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Overview
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 primitive, prebiotic forms of self-organization, 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 both in 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 order can emerge, emphasizing the concept of chemical organization (a closed and self-maintaining set of chemicals); and surveys a range of applications, which include computing, systems modeling in biology, and synthetic life. An appendix provides a Python toolkit for implementing ACs.
Product Details
| ISBN-13: | 9780262551526 |
|---|---|
| Publisher: | MIT Press |
| Publication date: | 03/19/2024 |
| Pages: | 576 |
| Product dimensions: | 7.00(w) x 9.25(h) x (d) |
About the Author
Lidia Yamamoto is a former Postdoctoral Researcher at the University of Basel.
Table of Contents
Preface xi
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
Further Reading 461
Appendix: Setting up Your Own Artificial Chemistry System 465
The PyCellChemistry Package 465
Writing Your Own Artificial Chemistry in Python 468
Further Resources 478
Bibliography 481
Author Index 531
Subject Index 545
What People are Saying About This
This book by Banzhaf and Yamamoto provides an excellently written introduction and survey on the state of the art in the young new discipline of artificial chemistries and has the potential to become the key publication in the field.
I found this to be a fascinating and essential read for anyone interested in artificial life research. The book is very well-organized and provides both the specialist and non-specialist alike with lots of well-referenced examples and also integrates over many of the most important fields from concepts of living systems to evolution, artificial chemistries, computational aspects, and the need for entire system exploration
A feast of theoretical and practical information about contemporary computational models of fundamental chemical phenomena, including chemical reaction networks, autocatalytic networks, organizations and self-organization, autopoiesis, the origin of life, and even the emergence and open-ended evolution of chemical novelty and complexity. This is the go-to-first source for any question about artificial chemistry.
This book by Banzhaf and Yamamoto provides an excellently written introduction and survey on the state of the art in the young new discipline of artificial chemistries and has the potential to become the key publication in the field.
—Peter Schuster, Professor Emeritus, Institute for Theoretical Chemistry, University of Vienna
A feast of theoretical and practical information about contemporary computational models of fundamental chemical phenomena, including chemical reaction networks, autocatalytic networks, organizations and self-organization, autopoiesis, the origin of life, and even the emergence and open-ended evolution of chemical novelty and complexity. This is the go-to-first source for any question about artificial chemistry.
—Mark A. Bedau, Professor of Philosophy and Humanities, Reed College; Adjunct Professor of Systems Science, Portland State University; and Editor-in-Chief of Artificial LifeI found this to be a fascinating and essential read for anyone interested in artificial life research. The book is very well-organized and provides both the specialist and non-specialist alike with lots of well-referenced examples and also integrates over many of the most important fields from concepts of living systems to evolution, artificial chemistries, computational aspects, and the need for entire system exploration
—Leroy (Lee) Cronin, Regius Professor of Chemistry, School of Chemistry, University of GlasgowThis book by Banzhaf and Yamamoto provides an excellently written introduction and survey on the state of the art in the young new discipline of artificial chemistries and has the potential to become the key publication in the field.
—Peter Schuster, Professor Emeritus, Institute for Theoretical Chemistry, University of Vienna