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  1. The Multiple Realizability of Biological Individuals.Ellen Clarke - 2013 - Journal of Philosophy 110 (8):413-435.
    Biological theory demands a clear organism concept, but at present biologists cannot agree on one. They know that counting particular units, and not counting others, allows them to generate explanatory and predictive descriptions of evolutionary processes. Yet they lack a unified theory telling them which units to count. In this paper, I offer a novel account of biological individuality, which reconciles conflicting definitions of ‘organism’ by interpreting them as describing alternative realisers of a common functional role, and then defines individual (...)
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  • Cohesion, Gene Flow, and the Nature of Species.Matthew J. Barker & Robert A. Wilson - 2010 - Journal of Philosophy 107 (2):59-77.
    A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene flow that (...)
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  • It’s the Song, Not the Singer: An Exploration of Holobiosis and Evolutionary Theory.W. Ford Doolittle & Austin Booth - 2017 - Biology and Philosophy 32 (1):5-24.
    That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...)
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  • Pathways to Pluralism About Biological Individuality.Beckett Sterner - 2015 - Biology and Philosophy 30 (5):609-628.
    What are the prospects for a monistic view of biological individuality given the multiple epistemic roles the concept must satisfy? In this paper, I examine the epistemic adequacy of two recent accounts based on the capacity to undergo natural selection. One is from Ellen Clarke, and the other is by Peter Godfrey-Smith. Clarke’s position reflects a strong monism, in that she aims to characterize individuality in purely functional terms and refrains from privileging any specific material properties as important in their (...)
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  • Towards a Multidimensional Metaconception of Species.Catherine Kendig - 2014 - Ratio 27 (2):155-172.
    Species concepts aim to define the species category. Many of these rely on defining species in terms of natural lineages and groupings. A dominant gene-centred metaconception has shaped notions of what constitutes both a natural lineage and a natural grouping. I suggest that relying on this metaconception provides an incomplete understanding of what constitute natural lineages and groupings. If we take seriously the role of epigenetic, behavioural, cultural, and ecological inheritance systems, rather than exclusively genetic inheritance, a broader notion of (...)
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  • Bacteria, Sex, and Systematics.L. R. Franklin - 2007 - Philosophy of Science 74 (1):69-95.
    Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...)
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  • Thinking About Populations and Races in Time.Roberta L. Millstein - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 52:5-11.
    Biologists and philosophers have offered differing concepts of biological race. That is, they have offered different candidates for what a biological correlate of race might be; for example, races might be subspecies, clades, lineages, ecotypes, or genetic clusters. One thing that is striking about each of these proposals is that they all depend on a concept of population. Indeed, some authors have explicitly characterized races in terms of populations. However, including the concept of population into concepts of race raises three (...)
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  • The Composite Species Concept: A Rigorous Basis for Cladistic Practice.D. J. Kornet & James W. McAllister - 2005 - In Thomas Reydon & Lia Hemerik (eds.), Current Themes in Theoretical Biology. Springer. pp. 95--127.
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  • The Concepts of Population and Metapopulation in Evolutionary Biology and Ecology.Roberta L. Millstein - 2010 - In M. A. Bell, D. J. Futuyma, W. F. Eanes & J. S. Levinton (eds.), Evolution Since Darwin: The First 150 Years. Sinauer.
    This paper aims to illustrate one of the primary goals of the philosophy of biology⎯namely, the examination of central concepts in biological theory and practice⎯through an analysis of the concepts of population and metapopulation in evolutionary biology and ecology. I will first provide a brief background for my analysis, followed by a characterization of my proposed concepts: the causal interactionist concepts of population and metapopulation. I will then illustrate how the concepts apply to six cases that differ in their population (...)
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  • Populations as Individuals.Roberta L. Millstein - 2009 - Biological Theory 4 (3):267-273.
    Biologists studying ecology and evolution use the term “population” in many different ways. Yet little philosophical analysis of the concept has been done, either by biologists or philosophers, in contrast to the voluminous literature on the concept of “species.” This is in spite of the fact that “population” is arguably a far more central concept in ecological and evolutionary studies than “species” is. The fact that such a central concept has been employed in so many different ways is potentially problematic (...)
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  • Darwinian Spaces: Peter Godfrey-Smith on Selection and Evolution.Kim Sterelny - 2011 - Biology and Philosophy 26 (4):489-500.
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  • Agents and Acacias: Replies to Dennett, Sterelny, and Queller.Peter Godfrey-Smith - 2011 - Biology and Philosophy 26 (4):501-515.
    The commentaries by Dennett, Sterelny, and Queller on Darwinian Populations and Natural Selection (DPNS) are so constructive that they make it possible to extend and improve the book’s framework in several ways. My replies will focus on points of disagreement, and I will pick a small number of themes and develop them in detail. The three replies below are mostly self-contained, except that all my comments about genes, discussed by all three critics, are in the reply to Queller. Agential views (...)
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  • Biological Individuality: The Case of Biofilms.Marc Ereshefsky & Makmiller Pedroso - 2013 - Biology and Philosophy 28 (2):331-349.
    This paper examines David Hull’s and Peter Godfrey-Smith’s accounts of biological individuality using the case of biofilms. Biofilms fail standard criteria for individuality, such as having reproductive bottlenecks and forming parent-offspring lineages. Nevertheless, biofilms are good candidates for individuals. The nature of biofilms shows that Godfrey-Smith’s account of individuality, with its reliance on reproduction, is too restrictive. Hull’s interactor notion of individuality better captures biofilms, and we argue that it offers a better account of biological individuality. However, Hull’s notion of (...)
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  • Towards a Processual Microbial Ontology.Eric Bapteste & John Dupré - 2013 - Biology and Philosophy 28 (2):379-404.
    Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...)
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  • Functionalism and Structuralism as Philosophical Stances: Van Fraassen Meets the Philosophy of Biology.Sandy C. Boucher - 2015 - Biology and Philosophy 30 (3):383-403.
    I consider the broad perspectives in biology known as ‘functionalism’ and ‘structuralism’, as well as a modern version of functionalism, ‘adaptationism’. I do not take a position on which of these perspectives is preferable; my concern is with the prior question, how should they be understood? Adapting van Fraassen’s argument for treating materialism as a stance, rather than a factual belief with propositional content, in the first part of the paper I offer an argument for construing functionalism and structuralism as (...)
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  • The Birth of the Holobiont: Multi-Species Birthing Through Mutual Scaffolding and Niche Construction.Lynn Chiu & Scott F. Gilbert - 2015 - Biosemiotics 8 (2):191-210.
    Holobionts are multicellular eukaryotes with multiple species of persistent symbionts. They are not individuals in the genetic sense— composed of and regulated by the same genome—but they are anatomical, physiological, developmental, immunological, and evolutionary units, evolved from a shared relationship between different species. We argue that many of the interactions between human and microbiota symbionts and the reproductive process of a new holobiont are best understood as instances of reciprocal scaffolding of developmental processes and mutual construction of developmental, ecological, and (...)
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  • Darwinian Populations and Natural Selection.Peter Godfrey-Smith - 2009 - Oxford University Press.
    The book presents a new way of understanding Darwinism and evolution by natural selection, combining work in biology, philosophy, and other fields.
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  • Defining Paradigm Darwinian Populations.John Matthewson - 2015 - Philosophy of Science 82 (2):178-197.
    This paper presents an account of the biological populations that can undergo paradigmatic natural selection. I argue for, and develop Peter Godfrey-Smith’s claim that reproductive competition is a core attribute of such populations. However, as Godfrey-Smith notes, it is not the only important attribute. I suggest what the missing element is, co-opting elements of Alan Templeton’s notion of exchangeability. The final framework is then compared to two recent discussions regarding biological populations proposed by Roberta Millstein and Jacob Stegenga.
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  • Causal Processes, Fitness, and the Differential Persistence of Lineages.Frédéric Bouchard - 2008 - Philosophy of Science 75 (5):560-570.
    Ecological fitness has been suggested to provide a unifying definition of fitness. However, a metric for this notion of fitness was in most cases unavailable except by proxy with differential reproductive success. In this article, I show how differential persistence of lineages can be used as a way to assess ecological fitness. This view is inspired by a better understanding of the evolution of some clonal plants, colonial organisms, and ecosystems. Differential persistence shows the limitation of an ensemblist noncausal understanding (...)
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  • Individuality, Subjectivity, and Minimal Cognition.Peter Godfrey-Smith - 2016 - Biology and Philosophy 31 (6):775-796.
    The paper links discussions of two topics: biological individuality and the simplest forms of mentality. I discuss several attempts to locate the boundary between metabolic activity and ‘minimal cognition.’ I then look at differences between the kinds of individuality present in unicellular life, multicellular life in general, and animals of several kinds. Nervous systems, which are clearly relevant to cognition and subjectivity, also play an important role in the form of individuality seen in animals. The last part of the paper (...)
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  • Levels of Selection in Biofilms: Multispecies Biofilms Are Not Evolutionary Individuals.Ellen Clarke - 2016 - Biology and Philosophy 31 (2):191-212.
    Microbes are generally thought of as unicellular organisms, but we know that many microbes live as parts of biofilms—complex, surface-attached microbial communities numbering millions of cells. Some authors have recently argued in favour of reconceiving biofilms as biological entities in their own right. In particular, some have claimed that multispecies biofilms are evolutionary individuals : 10126–10132 2015). Against this view, I defend the conservative consensus that selection acts primarily upon microbial cells.
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  • Bodily Parts in the Structure-Function Dialectic.Ingo Brigandt - 2017 - In Scott Lidgard & Lynn K. Nyhart (eds.), Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. Chicago: University of Chicago Press. pp. 249–274.
    Understanding the organization of an organism by individuating meaningful parts and accounting for organismal properties by studying the interaction of bodily parts is a central practice in many areas of biology. While structures are obvious bodily parts and structure and function have often been seen as antagonistic principles in the study of organismal organization, my tenet is that structures and functions are on a par. I articulate a notion of function (functions as activities), according to which functions are bodily parts (...)
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  • Are Species Really Individuals?David L. Hull - 1976 - Systematic Zoology 25:174-191.
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  • The Informational Gene and the Substantial Body: On the Generalization of Evolutionary Theory by Abstraction.James R. Griesemer - 2005 - Poznan Studies in the Philosophy of the Sciences and the Humanities 86 (1):59-116.
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  • From Embryology to Evo-Devo: A History of Developmental Evolution.M. Laubichler & J. Maienschein (eds.) - 2007 - MIT Press.
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  • Philosophy of Microbiology.Maureen O'Malley - 2014 - Cambridge University Press.
    Microbes and microbiology are seldom encountered in philosophical accounts of the life sciences. Although microbiology is a well-established science and microbes the basis of life on this planet, neither the organisms nor the science have been seen as philosophically significant. This book will change that. It fills a major gap in the philosophy of biology by examining central philosophical issues in microbiology. Topics are drawn from evolutionary microbiology, microbial ecology, and microbial classification. These discussions are aimed at philosophers and scientists (...)
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  • Individuality and Selection.David L. Hull - 1980 - Annual Review of Ecology and Systematics 11:311-332.
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  • The General Lineage Concept of Species, Species Criteria, and the Process of Speciation.Kevin de Queiroz - 1998 - In D. J. Howard & S. H. Berlocher (eds.), Endless Forms: Species and Speciation. Oxford University Press. pp. 57-75.
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  • The General Lineage Concept of Species and the Defining Properties of the Species Category.Kevin de Queiroz - 1999 - In R. A. Wilson (ed.), Species: New Interdisciplinary Essays. MIT Press. pp. 49-89.
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  • Principles of Animal Taxonomy.G. G. Simpson - 1961 - Columbia University Press.
    The Development of Modern Taxonomy Taxonomy has a long history, going back to the ancient Greeks and to forerunners even less sophisticated in systematics. Our interest here is centered on modern taxonomy itself, and we shall largely ...
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