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Elsevier

Systems Biology

Philosophical Foundations

  • 1 Edición - 20 de marzo de 2007
  • Última edición
  • Editores: Fred Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr, H.V. Westerhoff
  • Idioma: Inglés

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… Leer más

Descripción

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.

Puntos claves

* 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

De interès para

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

Índice

  • 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

Detalles del producto

  • Edición: 1
  • Última edición
  • Publicado: 20 de marzo de 2007
  • Idioma: Inglés

Sobre los editores

FB

Fred Boogerd

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

FB

Frank J. Bruggeman

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

JH

Jan-Hendrik S. Hofmeyr

Afiliaciones y experiencia
University of Stellenbosch, Faculty of Science, Department of Biochemistry, Matieland, South Africa

HW

H.V. Westerhoff

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

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