Everything Flows. Towards a Processual Philosophy of Biology

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Everything Flows: Towards a Processual Philosophy of Biology
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Contents
Acknowledgements
Contributors
Foreword
	References
PART I: Introduction
	1: A Manifesto for a Processual Philosophy of Biology
		1. Introduction
		2. Historical Background
		3. The Organicist Precedent
		4. Processes and Things
		5. Empirical Motivations
			5.1. Metabolic turnover
			5.2. Life cycles
			5.3. Ecological interdependence
		6. Philosophical Payoffs
			6.1. Grounding critiques of essentialism
			6.2. Grounding critiques of reductionism
			6.3. Grounding critiques of mechanicism
		7. Biological Consequences
			7.1. Physiology
			7.2. Genetics
			7.3. Evolution
			7.4. Medicine
		8. Conclusions
		9. Overview of Contributions
		References
PART II: Metaphysics
	2: Processes and Precipitates
		1. Introduction
		2. The Continuant/Occurrent Duality
		3. Specification
		4. The Priority Question
		5. Reasons to Take Processes as Fundamental
		6. (Just a Few) Kinds of Processes in Biology
		7. Continuants out of Processes
		8. Abstraction
		9. Abstracting to Continuants
		10. Modal Properties
		11. Consequences for Biology
		References
	3: Dispositionalism: A Dynamic Theory of Causation
		1. A Received Orthodoxy
		2. Causation in Biology
		3. Dispositions and Processes
		4. Static or Dynamic?
		5. Conclusions
		Acknowledgements
		References
	4: Biological Processes: Criteria of Identity and Persistence
		1. Introduction
		2. Ontological Explanation for Scientific Domains
		3. An Argument for Biological Process Ontology
		4. Criteria of Identity and the Individuation of Processes
		5. Process Persistence: Identity versus Composition
			5.1. The endurance of substances
			5.2. The perdurance of processes
		6. Conclusions
		Acknowledgements
		References
	5: Genidentity and Biological Processes
		1. Introduction
		2. What Is Genidentity? And How Can It Be Applied to the Living World?
		3. The Inconspicuous Centrality of Genidentity in Hull’s Conception of Biological Individuality
		4. Why Cases of Symbiosis Strengthen the Genidentity View
		5. How Genidentity Helps Define What an Organism Is
		6. Genidentity as a Way to Shed Light on the Notion of Biological Process: ‘Priority’ as the Central Question
		7. Conclusions
		Acknowledgements
		References
	6: Ontological Tools for the Process Turn in Biology: Some Basic Notions of General Process Theory
		1. Introduction
		2. General Processes or Dynamics: A New Category
		3. Relationships among General Processes: GPT’s ‘Levelled Mereology’
		4. A Typology of Processes
			4.1. Spatio-temporal signature
			4.2. Participant structure
			4.3. Dynamic composition
			4.4. Dynamic shape
			4.5. Dynamic context
		5. Applying GPT in the Philosophy of Biology
			5.1. Biological individuality
			5.2. Biological composition
			5.3. Emergence
		6. Conclusions
		Acknowledgements
		References
PART III: Organisms
	7: Reconceptualizing the Organism: From Complex Machine to Flowing Stream
		1. Introduction
		2. Organisms ≠ Machines: The Argument from Thermodynamics
			2.1. Addressing potential objections to the argument
		3. The Stream of Life: A Processual Conception of the Organism
		4. Organisms as Streams: Three Lessons for Biological Ontology
			4.1. First ontological lesson: ‘Activity is a necessary condition for existence’
			4.2. Second ontological lesson: ‘Persistence is grounded in the continuous self-maintenance of form’
			4.3. Third ontological lesson: ‘Order does not entail design’
		5. Conclusions
		Acknowledgements
		References
	8: Objectcy and Agency: Towards a Methodological Vitalism
		1. Introduction
		2. An Ontological Surprise
		3. Phases
		4. Agential Dynamics
		5. Object Theories and Agent Theories
			5.1. Objectcy
			5.2. Agency
		6. Evolution and Agency
		7. Conclusions
		Acknowledgements
		References
	9: Symbiosis, Transient Biological Individuality, and Evolutionary Processes
		1. Introduction
		2. Beyond Replicators
		3. Seeing the Light
		4. Transient and Intermittent Individuals
		5. Conclusions
		Acknowledgements
		References
	10: From Organizations of Processes to Organisms and Other Biological Individuals
		1. Introduction
		2. Some Implications of the Promiscuous Individualism Thesis Combined with a Hypercollaborative View of Life
		3. A Process-Based Organizational Ontology for Biology
			3.1. Simple self-maintenance
			3.2. Minimal recursive self-maintenance and biological individuality
			3.3. Recursive self-maintenance and the organismality of unicellular organizations
		4. Collaboration and Multicellular Systems
			4.1. A case of collaboration among single-species bacteria
			4.2. A case of early eukaryotic collaboration
			4.3. A case of eumetazoan collaboration
		5. Revisiting the Implications of Promiscuous Individualism and an Excessively Collaborative View of Life
			5.1. Organisms and other biological individuals
			5.2. The individual and the organismal status of microbial communities
			5.3. The distinction between life and non-life
		6. Conclusions
		Acknowledgements
		References
PART IV: Development and Evolution
	11: Developmental Systems Theory as a Process Theory
		1. Introduction
		2. Process Biology
		3. Process in the Developmental Systems Tradition
		4. Core Ideas in DST: Epigenesis and Developmental Dynamics
			4.1. Epigenesis
			4.2. Developmental dynamics
		5. An Ontology for DST: Genomes, Epigenomes, and Developmental Niches
		6. DST as a Process Theory of the Organism
		7. Conclusions
		Acknowledgements
		References
	12: Waddington’s Processual Epigenetics and the Debate over Cryptic Variability
		1. Introduction
		2. Substance versus Process: Two Conflicting Ontologies for Biology
		3. Waddington’s Epigenetics in the Context of Dynamical Systems Theory
		4. Development as the Homeorhetic Balance between Robustness and Plasticity
		5. Evolutionary Implications: The Genetic Assimilation of Acquired Characters
		6. Assessing Two Contemporary Models of the Canalization of Development
			6.1. How the two models differ in their interpretation of cryptic variability
			6.2. Do both models capture the homeorhetic nature of canalization?
		7. Conclusions
		Acknowledgements
		References
	13: Capturing Processes: The Interplay of Modelling Strategies and Conceptual Understanding in Developmental Biology
		1. Introduction
		2. In Vivo Imaging and the Four-Dimensional Conceptualization of Life
		3. Resolution, Contextuality, and the Return of Organicism
		4. Reconstructing and Explaining Developmental Processes
		5. Conclusions
		Acknowledgements
		References
	14: Intersecting Processes Are Necessary Explanantia for Evolutionary Biology, but Challenge Retrodiction
		1. Introduction
		2. An Increasingly Appreciated Issue: The Underdetermination of Phylogenetic Trees
		3. Intersecting Processes Are Also Absent from Phylogenetic Networks
		4. The Need to Investigate Reticulate Intersecting Processes in Evolutionary Studies
			4.1. Explaining the evolution of translation with a hypercycle
			4.2. Explaining the evolution of biological functions by network analyses
		5. Processes, and Hence Explanantia, Evolve
		6. Conclusions: Towards a Typology of Processes
		Acknowledgements
		References
PART V: Implications and Applications
	15: A Process Ontology for Macromolecular Biology
		1. Introduction
		2. The Ecological Model of the World
			2.1. Ecosystems, machines, and the environment
			2.2. Internal versus external relations
			2.3. Substance versus process
		3. Problems with the Ecological Model
		4. Symbiosis and the Importance of Integrated Capacities
			4.1. Termites and their capacity to survive and reproduce
			4.2. Process and individuality
			4.3. Distributed capacities
			4.4. The ecology of powers
			4.5. Component versus integrated capacities
			4.6. Integrated capacities at all levels?
		5. Proteins, Structure, and Capacities
			5.1. From structure to power?
			5.2. More than just collaboration
			5.3. Towards a general process account for macromolecular biology
		6. Conclusions
		Acknowledgements
		References
	16: A Processual Perspective on Cancer
		1. Introduction
		2. Cancer as a Process
		3. The Relational Ontology of Levels
		4. Morphogenetic Fields
		5. Conclusions
		Acknowledgements
		References
	17: Measuring the World: Olfaction as a Process Model of Perception
		1. Introduction: Why Things Stink
		2. The Received View: The Input Determines the Perceptual Experience
		3. The Neural Basis of Olfaction and the Idea of Forecasting in Perception
		4. The Interactivity of Forecasting and Stimulus Input in Perception
		5. Conclusions: Perception as a Measure of Changing Signal Ratios and Expectancy Effects
		Acknowledgements
		References
	18: Persons as Biological Processes: A Bio-Processual Way Out of the Personal Identity Dilemma
		1. Introduction
		2. Elimination or Mystification: The Personal Identity Dilemma
		3. The Thing-Ontological Roots of the Dilemma: Substances, Bundles, and the Disappearance of Change
		4. A Way Out: Persons as Biological Processes
		5. Conclusions
		Acknowledgements
		References
Index