Untangling Molecular Biodiversity: Explaining Unity and Diversity Principles of Organization with Molecular Structure and Evolutionary Genomics

Description

Untangling Molecular Biodiversity presents a unique global framework to explain molecular and organismal biodiversity that is grounded in evolutionary genomics. This book will tackle important questions such as the origin of life, the emergence of biochemistry, the origin of viruses, the nature of the last universal common ancestor responsible for diversified life, the role of information and thermodynamics in evolution, the reason for having three cellular domains in life, and the centrality of modules in biology.This book will explore six themes: (1) Explanatory frameworks for biological organization; (2) Evolutionary patterns and biodiversity; (3) Molecular structure and evolutionary genomics; (4) A framework of persistence strategies that borrows from engineering and systems biology; (5) Use of this framework to explain diversity in the molecular world; and (6) Exploring the origin and evolution of cells and viruses.Consequently, this book represents a very unique collection of ideas that can attract the attention of a broad readership interested in life sciences/biology. Contents Preface: Untangling molecular biodiversity List of Contributors Unity On unity in organisms and its evolution 1. Introduction 2. Unity as coordination 2.1. Linkage, constraints, and degrees of freedom 2.2. Economy, flexibility and robustness 2.3. Other meanings of unity 3. Kinds of coordination 3.1. Molecular coordination 3.2. Coordination in organisms 3.2.1. Physiology 3.2.2. Development 3.3. Synthesis 4. The evolution of coordination 4.1. The evolution of modules through diversification and unification 4.2. The evolution of networks of modules 5. Conclusion: Toward a theory of integration in organisms Acknowledgments References Memory Retrodiction — Exploring the history of parts and wholes in the biosystems of life 1. Introduction 2. Scientific progress and the search for truth Nomothetic and ideographic scientific pursuit 3. Retrodiction, explanatory power and phylogenetic analysis 4. Rooting undirected networks 5. Characters must serve as independent evolutionary hypotheses of homology 6. Parts and wholes: A new phylogenetic framework 7. Occurrence and abundance 8. Levels of universality and corollaries 9. The power of “serial” homologies 10. Effects of organismal lifestyles, problematic taxa and character ontology in tree reconstruction 11. Levels of selection, evolutionary units and the primacy of cellular processes over replicators 12. Conclusions References Linkage A “double tale” of module creation in evolving networks 1. Introduction 2. Understanding biological systems with network abstractions 3. Network modularity 4. A structural morphospace of networks 5. Hierarchical modularity 6. A morphospace of hierarchy describes flows along wiring diagrams 7. Evolutionary drivers of network structure in biological systems 8. Temporal biphasic patterns of diversification are widespread in evolution 9. A linkage-based biphasic model of module creation 10. Phylogenomic analyses of biological networks test the linkage hypothesis 11. A “principle of granularity” in the hierarchical structure of networks 12. Conclusions References Structure RNA structure and diversified life 1. Introduction 2. A novel phylogenetic approach based on macromolecular structure 2.1. Structural characters and derived phylogenetic trees 2.2. Phylogenetic analysis of RNA structural characters 2.3. Major properties of phylogenetic trees derived from RNA structure 2.4. Potential limitations of the methodology 3. Applications 3.1. tRNA 3.2. 5S rRNA 3.3. RNase P RNA 3.4. SINE RNA 3.5. rRNA 4. Conclusions References Origins It takes a well rooted trunk to bear a tree — reductionist models of divergent evolution and further aspects of reality 1. Introduction 2. The Woesean perspective on biodiversity in molecular phylogenies 3. Origins of Darwinian speciation 4. Origins of energy procurement, compartmentalization and genuine cells 5. Origins of modular genomes 5.1. The rise of akaryotic bacterial genomes 5.2. Asgard archaea: “Jokers” of the game 5.3. Protobiofilm to biofilm transition: a mixed model to bridge deep knowledge gaps 5.4. Founding the organismal ToL: the first dichotomy between Archaea and Bacteria 5.5. Consolidation of eukaryotic genomes 6. Origins of protein domains and fold families 7. Origins of functional and replicating RNA molecules 8. Outlook and synopsis: A Tree is a Tree is a Tree — or is it? References Language The language of biomolecular communication 1. Introduction 2. Connecting linguistics and molecular biology at different levels of organization 2.1. The lexicon and syntaxis of natural languages and their correspondence to the structure of macromolecules 2.2. Semantics and its correspondence to components, events and activities of the cell 2.3. Pragmatics and its correspondence to fitness 3. A Chomsky’s hierarchy of formal language in biomolecules 4. Quantitative linguistics and universal stochastic hypotheses 4.1. Probability distribution laws 4.2. Functional type laws 4.3. Developmental type laws 5. Laws of language in the structure and organization of macromolecules 6. Communication and the persistence triangle 7. The semantic and pragmatic compression of “omic” vocabularies 8. The evolution of semantic and pragmatic compression in molecules 9. Conclusions References Growth Molecular accretion, growth and innovation 1. Introduction 2. Macromolecular accretion 3. Genomic abundance and the shape of phylogenetic trees 4. Macromolecular growth and the Heaps law 5. Modeling processes of macromolecular growth and innovation 6. Innovation and the diffusion of mutations in sequence and structure space 7. Conclusions and prospects References Persistence A model of lineage evolution based on the persistence strategy hypothesis 1. Introduction 2. Interpretation of the persistence triangle 3. A method of modeling evolutionary movements of organisms on the persistence triangle 3.1. Simulating scope/umwelt/gap 3.2. Simulating the mechanisms of flexibility and robustness 4. Movements within the persistence triangle 4.1. Evolutionary movements 4.2. Lifetime movements 4.3. Bifurcations into new lineages 5. Conclusions and outlook References Panspermia An early cellular origin of viruses 1. Introduction 2. Basic science questions are often the hardest 3. Standard methods are not suited for Tree of Life research 4. Protein structures offer many more useful characters to study virus origins 5. Infection: An atypical way to study virus origins? 6. Morphological characters may indicate a polyphyletic origin of virus 7. An “extrusion” model of viral panspermia: from vesicles to viruses 8. Synthesis Acknowledgements References Complexity Some considerations towards a predictive theory of life 1. Introduction 2. Biology and the scientific method 2.1. Probability in modern biology 3. Promising paths: joining visions of the organism 3.1. The accuracy of phylogenomics in the context of living systems 3.2. Structural bioinformatics: function robustness in a sea of opportunity 3.3. Network theory: the path beyond trees 4. Biological entities as complex systems: some epistemological conclusions Acknowledgments References Power Life as a tendency to go beyond itself — The struggle for power 1. Introduction 1.1. Why we need to talk about Nietzsche 1.2. What nobody will say about molecular biology today 1.3. Objective 2. Biology and the will to power 3. Nietzsche’ criticism of Darwin 4. Nietzsche’s subversion 5. Nietzsche’ update 5.1. Multiplicity 5.2. The fluid self 5.3. The pre-individual being and viruses 5.4. Perspectivism and pragmatism Acknowledgments References Time Temporal parts and biological change 1. Introduction 2. Temporal parts 3. Temporal parts and growth 4. Temporal parts and change 5. Evolution of parts 6. Causation 7. Origin of causation 8. Modular parts as entropically entangled occurrents 9. Dynamic patchworks of temporal parts 10. Toward long-lived occurrents 11. Conclusions References Foresight Empedocles’ On Nature, P. Strasb. Gr. Inv. 1665–6, a theory of networks and evolutionary growth ~2,400 years before Darwin 1. Introduction 2. The editions of the Strasbourg fragments 3. Biological interpretation 4. The “Ship of Theseus” paradox: Evolutionary modules and growth 5. Spiral movement describes the frustrated dynamics of unification and change 6. Foresight and evolution References Appendix A The spiral, the wheel, the triskelion and a double tale of the sun Index