorithmic model (a formal step-by-step procedure) of how adaptation may take place in biological systems. However, the simple process of linear incremental improvement that he described is only one algorithmic possibility, and certain biological phenomena provide the possibility of implementing alternative processes. In Compositional Evolution, Richard Watson uses the tools of computer science and computational biology to show that certain mechanisms of genetic variation (such as sex, gene transfer, and symbiosis) allowing the combination of preadapted genetic material enable an evolutionary process, compositional evolution, that is algorithmically distinct from the Darwinian gradualist framework.

After reviewing the gradualist framework of evolution and outlining the analogous principles at work in evolutionary computation, Watson describes the compositional mechanisms of evolutionary biology and provides computational models that illustrate his argument. He uses models such as the genetic algorithm as well as novel models to explore different evolutionary scenarios, comparing evolution based on spontaneous point mutation, sexual recombination, and symbiotic encapsulation. He shows that the models of sex and symbiosis are algorithmically distinct from simpler stochastic optimization methods based on gradual processes. Finally, Watson discusses the impact of compositional evolution on our understanding of natural evolution and, similarly, the utility of evolutionary computation methods for problem solving and design.

Contents:

1.1 Gradual and Compositional Evolution 3

1.2 The Algorithmic Paradigms of Evolution 8

1.3 Complex Systems with Modular Interdependency and Their (Un)evolvability 12

1.4 Compositional Mechanisms 16

1.5 The Impact on Gradualism 19

1.6 Some Related Issues 24

2 Gradual Evolution 29

2.1 The Gradualist Framework of Evolution 29

2.2 Evolutionary Algorithms 31

2.3 Concepts of Evolutionary Difficulty 35

3 Compositional Evolution 45

3.1 Compositional Mechanisms 45

3.2 Models of Composition 55

3.3 Some Issues in the Use of Compositional Mechanisms 81

3.4 Some Conceptual Issues of Compositional Evolution 90

4 Modularity 101

4.1 Interdependency 101

4.2 Modular Interdependency 109

4.3 Hierarchical Modular Interdependency 117

4.4 Hierarchical-If-and-Only-If (HIFF) 125

5 Mutation 149

5.1 Examining the Fitness Landscape 149

5.2 Difficulty of Modular Interdependency for Gradual Mechanisms 150

5.3 Expected Time to Solution for Gradual Mechanisms 155

5.4 Simulation Results for Mutation 157

6 Sexual Recombination 163

6.1 Overview of Models 164

6.2 Results for a Single Panmictic Population-The Simple GA 165

6.3 Results for a Subdivided or Niched Population-GA with Crowding 167

6.4 The Dependence on Physical Linkage 174

6.5 The Impact for GA Theory 183

7 Symbiotic Encapsulation 191

7.1 An Overview of the Symbiotic Encapsulation Model 191

7.2 Entities and Their Encapsulation 193

7.3 Evaluation and Selection 200

7.4 The Symbiogenic Evolutionary Adaptation Model (SEAM) 205

7.5 Simulation Results for Symbiotic Encapsulation 205

7.6 The Relationship of SEAM to Other Algorithmic Methods 210

8 How Fast Is Fast? 219

8.1 An Analysis of Sexual Recombination on HIFF 219

8.2 An Analysis of SEAM on Shuffled HIFF 234

9 Scaling Up Evolution 245

9.1 Units in Sexual Populations 247

9.2 Scaling Up Evolution with Symbiotic Encapsulation 255

9.3 The Inherent Tension of Innovation and Reproductive Fidelity 265

10 The Impact of Compositional Evolution 267

10.1 Future and Ongoing Research 267

10.2 Large Directed Adaptive Genetic Changes 274

10.3 Symbiosis as a Source of Evolutionary Innovation 276

10.4 Evolutionary Difficulty and Gradualism 277

10.5 Algorithmic Principles of Adaptation 277

10.6 The Availability and Impact of Compositional Mechanisms in Nature 279

10.7 Modularity in Natural Systems 280.

Notes:

Includes bibliographical references (pages [301]-318) and index.

ISBN:

026223243X

OCLC:

58985705