Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory

Preface
Acknowledgments
Contents
Contributors
1: Introduction
	1.1 Introduction
	1.2 Extending the Modern Synthesis
	1.3 This Book
	1.4 Summary and Conclusion
	References
Part I
	2: Every Evolutionist Their Own Historian: The Importance of History, Context, and the Extended Evolutionary Synthesis
		2.1 Introduction: Every Evolutionist Their Own Historian
		2.2 Laying the Groundwork: Historicism, Contextualism, Presentism, and the Language of Synthesis
		2.3 The Modern Synthesis, The Evolutionary Synthesis, and Neo-Darwinism: Drawing Distinctions
		2.4 Moving Targets, Déjà Vu Moments, and the Importance of History to the EES
		2.5 History and the EES
		2.6 ``Every Evolutionist Their Own Historian´´: Summation and Closing Thoughts
		References
	3: Yes Indeed, Evolutionary Biologists Should Pay More Attention to History: A Commentary on Smocovitis
		References
	4: History, Evolution, and the ``Rashomon Effect´´: A Reply to Svensson
		References
Part II
	5: The Creativity of Natural Selection and the Creativity of Organisms: Their Roles in Traditional Evolutionary Theory and Som...
		5.1 Introduction
		5.2 How Natural Selection Is a Creative Process: Speleology and Teleology
			5.2.1 Blind Cave Fish: Creativity as a Source of Directionality
			5.2.2 Blind Watchmakers: Creativity as a Source of Purpose
			5.2.3 Complex Adaptations and the Lack of Creative Direction
		5.3 Processes That Are Creative in Other Ways: Balance and Bias
			5.3.1 Creativity as Increasing Evolvability
				5.3.1.1 Creative But Unimportant?
				5.3.1.2 What Needs to be Explained?
			5.3.2 Creativity as Choice Between Peaks
			5.3.3 Summary So Far
		5.4 The Organism as a Source of Creativity: Agency Work and Make-Work
			5.4.1 The Art of Misdirection: Human Creativity as a Novel Source of Purpose
			5.4.2 Theories of Adaptation Without Purpose
				5.4.2.1 Popper: The Genetic Fallacy
				5.4.2.2 Waddington: Plasticity First and Last
				5.4.2.3 Lewontin: Changing the Subject
		5.5 Conclusion: Creative Ambiguity
		References
	6: Let there Be Light: A Commentary on Welch
		References
	7: Creative Destruction: A Reply to Haig
		References
Part III
	8: The Organism in Evolutionary Explanation: From Early Twentieth Century to the Extended Evolutionary Synthesis
		8.1 Introduction
		8.2 The Organism Before the Modern Synthesis
		8.3 Three Explanatory Roles of the Organism in the Organicist Movement
			8.3.1 Contextualizing Genes and Cells in Development
			8.3.2 Organism-Environment Reciprocity
			8.3.3 Organismal Agency
		8.4 Streamlining the Organism After the Modern Synthesis
		8.5 Rediscovering Explanatory Roles of the Organism in the EES
		8.6 Conclusions
		References
	9: Causes and Consequences of Selection: A Commentary on Baedke and Fbregas-Tejeda
		References
	10: Organisms and the Causes and Consequences of Selection: A Reply to Vidya et al.
		10.1 The Evolutionary Stance of Vidya and Colleagues
		10.2 Organisms as Evolutionary Agents
		References
Part IV
	11: The Structure of Evolutionary Theory: Beyond Neo-Darwinism, Neo-Lamarckism and Biased Historical Narratives About the Mode...
		11.1 Introduction
		11.2 What the Modern Synthesis Was (and Was Not)
		11.3 Gould´s Mixed Legacy: Strawman Arguments and Myths About the MS
		11.4 Extrascientific Criticisms of the MS: Adaptation Without Natural Selection?
		11.5 Scientific Criticisms of the MS: From Waddington and Gould to the EES
		11.6 Recent Challenges to the MS
		11.7 The Re-emergence of Mutation-Driven Evolution and Directed Variation?
		11.8 Developmental Bias, Niche Construction, Non-Genetic Inheritance, and Plasticity
		11.9 Where Are We?
		11.10 Looking Forward
		11.11 Conclusions
		References
	12: It Is the Endless Forms, Stupid: A Commentary on Svensson
		References
	13: Ecology, Agents, and the Causes of Selection: A Reply to Shuker
		References
Part V
	14: Hypertextuality of a Hyperextended Synthesis: On the Interpretation of Theories by Means of Selective Quotation
		14.1 Introduction
		14.2 Engaging the Extended Evolutionary Synthesis
		14.3 Differences that Make a Difference
		14.4 Exaptations, Spandrels, and Constraints
		14.5 Purpose, Goal, and Direction
		14.6 Karl Ernst von Baer and Zielstrebigskeit (Goal-Directedness)
		14.7 Directedness
		14.8 Directed Variation
		14.9 The Poetry of Life
		References
	15: Teleology, Organisms, and Genes: A Commentary on Haig
		15.1 Introduction: A Zone of Agreement
		15.2 Disentangling Types of Teleology in Biological Explanations
		15.3 Teleology and the Extended Evolutionary Synthesis
		15.4 What Constitutes a Teleological Explanation?
		15.5 Difference-Makers in Evolution or ``Where is the Organism?´´
		15.6 Conclusions: What Can Biologists Build with Haig´s Hammer?
		References
	16: A Token Response: A Reply to Fbregas-Tejeda and Baedke
		Reference
Part VI
	17: The Darwinian Core of Evolutionary Theory and the Extended Evolutionary Synthesis: Similarities and Differences
		17.1 Introduction
		17.2 The Darwinian Core (DC) of Evolutionary Theory
			Box 17.1 Transmission Fidelity and Change in Frequency of Trait-variants
		17.3 The Crystallization of the Modern Synthesis (MS)
			Box 17.2 Transmission Fidelity in Population and Quantitative Genetic Models
		17.4 Quantitative Genetics as a Phenotypic Theory
		17.5 The Nature(s) of Fitness, and a Micro-Evolutionary Red-Herring
		17.6 One Gene´s Eye View of Evolution, or Two?
		17.7 The Evolutionary Shaping of the Distribution of Phenotypes
		17.8 The Extended Evolutionary Synthesis (EES) in the Context of the Darwinian Core (DC) and the Modern Synthesis (MS)
		17.9 Summary and Conclusions
		References
	18: Evolution Is Bigger than All of Us: A Commentary on Vidya, Dey, Prasad, and Joshi
		References
	19: Why Evolution Is Bigger than all of Us: A Reply to Smocovitis
		References
Part VII
	20: Inclusive Fitness: A Scientific Revolution
		20.1 Introduction
		20.2 The Inclusive Fitness Revolution
		20.3 The Laundry List in the Light of Inclusive Fitness
			Box 20.1 Price´s Equation, Kin Selection, Inclusive Fitness and Multi-Level Selection
		20.4 Conclusions
		References
	21: Phenotypes, Organisms, and Individuals: A Commentary on Rodrigues and Gardner
		References
	22: On Monism and Pluralism: A Reply to Dickins, T. E.
		References
Part VIII
	23: Evolution of Bacteriophage Latent Period Length
		23.1 Introduction
		23.2 Some Phage Biology and Ecology
			23.2.1 Latent Periods Are Infection Periods
			23.2.2 Latent Period Length Variation
			23.2.3 The Eclipse and Post-Eclipse Are Ecological Phenomena
			23.2.4 Burst Size and Absolute Fitness
			23.2.5 Pre-Reproductive vs. Reproductive Periods
			23.2.6 Chronic Release Extends the Post-Eclipse
			23.2.7 Virocells vs. the Extracellular Search
			23.2.8 Extracellular Searches Can Be Costly
			23.2.9 Temperate Phages Can Vary Their Infection Period Durations
			23.2.10 Infection Duration Optimization
		23.3 Best of Times, Worst of Times
			23.3.1 Virion Hard Times
			23.3.2 Gadagkar and Gopinathan (1980)
			23.3.3 Optimization of Latent Period Duration
		23.4 Core Concept: Tradeoff Hypothesis
			23.4.1 Shorter vs. Longer Latent Periods
			23.4.2 Even Stronger Selection for Shorter Latent Periods?
			23.4.3 The Eclipse as a Juggernaut
			23.4.4 Importance of Adsorption Kinetics
		23.5 Further Tradeoff Hypothesis Considerations
			23.5.1 Role of Effective Burst Size (II)
			23.5.2 Exploitative Competition (III)
				23.5.2.1 SLP Phage Invasion and Invasion Resistance
				23.5.2.2 Limitations on Invasion Avoidance
			23.5.3 Bacterial Spatial Structure (IV)
				23.5.3.1 Well-Separated Microcolonies
				23.5.3.2 Clustered Microcolonies
			23.5.4 Environmental Change (V)
			23.5.5 Other than Lytic Phage Infections (VI)
				23.5.5.1 Lysogenizing the Winner?
				23.5.5.2 Also Lysogenizing Losers?
				23.5.5.3 Chronic Release
			23.5.6 Infection Duration Plasticity (VII)
				23.5.6.1 Extended Rise
				23.5.6.2 Lysis Inhibition
			23.5.7 Weak Selection? (VIII)
		23.6 Related Phenomena
			23.6.1 Michaelis-Menten Kinetics Analogy
			23.6.2 Virulence Evolution
			23.6.3 Intercellular Communication
		23.7 Conclusions
		References
	24: Optimality and Idealisation in Models of Bacteriophage Evolution: A Commentary on Abedon
		References
	25: On r-K Selection in the Evolution of Bacteriophages: A Reply to Dickins
		25.1 Molecular Details
		25.2 Constraints
		25.3 Adaptive Physiological Responses
		25.4 Megafauna and Cheats
		References
Part IX
	26: Plasticity and Information
		26.1 Introduction
		26.2 What Is Plasticity?
			26.2.1 Development and the Instructional Gene
		26.3 The Role of Information
		26.4 Levels of Abstraction
		26.5 Conclusion
		References
	27: Phenotypic Plasticity and Evolutionary Syntheses: A Commentary on Dickins, T.E.
		References
	28: On Rhetoric and Conceptual Frames: A Reply to Futuyma
		References
Part X
	29: The Curious Incident of the Wasp in the Fig Fruit: Sex Allocation and the Extended Evolutionary Synthesis
		29.1 Introduction
		29.2 What Is Sex Allocation?
		29.3 What Is the Extended Evolutionary Synthesis?
		29.4 Sex Allocation in EES Terms
			29.4.1 Sex Allocation as Behaviour (Organismal Agency)
			29.4.2 Sex Allocation as Phenotypic Plasticity
			29.4.3 Sex Allocation as Niche Construction
			29.4.4 Sex Allocation as Ontogeny
			29.4.5 Sex Allocation as Epigenetics
			29.4.6 Sex Allocation and Trans-Generational Effects
			29.4.7 Sex Allocation as Culture
		29.5 Discussion
		References
	30: The Nuances of Biological Syntheses: A Commentary on Shuker
		References
	31: On Genetics, Ecology, and the Role of Philosophy in Evolutionary Biology: A Reply to Distin
		References
Part XI
	32: The Evolving Evolutionary Synthesis
		32.1 Evolutionary Biology and the Evolutionary Synthesis
		32.2 Controversies
			32.2.1 Neutral Theory
			32.2.2 Levels of Selection
			32.2.3 Sympatric Speciation
			32.2.4 Punctuated Equilibria
			32.2.5 Adaptation and Constraint
		32.3 The Extended Evolutionary Synthesis
			32.3.1 Niche Construction
			32.3.2 Evolutionary Developmental Biology
			32.3.3 Phenotypic Plasticity
			32.3.4 Inclusive Inheritance
			32.3.5 Overview
		32.4 Summary
		References
	33: Inclusive Fitness Theory as a Scientific Revolution: A Commentary on Futuyma
		References
	34: Inclusive Fitness Theory Prefigured: A Reply to Rodrigues and Gardner
		References
Part XII
	35: Genes and Organisms in the Legacy of the Modern Synthesis
		35.1 Introduction
		35.2 The Core Argument of the Gene´s-Eye View
		35.3 The Genesis of the Gene´s-Eye View
		35.4 Has Evolutionary Biology Forgotten About Organisms?
		35.5 Conclusion
		References
	36: The Parallax View: A Commentary on Ågren
		36.1 Fisher
		36.2 Lewontin
		36.3 Discussion
		References
	37: Why We Disagree About Selfish Genes: A Reply to Welch
		References
Part XIII
	38: Genetic Evolvability: Using a Restricted Pluralism to Tidy up the Evolvability Concept
		38.1 Genetic Evolvability: Using a Restricted Pluralism to Tidy up the Evolvability Concept
		38.2 The Neglected Long Past of Genetic Evolvability
		38.3 Evolvability Theory Today: The Issue(s) with Evolvability
		38.4 Non-Genetic (or Evo-Devo) Evolvability
		38.5 Drawing a Causal Distinction Between Non-genetic and Genetic Evolvability
		38.6 Prescribing a Restrictive Pluralism to Solve Evolvability´s Conceptual Issues
		38.7 Theoretical Progress in Biology and the Failures of Modern Science
		References
	39: Pluralism and Progress in Evolutionary Biology: A Commentary on Distin
		References
	40: Genetic Evolvability: A Reply to Ågren
		References
Index