Artificial chemistries / Wolfgang Banzhaf and Lidia Yamamoto.

Format:

• Book

Author/Creator:

• Banzhaf, Wolfgang, 1955- author.
• Yamamoto, Lidia, author.

Language:

English

Subjects (All):

• Biochemistry.
• Molecular evolution.
• Chemistry, Physical and theoretical.
• Evolution (Biology).
• Life--Origin.

Physical Description:

1 online resource (xv, 555 pages) : illustrations (some color)

Place of Publication:

Cambridge, MA : The MIT Press, [2015]

System Details:

text file

Summary:

The field of Artificial life (ALife) is now firmly established in the scientific world, but it has yet to achieve one of its original goals: an understanding of the emergence of life on Earth. The new field of artificial chemistries draws from chemistry, biology, computer science, mathematics, and other disciplines to work toward that goal. For if, as it has been argued, life emerged from pirmitive, prebiotic forms of self-organizations, then studying models of chemical reaction systems could bring ALife closer to understanding the origins of life. In artificial chemistries (ACs), the emphasis is on creating new interactions rather than new materials. The results can be found in both the virtual world, in certain multiagent systems, and in the physical world, in new (artificial) reaction systems. This book offers an introduction to the fundamental concepts of ACs, covering both theory and practical applications. After a general overview of the field and its methodology, the book reviews important aspects of biology, including basic mechanisms of evolution; discusses examples of ACs drawn from the literature; considers fundamental questions of how surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs. -- from back cover.

Contents:

• I Foundations 1
• 1 Introduction 3
• 2 Basic Concepts of Artificial Chemistries 11
• 2.1 Modeling and Simulation 11
• 2.2 Chemistry Concepts 15
• 2.3 General Structure of an Artificial Chemistry 25
• 2.4 A Few Important Distinctions 31
• 2.5 Two Examples 33
• 2.6 Frequently Used Techniques in ACs 38
• 2.7 Summary 43
• 3 The Matrix Chemistry as an Example 45
• 3.1 The Basic Matrix Chemistry 46
• 3.2 The Simplest System, N = 4 50
• 3.3 The System N = 9 55
• 3.4 Systems with Larger N 59
• 3.5 Summary 61
• 4 Computing Chemical Reactions 63
• 4.1 From Macroscopic to Microscopic Chemical Dynamics 63
• 4.2 Stochastic Reaction Algorithms 65
• 4.3 Spatial and Multicompartmental Algorithms 71
• 4.4 Summary 73
• II Life and Evolution 75
• 5 The Chemistry of Life 77
• 5.1 What Is Life? 79
• 5.2 The Building Blocks of Life 80
• 5.3 The Organization of Modern Cells 93
• 5.4 Multicellular Organisms 100
• 5.5 Summary 109
• 6 The Essence of Life 111
• 6.1 A Minimal Cell 111
• 6.2 Origin of Life 119
• 6.3 Artificial Chemistry Contributions to Origin of Life Research 130
• 6.4 Summary 136
• 7 Evolution 139
• 7.1 Evolution: Taming Combinatorics to Improve Life 140
• 7.2 Evolutionary Dynamics from an AC Perspective 141
• 7.3 Artificial Chemistries for Evolution 154
• 7.4 Summary and Open Issues 157
• 8 Complexity and Open-Ended Evolution 159
• 8.1 Evolution: Steering Self-Organization and Promoting Innovation 159
• 8.2 Revolutionary Dynamics in Ecologies 161
• 8.3 Robustness and Evolvability 165
• 8.4 Complexity Growth 169
• 8.5 Toward Open-Ended Artificial Evolution 175
• 8.6 Summary 177
• III Approaches to Artificial Chemistries 179
• 9 Rewriting Systems 181
• 9.1 Lambda Calculus 182
• 9.2 Gamma 184
• 9.3 The Chemical Abstract Machine 186
• 9.4 Chemical Rewriting System on Multisets 187
• 9.5 P systems 188
• 9.6 MGS 191
• 9.7 Other Formal Calculi Inspired by a Chemical Metaphor 193
• 9.8 L-Systems and Other Rewriting Systems 193
• 9.9 Summary 194
• 10 Automata and Machines 195
• 10.1 Finite State Automata 196
• 10.2 Turing Machines 197
• 10.3 Von Neumann Machines 198
• 10.4 Cellular Automata 200
• 10.5 Examples of Artificial Chemistries Based on Turing Machines 202
• 10.6 Artificial Chemistries Based on von Neumann Machines 207
• 10.7 Artificial Chemistries Based on Cellular Automata 215
• 10.8 Summary 222
• 11 Bio-inspired Artificial Chemistries 225
• 11.1 String-Based Artificial Chemistries 225
• 11.2 Lock-and-Key Artificial Chemistries 234
• 11.3 Networks 240
• 11.4 Spatial Structuring and Movement in Artificial Chemistries 248
• 11.5 Summary 254
• IV Order Construction 255
• 12 The Structure of Organizations 257
• 12.1 Basic Definitions 259
• 12.2 Generators 262
• 12.3 Bringing Order into Organizations 263
• 12.4 Novelty and Innovation 265
• 12.5 Examples of the Statics of Organizations 266
• 12.6 How to Calculate Closed and Self-Maintaining Sets 270
• 12.7 Summary 273
• 13 The Dynamics of Organizations 275
• 13.1 Flows, Stoichiometry and Kinetic Constants 275
• 13.2 Examples of the Dynamics of Organization 277
• 13.3 Observing Organizations 282
• 13.4 Probabilistic Notions of Closure and Self-Maintenance 283
• 13.5 Summary 285
• 14 Self-Organization and Emergent Phenomena 287
• 14.1 Examples of Self-Organizing Systems 288
• 14.2 Explanatory Concepts of Self-Organization 289
• 14.3 The Emergence of Phenomena 295
• 14.4 Explanatory Concepts of Emergence 298
• 14.5 Emergence and Top-Down Causation 304
• 14.6 Summary 306
• 15 Constructive Dynamical Systems 307
• 15.1 Novelty, Innovation, Emergence 307
• 15.2 Birth Processes at the Same Level 309
• 15.3 The Emergence of Entities on a Higher Level 317
• 15.4 Summary 319
• V Applications 321
• 16 Applications of Artificial Chemistries 323
• 16.1 Robots Controlled by Artificial Chemistries 324
• 16.2 ACs for Networking 330
• 16.3 Language Dynamics and Evolution 334
• 16.4 Music Composition Using Algorithmic Chemistries 338
• 16.5 Proof Systems 339
• 16.6 Artificial Chemistry and Genetic Programming 340
• 16.7 Summary 344
• 17 Computing with Artificial Chemistries 345
• 17.1 Principles of implementation 346
• 17.2 Search and Optimization Algorithms Inspired by Chemistry 355
• 17.3 Distributed Algorithms Using Chemical Computing 358
• 17.4 In Silico Simulation of Wet Chemical Computing 366
• 17.5 Summary 372
• 18 Modeling Biological Systems 373
• 18.1 Folding Algorithms 374
• 18.2 Basic Kinetics of Biomolecular Interactions 379
• 18.3 Biochemical Pathways 383
• 18.4 Modeling Genetic Regulatory Networks 391
• 18.5 Cell Differentiation and Multicellularity 396
• 18.6 Morphogenesis 398
• 18.7 Summary 403
• 19 Wet Artificial Chemistries 405
• 19.1 Artificial Building Blocks of Life 405
• 19.2 Synthetic Life and Protocells 411
• 19.3 Chemical and Biochemical Computation 417
• 19.4 In Vivo Computing with Bacteria and Other Living Organisms 431
• 19.5 Ethical Issues 435
• 19.6 Summary 437
• 20 Beyond Chemistry and Biology 439
• 20.1 Mechanical Self-Assembly 439
• 20.2 Nuclear and Particle Physics 442
• 20.3 Economic Systems 444
• 20.4 Social Systems 446
• 20.5 Summary 448
• VI Conclusions 449
• 21 Summary and Perspectives 451
• 21.1 Some Common Criticisms of the Artificial Chemistry Approach 451
• 21.2 Delimiting the Borders of the Field 453
• 21.3 Main Features of Artificial Chemistries 456
• 21.4 Conclusion 459.

Notes:

OCLC-licensed vendor bibliographic record.

ISBN:

• 9780262329460
• 0262329468

OCLC:

913742479

Publisher Number:

40025104169

Access Restriction:

Restricted for use by site license.