Note: Front Cover -- Evolution of Primary Production in the Sea -- Copyright Page -- Contents -- List of Contributors -- Preface -- Chapter 1: An Introduction to Primary Producers in the Sea: Who They Are, What They Do, and When They Evolved -- I. What Is Primary Production? -- II. How Is Photosynthesis Distributed in the Oceans? -- III. What Is the Evolutionary History of Primary Production in the Oceans? -- IV. Concluding Comments -- References -- Chapter 2: Oceanic Photochemistry and Evolution of Elements and Cofactors in the Early Stages of the Evolution of Life -- I. Energy Requirements for Life -- II. Prebiotic Photochemistry-UV and Oceanic Photochemistry -- III. Evolution of Cofactors -- A. Metals -- B. Cofactors -- IV. Conclusions -- Acknowledgments -- References -- Chapter 3: The Evolutionary Transition from Anoxygenic to Oxygenic Photosynthesis -- I. Earliest Evidence for Photosynthesis and the Nature of the Earliest Phototrophs -- II. Structural Conservation of the Core Structure of Photosynthetic Reaction Centers During Evolution -- III. The Structural and Mechanistic Differences Between the Anoxygenic Reaction Centers of Type II and Photosystem II of Oxygenic Organisms -- IV. Evolutionary Scenarios for How the Transition from Anoxygenic to Oxygenic Photosynthesis May Have Taken Place -- V. Conclusions and Prospects for the Future -- Acknowledgments -- References -- Chapter 4: Evolution of Light-Harvesting Antennas in an Oxygen World -- I. How Cyanobacteria Changed the World -- II. Light-Harvesting Antennas and the Evolution of the Algae -- III. Phycobilisomes -- IV. The ISIA/PCB Family -- V. About Chlorophylls -- VI. The LHC Superfamily -- A. The Light-Harvesting Antennas -- B. The Stress-Response Connection -- C. Prokaryotic Ancestry of the LHC Superfamily -- VII. Overview -- Acknowledgments -- References. , Chapter 5: Eukaryote and Mitochondrial Origins: Two Sides of the Same Coin and Too Much Ado About Oxygen -- I. Cell Evolution With and Without Endosymbiosis -- II. The Standard Model of How and Why the Mitochondrion Become Established -- III. There are at Least 12 Substantial Problems with the Standard Model -- IV. The Same 12 Issues from the Standpoint of an Alternative Theory -- V. Criticism and Defense of the Hydrogen Hypothesis -- VI. Intermezzo -- VII. Conclusions -- Acknowledgments -- References -- Chapter 6: Photosynthesis and the Eukaryote Tree of Life -- I. The Eukaryotes -- II. Overview of the Tree -- A. Opisthokonts -- B. Amoebozoa -- C. Rhizaria (Formerly Cercozoa) -- D. Archaeplastida -- E. Chromalveolates -- F. Excavates -- G. Incertae Sedis -- III. The Eukaryote Root -- IV. Oxygenic Photosynthesis Across the Eukaryote Tree of Life -- A. Opisthokonts -- B. Amoebozoa -- C. Rhizaria -- D. Archaeplastida -- E. Chromalveolates -- F. Excavates and Incertae Sedis -- V. Conclusions -- References -- Chapter 7: Plastid Endosymbiosis: Sources and Timing of the Major Events -- I. General Introduction to Plastid Endosymbiosis -- II. Primary Plastid Origin and Plantae Monophyly -- A. Generating the Eukaryotic Phylogeny -- B. Molecular Clock Analyses -- C. Conclusions of Plantae Phylogenetic and Molecular Clock Analyses -- III. Secondary Plastid Endosymbiosis -- IV. Tertiary Plastid Endosymbiosis -- V. Summary -- References -- Chapter 8: The Geological Succession of Primary Producers in the Oceans -- I. Records of Primary Producers in Ancient Oceans -- A. Microfossils -- B. Molecular Biomarkers -- II. The Rise of Modern Phytoplankton -- A. Fossils and Phylogeny -- B. Biomarkers and the Rise of Modern Phytoplankton -- C. Summary of the Rise of Modern Phytoplankton -- III. Paleozoic Primary Production -- A. Microfossils. , B. Paleozoic Molecular Biomarkers -- C. Paleozoic Summary -- IV. Proterozoic Primary Production -- A. Prokaryotic Fossils -- B. Eukaryotic Fossils -- C. Proterozoic Molecular Biomarkers -- D. Summary of the Proterozoic Record -- V. Archean Oceans -- VI. Conclusions -- A. Directions for Continuing Research -- Acknowledgments -- References -- Chapter 9: Life in Triassic Oceans: Links Between Planktonic and Benthic Recovery and Radiation -- I. Benthos -- A. Benthic Wastelands of the Early Triassic -- B. Middle Triassic Recovery of Benthic Ecosystems -- C. Late Triassic Benthic Boom: Supersize Me -- II. Plankton -- A. Early Triassic Disaster Species -- B. Middle Triassic Oxygen and Evolution -- C. Late Triassic Rise of Modern Phytoplankton -- III. Benthic-Planktonic Coupling in Triassic Oceans -- A. Common Driver -- B. Plankton Control -- C. Feedback from the Benthos -- D. Assistance from the Plankton -- IV. Conclusions -- Acknowledgments -- References -- Chapter 10: The Origin and Evolution of Dinoflagellates -- I. Paleontological Data -- II. Phylogeny of Dinoflagellates -- A. Sources of Information -- B. The Phylogeny -- C. Reconciling Molecular and Morphological Phylogenies -- III. The Plastids of Dinoflagellates -- IV. Dinoflagellates in the Plankton -- References -- Chapter 11: The Origin and Evolution of the Diatoms: Their Adaptation to a Planktonic Existence -- I. The Hallmark of the Diatoms: The Silica Frustule -- A. Frustule Shape and Ornamentation and Their Bearings on Diatom Taxonomy -- B. Frustule Construction -- II. Diatom Phylogeny -- A. The Heterokont Ancestry of the Diatoms -- B. Diatom Phylogenies -- C. The Life Cycle and Its Bearings on Phylogeny -- III. The Origin of the Frustule -- A. The Origin of Silica Sequestering and Metabolism -- B. The Evolution of the Frustule in Vegetative Cells -- IV. The Fossil Record. , A. The Early Fossil Record of the Heterokontophytes -- B. The Fossil Record of the Diatoms -- V. The Success of the Diatoms in the Plankton -- A. The Paleo-Environmental Settings and the Fates of the Various Phytoplankton Lineages -- B. Why Did Chromists Win Over Prasinophytes or Red Microalgae? -- C. Why Did Heterokontophytes Win Over Haptophytes and Dinoflagellates? -- D. Why Did Diatoms Win Over Other Heterokontophytes? -- VI. Cryptic Diversity in Planktonic Diatoms and Its Bearing on Evolution -- VII. The Dawning Future of Diatom Research: Genomics -- Acknowledgments -- References -- Chapter 12: Origin and Evolution of Coccolithophores: From Coastal Hunters to Oceanic Farmers -- I. Coccolithophores and the Biosphere -- II. What Is a Coccolithophore? -- A. Coccoliths and Coccolithogenesis -- III. The Haptophytes -- IV. Tools and Biases in the Reconstruction of Coccolithophore Evolution -- V. The Evolution of Haptophytes up to the Invention of Coccoliths: From Coastal Hunters to Oceanic Farmers? -- A. The Origin of the Haptophytes and Their Trophic Status -- B. Paleozoic Haptophytes and the Ancestors of the Coccolithophores -- VI. The Origin of Calcification in Haptophytes: When, How Many Times, and Why? -- A. Genetic Novelties? -- B. Multiple Origins for Coccolithogenesis? -- C. Environmental Forcing on the Origin of Haptophyte Calcification -- D. Why Were Coccoliths Invented? -- VII. Macroevolution Over the Last 220 Million Years -- A. Forces Shaping the Evolution of Coccolithophores and Coccolithogenesis -- B. Broad Patterns of Morphological Diversity -- C. Oligotrophy and Water Chemistry -- D. Changes in Morphostructural Strategies -- VIII. The Future of Coccolithophores -- Acknowledgments -- References -- Chapter 13: The Origin and Early Evolution of Green Plants -- I. Green Plants Defined -- II. Green Plant Body Plans. , A. Green Plant Life Histories -- III. The Core Structure of the Green Plant Phylogenetic Tree -- A. The Archegoniate Line -- B. The Chlorophyte Line -- C. The Prasinophytes -- IV. Difficulties in the Green Plant Phylogenetic Tree -- A. The Identity of the Lineage Ancestral to Green Plants -- B. The Early Diversification of the "Seaweed" Orders -- V. Green Plants in the Modern Marine Environment -- VI. Conclusions -- Acknowledgments -- References -- Chapter 14: Armor: Why, When, and How -- I. Why Armor -- A. History of The Concept "Armor" Applied to Plankton -- B. Why Should Protists and the Pelagial Be Different? -- C. Form and Function in Sessile and Drifting Photoautotrophs -- D. Attacking Organisms/Attacking Tools -- E. Ingestors or Predators -- II. When -- III. How -- A. Material -- B. The Geometry -- C. Lightweight Constructions of Phytoplankton Armor -- D. Spines and Large Size -- E. Other Functional Explanations -- IV. Conclusions -- Acknowledgments -- References -- Chapter 15: Does Phytoplankton Cell Size Matter? The Evolution of Modern Marine Food Webs -- I. Size Matters: From Physiological Rates to Ecological and Evolutionary Patterns -- A. Size Scaling of Physiological Rates -- B. Size-Abundance Relationship -- C. Size-Diversity Relationship -- D. Size Matters: Food Web Structure and Function -- II. Resource Availability, Primary Production, and Size Structure of Planktonic and Benthic Food Webs -- III. Size and the Evolution of Marine Food Webs -- A. Increase in the Maximum Size of Living Organisms Through Time -- B. Organism Size Within Lineages Through Time (Cope's Rule) -- C. Climatically Driven Macroevolutionary Change in Organism Size -- D. The Evolution of the Modern Marine Food Web -- Acknowledgments -- References -- Chapter 16: Resource Competition and the Ecological Success of Phytoplankton. , I. Resource Acquisition and Measures of Competitive Ability.

Note: Cover -- Title -- Copyright -- Dedication -- Contents -- Acknowledgments -- Preface to the New Paperback Edition -- Prologue -- Chapter 1 In the Beginning? -- Chapter 2 The Tree of Life -- Chapter 3 Life's Signature in Ancient Rocks -- Chapter 4 The Earliest Glimmers of Life -- Chapter 5 The Emergence of Life -- Chapter 6 The Oxygen Revolution -- Chapter 7 The Cyanobacteria, Life's Microbial Heroes -- Plate 1 -- Plate 2 -- Plate 3 -- Plate 4 -- Plate 5 -- Plate 6 -- Plate 7 -- Plate 8 -- Chapter 8 The Origins of Eukaryotic Cells -- Chapter 9 Fossils of Early Eukaryotes -- Chapter 10 Animals Take the Stage -- Chapter 11 Cambrian Redux -- Chapter 12 Dynamic Earth, Permissive Ecology -- Chapter 13 Paleontology ad Astra -- Epilogue -- Further Reading -- Index.

Note: Intro -- Title Page -- Dedication -- Contents -- Prologue: An Invitation -- 1: Chemical Earth -- 2: Physical Earth -- 3: Biological Earth -- 4: Oxygen Earth -- 5: Animal Earth -- 6: Green Earth -- 7: Catastrophic Earth -- 8: Human Earth -- Acknowledgments -- Further Reading -- Index -- About the Author -- Also by Andrew H. Knoll -- Copyright -- About the Publisher.

Note: Intro -- FUNDAMENTALS OF GEOBIOLOGY -- Contents -- Contributors -- 1. What is Geobiology? -- 1.1 Introduction -- 1.2 Life interacting with the Earth -- 1.3 Pattern and process in geobiology -- 1.4 New horizons in geobiology -- References -- 2. The Global Carbon Cycle: Biological Processes -- 2.1 Introduction -- 2.2 A brief primer on redox reactions -- 2.3 Carbon as a substrate for biological reactions -- 2.4 The evolution of photosynthesis -- 2.5 The evolution of oxygenic phototrophs -- 2.6 Net primary production -- 2.7 What limits NPP on land and in the ocean? -- 2.8 Is NPP in balance with respiration? -- 2.9 Conclusions and extensions -- References -- 3. The Global Carbon Cycle: Geological Processes -- 3.1 Introduction -- 3.2 Organic carbon cycling -- 3.3 Carbonate cycling -- 3.4 Mantle degassing -- 3.5 Metamorphism -- 3.6 Silicate weathering -- 3.7 Feedbacks -- 3.8 Balancing the geological carbon cycle -- 3.9 Evolution of the geological carbon cycle through Earth's history: proxies and models -- 3.10 The geological C cycle through time -- 3.11 Limitations and perspectives -- References -- 4. The Global Nitrogen Cycle -- 4.1 Introduction -- 4.2 Geological nitrogen cycle -- 4.3 Components of the global nitrogen cycle -- 4.4 Nitrogen redox chemistry -- 4.5 Biological reactions of the nitrogen cycle -- 4.6 Atmospheric nitrogen chemistry -- 4.7 Summary and areas for future research -- References -- 5. The Global Sulfur Cycle -- 5.1 Introduction -- 5.2 The global sulfur cycle from two perspectives -- 5.3 The evolution of S metabolisms -- 5.4 The interaction of S with other biogeochemical cycles -- 5.5 The evolution of the S cycle -- 5.6 Closing remarks -- Acknowledgements -- References -- 6. The Global Iron Cycle -- 6.1 Overview -- 6.2 The inorganic geochemistry of iron: redox and reservoirs -- 6.3 Iron in modern biology and biogeochemical cycles. , 6.4 Iron through time -- 6.5 Summary -- Acknowledgements -- References -- 7. The Global Oxygen Cycle -- 7.1 Introduction -- 7.2 The chemistry and biochemistry of oxygen -- 7.3 The concept of redox balance -- 7.4 The modern O2 cycle -- 7.5 Cycling of O2 and H2 on the early Earth -- 7.6 Synthesis: speculations about the timing and cause of the rise of atmospheric O2 -- References -- 8. Bacterial Biomineralization -- 8.1 Introduction -- 8.2 Mineral nucleation and growth -- 8.3 How bacteria facilitate biomineralization -- 8.4 Iron oxyhydroxides -- 8.5 Calcium carbonates -- Acknowledgements -- References -- 9. Mineral-Organic-Microbe Interfacial Chemistry -- 9.1 Introduction -- 9.2 The mineral surface (and mineral-bio interface) and techniques for its study -- 9.3 Mineral-organic-microbe interfacial processes: some key examples -- Acknowledgements -- References -- 10. Eukaryotic Skeletal Formation -- 10.1 Introduction -- 10.2 Mineralization by unicellular organisms -- 10.3 Mineralization by multicellular organisms -- 10.4 A brief history of skeletons -- 10.5 Summary -- Acknowledgements -- References -- 11. Plants and Animals as Geobiological Agents -- 11.1 Introduction -- 11.2 Land plants as geobiological agents -- 11.3 Animals as geobiological agents -- 11.4 Conclusions -- Acknowledgements -- References -- 12. A Geobiological View of Weathering and Erosion -- 12.1 Introduction -- 12.2 Effects of biota on weathering -- 12.3 Effects of organic molecules on weathering -- 12.4 Organomarkers in weathering solutions -- 12.5 Elemental profiles in regolith -- 12.6 Time evolution of profile development -- 12.7 Investigating chemical, physical, and biological weathering with simple models -- 12.8 Conclusions -- Acknowledgements -- References -- 13. Molecular Biology's Contributions to Geobiology -- 13.1 Introduction -- 13.2 Molecular approaches used in geobiology. , 13.3 Case study: anaerobic oxidation of methane -- 13.4 Challenges and opportunities for the next generation -- Acknowledgements -- References -- 14. Stable Isotope Geobiology -- 14.1 Introduction -- 14.2 Isotopic notation and the biogeochemical elements -- 14.3 Tracking fractionation in a system -- 14.4 Applications -- 14.5 Using isotopes to ask a geobiological question in deep time -- 14.6 Conclusions -- Acknowledgements -- References -- 15. Biomarkers: Informative Molecules for Studies in Geobiology -- 15.1 Introduction -- 15.2 Origins of biomarkers -- 15.3 Diagenesis -- 15.4 Isotopic compositions -- 15.5 Stereochemical considerations -- 15.6 Lipid biosynthetic pathways -- 15.7 Classification of lipids -- 15.8 Lipids diagnostic of Archaea -- 15.9 Lipids diagnostic of Bacteria -- 15.10 Lipids of Eukarya -- 15.11 Preservable cores -- 15.12 Outlook -- Acknowledgements -- References -- 16. The Fossil Record of Microbial Life -- 16.1 Introduction -- 16.2 The nature of Earth's early microbial record -- 16.3 Paleobiological inferences from microfossil morphology -- 16.4 Inferences from microfossil chemistry and ultrastructure (new technologies) -- 16.5 Inferences from microbialites -- 16.6 A brief history, with questions -- 16.7 Conclusions -- Acknowledgements -- References -- 17. Geochemical Origins of Life -- 17.1 Introduction -- 17.2 Emergence as a unifying concept in origins research -- 17.3 The emergence of biomolecules -- 17.4 The emergence of macromolecules -- 17.5 The emergence of self-replicating systems -- 17.6 The emergence of natural selection -- 17.7 Three scenarios for the origins of life -- Acknowledgements -- References -- 18. Mineralogical Co-evolution of the Geosphere and Biosphere -- 18.1 Introduction -- 18.2 Prebiotic mineral evolution I - evidence from meteorites -- 18.3 Prebiotic mineral evolution II - crust and mantle reworking. , 18.4 The anoxic Archean biosphere -- 18.5 The Great Oxidation Event -- 18.6 A billion years of stasis -- 18.7 The snowball Earth -- 18.8 The rise of skeletal mineralization -- 18.9 Summary -- Acknowledgements -- References -- 19. Geobiology of the Archean Eon -- 19.1 Introduction -- 19.2 Carbon cycle -- 19.3 Sulfur cycle -- 19.4 Iron cycle -- 19.5 Oxygen cycle -- 19.6 Nitrogen cycle -- 19.7 Phosphorus cycle -- 19.8 Bioaccretion of sediment -- 19.9 Bioalteration -- 19.10 Conclusions -- References -- 20. Geobiology of the Proterozoic Eon -- 20.1 Introduction -- 20.2 The Great Oxidation Event -- 20.3 The early Proterozoic: Era geobiology in the wake of the GOE -- 20.4 The mid-Proterozoic: a last gasp of iron formations, deep ocean anoxia, the 'boring' billion, and a mid-life crisis -- 20.5 The history of Proterozoic life: biomarker records -- 20.6 The history of Proterozoic life: mid-Proterozoic fossil record -- 20.7 The late Proterozoic: a supercontinent, oxygen, ice, and the emergence of animals -- 20.8 Summary -- Acknowledgements -- References -- 21. Geobiology of the Phanerozoic -- 21.1 The beginning of the Phanerozoic Eon -- 21.2 Cambrian mass extinctions -- 21.3 The terminal Ordovician mass extinction -- 21.4 The impact of early land plants -- 21.5 Silurian biotic crises -- 21.6 Devonian mass extinctions -- 21.7 Major changes of the global ecosystem in Carboniferous time -- 21.8 Low-elevation glaciation near the equator -- 21.9 Drying of climates -- 21.10 A double mass extinction in the Permian -- 21.11 The absence of recovery in the early Triassic -- 21.12 The terminal Triassic crisis -- 21.13 The rise of atmospheric oxygen since early in Triassic time -- 21.14 The Toarcian anoxic event -- 21.15 Phytoplankton, planktonic foraminifera, and the carbon cycle -- 21.16 Diatoms and the silica cycle -- 21.17 Cretaceous climates. , 21.18 The sudden Paleocene-Eocene climatic shift -- 21.19 The cause of the Eocene-Oligocene climatic shift -- 21.20 The re-expansion of reefs during Oligocene time -- 21.21 Drier climates and cascading evolutionary radiations on the land -- References -- 22. Geobiology of the Anthropocene -- 22.1 Introduction -- 22.2 The Anthropocene -- 22.3 When did the Anthropocene begin? -- 22.4 Geobiology and human population -- 22.5 Human appropriation of the Earth -- 22.6 The carbon cycle and climate of the Anthropocene -- 22.7 The future of geobiology -- Acknowledgements -- References -- Index -- Colour plates.