Organisms Amplify Diversity: An Autocatalytic Hypothesis

Cover
Half Title
Title Page
Copyright Page
Dedication
Table of Contents
Acknowledgments
About the Author
1 Introduction
	References
2 Life Regulates the Atmosphere’s Greenhouse Gas Levels and the Earth’s Temperature
	2.1 Terminology
	2.2 The Carbon Cycle and Negative Feedback Loops
	2.3 Life Is the Main Regulator of Atmospheric Carbon
	2.4 Life Conserves Carbon for the Biosphere, Even as It Regulates It
	2.5 Life Likely Regulates Temperature With Negative Feedback and Dimethyl Sulfide
	2.6 Coccolithophores May Regulate Temperature Through Negative Feedback
	2.7 Organisms Regulate Silicon, Helping Life
	2.8 Biology Might Aid Life By Regulating the Ocean’s Salt Content
	2.9 Venus and Human Impacts Show That Organisms Have Profoundly Helped Life By Regulating Atmospheric Greenhouse Gases and Temperature
	2.10 The Detrimental Impacts of High Atmospheric Carbon Dioxide Levels On Life Are Not Limited to Temperature Effects
	2.11 Did Biology Create Optimal Conditions for Life?
	2.12 Conclusion
	References
3 Organisms Created High Oxygen Levels, Which Allowed Complex Life to Evolve and Diversify
	3.1 Life Increased Earth’s Oxygen Level in the Great Oxidation Event
	3.2 High Oxygen Levels Diversified Minerals and Increased the Number of Amino Acids Used By Life. Both of These Increased Biodiversity
		3.3 Life Caused Further Rises in Oxygen Levels After the GOE
	3.4 The Amazon River and Phytoplankton Together Produce Great Quantities of Oxygen
	3.5 Life’s Production of High Oxygen Levels Helps Diversity in Many Ways Besides Providing an Energy Source...
	3.6 Oxygen and Fire Are Regulated By Negative Feedback Mediated By Life
	3.7 Life Stabilized Atmospheric Oxygen Levels for the Last 350 Million Years With Imperfect Negative Feedback
	3.8 The GOE May Have Caused a Glaciation, But Almost Surely Not a Mass Extinction
	3.9 Anoxygenic and Oxygenic Photosynthesis and the Use By Life of What Is Available
	3.10 Life Coevolved With the Atmosphere
	Note
	References
4 Species Profoundly Affect the Evolution of Other Species: Coevolution Is Fundamentally Important and Was Involved in...
	References
5 In Ecological Succession, Communities Create Favorable Environmental Conditions for Succeeding, Usually More Diverse and Complex, Communities
	References
6 Life Is the Main Creator of Soil, a Diverse Ecosystem That Benefits Life in the Soil and Above It
	Note
	References
7 Eukaryotes Are Complex Ecosystems With Diverse Microbiomes, Showing the Importance...
	7.1 All Eukaryotes Are Ecosystems With Diverse Microbiomes, With a Great Deal of Symbiosis and Commensalism
	7.2 Unicellular Eukaryotes Have Microbiomes
	7.3 About the Microbiome
	7.4 The Microbiome Aids Digestion and Absorption, and the Digestive System
	7.5 The Microbiome Makes Vitamins That Its Host Needs
	7.6 The Microbiome Helps the Intestine of Its Host
	7.7 The Microbiome Is Necessary for the Nervous System
	7.8 The Microbiome Is Essential to the Function of the Immune System, and Directly Competes With Pathogens
	7.9 The Microbiome Protects Its Host From Allergies
	7.10 Probiotic Bacteria Help Keep the Host Free of Infections, and Help It in Other Ways
	7.11 The Skin Is a Diverse Ecosystem of Microbes That Are Essential to Skin Health
	7.12 The Microbiome Is Involved in Gene Expression
	7.13 Other Benefits of the Microbiome
	7.14 Helicobacter Pylori Causes Peptic Ulcers, But Also Helps Its Host
	7.15 The Appendix Functions to Ensure That the Host Does Not Lose Its Microbiome
	7.16 Low Microbiome Diversity Is Correlated With Obesity and Other Problems
	7.17 Other Benefits of a Diverse Microbiome
	7.18 Plant Microbiomes
	7.19 The Microbiomes of Invertebrates
	7.20 Ruminants Have Complex Microbiome Ecosystems
	7.21 The Microbiome Can Aid Speciation
	7.22 More Facts About the Microbiome
	7.23 Implications of the Microbiome
	Notes
	References
8 Viruses Are By Far the Most Genetically Variable and Biodiverse Group of Organisms, Generate High Diversity in Cellular Organisms, and...
	8.1 Viruses Are the Most Diverse and Abundant Life Form
	8.2 There Is a Continuum of Replicating Segments of Genetic Material From Selfish Parasite to Full Cooperator With Respect to the Host
	8.3 Viruses Increase the Diversity of Cellular Organisms
	8.4 Viruses Exchange Genetic Material, Including Genes, With Their Hosts
	8.5 Bacteriophage Release Nutrients in Deep-Sea Sediments
	8.6 Viral Infection Reduces Phytoplankton Nutrient Quality, Contradicting the ABH
	8.7 Coevolution of Phage With the Bacteria Group Called SAR11 Is Important in Nutrient Cycles
	8.8 Viruses Caused Macroevolutionary Innovations and Tremendous Diversification in Prokaryotes and EUKARYOTIC Phytoplankton
	8.9 Viruses Were Important in Promoting Major Macroevolutionary Breakthroughs in Cellular Organisms
	References
9 Genomes and Their Behaviors Promote Genetic Variability, Evolution, Large Adaptive Evolutionary Innovations, and Diversification: The Amount and Nature of Genetic Variability Is Subject to Natural Selection
	9.1 The Behaviors of Genomes Promote Variability, Diversity, Evolution, and Even Large, Adaptive Macroevolutionary Breakthroughs
	9.2 Natural Selection Optimizes the Amount and Nature of Genetic Variability
	9.3 Sexual Reproduction Increases Variability While Maintaining the Integration and Self-Compatibility of the Genotype and Phenotype, and Can Promote Evolutionary Innovation and Diversity
	9.4 Horizontal Gene Transfer
	9.5 Bacterial Conjugation
	9.6 Gene Transfer Agents
	9.7 Transformation
	9.8 Transduction and Viral Incorporation of Host Genes
	9.9 Transposable Elements
	9.10 Transposable Elements Affect Genome Size, Influencing the Phenotype and Increasing Biodiversity
	9.11 The Microbiome Can Supply Genes to Its Eukaryotic Host
	9.12 Exon Shuffling and Protein Domains
	9.13 New Genes Can Originate From Noncoding DNA AND NONCODING RNA
	9.14 Duplication of DNA Segments
	9.15 Repetitive DNA Sequences
	9.16 DNA Base Repeats
	9.17 Polyploidy
	9.18 Creation of New Species By Hybridization Between Two Different Species
	9.19 Deletion of Segments of DNA
	9.20 Regulatory Genes and Evolution
	9.21 Exaptation and Evolution
	9.22 Special Chromosomes Promoted Songbird Diversification
	9.23 CONCLUSION
	Notes
	References
10 Altruism and Cooperation Within Populations Are Often Adaptive, and Maintain Populations and Diversity
	10.1 Kin Selection
	10.2 The Green Beard Effect
	10.3 Warning Others May Be Kin Selection Or a Side Effect of Selfishness
	10.4 Reciprocal Altruism
	10.5 Group Selection
	10.6 Kin Selection With Possible Group Selection
	10.7 Unexplained Altruism
	10.8 Cooperation and Altruism Can Be Transmitted Culturally
	10.9 Conflict Resolution Without Fighting
	10.10 The Superorganism
	References
11 Network Theory Models and Empirical Evidence Support the Thesis That Coevolved Diversity and Connectance Correlate...
	11.1 Life Promotes Regulation of Earth’s System
	11.2 Network Theory
	11.3 A New Proposed Principle of Ecology and Evolution: Links Between Species Are Fundamental
	11.4 Conclusion
	Note
	References
12 Scientific Laws Indicate the Essential Inevitability of the Chemical Evolution of Life Under Favorable Conditions: A Hypothesis That Incorporates the Autocatalytic Biodiversity...
	12.1 Precursors to Large Biological Molecules Were Delivered From Space
	12.2 How Lipids and Amino Acids Are Formed in Molecular Clouds and Possibly How Amino Acids Are Formed On Earth
	12.3 Source of Nucleotides Not Fully Worked Out
	12.4 Source of Earth’s Water
	12.5 Volcanoes Provided Land: Solar Distillation of Water
	12.6 How the Building Blocks of RNA Were Joined Together to Make RNA and How RNA Increased in Complexity
	12.7 How the First Cells Were Made
	12.8 Life’s Earliest Fossils Are Consistent With the Inevitability of Life’s Origin
	12.9 A General Hypothesis That Incorporates the ABH
	Notes
	References
13 The Solar System, Sun, Jupiter, Earth’s Moon, and Nonbiological Earth All Aid Life, Suggesting the Autocatalytic Biodiversity Hypothesis Does Not Account for All of Earth’s Biodiversity
	13.1 The Sun Supports Life
	13.2 The Earth Is Placed Well for Life
	13.3 Volcanoes and Earth’s Internal Heat Aid Life
	13.4 Upwelling Is Caused By a Combination of Nonbiological and Biological Factors and Brings the Nutrients That Support Many of the Ocean’s Food Webs to the Photic Zone
	13.5 Deep-Sea Eruptions Create Habitats for Diverse Floating Communities of Species
	13.6 Plate Tectonics and Continental Drift Increased Diversity and Aided the Evolution of Upright Walking in Human Ancestors
		13.7 The Magnetic Field Protects and Is Used By Life On Earth
	13.9 Nonbiological Transport of Nutrients Between Ecosystems
	13.10 Lightning Helps Life
	13.11 THE MOON AIDS LIFE AND MAY HAVE CAUSED MAJOR EVOLUTIONARY BREAKTHROUGHS
	13.12 JUPITER AND SATURN MAY HAVE HELPED MAKE EARTH ABLE TO SUPPORT LIFE
	13.13 The Galactic Tide May Have Aided Biology
	13.14 The Possibility of Life On Other Planets
	13.15 Are the Parameters On Earth Close to Optimal for Life? If So, Is this Due to Life?
	References
14 Counterexamples to and Arguments Against the Autocatalytic Biodiversity Hypothesis and Answers to Them
	14.1 The Medea Hypothesis
	14.2 Human Impacts and the Autocatalytic Biodiversity Hypothesis/Pachamama Hypothesis
	References
15 Implications
	References
Index