Self-Organization as a New Paradigm in Evolutionary Biology: From Theory to Applied Cases in the Tree of Life

Contents
1: Introduction: Understanding the Origins and Evolution of Living Organisms-The Necessity of Convergence Between Old and New ...
	1.1 Introduction
	References
Part I: The Modernity of Old Paradigms
	2: Self-Organization Meets Evolution: Ernst Haeckel and Abiogenesis
		2.1 Introduction
		2.2 The Philosophical Background to Haeckel´s Theory of Abiogenesis
		2.3 Spontaneous Generation and Early Evolution in Haeckel´s Writings
		2.4 Trees and Bushes: Polyphyletic vs. Monophyletic Evolution
		2.5 Conclusions
		References
	3: D´Arcy Wentworth Thompson´s ``Physico-Mathematical´´ Approach to the Investigation of Morphogenesis and Its Pertinence to C...
		3.1 Introduction: D´Arcy Wentworth Thompson and the Aristotelian Foundations of Morphology
		3.2 Aristotle´s Philosophy of Nature and Metaphysics
		3.3 Kant on Substance, Teleology, and Mechanism
		3.4 Thompson´s ``Physico-Mathematical´´ Approach to the Study of Morphogenesis and His Criticisms of Vitalism, Natural Selecti...
		3.5 Thompson´s Notion of ``Mechanical Efficiency´´ and the Baldwin Effect
		3.6 Ginsburg and Jablonka´s Cognitive-Behavioral and/or Learning-Based Account of the Causal Fuses Leading to the Cambrian Exp...
		3.7 Embodying the Baldwin Effect: Complementing Ginsburg and Jablonka´s Cognitive-Behavioral and/or Learning-Based Account of ...
		3.8 Conclusion: The Importance of D´Arcy Thompson´s Physico-Mathematical Approach to the Study of Morphogenesis-Teleology and ...
		References
	4: From Dissipative Structures to Biological Evolution: A Thermodynamic Perspective
		4.1 Self-Organization in Non-equilibrium Systems
			4.1.1 Classical and Modern Thermodynamics
			4.1.2 Self-Organization in Systems Far from Thermodynamic Equilibrium
			4.1.3 Dissipative Structures
				4.1.3.1 Instability, Amplification of Fluctuations, and Establishment of a New Structure
				4.1.3.2 Spontaneous Symmetry Breaking, States Selection, and Sensitivity
				4.1.3.3 Self-Healing
		4.2 Universal Chiral Asymmetry in Biological Realm
		4.3 Bio-Analog Dissipative Structures
		4.4 Thermodynamics, Self-Organization, Dissipative Structures, and Evolution
			4.4.1 Self-Replication and End-Directed Behavior
			4.4.2 Nonequilibrium Sensitivity
			4.4.3 Self-Healing
			4.4.4 Mutations and Appearance of New Traits
			4.4.5 Competition and Survival of the Fittest
			4.4.6 Complexity and Complexification Through Evolution
		References
	5: Self-Organization at Different Levels of Metazoan Complexity in Comparative Genomic-Phenomic Context
		5.1 Introduction
		5.2 Self-Organization in Cyanobacteria Cell Communities
		5.3 Cell Social Behavior and Self-Organization in Metazoan Cell Assemblies In Vitro
			5.3.1 Myogenic Cells In Vitro
			5.3.2 Hemocyte Aggregation In Vitro
			5.3.3 Metazoan Embryonic Cells
		5.4 Topological Approach: Transformations in Metazoan Development and Evolution
		5.5 Metazoan Body Plan in Molecular-Genetic and Macroevolutionary Context
			5.5.1 Gene Regulatory Networks: The Inevitability of Self-Organization
			5.5.2 Genome-Phenome Mapping/Correlations
			5.5.3 Developmental Molecular-Genetic Machinery in Vertebrates
			5.5.4 Molecular-Genetic Background of Metazoan Axial Body Plan
		5.6 Social Behavior in Vertebrate Communities
		5.7 Conclusions
		References
	6: Instinct as Form: The Challenge of Bergson
		6.1 Introduction
		6.2 The Problem of Commonsense Knowledge
			6.2.1 DNA and Coding ``Commonsense´´
		6.3 Consciousness, the Hard Problem, and Evolution
		6.4 The Intellect, the Classic Metaphysic
			6.4.1 Instinct
			6.4.2 Intuition
			6.4.3 The Eye
			6.4.4 To Return: Creating Mousetraps and Wasps
			6.4.5 Bergson´s Larger Vision of the Transforming Field
		References
Part II: Modernity of Self-Organization and Emerging Paradigms
	7: Biological Evolution of Microorganisms
		7.1 Introduction
		7.2 Molecular Genetics of Escherichia coli Bacteria and Their Phages
		7.3 Mechanisms of Genetic Variation in Bacterial Genomes
		7.4 Bacterial Restriction and Modification Systems
		7.5 Role of Restriction Enzymes in Structural and Functional Genome Analysis and Genetic Engineering
		7.6 Evolution Genes and the Duality of the Bacterial Genome
		7.7 Self-Organization of the Biological Evolution of Microorganisms by Permanent Creation
		7.8 Conclusions
		References
	8: Self-Organization in Embryonic Development: Myth and Reality
		8.1 Introduction
		8.2 Metazoan Matter: Physical Bases of Self-Organization
		8.3 Evidence for and Against Developmental Self-Organization
			8.3.1 Gastrulation
			8.3.2 Somitogenesis
			8.3.3 Limb Skeletogenesis
		8.4 Conclusions
		References
	9: The Morphoprocess and the Diversity of Evolutionary Mechanisms of Metastable Structures
		9.1 Introduction
		9.2 Major Problems in Understanding Evolutionary Mechanisms
			9.2.1 Epistemological Problem of the Ambiguity of the Notion of Evolution and the Associated Problem of Uncertainty of the Ter...
			9.2.2 The Problem of Uncertainty of Direct Observation
			9.2.3 The Problem of Uncertainty of Applicability
		9.3 Conceptualization of the Morphoprocess
		9.4 Three Conceptual Models of Microevolution of Highly Integrated Metastable Structures-Processes
			9.4.1 The Model of Indirect Adaptogenesis (Granovitch 2018, 2021)
			9.4.2 The Model of Direct Adaptogenesis (Granovitch 2018, 2021)
			9.4.3 The Model of Constructional Transformism (Granovitch 2018, 2021), syn. Orthogenesis (Term-Haacke 1893, cit. ex. Popov 20...
				9.4.3.1 Evidence of a Limited and ``Non-homogenous´´ Character of Variation Has Been Analysed Before (Granovitch 2018, 2021), ...
				9.4.3.2 Evidence of a Regular and Correlated Character of the Morphogenetic Processes in Multicellular Organisms
				9.4.3.3 Evidence of Self-Assembly of Molecular and Cellular Structures
		9.5 Conclusion
		References
	10: Mesological Plasticity as a New Model to Study Plant Cognition, Interactive Ecosystems, and Self-Organized Evolutionary Pr...
		10.1 Introduction
		10.2 The Epistemic Concept of Plasticity: Ontology and Complexion
		10.3 The Concept of Mesology: Being, Environment, and Trajection
		10.4 Plant Electrome and Cognition
			10.4.1 Behaviors and Signalization in Plants
			10.4.2 Role of Low-Voltage Spontaneous Variations or Electrophytograms (EPGs) Recorded at the Whole Plant Level: Dynamics of t...
			10.4.3 Signature of the Electrome and Plant Cognition: A New Electromic Reading Grid
		10.5 Mesological Plasticity as a New Model to Study Plant Evolutionary Biology
			10.5.1 Plasticity as the ``as that´´ or the Third Included of the Mesological Formulation
			10.5.2 Mesological Relationships Between Plants and Their Milieu: The Uexküll´s Gap
			10.5.3 Semiosis, Uexküll´s Primary-Meaning Making and Functional Circle: An Ecosensitive Complexion?
			10.5.4 Phyto- vs Ecosemiotics as an Experimental Field of Mesological Plasticity: Evolutionary Biology and the Umvelt of Plants
		10.6 Assessments of in Loco Mesological Plasticity Using Monitored EPG Kits: A Key Approach to Study Electrome Patterns in Nat...
		10.7 The Plant Mesological Plasticity: A Unique Cognitive, Electromic, and Ecosemiotic Interface
		References
	11: Quantum Fractal Thermodynamics to Describe the Log-Periodicity Law in Species Evolution and Human Organizations
		11.1 Introduction
			11.1.1 Length of a Fractal Interaction: Homogeneous Time and Entropic Fractal Time
			11.1.2 The States of a Fractal: Application to the Generalized Surface Cantor Fractal
		11.2 Interaction Time of a Fractal State
		11.3 Energy of a Fractal State
		11.4 The Mass of a Fractal State: The Variation of Mass with the Order of the Fractal State
		11.5 A Planck-Einstein-Like Law for the Fractal State Energy
		11.6 Kinetic Chain Temperature, Exergy, and Dispergy of a Fractal State
		11.7 Entropy Production Between the Fractal States: The Kinetic Chain Temperature
		11.8 Irreversibility and the Structuration Efficiency of a Log-Periodic Phenomenon
		11.9 Conclusion
		References
	12: Sapiens and Cognition: The Optimal Vertical Nervous System-The Last Threshold of Self-Organized and Self-Memorizing Increa...
		12.1 The Premises
		12.2 Lamarck and Darwin, Pioneers of the Self-Organized Evolution
		12.3 Orthogenesis, Macroevolution, and the Synthetic Theory (Princeton, 1947)
		12.4 Posing the Evolutionary Problem: The Embryonic Trajectories of the Nervous System Versus Locomotion
			12.4.1 Locomotion
			12.4.2 More Precise Vocabulary to Clarify the Problem: The Endoskeleton of the Axial Skeleton
			12.4.3 The Straightened Axial Endoskeleton: The Result of an Internal Evolutionary Process
			12.4.4 Human Paleontology and the Neural Straightening: One Century of Dilemma Between Locomotion and Encephalon
		12.5 The Straightening, an Embryonic Dynamical Reality
			12.5.1 A Bibliographic Rediscovery
			12.5.2 The Mandible, the Double Pantograph, and the Craniofacial Contraction
			12.5.3 The Embryonic Origin of the Neural Straightening
			12.5.4 Nonhuman Primate Embryogenesis
			12.5.5 Embryogenesis, Homeotic Genes, and Viscoelastic Dynamics
				12.5.5.1 Hominins Verticality and Homeotic Genes
				12.5.5.2 Embryonic Straightening and Viscoelastic Dynamics
		12.6 Embryogenesis and Paleontology: Consequences for the Recognition of Extinct Taxa in the Fossil Records
			12.6.1 Craniocaudal Discontinuities in Phylogenetic Continuities
			12.6.2 A Key Distinction: Different Appendicular Adaptations for a Same Embryonic Axial Straightening
			12.6.3 Wet Woodland and the Role of Females in Hominization Processes
			12.6.4 Cerebro-Cerebellar Rubicon, Psychomotricity, Mother-Infant Interactions, and Cognitive Implications
		12.7 An Emerging Evolutionary Problematic
			12.7.1 Environments and Self-Memorizing Evolutionary Processes
				12.7.1.1 Dissipative Structures and Unpredictability
				12.7.1.2 Self-Memorization, Conservative Dynamics with Innovative Organization
			12.7.2 Self-Organization, Self-Memorization, and Predictability
			12.7.3 Examples of Memory in Nonlinear Systems
			12.7.4 Macroevolutionary Straightening and Self-Memorization Versus Random Ecological Epiphenomenon
		12.8 Conclusion: The Emergence of Life Helps to Understand the Phylogenetic Neuraxis Straightening
		References
	13: Evolutionary Creativity
		13.1 Introduction
		13.2 The Complexity of Autos
		13.3 Our Reality Is Not Primary, It Is Emergent
		13.4 Autos Revealed and Hidden
			13.4.1 The Emergence of Autos
			13.4.2 The Constellation of Autos
		13.5 The Unity of Duality
			13.5.1 The  Organizing Loop
			13.5.2 Computing Apparatus and Geno-Phenomenal Transformations
		13.6 The Duality of the Unity
			13.6.1 Symbiotic Uniduality
			13.6.2 Internal Competition and Antagonism
			13.6.3 The Struggle to the Death
			13.6.4 Dialogical Unity
			13.6.5 The Republic of the Complex: Between the Empire of the Genes and the Empire of the Environment
		13.7 Generativity and Genesis
			13.7.1 Generativity and Genesis
			13.7.2 The Resurrection of the Past
		13.8 Biological Oscillation, a Principle of Uncertainty
			13.8.1 Biological Individuality and the Living Individual
			13.8.2 Individuality and Individual
			13.8.3 Individual Autonomy
			13.8.4 The Individual Being
			13.8.5 The Non-Elementary Individual
		13.9 Reason and Unreason in Life
			13.9.1 The First Level of Rationality
			13.9.2 The Second Level of Irrationality
			13.9.3 The Third Level: Complex Rationality
			13.9.4 The Fourth Level: The Reverse Side of Rationality: Infra? Meta? Rationality
			13.9.5 Inoptimization
			13.9.6 Toward an Open Rationality
			13.9.7 Open Life
		13.10 Living Creativity
			13.10.1 Life Is a Creator of Creativity
			13.10.2 The Challenge
			13.10.3 Generalized Life
		13.11 Conclusion
		References