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Systems Biology
Philosophical Foundations
1st Edition - March 20, 2007
Editors: Fred Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr, H.V. Westerhoff
Language: English
Hardback ISBN:9780444520852
9 7 8 - 0 - 4 4 4 - 5 2 0 8 5 - 2
eBook ISBN:9780080475271
9 7 8 - 0 - 0 8 - 0 4 7 5 2 7 - 1
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…Read more
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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
Computational biologists, Molecular biologists, Cellular biologists, Systems biologists, Bioinformaticians, Philosophers of Science, Philosophers of Biology
List of Contributors
Contributor Biographies
Preface
Chapter 1: Towards philosophical foundations of Systems Biology: introduction
Publisher Summary
1. SYSTEMS BIOLOGY: A NEW SCIENCE IN SEARCH OF METHODOLOGIES AND PHILOSOPHICAL FOUNDATIONS
2. SYSTEMS BIOLOGY
3. TOWARDS A PHILOSOPHY OF SYSTEMS BIOLOGY
4. INTRODUCTION OF A NUMBER OF PHILOSOPHICAL ASPECTS OF SYSTEMS BIOLOGY
5. AIM AND OVERVIEW OF THE BOOK
Chapter 2: The methodologies of systems biology
Publisher Summary
SUMMARY
1. THE METHODOLOGY AND PHILOSOPHICAL FOUNDATIONS OF THE VARIOUS SCIENCES
2. LIMITATIONS TO THE SCIENTIFIC STATUS OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
3. RISING ABOVE THE LIMITATIONS
4. TOWARDS A SYSTEMATIC METHODOLOGY OF SYSTEMS BIOLOGY
Chapter 3: Methodology is Philosophy
Publisher Summary
SUMMARY
1. INTRODUCTION
2. FROM MOLECULES TO DIABETES VIA METABOLISM AND SYSTEMIC PHYSIOLOGY
3. MRS AND MCA FORM A SUCCESSFUL METHODOLOGY FOR SYSTEMS BIOLOGY
4. CONCLUSION
Chapter 4: How can we understand metabolism?
Publisher Summary
SUMMARY
1. INTRODUCTION
2. TRADITIONAL PRINCIPLES OF METABOLISM
3. THE RISE OF SYSTEMS ANALYSIS OF METABOLISM
4. SHOULD WE EXPECT METABOLISM TO BE UNDERSTANDABLE?
5. IS SIMULATING CELL METABOLISM THE SAME AS UNDERSTANDING IT?
Chapter 5: On building reliable pictures with unreliable data: An evolutionary and developmental coda for the new systems biology
Publisher Summary
SUMMARY
1. INTRODUCTION
2. THE NEW SYSTEMS BIOLOGY AND EVO-DEVO
3. THE PROBLEM OF DATA RELIABILITY IN THE ANALYSIS OF LARGE SYSTEMS
4. DATA ERRORS AND MOLAR SYSTEM PROPERTIES
5. ROBUSTNESS AND THE MANAGEMENT OF UNCERTAINTY
6. GENERATIVE ENTRENCHMENT
Chapter 6: Mechanism and mechanical explanation in systems biology
Publisher Summary
SUMMARY
1. INTRODUCTION: MECHANISTIC EXPLANATION AND REDUCTION
2. LEVELS OF ORGANIZATION AND DEGREES OF RESOLUTION
3. THE DEVELOPMENT OF THE LAC OPERON AS A MECHANISTIC MODEL
4. MECHANISM AND EMERGENCE
5. CONCLUSION: MECHANISTIC EXPLANATION AND SYSTEMS BIOLOGY
Chapter 7: Theories, models, and equations in systems biology
Publisher Summary
SUMMARY
1. INTRODUCTION: THE STRUCTURE OF BIOLOGICAL THEORIES
2. THE DEVELOPMENT OF THE HODGKIN–HUXLEY GIANT SQUID MODEL FOR ACTION POTENTIALS AS A CLASSICAL EXAMPLE OF SYSTEMS BIOLOGY
3. IMPLICATIONS OF THE HODGKIN–HUXLEY MODEL AND THEIR METHODOLOGY
4. A NEUROSCIENTIFIC ACCOUNT OF BEHAVIOR IN C. ELEGANS
5. IMPLICATIONS OF THE FERRÉE AND LOCKERY MODEL FOR C. ELEGANS CHEMOTAXIS
6. EIGHT IMPLICATIONS OF THE TWO EXEMPLARS FOR SYSTEMS BIOLOGY
Chapter 8: All models are wrong: … some more than others
Publisher Summary
SUMMARY
1. INTRODUCTION
2. MODELLING THE MODELLING PROCESS
3. ANALYTICAL MODELLING
4. SYNTHETIC MODELLING
5. SYNTHETIC VS. ANALYTIC MODELLING
6. DYNAMIC PATHWAY MODELLING
7. ALL MODELS ARE WRONG, SOME ARE USEFUL
ACKNOWLEDGEMENTS
Chapter 9: Data without models merging with models without data
Publisher Summary
SUMMARY
1. INTRODUCTION
2. PRELIMINARY TOPOGRAPHY OF THE FIELD
3. THE FIRST ROOT OF SYSTEMS BIOLOGY: MODELS OF METABOLIC AND SIGNALING PATHWAYS
4. THE SECOND ROOT OF SYSTEMS BIOLOGY: BIOLOGICAL CYBERNETICS AND MATHEMATICAL SYSTEMS ANALYSIS
5. THE THIRD ROOT OF SYSTEMS BIOLOGY: ‘OMICS’
6. THE BRANCHES OF SYSTEMS BIOLOGY: MERGERS OF THE DIFFERENT ROOTS
7. THE STRUCTURE OF THE FIELD
8. EPISTEMOLOGICAL AND ONTOLOGICAL ISSUES REGARDING TOP-DOWN SYSTEMS BIOLOGY
9. CONCLUSION
Chapter 10: The biochemical factory that autonomously fabricates itself: A systems biological view of the living cell
Publisher Summary
SUMMARY
1 HOW TO BE A SYSTEMS BIOLOGIST
2 THE SELF-FABRICATING CELL: A CONTEXT FOR SYSTEMS BIOLOGY
3 AUTONOMY OF MATERIAL SYSTEMS: THE NEED FOR SPECIFIC CATALYSIS
4 FABRICATION AND THE LOGIC OF LIFE
5 HOW TO CONSTRUCT A SELF-FABRICATING FACTORY
6 SELF-FABRICATION IN LIVING SYSTEMS
7 CONCLUSION
ACKNOWLEDGEMENTS
Chapter 11: A systemic approach to the origin of biological organization
Publisher Summary
SUMMARY
1 INTRODUCTION
2 THE ORGANIZATIONAL PERSPECTIVE
3 THE STARTING POINT: NONTRIVIAL SELF-MAINTENANCE
4 NTSM ORGANIZATION AND AUTONOMY
5 THE EMERGENCE OF A HISTORICAL–COLLECTIVE DIMENSION
6 THE OPEN STRUCTURE OF DARWINIAN EVOLUTION
7 CONCLUDING REMARKS
ACKNOWLEDGMENTS
Chapter 12: Biological mechanisms: organized to maintain autonomy
Publisher Summary
SUMMARY
1. INTRODUCTION
2. THE BASIC CONCEPTION OF MECHANISM
3. THE VITALIST CHALLENGE
4. FIRST STEPS: BERNARD, CANNON, AND CYBERNETICS
5. CYCLIC ORGANIZATION AND GÁNTI’S CHEMOTON
6. FROM GÁNTI’S CHEMOTON TO AUTONOMOUS SYSTEMS
7. CONCLUDING THOUGHTS: BEYOND BASIC AUTONOMY
Chapter 13: The disappearance of function from ‘self-organizing systems’
Publisher Summary
SUMMARY
Chapter 14: Afterthoughts as foundations for systems biology
Publisher Summary
1. SYSTEMS BIOLOGY IS FUNCTIONAL AND MECHANISTIC RATHER THAN EVOLUTIONARY BIOLOGY
2. SYSTEMS BIOLOGICAL EXPLANATIONS ARE OFTEN MECHANISTIC EXPLANATIONS
3. OTHER TYPES OF EXPLANATION ARE ALSO IMPORTANT FOR SYSTEMS BIOLOGY
4. DESCRIPTION OF MOLECULAR MECHANISMS USING MODELS
5. MODELS AND THE NONEQUILIBRIUM ORGANIZATION OF LIVING SYSTEMS
6. EMERGENT PROPERTIES
7. THEORIES AND LAWS IN SYSTEMS BIOLOGY
8. EXPLANATORY PLURALISM: INTRALEVEL AND INTERLEVEL THEORIES
9. WHAT IS LIFE?
10. CONCLUDING REMARKS
Subject Index
No. of pages: 360
Language: English
Edition: 1
Published: March 20, 2007
Imprint: Elsevier Science
Hardback ISBN: 9780444520852
eBook ISBN: 9780080475271
FB
Fred Boogerd
Affiliations and expertise
Vrije Universiteit, Faculty of Earth and Life Sciences, Dept. of Molecular Cell Physiology, Amsterdam, The Netherlands
FB
Frank J. Bruggeman
Affiliations and expertise
Vrije Universiteit, Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Amsterdam, The Netherlands
JH
Jan-Hendrik S. Hofmeyr
Affiliations and expertise
University of Stellenbosch, Faculty of Science, Department of Biochemistry, Matieland, South Africa
HW
H.V. Westerhoff
Affiliations and expertise
Vrije Universiteit, Faculty of Earth and Life Sciences, Dept. of Molecular Cell Physiology, Amsterdam, The Netherlands