Towards Revealing the Origin of Life : Presenting the GADV Hypothesis

The origin of life has been investigated by many researchers from various research fields, such as Geology, Geochemistry, Physics, Chemistry, Molecular Biology, Astronomy and so on. Nevertheless, the origin of life remains unsolved. One of the reasons for this could be attributed to the different approaches that researchers have used to understand the events that happened on the primitive Earth. The origins of the main three members of the fundamental life system, as gene, genetic code and protein, could be only separately understood with these approaches. Therefore, it is necessary to understand the origins of gene, the genetic code, tRNA, metabolism, cell structure and protein not separately but comprehensively under a common concept in order to understand the origin of life, because the six members are intimately related to each other. In this monograph, the author offers a comprehensive hypothesis to explain the origin of life under a common concept. At the same time, the author offers the [GADV] hypothesis contrasting it with other current hypotheses and discusses the results of analyses of genes/proteins and the experimental data available in the exploration of the current knowledge in the field. This book is of interest for science students, researchers and the general public interested in the origin of life. Foreword Preface Acknowledgments Contents About the Author Abbreviations Chapter 1: Introduction 1 Why Has Not the Origin of Life Been Solved Still Now? 1.1 The Reasons from Viewpoint of Research Methodology 1.1.1 The Research on the Origin of Life Usually Carried Out with the “Bottom-Up Approach” 1.1.2 Reproducibility Problem of the Events, Which Occurred on the Primitive Earth 1.1.3 Long-Time Phenomena 1.1.4 Repeating Phenomena 1.1.5 Another Difficulty in the Origin-Life Research 1.2 How Could the Three Main Members in the Fundamental Life System Be Created Through Random Processes? 1.3 Then, Is It Impossible to Unravel the Riddle of the Origin of Life? 2 My Idea About the Origin of Life 2.1 I Might Be Able to Solve the Riddle of the Origin of Life from My Own Viewpoint 2.2 The Reason Why I Could Reach a Novel Idea, with Which the Riddle of the Origin of Life Might Be Solved 3 Overview of This Book References Chapter 2: Modern Fundamental Life System 1 Towards Solving the Riddle of the Origin of Life 1.1 The Mechanism How Life Is Living 1.1.1 Problem About the “Central Dogma” 1.1.2 Proposition of “Core Life System” Instead of the “Central Dogma” 1.2 Necessary Matters for Solving the Riddle of the Origin of Life 1.3 Significance of Theoretical Approach 1.3.1 The Origin of a Member Must Be Narrowed Down to a Reasonable One with Theoretical Approach 1.3.2 Even the Most Primitive Member Must Have Basic Features Similar to Modern One 1.3.3 Something Assumed as the Origin Must Be the Most Primitive One, Which Could Evolve to Modern One 2 Overview of [GADV]-Protein World Hypothesis (GADV Hypothesis) 2.1 Establishment Process of the Fundamental Life System (Outline) 2.2 The Steps from Chemical Evolution to the Emergence of Life References Chapter 3: The Origin of Protein 1 Introduction: Towards Solving the Riddle of the Origin of Protein 1.1 Necessary Matters for Exploring the Origin of Protein 1.2 General Structural Features of Modern Protein (Enzyme) 1.3 General Functional Features of Modern Protein (Enzyme) 2 Structure Formation of Protein Under the Modern Genetic System 3 The Ideas on the Origin of Protein Advocated by Other Researchers 3.1 Amino Acid Sequence Hypothesis 3.2 Protein Structure Hypothesis 3.3 Short Peptide (Motif) Theory 3.4 The Reason Why the Origin of Protein-II Has Not Been Solved Still Now 4 My Idea About the Origin of Protein 4.1 Chemical Evolution 4.1.1 The First Life Should Emerge with Organic Compounds Accumulated at a Large Amount on the Primitive Earth 4.1.2 The Problem of Homochirality on the Origin of Life 4.2 [GADV]-Amino Acids Could Be Produced at Large Amounts Through Prebiotic Means 4.3 Immature [GADV]-Protein Could Be Produced Through a Random Process 4.4 [GADV]-Amino Acid Composition Is One of Protein 0th-Order Structures 4.5 From Production of Immature Protein to Formation of Double-Stranded (GNC)n Gene 4.5.1 Production of Immature Protein by Direct Random Joining of [GADV]-Amino Acids 4.5.2 Formation of Primitive Cell Structure or [GADV]-Microsphere and a Primitive Metabolic System 4.5.3 Production of Immature Protein by Random Joining of Activated [GADV]-Amino Acids 4.5.4 Formation of Four AntiC-SL tRNAs Carrying [GADV]-Amino Acid and Synthesis of Immature [GADV]-Protein 4.5.5 Creations of Single-Stranded (GNC)n RNA and Double-Stranded (GNC)n RNA 4.6 The Formation of the First ds-(GNC)n RNA Led to Creation of the First Mature [GADV]-Protein 4.6.1 Creation of a Mature [GADV]-Protein Was Triggered by the Formation of ds-(GNC)n RNA 4.7 Immature Protein Is Pluripotent 4.7.1 Evidence Showing That an Immature Protein Is Pluripotent 4.8 Creation of an Entirely New Mature Protein Through the First Double-Stranded (GNC)n RNA 4.8.1 No Mature Protein Could Be Produced Through Random Process 4.8.2 Every Mature Protein Was Always Created Through Maturation Process from an Immature Protein 4.8.3 Creation of Mature Protein Was Always Led by Not Gene But the Protein Itself 4.8.4 Formation of an Active Site of an Induced-Fit Type Mature Protein 5 Discussion 6 Conclusion References Chapter 4: The Origin of Cell Structure 1 Towards Solving the Riddle of the Origin of Cell Structure 1.1 Necessary Matters for Exploration of the Origin of Cell Structure 1.2 General Structural Features of Modern Cell (Cell Structure) 1.3 General Functional Features of Modern Cell (Cell Structure) 2 The Ideas on the Origin of Cell Structure Advocated by Other Researchers 2.1 Amphiphile Membrane Theory 2.2 Protenoid Microsphere Theory 3 My Idea About the Origin of Modern Cell 3.1 For What Purpose Was the First Cell Structure Created? 3.2 [GADV]-Microsphere Hypothesis 3.2.1 Formation of [GADV]-Microsphere 3.2.2 Properties of [GADV]-Microsphere 4 Discussion 5 Conclusion References Chapter 5: The Origin of Metabolism 1 Introduction: Towards Solving the Riddle of the Origin of Metabolism 1.1 Necessary Matters for Exploration of the Origin of Metabolism 1.2 General Features of Modern Metabolism 1.3 Basic Features of Modern Metabolism 1.4 Significance of Establishment of the Primitive Metabolic System for the Emergence of Life 2 The Ideas on the Origin of Metabolism Advocated by Other Researchers 2.1 Surface Metabolism Theory 2.2 Clay World Theory 2.3 Hydrothermal Vent Theory 2.4 Three Hypotheses Proposed by Other Researchers and the Origin of Metabolism 3 My Idea on the Origin of Metabolism 3.1 For What Purpose Was the First Metabolism Created? 3.2 The Initial Metabolism Must Be Formed Before the Emergence of Life 3.3 The Role of [GADV]-Amino Acids or Protein 0th-Order Structure in the Origin of Metabolism 3.4 What Kinds of Catalytic Reactions Were Used in the Initial Metabolism 3.4.1 What Organic Compounds Were Accumulated on the Primitive Earth? 3.4.2 What Organic Compounds Were Required for the First Life to Emerge? 3.4.3 Nucleotide Synthetic Pathways Were Integrated at the Second Phase of the Initial Metabolism 3.5 Proposition of GoGaPyr Hypothesis on the Origin of Metabolism 3.5.1 Validity of GoGaPyr Hypothesis on the Origin of Metabolism 3.5.2 Synthetic Reactions Preferentially Proceeded in the Initial Metabolism 3.6 Immature Proteins, Which Were Produced in the Absence of Gene, Could Catalyze All Metabolic Reactions in the Initial Metabolism 3.7 Evolution of Metabolic Pathways from the Most Primitive Metabolic System 3.7.1 Formation of Linear Metabolic Pathway 3.7.2 Formation of Circular Metabolic Pathway 3.7.3 Formation of Branched Metabolic Pathway 4 Discussion 5 Conclusion References Chapter 6: The Origin of tRNA 1 Introduction: Towards Solving the Riddle of the Origin of tRNA 1.1 Necessary Matters for Exploration of the Origin of tRNA 1.2 General Structural Features of tRNA 1.3 General Functional Features of tRNA 2 The Ideas on the Origin of tRNA Advocated by Other Researchers 2.1 Minihelix Theory 2.2 Double-Hairpin and tRNA Split Gene Hypothesis 2.3 A Small Hairpin-Loop RNA Hypothesis 3 My Idea on the Origin of tRNA 3.1 For What Purpose Was the First tRNA Created? 3.2 Exploring the Origin of tRNA 3.3 Exploring the First Primeval AntiC-SL tRNA 3.4 Modern tRNA Originated from One Nonspecific Anticodon Stem-Loop RNA 3.5 Properties of the First AntiC-SL tRNA 4 Evolutionary Process Deduced from Anticodon Stem-Loop Hypothesis 4.1 Evolutionary Pathway of tRNA Deduced from Mutual Relation Network of 5′ AntiC-Stem Sequences 4.2 Evolutionary Process from the Primitive AntiC-SL tRNA to L-form tRNA 4.2.1 L-form tRNA Was Created by Combination of Four AntiC-SL tRNAs 4.2.2 Deduced Evolutionary Steps from the First AntiC-SL tRNA to L-form tRNA 5 Discussion 6 Conclusion References Chapter 7: The Origin of the Genetic Code 1 Introduction: Towards Solving the Riddle of the Origin of the Genetic Code 1.1 Necessary Matters for Exploration of the Origin of the Genetic Code 1.2 General Structural Features of the Genetic Code 1.3 General Functional Features of the Genetic Code 1.4 There Are Two Sides for Exploring the Origin of the Genetic Code 2 The Ideas on the Origin of the Genetic Code Advocated by Other Researchers 2.1 RNY Hypothesis 2.2 GC Hypothesis 2.3 Four Column Theory 2.4 GCU Code Hypothesis 2.5 Stereochemical Theory 2.5.1 Search for Specific Interactions Between a Codon/Anticodon and an Amino Acid 2.5.2 Was the Genetic Code Established as Expected by the Stereochemical Theory? 2.5.3 Can the Complexes Between a Codon/Anticodon and an Amino Acid Function in Protein Synthesis? 2.6 Crick’s Frozen-Accident Theory 3 My Idea on the Origin of the Genetic Code 3.1 For What Purpose Was the First Genetic Code Created? 3.2 GNC-SNS Primitive Genetic Code Hypothesis 3.2.1 SNS Primitive Genetic Code Hypothesis 3.2.2 GNC Primeval Genetic Code Hypothesis 3.3 GNC Code Frozen-Accident Theory 3.3.1 A Novel Idea for Solving the Enigma of the Origin of the Genetic Code-II 3.3.2 Proposition of a Novel Idea on the Origin of the Genetic Code or “GNC Code-Frozen Accident Theory” 4 Discussion 5 Conclusion References Chapter 8: The Origin of Gene 1 Introduction: Towards Solving the Riddle of the Origin of Gene 1.1 Necessary Matters for Exploring the Origin of Gene 1.2 General Structural Features of Gene (Basic Features of Gene) 1.3 General Functional Features of Gene 1.4 There Are Two Sides for Exploring the Origin of Gene 2 The Ideas on the Origin of Gene Advocated by Other Researchers 2.1 Gene-Duplication Theory 2.2 Exon-Shuffling Theory 2.3 Self-Replicated RNA Theory (RNA World Hypothesis) 3 My Idea About the Origin of Gene 3.1 For What Purpose Was the First Genetic Information (Gene) Created? 3.2 Anticodon Joining Hypothesis 3.2.1 Creation Process of Single-Stranded (GNC)n RNA 3.2.2 Formation of Double-Stranded (GNC)n RNA 3.2.3 Creation of the First Double-Stranded (GNC)n RNA Gene Encoding a Mature [GADV]-Protein 3.3 Creation of an Entirely New Gene After Formation of the First Double-Stranded (GNC)n RNA Gene 3.3.1 Creation of an Entirely New Gene Under GNC Primeval Genetic Code (GC-(GNC)n-NSF(a) Hypothesis) 3.3.2 An Immature [GADV]-Protein-2 is More Flexible Than a Mature Protein 3.3.3 Creation of an Entirely New Gene Under SNS Primitive Genetic Code (GC-(SNS)n-NSF(a) Hypothesis) 3.3.4 Creation of an Entirely New Gene Under the Universal Genetic Code (GC-NSF(a) Hypothesis) 3.4 Evidence Showing that Modern Entirely New Proteins Have Been Produced Through Essentially Random Process 3.4.1 Appearance Frequency of Neighboring Two Amino Acids in Proteins 3.4.2 Dependency of Hydrophilic Amino Acid Content of a Modern Protein on the Amino Acid Number of the Protein 3.4.3 Direct Evidence for Creation of a Mature Protein from an Immature Protein-2 3.4.4 Pan-GC-NSF(a) Hypothesis on the Origin of Gene-II 4 Discussion 4.1 Anticodon Joining Hypothesis 4.1.1 Qualitative Change from RNA without Genetic Information to RNA Gene 4.2 Grounds for Pan-GC-NSF(a) Hypothesis 5 Conclusion References Chapter 9: The Origin of Life 1 Introduction: Towards Solving the Riddle of the Origin of Life 1.1 Necessary Matters for Exploration of the Origin of Life 1.2 General Structural Features of Modern Life 1.3 General Functional Features of Modern Life 2 The Ideas About the Origin of Life Advocated by Other Researchers 2.1 RNA World Hypothesis 2.2 Hydrothermal Vent Theory 2.3 Protein World Theory 2.3.1 Amyloid World Theory 2.3.2 α-Helical Peptide Theory 2.4 Coenzyme World Hypothesis 2.5 tRNA Core Hypothesis 2.6 Space-Origin Hypothesis 2.7 Common Weaknesses of Other Hypotheses for Exploration of the Origin of Life 3 My Idea About the Origin of Life 3.1 [GADV]-Protein World Hypothesis (GADV Hypothesis) 3.2 Establishment Process of the Fundamental Life System 4 Three Keys for Solving the Riddle of the Origin of Life 4.1 Can Biopolymers with Ordered Sequence Be Produced Through Random Processes? 4.2 How Could the Three Keys for Solving the Riddle of the Origin of Life Be Formed During Random Processes 4.2.1 The First Key: Immature Water-Soluble Globular [GADV]-Protein with Some Flexibility 4.2.2 The Second Key: Anticodon Stem-Loop tRNA 4.2.3 The Third Key: Single-Stranded (GNC)n RNA 4.2.4 The Genuine Life Emerged Upon Acquisition of Double-Stranded (GNC)n Gene 4.2.5 The Steps to the Emergence of Life Viewed from the Three Keys 5 Discussion 6 Conclusion References Chapter 10: General Discussion 1 What is the Significance of the Origin-Life Research? 2 Establishment Process of the Fundamental Life System 3 About Another Possibility of the Establishment Process of the Fundamental Life System 4 Bottom-Up and Top-Down Approaches for Elucidation of the Origin of Life 5 Did the Events Deduced from GADV Hypothesis Really Occur on the Primitive Earth? 6 Evolution of Organisms 7 Why Have So Splendid Organisms Flourished on the Present Earth? Reference Index