Conflicting Models for the Origin of 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