Prebiotic Chemistry and the Origin of Life

Preface
Contents
1 Transition Metal Organometallic/Metallorganic Chemistry: Its Role in Prebiotic Chemistry and Life's Origin
	1.1 Transition Metals: Elegance in Chemistry
	1.2 TM Astro-Genesis
		1.2.1 TM Condensation
		1.2.2 Physical-Chemistry of TM
	1.3 Organometallic and Metal-Organic Compounds
	1.4 Organometallic-Astrochemistry
	1.5 OC in Pre-biotic and Life's Origin
		1.5.1 Exogenous Delivery
			1.5.1.1 Organic-Mineral Interactions in Meteorites
			1.5.1.2 First Organometallics in Meteorites
			1.5.1.3 First Metallorganics in Meteorites
		1.5.2 Endogeneous Synthesis
			1.5.2.1 TM Distribution in the Hadean Eon
			1.5.2.2 Metabolism First
			1.5.2.3 Genetics First
	1.6 Final Considerations
	References
2 Mineralogical Environments of the Hadean Eon: Rare Elements Were Ubiquitous in Surface Sites of Rock-Forming Minerals
	2.1 Introduction
	2.2 An Evolutionary System of Mineralogy
	2.3 Trace and Minor Elements in Common Rock-FormingMinerals
	2.4 Conclusions
	References
3 The Geological Platform for the Origin of Life on Earth
	3.1 Introduction: Life Did Not Emerge in a Beaker
	3.2 A Geologist's Recipe for Life
		3.2.1 CHNOPS Sources and Activation Energy for Organic Synthesis
		3.2.2 Polymerisation
		3.2.3 Encapsulation
		3.2.4 Redox Gradients and Mineral Catalysis
	3.3 What Did the Earth Look Like When Life Emerged?
		3.3.1 The Solid Earth
			3.3.1.1 The Hadean to Eoarchean: The Earliest Fragments
			3.3.1.2 The 3.5–3.2 Ga East Pilbara Terrane: Geodynamics and Continental Emergence
			3.3.1.3 Surficial Expressions of an Archean Volcanic Plateau
		3.3.2 The Atmospheric Envelope
			3.3.2.1 The Composition of Earth's Atmosphere
			3.3.2.2 Lightning and Photochemistry
			3.3.2.3 Aerosols
		3.3.3 The Ocean
			3.3.3.1 Seawater Composition
			3.3.3.2 The Ocean-Atmosphere Interface
			3.3.3.3 Beaches and Shorelines
			3.3.3.4 Sea Ice
			3.3.3.5 Deep-Sea Hydrothermal Vents
	3.4 Summary and Conclusions: The Earth Was a Global Chemical Reactor
	References
4 Homochirality: A Prerequisite or Consequence of Life?
	4.1 Introduction
	4.2 Enantiomeric Cross Inhibition: The Need for Homochirality
	4.3 The Weak Force: Non-mirrorsymmetry in Nature
	4.4 Chiral Amino Acids in Meteorites
	4.5 The Basic Idea Behind the Frank Mechanism
	4.6 Evidence for Autocatalysis
	4.7 The Effect of an External Chiral Influence
	4.8 Polymerization Model of San03
	4.9 Spatiotemporal Chirality Dynamics
	4.10 Recycling Frank: The Peptide Model of Plasson et al.
	4.11 Fluctuations Instead of Autocatalysis or Enantiomeric Cross-Inhibition
	4.12 Chirality from a Martian Labeled Release Experiment
	4.13 Conclusions
	References
5 Origin of Nucleic Acids
	5.1 Introduction
	5.2 The Strange Ubiquity of AMP
	5.3 Nucleotides and the Creative Power of Standardization
	5.4 A Paradox Falls into Water
	5.5 The Crystalline Womb
	5.6 Informed Molecules Chain Order with Chaos
	5.7 What Is the Code About, Basically?
	5.8 Who Holds the Copyright? The Case Nucleic Acids Versus Amino Acids
	5.9 A New Form of Stability Arises
	5.10 Summary and Outlook
	References
6 Abiotic Synthesis and Role of Amphiphiles in the Encapsulation Process in Life's Origin
	6.1 Introduction
	6.2 Why Is the Emergence of Life Related to the Encapsulation Phenomenon?
		6.2.1 Encapsulation Improves the Efficiency of a Self-Sustaining Chemical System
		6.2.2 Encapsulation Is a Key Step Towards Darwinian Evolution
	6.3 Which Compartments for the First Encapsulations?
	6.4 Why Lipids as the First Membranogenic Components for Protocells?
		6.4.1 Which Lipids on the Early Earth?
		6.4.2 Prebiotic Precursors of Lipids
	6.5 Which Composition for Prebiotic Lipidic Compartments?
	6.6 Non-lipidic Prebiotic Compartments
	6.7 The Peculiar Case of Minerals: The Case Study of Mica
	6.8 How to Encapsulate?
	6.9 Conclusions
	References
7 First Steps Towards Molecular Evolution
	7.1 Introduction
	7.2 Evolution on a Molecular Level
	7.3 Selective Formation of Deoxyribonucleosides Directed by Activation with Nucleobases
	7.4 Summary and Outlook
	References
8 Virus Origins and the Origin of Life
	8.1 Introduction
	8.2 The Place of Viruses in Origin of Life Studies
	8.3 What Are Viruses? Evolution of the Virus Concept
		8.3.1 Are Viruses Alive?
		8.3.2 Evidence for Primordial Viruses
			8.3.2.1 Viruses Co-evolved with Cellular Life on Earth
			8.3.2.2 Viruses Share Homologous Genes Not Found in Cellular Life Forms
			8.3.2.3 Viruses Utilize Diverse Modes of Replication
			8.3.2.4 Giant Viruses
	8.4 Virus Origin Scenarios
		8.4.1 Virus-First Hypothesis
			8.4.1.1 Viroids and RNA Viruses in the RNA World
		8.4.2 Cell Reduction or Regression Hypothesis
		8.4.3 Escape or Endogenous Hypothesis
	8.5 Other Early Evolutionary Scenarios
	8.6 Conclusion
	References
9 Reconstructing the Last Universal Common Ancestor
	9.1 Introduction
	9.2 LUCA and Lost Signal: An Insurmountable Challenge?
	9.3 Approaches to LUCA
		9.3.1 Tree of Life (TOL) LUCA
		9.3.2 Planetary Megaorganism LUCA
		9.3.3 Non-orthologous Gene Displacement (NOGD) LUCA
	9.4 The Ship of Theseus and Genes Refractory to HGT
	9.5 Rescuing LUCA from Theseus?
	9.6 Are There Other General Traits That We Might Placein LUCA?
		9.6.1 Membrane-Associated Proteins Support a Cellular, Membrane-Bound LUCA
		9.6.2 Positional Conservation of RNA Modifications Places them in LUCA
	9.7 Towards a Lo-fi or Jack-of-all-Trades LUCA
	9.8 Concluding Remarks: A Path Towards a Trait-Based LUCA?
	References
10 Earliest Traces of Life as a Window on Life's Origins
	10.1 Introduction
	10.2 The Record of Early Life
		10.2.1 Indicators of Early Life
			10.2.1.1 Cellular Remains
			10.2.1.2 Microbialites
			10.2.1.3 Biogeochemical Signals of the Co-evolving Geosphere and Biosphere
			10.2.1.4 Biominerals
			10.2.1.5 Bioalteration
	10.3 Relevance of the Palaeobiological Record for Life's Origin
	References
11 Origin and Early Evolution of the Eukaryotes: Perspectives from the Fossil Record
	11.1 Introduction
	11.2 Early Eukaryotes and Where to Find Them
		11.2.1 A Key to Identifying Ancient Eukaryotes in the Fossil Record
			11.2.1.1 Size
			11.2.1.2 Shapeshifting
			11.2.1.3 Cyst Production: Openings, Sturdy Walls, and Intracellular Complexity
			11.2.1.4 Life Cycle and Reproduction
			11.2.1.5 Preservation
	11.3 Early Eukaryotic Body Fossils
		11.3.1 Macroscopic Compressions
		11.3.2 The Oldest OWM Assemblages
		11.3.3 OWM Indicative of Cytoskeletal Complexity
		11.3.4 Multicellularity and Cellular Differentiation
		11.3.5 Early Eukaryotic Diversity
	11.4 Molecular Fossils (Biomarkers)
	11.5 How Can the Fossil Record Inform Us About the Sequence of Events in Eukaryotic Evolution?
	11.6 Takeaways
	References
Index