Conflicting Models for the Origin of Life

Description

The number of publications on the origin of life has been doubling every decade from 1970 until today and now exceeds 70,000, illustrating the ever-growing interest of the scientific community and the public in this area. With our explosion of knowledge about the niches of extremophiles, discoveries of the vast numbers and varieties of exoplanets, and new fossil evidence for life extending nearly to Earth's beginning, many hypotheses have been put forth on the place, timing and manner for the origin of life. Old and new debates abound in the scientific community, demonstrating the lack of consensus among scholars with the emergence of champions for one point of view over another. The purpose of this book is to bring together the various arguments and points of view on the origin of life, highlighting their differences and conflicts, illustrating these various points of view in relation to concept, mechanism and plausibility for each of the theories. In this book we include dialogue between proponents of alternative hypotheses by giving them consecutive chapters, and allowing for criticisms and response sections after each chapter. In addition, an attempt is made to elicit definitions for life that are more rigorous and consistent than currently available. The use of consistent approaches has also resulted in the logical inclusion of minimal approaches to the origin of life, both investigating the original origin, and the possibility of an impending second creation - of artificial life. Cover Title Page Copyright Page Contents Foreword, “Are There Men on the Moon?” by Winston S. Churchill Preface Appendix to Preface by Richard Gordon and George Mikhailovsky Part I: Introduction to the Origin of Life Puzzle Chapter 1 Origin of Life: Conflicting Models for the Origin of Life 1.1 Introduction 1.2 Top-Down Approach—The Phylogenetic Tree of Life 1.3 Bottom-Up Approach—The Hypotheses 1.4 The Emergence of Chemolithoautotrophs and Photolithoautotrophs? 1.5 Viruses: The Fourth Domain of Life? 1.6 Where are We with the Origin of Life on Earth? References Chapter 2 Characterizing Life: Four Dimensions and their Relevance to Origin of Life Research 2.1 Introduction 2.2 The Debate About (Defining) Life 2.2.1 The Debate and the Meta-Debate 2.2.2 Defining Life is Only One Way to Address the Question “What is Life?” 2.3 Does Origin of Life Research Need a Characterization of Life? 2.4 Dimensions of Characterizing Life 2.4.1 Dimension 1: Dichotomy or Matter of Degree? 2.4.2 Dimension 2: Material or Functional? 2.4.3 Dimension 3: Individual or Collective? 2.4.4 Dimension 4: Minimal or Inclusive 2.4.5 Summary Discussion of the Dimensions 2.5 Conclusion Acknowledgments References Chapter 3 Emergence, Construction, or Unlikely? Navigating the Space of Questions Regarding Life’s Origins 3.1 How Can We Approach the Origins Quest(ion)? 3.2 Avian Circularities 3.3 Assuming That... 3.4 Unlikely 3.5 Construction 3.6 Emergence References Part II: Chemistry Approaches Chapter 4 The Origin of Metabolism and GADV Hypothesis on the Origin of Life 4.1 Introduction 4.2 [GADV]-Amino Acids and Protein 0th-Order Structure 4.3 Exploration of the Initial Metabolism: The Origin of Metabolism 4.3.1 From What Kind of Enzymatic Reactions Did the Metabolic System Originate? 4.3.2 What Kind of Organic Compounds Accumulated on the Primitive Earth 4.3.3 What Organic Compounds were Required for the First Life to Emerge? 4.4 From Reactions Using What Kind of Organic Compounds Did the Metabolism Originate? 4.4.1 Catalytic Reactions with What Kind of Organic Compounds Were Incorporated Into the Initial Metabolism? 4.4.2 Search for Metabolic Reactions Incorporated Into the Initial Metabolism 4.4.3 Syntheses of [GADV]-Amino Acids Leading to Produce [GADV]-Proteins/Peptides Were One of the Most Important Matters for the First Life 4.4.4 Nucleotide Synthetic Pathways were Integrated at the Second Phase in the Initial Metabolism 4.5 Discussion 4.5.1 Protein 0th-Order Structure Was the Key for Solving the Origin of Metabolism 4.5.2 Validity of GPG-Three Compounds Hypothesis on the Origin of Metabolism 4.5.3 Establishment of the Metabolic System and the Emergence of Life 4.5.4 The Emergence of Life Viewed from the Origin of Metabolism Acknowledgments References Chapter 5 Chemical Automata at the Origins of Life 5.1 Introduction 5.2 Theoretical Models 5.2.1 The Chemoton Model 5.2.2 Autopoiesis 5.2.3 Biotic Abstract Dual Automata 5.2.4 Automata and Diffusion-Controlled Reactions 5.2.5 Quasi-Species and Hypercycle 5.2.6 Computer Modeling 5.2.7 Two-Dimensional Automata 5.3 Experimental Approach 5.3.1 The Ingredients for Life 5.3.2 Capabilities Required for the Chemical Automata 5.3.2.1 Autonomy 5.3.2.2 Self-Ordering and Self-Organization 5.3.2.3 About Discriminating Aggregation 5.3.2.4 Autocatalysis and Competition 5.4 Conclusion References Chapter 6 A Universal Chemical Constructor to Explore the Nature and Origin of Life 6.1 Introduction 6.2 Digitization of Chemistry 6.3 Environmental Programming, Recursive Cycles, and Protocells 6.4 Measuring Complexity and Chemical Selection Engines 6.5 Constructing a Chemical Selection Engine Acknowledgements References Chapter 7 How to Make a Transmembrane Domain at the Origin of Life: A Possible Origin of Proteins 7.1 Introduction 7.2 The Initial “Core” Amino Acids 7.3 The Thickness of Membranes of the First Vesicles 7.4 Carbon–Carbon Distances Perpendicular to a Membrane 7.5 The Thickness of Modern Membranes 7.6 A Prebiotic Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides 7.7 A Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides 7.8 RNA World with the Protein World 7.9 Conclusion Acknowledgements References Part III: Physics Approaches Chapter 8 Patterns that Persist: Heritable Information in Stochastic Dynamics 8.1 Introduction 8.2 Markov Processes 8.2.1 Simple Examples of Markov Processes 8.2.2 Stochastic Dynamics 8.2.3 Master Equation 8.2.4 Dynamic Persistence 8.2.5 Coarse Graining 8.2.6 Entropy Production 8.3 Results 8.3.1 The Persistence Filter 8.4 Mechanisms of Persistence 8.5 Effects of Size N and Disequilibrium γ 8.6 Probability of Persistence 8.6.1 Continuity Constraint 8.6.2 Locality Constraint 8.6.3 New Strategies for Persistence 8.7 Measuring Persistence in Practice 8.7.1 Computable Information Density (CID) 8.7.2 Quantifying Persistence in Dynamic Assemblies of Colloidal Rollers 8.8 Conclusions 8.9 Methods 8.9.1 Coarse-Graining 8.10 Monte Carlo Optimization 8.11 Experiments on Ferromagnetic Rollers 8.12 A Persistence in Equilibrium Systems Acknowledgements References Chapter 9 When We Were Triangles: Shape in the Origin of Life via Abiotic, Shaped Droplets to Living, Polygonal Archaea During the Abiocene 9.1 Introduction 9.1.1 What Correlates with Archaea Shape? Nothing! 9.1.2 Archaea’s Place in the Tree of Life 9.1.3 The Discovery and Exploration of Shaped Droplets 9.1.4 Shaped Droplets as Protocells 9.1.5 Comparison of Shaped Droplets with Archaea 9.1.6 The S-Layer 9.1.7 The S-Layer as a Two-Dimensional Liquid with Fault Lines 9.1.8 The Analogy of the S-Layer to Bubble Rafts 9.1.9 Energy Minimization Model for the S-Layer in Polygonal Archaea 9.2 Discussion 9.3 Conclusion Acknowledgements References Chapter 10 Challenges and Perspectives of Robot Inventors that Autonomously Design, Build, and Test Physical Robots 10.1 Introduction 10.2 Physical Evolutionary-Developmental Robotics 10.2.1 Robotic Invention 10.2.2 Physical Morphology Adaptation 10.3 Falling Paper Design Experiments 10.3.1 Design–Behavior Mapping 10.3.2 More Variations of Paper Falling Patterns 10.3.3 Characterizing Falling Paper Behaviors 10.4 Evolutionary Dynamics of Collective Bernoulli Balloons 10.5 Discussions and Conclusions Acknowledgments References Part IV: The Approach of Creating Life Chapter 11 Synthetic Cells: A Route Toward Assembling Life 11.1 Compartmentalization: Putting Life in a Box 11.2 The Making of Cell-Sized Giant Liposomes 11.3 Coacervate-Based Synthetic Cells 11.4 Adaptivity and Functionality in Synthetic Cells 11.5 Synthetic Cell Information Processing and Communication 11.6 Intracellular Information Processing: Making Decisions with All the Noise 11.7 Extracellular Communication: the Art of Talking and Selective Listening 11.8 Conclusions Acknowledgments References Chapter 12 Origin of Life from a Maker’s Perspective–Focus on Protocellular Compartments in Bottom-Up Synthetic Biology 12.1 Introduction 12.2 Unifying the Plausible Protocells in Line with the Crowded Cell 12.3 Self-Sustained Cycles of Growth and Division 12.4 Transport and Energy Generation at the Interface 12.4.1 Energy and Complexity 12.4.2 Energy Compartmentation 12.5 Synergistic Effects Towards the Origin of Life References Part V: When and Where Did Life Start? Chapter 13 A Nuclear Geyser Origin of Life: Life Assembly Plant – Three-Step Model for the Emergence of the First Life on Earth and Cell Dynamics for the Coevolution of Life’s Functions 13.1 Introduction 13.2 Natural Nuclear Reactor 13.2.1 Principle of a Natural Nuclear Reactor 13.2.2 Natural Nuclear Reactor in Gabon 13.2.3 Radiation Chemistry to Produce Organics 13.2.4 Hadean Natural Nuclear Reactor 13.3 Nuclear Geyser Model as a Birthplace of Life on the Hadean Earth 13.4 Nine Requirements for the Birthplace of Life 13.5 Three-Step Model for the Emergence of the First Life on Hadean Earth 13.5.1 The Emergence of the First Proto-Life 13.5.1.1 Domain I: Inorganics 13.5.1.2 Domain II: From Inorganic to Organic 13.5.1.3 Domain III: Production of More Advanced BBL 13.5.1.4 Domain IV: Passage Connecting Geyser Main Room with the Surface and Fountain Flow 13.5.1.5 Domain V: Production of BBL in an Oxidizing Wet–Dry Surface Environment 13.5.1.6 Domain VI: Birthplace of the First Proto-Life 13.5.1.7 Utilization of Metallic Proteins 13.5.2 The Emergence of the Second Proto-Life 13.5.2.1 Drastic Environmental Change from Step 1 to Step 2 13.5.2.2 Biological Response from Step 1 to Step 2 13.5.3 The Emergence of the Third Proto-Life, Prokaryote 13.5.3.1 Drastic Environmental Changes from Step 2 to Step 3 13.5.3.2 Biological Response from Step 2 to Step 3 13.6 Concept of the Cell Dynamics: Life Assembly Plant Acknowledgments References Chapter 14 Comments on the Nuclear Geyser Origin of Life Proposal of the Authors S. Maruyama and T. Ebisuzaki and Interstellar Medium as a Possible Birthplace of Life References Chapter 15 Nucleotide Photochemistry on the Early Earth 15.1 Introduction 15.2 Pyrimidine Photochemistry 15.2.1 Photohydrates 15.2.2 Photodimers 15.2.3 Glycosidic Bond Cleavage 15.2.4 Addition of Nucleophiles to C2 15.3 Purine Photochemistry 15.4 Photochemistry of Noncanonical Nucleosides 15.4.1 Photochemical Anomerization of Cytidine Nucleosides 15.4.2 Thiobase Irradiation Products 15.4.3 Photochemical Decarboxylation of Orotidine 15.4.4 Photochemical Synthesis of AICN, a Possible Synthetic Precursor to the Purines 15.5 Considering More Complex Photochemical Systems 15.6 Concluding Remarks References Chapter 16 Origins of Life on Exoplanets 16.1 Introduction 16.2 How to Test Origins Hypotheses 16.3 Exoplanets as Laboratories 16.4 The Scenario 16.5 Initial Conditions 16.5.1 Chemical Initial Conditions 16.5.1.1 Hydrogen Cyanide 16.5.1.2 Sulfite and Sulfide 16.5.2 Physical Initial Conditions 16.6 Chances of Success 16.7 Relevance of the Outcome 16.8 Conclusions Acknowledgements References Chapter 17 The Fish Ladder Toy Model for a Thermodynamically at Equilibrium Origin of Life in a Lipid World in an Endoreic Lake 17.1 The Fish Ladder Model for the Origin of Life 17.2 Could the Late Heavy Bombardment have Supplied Enough Amphiphiles? 17.3 How Many Uphill Steps to LUCA? 17.4 How Long Would the Origin of Life Take After the CVC is Achieved? 17.5 Conclusion Acknowledgements Appendix (Discussion with David Deamer) References Index EULA