Stepping Stones to Synthetic Biology

Description

This book explores fascinating topics at the edge of life, guiding the reader all the way from the relation of life processes to the second law of thermodynamics and the abundance of complex organic compounds in the universe through to the latest advances in synthetic biology and metabolic engineering. The background to the book is the extraordinary scientific adventures that are being undertaken as progress is made toward the creation of an artificial cell and the control of life processes. This journey involves input from research areas as diverse as genetic engineering, physical chemistry, and information theory. Life is to be thought of not only as a chemical event but also as an information process, with the genome a repository of information gathered over time through evolution. Knowledge of the mechanisms affecting the increase in complexity associated with evolutionary paths is improving, and there appear to be analogies with the evolution of the technologies promoting the development of our society. The book will be of wide interest to students at all levels and to others with an interest in the subject.  Read more... Abstract: This book explores fascinating topics at the edge of life, guiding the reader all the way from the relation of life processes to the second law of thermodynamics and the abundance of complex organic compounds in the universe through to the latest advances in synthetic biology and metabolic engineering.  Read more... Content: Intro Preface Contents Employed Symbols Mathematical Notation Physical Constants Chapter 1: Devils, Ratchets and Biomolecular Motors 1.1 The Century of the Devils 1.2 The Unbearable Attractiveness of Irreversibility 1.3 The Devil Is a Pawl 1.4 Swimming in Molasses 1.5 Down in the Bioworld References Chapter 2: Entropy and Information 2.1 Back to Thermodynamics 2.2 The Statistical Character of Entropy 2.3 Out of Equilibrium 2.4 Shaping the World 2.5 The Role of Information 2.6 The Physics of Neglecting References Chapter 3: A Computer Called the Universe 3.1 A Controversial Origin3.2 The Atomic Universe 3.3 The Molecular Universe 3.4 The Birth of Chemistry 3.5 Back to Earth 3.6 The Computing Universe References Chapter 4: Biomolecules, Networks and Bioenergetics: System Approach to Biology 4.1 A New Paradigm 4.2 The Molecules of Life 4.3 Building the Cells 4.4 Viruses 4.5 Thermodynamics in Action 4.6 The Path of Bioenergy 4.7 Life and Energy 4.8 Taming the Rates 4.9 Towards a System Biology References Chapter 5: Making Sense of Life 5.1 An Enlightening Contribution 5.2 The Nature and Role of Free Energy 5.3 The Eighth Day of Creation5.4 A Gentlemenś Club 5.5 Central Dogma at Work 5.6 Feedback Control 5.7 Regulator Gene 5.8 Final Remark References Chapter 6: Complexity and Information: A Metaphor of Natural and Technological Systems 6.1 Complexity: A Philosophy or a Tool? 6.2 A World Patterned by Networks 6.3 The Language of Nature 6.4 Natural Computers 6.5 An Abundance of Energy (and Exergy) from the Top 6.6 The Emerald Planet 6.7 Eating the Sun 6.8 Back to the Macroworld 6.9 A Glance Towards the Future References Chapter 7: The Path of Evolution 7.1 The Informational Aspect of Evolution7.2 Evolution and Complexity 7.3 Simulating Evolution 7.4 Evolution in a Computer 7.5 Meta-Biological Darwinism References Chapter 8: Imitation of Life: The Cell in a Silicon Chip 8.1 The Chemoton 8.2 A Challenging Problem 8.3 Modeling of Metabolic Reaction Systems 8.4 FBA Approach 8.5 Exploring the Escherichia coli 8.6 Whole Cell References Chapter 9: Synthetic Biology at Work 9.1 The Synthetic Approach to Biology 9.2 Progress in Gene Manipulations 9.3 Frontier of Genome Engineering: The CRISPR/Cas System 9.4 Technical Issues 9.5 Works in Progress9.6 A Renewed Synthetic Chemistry 9.7 Metabolic Engineering 9.8 Towards a Post-petroleum Era? References Chapter 10: Why Life? 10.1 Resurrecting Prometheus 10.2 The Beginning of Life 10.3 Ideas and Theories on the Origin of Life 10.3.1 Protein First 10.3.2 Nucleic Acids First 10.3.3 The Chicken or the Egg? 10.3.4 RNA World 10.3.5 The Phase Transition Approach to the Emergence of Life 10.3.6 Back to Thermodynamics 10.3.7 The Revenge of Energy 10.3.8 A Merging Point? 10.4 The First Synthetic Cell References Glossary Sources General Titles in This Series