Boogerd / Bruggeman / Hofmeyr Systems Biology

Philosophical Foundations
1. Auflage 2007
ISBN: 978-0-08-047527-1
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark

E-Book, Englisch, 360 Seiten

Systems biology is a vigorous and expanding discipline, in many ways a successor to genomics and perhaps unprecedented in its combination of biology with a great many other sciences, from physics to ecology, from mathematics to medicine, and from philosophy to chemistry. Studying the philosophical foundations of systems biology may resolve a longer standing issue, i.e., the extent to which Biology is entitled to its own scientific foundations rather than being dominated by existing philosophies.
* Answers the question of what distinguishes the living from the non-living
* An in-depth look to a vigorous and expanding discipline, from molecule to system
* Explores the region between individual components and the system

Autoren/Hrsg.

Boogerd, Fred

Bruggeman, Frank J.

Hofmeyr, Jan-Hendrik S.

Westerhoff, H. V.

Inhaltsverzeichnis

1;Front Cover;1
2;Systems Biology;4
3;Copyright Page;5
4;Table of Contents;6
5;List of Contributors;8
6;Contributor Biographies;10
7;Preface;18
8;SECTION I Introduction;20
8.1;Chapter 1 Towards philosophical foundations of Systems Biology: introduction;22
8.1.1;1. SYSTEMS BIOLOGY: A NEW SCIENCE IN SEARCH OF METHODOLOGIES AND PHILOSOPHICAL FOUNDATIONS;22
8.1.2;2. SYSTEMS BIOLOGY;24
8.1.2.1;2.1. History of systems biology;24
8.1.2.2;2.2. What is contemporary systems biology?;25
8.1.2.3;2.3. Approaches to systems biology;25
8.1.3;3. TOWARDS A PHILOSOPHY OF SYSTEMS BIOLOGY;26
8.1.3.1;3.1. The philosophy of molecular biology itself needs no further elaboration;26
8.1.3.2;3.2. Philosophers focus on philosophy of evolutionary biology;27
8.1.3.3;3.3. A philosophy of systems biology is lacking but needed;28
8.1.4;4. INTRODUCTION OF A NUMBER OF PHILOSOPHICAL ASPECTS OF SYSTEMS BIOLOGY;29
8.1.4.1;4.1. Two types of reductionism;29
8.1.4.2;4.2. A continuum of reductionism to antireductionism;31
8.1.4.3;4.3. Types of explanation;31
8.1.4.4;4.4. Mechanistic explanation;32
8.1.4.5;4.5. Systems biology and models;33
8.1.4.6;4.6. What is life?;34
8.1.5;5. AIM AND OVERVIEW OF THE BOOK;35
8.1.6;REFERENCES;36
9;SECTION II Research programs of Systems Biology;40
9.1;Chapter 2 The methodologies of systems biology;42
9.1.1;SUMMARY;42
9.1.2;1. THE METHODOLOGY AND PHILOSOPHICAL FOUNDATIONS OF THE VARIOUS SCIENCES;42
9.1.2.1;1.1. Physics;42
9.1.2.2;1.2. Biology;43
9.1.2.3;1.3. Biochemistry and molecular biology;46
9.1.2.4;1.4. Cell Biology: The living cell;47
9.1.3;2. LIMITATIONS TO THE SCIENTIFIC STATUS OF BIOCHEMISTRY AND MOLECULAR BIOLOGY;52
9.1.3.1;2.1. Inaccuracy;52
9.1.3.2;2.2. Inability to deal with emergence;53
9.1.3.3;2.3. Frustrated aspiration of biochemistry and molecular biology to . . . biology;54
9.1.3.4;2.4. Irreducibility;55
9.1.3.5;2.5. Lack of testability because of undefinedness;56
9.1.3.6;2.6. Lack of experimental accessibility;57
9.1.3.7;2.7. Lack of analysability;57
9.1.4;3. RISING ABOVE THE LIMITATIONS;58
9.1.4.1;3.1. Genomics;58
9.1.4.2;3.2. Soon everything will be known . . . : Will biology become physics, at last?;61
9.1.4.3;3.3. Observing or understanding?;61
9.1.4.4;3.4. Systems biology;65
9.1.5;4. TOWARDS A SYSTEMATIC METHODOLOGY OF SYSTEMS BIOLOGY;66
9.1.5.1;4.1. The goals of systems biology;67
9.1.5.2;4.2. Systems biology: What it is;68
9.1.5.3;4.3. The spiral of knowledge;69
9.1.5.4;4.4. The special role of mathematics in systems biology: Calculating emergence;79
9.1.6;ACKNOWLEDGEMENTS;83
9.1.7;REFERENCES;84
9.2;Chapter 3 Methodology is Philosophy;90
9.2.1;SUMMARY;90
9.2.2;1. INTRODUCTION;91
9.2.3;2. FROM MOLECULES TO DIABETES VIA METABOLISM AND SYSTEMIC PHYSIOLOGY;100
9.2.4;3. MRS AND MCA FORM A SUCCESSFUL METHODOLOGY FOR SYSTEMS BIOLOGY;102
9.2.5;4. CONCLUSION;104
9.2.6;REFERENCES;105
9.3;Chapter 4 How can we understand metabolism?;106
9.3.1;SUMMARY;106
9.3.2;1. INTRODUCTION;107
9.3.3;2. TRADITIONAL PRINCIPLES OF METABOLISM;107
9.3.4;3. THE RISE OF SYSTEMS ANALYSIS OF METABOLISM;109
9.3.5;4. SHOULD WE EXPECT METABOLISM TO BE UNDERSTANDABLE?;114
9.3.6;5. IS SIMULATING CELL METABOLISM THE SAME AS UNDERSTANDING IT?;116
9.3.7;REFERENCES;118
9.4;Chapter 5 On building reliable pictures with unreliable data: An evolutionary and developmental coda for the new systems biology?;122
9.4.1;SUMMARY;122
9.4.2;1. INTRODUCTION;123
9.4.3;2. THE NEW SYSTEMS BIOLOGY AND EVO-DEVO;124
9.4.4;3. THE PROBLEM OF DATA RELIABILITY IN THE ANALYSIS OF LARGE SYSTEMS;125
9.4.5;4. DATA ERRORS AND MOLAR SYSTEM PROPERTIES;127
9.4.6;5. ROBUSTNESS AND THE MANAGEMENT OF UNCERTAINTY;130
9.4.7;6. GENERATIVE ENTRENCHMENT;133
9.4.8;REFERENCES;137
10;SECTION III Theory and models;140
10.1;Chapter 6 Mechanism and mechanical explanation in systems biology;142
10.1.1;SUMMARY;142
10.1.2;1. INTRODUCTION: MECHANISTIC EXPLANATION AND REDUCTION;143
10.1.3;2. LEVELS OF ORGANIZATION AND DEGREES OF RESOLUTION;148
10.1.4;3. THE DEVELOPMENT OF THE LAC OPERON AS A MECHANISTIC MODEL;153
10.1.5;4. MECHANISM AND EMERGENCE;158
10.1.6;5. CONCLUSION: MECHANISTIC EXPLANATION AND SYSTEMS BIOLOGY;161
10.1.7;REFERENCES;161
10.2;Chapter 7 Theories, models, and equations in systems biology;164
10.2.1;SUMMARY;164
10.2.2;1. INTRODUCTION: THE STRUCTURE OF BIOLOGICAL THEORIES;165
10.2.3;2. THE DEVELOPMENT OF THE HODGKIN–HUXLEY GIANT SQUID MODEL FOR ACTION POTENTIALS AS A CLASSICAL EXAMPLE OF SYSTEMS BIOLOGY;167
10.2.4;3. IMPLICATIONS OF THE HODGKIN–HUXLEY MODEL AND THEIR METHODOLOGY;172
10.2.4.1;3.1. One basic mechanism with many types of molecular realizations?;172
10.2.4.2;3.2. Genetic and epigenetic diversity accounts for ion channel diversity;173
10.2.4.3;3.3. The H and H ‘basic mechanism’ as an emergent simplification;174
10.2.5;4. A NEUROSCIENTIFIC ACCOUNT OF BEHAVIOR IN C. ELEGANS;175
10.2.6;5. IMPLICATIONS OF THE FERRÉE AND LOCKERY MODEL FOR C. ELEGANS CHEMOTAXIS;178
10.2.7;6. EIGHT IMPLICATIONS OF THE TWO EXEMPLARS FOR SYSTEMS BIOLOGY;179
10.2.8;REFERENCES;180
10.3;Chapter 8 All models are wrong . . . some more than others;182
10.3.1;SUMMARY;182
10.3.2;1. INTRODUCTION;183
10.3.3;2. MODELLING THE MODELLING PROCESS;185
10.3.4;3. ANALYTICAL MODELLING;186
10.3.5;4. SYNTHETIC MODELLING;191
10.3.6;5. SYNTHETIC VS. ANALYTIC MODELLING;193
10.3.7;6. DYNAMIC PATHWAY MODELLING;194
10.3.8;7. ALL MODELS ARE WRONG, SOME ARE USEFUL;196
10.3.9;ACKNOWLEDGEMENTS;198
10.3.10;REFERENCES;198
10.4;Chapter 9 Data without models merging with models without data;200
10.4.1;SUMMARY;200
10.4.2;1. INTRODUCTION;201
10.4.3;2. PRELIMINARY TOPOGRAPHY OF THE FIELD;203
10.4.4;3. THE FIRST ROOT OF SYSTEMS BIOLOGY: MODELS OF METABOLIC AND SIGNALING PATHWAYS;205
10.4.4.1;3.1. Regulatory metabolic and signaling systems;205
10.4.4.2;3.2. Modeling regulatory networks and gathering data;206
10.4.5;4. THE SECOND ROOT OF SYSTEMS BIOLOGY: BIOLOGICAL CYBERNETICS AND MATHEMATICAL SYSTEMS ANALYSIS;207
10.4.5.1;4.1. Cybernetic models in biology;208
10.4.5.2;4.2. Contents of the black boxes and the ‘direction’ of cybernetic modeling;209
10.4.6;5. THE THIRD ROOT OF SYSTEMS BIOLOGY: ‘OMICS’;210
10.4.6.1;5.1. Early genome projects: Chromosome maps;211
10.4.6.2;5.2. Molecular genome projects;211
10.4.6.3;5.3. Early proteomic projects;212
10.4.7;6. THE BRANCHES OF SYSTEMS BIOLOGY: MERGERS OF THE DIFFERENT ROOTS;213
10.4.7.1;6.1. The first branch of systems biology: Detailed bottom-up regulatory models;213
10.4.7.2;6.2. The second branch of systems biology: Making sense of ‘omic’ data by top-down modeling;215
10.4.8;7. THE STRUCTURE OF THE FIELD;216
10.4.9;8. EPISTEMOLOGICAL AND ONTOLOGICAL ISSUES REGARDING TOP-DOWN SYSTEMS BIOLOGY;219
10.4.9.1;8.1. Decomposition of large networks and functionality;220
10.4.9.2;8.2. The ‘holism’ of systems biology;223
10.4.9.3;8.3. ‘Realistic’ representation and systems biological ‘models of everything’;225
10.4.10;9. CONCLUSION;227
10.4.11;REFERENCES;228
11;SECTION IV Organization in biological systems;234
11.1;Chapter 10 The biochemical factory that autonomously fabricates itself: A systems biological view of the living cell;236
11.1.1;SUMMARY;236
11.1.2;1. HOW TO BE A SYSTEMS BIOLOGIST;237
11.1.3;2. THE SELF-FABRICATING CELL: A CONTEXT FOR SYSTEMS BIOLOGY;241
11.1.4;3. AUTONOMY OF MATERIAL SYSTEMS: THE NEED FOR SPECIFIC CATALYSIS;245
11.1.5;4. FABRICATION AND THE LOGIC OF LIFE;247
11.1.6;5. HOW TO CONSTRUCT A SELF-FABRICATING FACTORY;250
11.1.7;6. SELF-FABRICATION IN LIVING SYSTEMS;256
11.1.8;7. CONCLUSION;259
11.1.9;ACKNOWLEDGEMENTS;259
11.1.10;REFERENCES;260
11.2;Chapter 11 A systemic approach to the origin of biological organization;262
11.2.1;SUMMARY;262
11.2.2;1. INTRODUCTION;263
11.2.3;2. THE ORGANIZATIONAL PERSPECTIVE;265
11.2.4;3. THE STARTING POINT: NONTRIVIAL SELF-MAINTENANCE;266
11.2.4.1;3.1. From self-organization to NTSM;268
11.2.4.2;3.2. The problem of the origin of NTSMSs;271
11.2.5;4. NTSM ORGANIZATION AND AUTONOMY;272
11.2.6;5. THE EMERGENCE OF A HISTORICAL–COLLECTIVE DIMENSION;276
11.2.6.1;5.1. Autonomous systems with memory;276
11.2.6.2;5.2. The origin of an informational organization;279
11.2.7;6. THE OPEN STRUCTURE OF DARWINIAN EVOLUTION;282
11.2.8;7. CONCLUDING REMARKS;284
11.2.9;ACKNOWLEDGMENTS;285
11.2.10;REFERENCES;286
11.3;Chapter 12 Biological mechanisms: organized to maintain autonomy;288
11.3.1;SUMMARY;288
11.3.2;1. INTRODUCTION;289
11.3.3;2. THE BASIC CONCEPTION OF MECHANISM;294
11.3.4;3. THE VITALIST CHALLENGE;296
11.3.5;4. FIRST STEPS: BERNARD, CANNON, AND CYBERNETICS;298
11.3.6;5. CYCLIC ORGANIZATION AND GÁNTI’S CHEMOTON;300
11.3.7;6. FROM GÁNTI’S CHEMOTON TO AUTONOMOUS SYSTEMS;310
11.3.8;7. CONCLUDING THOUGHTS: BEYOND BASIC AUTONOMY;315
11.3.9;REFERENCES;318
11.4;Chapter 13 The disappearance of function from ‘self-organizing systems’;322
11.4.1;SUMMARY;322
11.4.2;REFERENCES;335
12;SECTION V Conclusion;338
12.1;Chapter 14 Afterthoughts as foundations for systems biology;340
12.1.1;1. SYSTEMS BIOLOGY IS FUNCTIONAL AND MECHANISTIC RATHER THAN EVOLUTIONARY BIOLOGY;344
12.1.2;2. SYSTEMS BIOLOGICAL EXPLANATIONS ARE OFTEN MECHANISTIC EXPLANATIONS;345
12.1.3;3. OTHER TYPES OF EXPLANATION ARE ALSO IMPORTANT FOR SYSTEMS BIOLOGY;346
12.1.4;4. DESCRIPTION OF MOLECULAR MECHANISMS USING MODELS;347
12.1.5;5. MODELS AND THE NONEQUILIBRIUM ORGANIZATION OF LIVING SYSTEMS;348
12.1.6;6. EMERGENT PROPERTIES;348
12.1.7;7. THEORIES AND LAWS IN SYSTEMS BIOLOGY;350
12.1.8;8. EXPLANATORY PLURALISM: INTRALEVEL AND INTERLEVEL THEORIES;352
12.1.9;9. WHAT IS LIFE?;352
12.1.10;10. CONCLUDING REMARKS;353
12.1.11;REFERENCES;354
12.2;Subject Index;356