Systems Biology - 1st Edition - ISBN: 9780444520852, 9780080475271

Systems Biology

1st Edition

Philosophical Foundations

Editors: Fred Boogerd Frank Bruggeman Jan-Hendrik Hofmeyr H.V. Westerhoff
Hardcover ISBN: 9780444520852
eBook ISBN: 9780080475271
Imprint: Elsevier Science
Published Date: 20th March 2007
Page Count: 360
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Description

  • 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

Key Features

  • 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

Readership

Computational biologists, Molecular biologists, Cellular biologists, Systems biologists, Bioinformaticians, Philosophers of Science, Philosophers of Biology

Table of Contents

  • 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

Details

No. of pages:
360
Language:
English
Copyright:
© Elsevier Science 2007
Published:
Imprint:
Elsevier Science
eBook ISBN:
9780080475271
Hardcover ISBN:
9780444520852

About the Editor

Fred Boogerd

Affiliations and Expertise

Vrije Universiteit, Faculty of Earth and Life Sciences, Dept. of Molecular Cell Physiology, Amsterdam, The Netherlands

Frank Bruggeman

Affiliations and Expertise

Vrije Universiteit, Faculty of Earth and Life Sciences, Department of Molecular Cell Physiology, Amsterdam, The Netherlands

Jan-Hendrik Hofmeyr

Affiliations and Expertise

University of Stellenbosch, Faculty of Science, Department of Biochemistry, Matieland, South Africa

H.V. Westerhoff

Affiliations and Expertise

Vrije Universiteit, Faculty of Earth and Life Sciences, Dept. of Molecular Cell Physiology, Amsterdam, The Netherlands