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hanczyc m conflicting models origin life 2023

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Textbook in PDF format 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. Foreword, “Are There Men on the Moon?” by Winston S Churchill Preface Appendix to Preface by Richard Gordon and George Mikhailovsky Introduction to the Origin of Life Puzzle Origin of Life: Conflicting Models for the Origin of Life Introduction Top-Down Approach—The Phylogenetic Tree of Life Bottom-Up Approach—The Hypotheses The Emergence of Chemolithoautotrophs and Photolithoautotrophs? Viruses: The Fourth Domain of Life? Where are We with the Origin of Life on Earth? References Characterizing Life: Four Dimensions and their Relevance to Origin of Life Research Introduction The Debate About (Defining) Life The Debate and the Meta-Debate Defining Life is Only One Way to Address the Question “What is Life?” Does Origin of Life Research Need a Characterization of Life? Dimensions of Characterizing Life Dimension : Dichotomy or Matter of Degree? Dimension : Material or Functional? Dimension : Individual or Collective? Dimension : Minimal or Inclusive Summary Discussion of the Dimensions Conclusion Acknowledgments References Emergence, Construction, or Unlikely? Navigating the Space of Questions Regarding Life’s Origins How Can We Approach the Origins Quest(ion)? Avian Circularities Assuming That Unlikely Construction Emergence References Chemistry Approaches The Origin of Metabolism and GADV Hypothesis on the Origin of Life Introduction [GADV]-Amino Acids and Protein th-Order Structure Exploration of the Initial Metabolism: The Origin of Metabolism From What Kind of Enzymatic Reactions Did the Metabolic System Originate? What Kind of Organic Compounds Accumulated on the Primitive Earth What Organic Compounds were Required for the First Life to Emerge? From Reactions Using What Kind of Organic Compounds Did the Metabolism Originate? Catalytic Reactions with What Kind of Organic Compounds Were Incorporated Into the Initial Metabolism? Search for Metabolic Reactions Incorporated Into the Initial Metabolism Syntheses of [GADV]-Amino Acids Leading to Produce [GADV]-Proteins/Peptides Were One of the Most Important Matters for the First Life Nucleotide Synthetic Pathways were Integrated at the Second Phase in the Initial Metabolism Discussion Protein th-Order Structure Was the Key for Solving the Origin of Metabolism Validity of GPG-Three Compounds Hypothesis on the Origin of Metabolism Establishment of the Metabolic System and the Emergence of Life The Emergence of Life Viewed from the Origin of Metabolism Acknowledgments References Chemical Automata at the Origins of Life Introduction Theoretical Models The Chemoton Model Autopoiesis Biotic Abstract Dual Automata Automata and Diffusion-Controlled Reactions Quasi-Species and Hypercycle Computer Modeling Two-Dimensional Automata Experimental Approach The Ingredients for Life Capabilities Required for the Chemical Automata Autonomy Self-Ordering and Self-Organization About Discriminating Aggregation Autocatalysis and Competition Conclusion References A Universal Chemical Constructor to Explore the Nature and Origin of Life Introduction Digitization of Chemistry Environmental Programming, Recursive Cycles, and Protocells Measuring Complexity and Chemical Selection Engines Constructing a Chemical Selection Engine Acknowledgements References How to Make a Transmembrane Domain at the Origin of Life: A Possible Origin of Proteins Introduction The Initial “Core” Amino Acids The Thickness of Membranes of the First Vesicles Carbon–Carbon Distances Perpendicular to a Membrane The Thickness of Modern Membranes A Prebiotic Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides A Model for the Coordinated Growth of Membrane Thickness and Transmembrane Peptides RNA World with the Protein World Conclusion Acknowledgements References Physics Approaches Patterns that Persist: Heritable Information in Stochastic Dynamics Introduction Markov Processes Simple Examples of Markov Processes Stochastic Dynamics Master Equation Dynamic Persistence Coarse Graining Entropy Production Results The Persistence Filter Mechanisms of Persistence Effects of Size N and Disequilibrium γ Probability of Persistence Continuity Constraint Locality Constraint New Strategies for Persistence Measuring Persistence in Practice Computable Information Density (CID) Quantifying Persistence in Dynamic Assemblies of Colloidal Rollers Conclusions Methods Coarse-Graining Monte Carlo Optimization Experiments on Ferromagnetic Rollers A Persistence in Equilibrium Systems Acknowledgements References When We Were Triangles: Shape in the Origin of Life via Abiotic, Shaped Droplets to Living, Polygonal Archaea During the Abiocene Introduction What Correlates with Archaea Shape? Nothing! Archaea’s Place in the Tree of Life The Discovery and Exploration of Shaped Droplets Shaped Droplets as Protocells Comparison of Shaped Droplets with Archaea The S-Layer The S-Layer as a Two-Dimensional Liquid with Fault Lines The Analogy of the S-Layer to Bubble Rafts Energy Minimization Model for the S-Layer in Polygonal Archaea Discussion Conclusion Acknowledgements References Challenges and Perspectives of Robot Inventors that Autonomously Design, Build, and Test Physical Robots Introduction Physical Evolutionary-Developmental Robotics Robotic Invention Physical Morphology Adaptation Falling Paper Design Experiments Design–Behavior Mapping More Variations of Paper Falling Patterns Characterizing Falling Paper Behaviors Evolutionary Dynamics of Collective Bernoulli Balloons Discussions and Conclusions Acknowledgments References The Approach of Creating Life Synthetic Cells: A Route Toward Assembling Life Compartmentalization: Putting Life in a Box The Making of Cell-Sized Giant Liposomes Coacervate-Based Synthetic Cells Adaptivity and Functionality in Synthetic Cells Synthetic Cell Information Processing and Communication Intracellular Information Processing: Making Decisions with All the Noise Extracellular Communication: the Art of Talking and Selective Listening Conclusions Acknowledgments References Origin of Life from a Maker’s Perspective–Focus on Protocellular Compartments in Bottom-Up Synthetic Biology Introduction Unifying the Plausible Protocells in Line with the Crowded Cell Self-Sustained Cycles of Growth and Division Transport and Energy Generation at the Interface Energy and Complexity Energy Compartmentation Synergistic Effects Towards the Origin of Life References When and Where Did Life Start? 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 Introduction Natural Nuclear Reactor Principle of a Natural Nuclear Reactor Natural Nuclear Reactor in Gabon Radiation Chemistry to Produce Organics Hadean Natural Nuclear Reactor Nuclear Geyser Model as a Birthplace of Life on the Hadean Earth Nine Requirements for the Birthplace of Life Three-Step Model for the Emergence of the First Life on Hadean Earth The Emergence of the First Proto-Life Domain I: Inorganics Domain II: From Inorganic to Organic Domain III: Production of More Advanced BBL Domain IV: Passage Connecting Geyser Main Room with the Surface and Fountain Flow Domain V: Production of BBL in an Oxidizing Wet–Dry Surface Environment Domain VI: Birthplace of the First Proto-Life Utilization of Metallic Proteins The Emergence of the Second Proto-Life Drastic Environmental Change from Step to Step Biological Response from Step to Step The Emergence of the Third Proto-Life, Prokaryote Drastic Environmental Changes from Step to Step Biological Response from Step to Step Concept of the Cell Dynamics: Life Assembly Plant Acknowledgments References 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 Nucleotide Photochemistry on the Early Earth Introduction Pyrimidine Photochemistry Photohydrates Photodimers Glycosidic Bond Cleavage Addition of Nucleophiles to C Purine Photochemistry Photochemistry of Noncanonical Nucleosides Photochemical Anomerization of Cytidine Nucleosides Thiobase Irradiation Products Photochemical Decarboxylation of Orotidine Photochemical Synthesis of AICN, a Possible Synthetic Precursor to the Purines Considering More Complex Photochemical Systems Concluding Remarks References Origins of Life on Exoplanets Introduction How to Test Origins Hypotheses Exoplanets as Laboratories The Scenario Initial Conditions Chemical Initial Conditions Hydrogen Cyanide Sulfite and Sulfide Physical Initial Conditions Chances of Success Relevance of the Outcome Conclusions Acknowledgements References The Fish Ladder Toy Model for a Thermodynamically at Equilibrium Origin of Life in a Lipid World in an Endoreic Lake The Fish Ladder Model for the Origin of Life Could the Late Heavy Bombardment have Supplied Enough Amphiphiles? How Many Uphill Steps to LUCA? How Long Would the Origin of Life Take After the CVC is Achieved? Conclusion Acknowledgements Appendix (Discussion with David Deamer) References Index EULA

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