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  1. Homology: A Comparative or a Historical Concept?Francisco Aboitiz - 1988 - Acta Biotheoretica 37 (1):27-29.
    The meaning of the word homology has changed. From being a comparative concept in pre-Darwinian times, it became a historical concept, strictly signifying a common evolutionary origin for either anatomical structures or genes. This historical understanding of homology is not useful in classification; therefore I propose a return to its pre-Darwinian meaning.
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  2. Accounting For Vertebrate Limbs: From Owen's Homology To Novelty In Evo-Devo.Ron Amundson - unknown
    This article reviews the recent reissuing of Richard Owen’s On the Nature of Limbs and its three novel, introductory essays. These essays make Owen’s 1849 text very accessible by discussing the historical context of his work and explaining how Owen’s ideas relate to his larger intellectual framework. In addition to the ways in which the essays point to Owen’s relevance for contemporary biology, I discuss how Owen’s unity of type theory and his homology claims about fins and limbs compare with (...)
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  3. Once More on the Homology Thesis: A Response to Smith's Reply.Christopher Arthur - 2003 - Historical Materialism 11 (1):195-198.
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  4. Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution.Leandro Assis & Ingo Brigandt - 2009 - Evolutionary Biology 36:248-255.
    Taxa and homologues can in our view be construed both as kinds and as individuals. However, the conceptualization of taxa as natural kinds in the sense of homeostatic property cluster kinds has been criticized by some systematists, as it seems that even such kinds cannot evolve due to their being homeostatic. We reply by arguing that the treatment of transformational and taxic homologies, respectively, as dynamic and static aspects of the same homeostatic property cluster kind represents a good perspective for (...)
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  5. Chaos in Plant Morphology.Denis Barabé - 1991 - Acta Biotheoretica 39 (2):157-159.
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  6. On the Interpretation of the Asymmetrical Leaf of Begonia by D'Arcy Thompson.Denis Barabé, Stéphane Daigle & Luc Brouillet - 1992 - Acta Biotheoretica 40 (4):329-332.
  7. Developmental Causation and the Problem of Homology.David A. Baum - 2013 - Philosophy and Theory in Biology 5 (20150505).
    While it is generally agreed that the concept of homology refers to individuated traits that have been inherited from common ancestry, we still lack an adequate account of trait individuation or inheritance. Here I propose that we utilize a counterfactual criterion of causation to link each trait with a developmental-causal (DC) gene. A DC gene is made up of the genetic information (which might or might not be physically contiguous in the genome) that is needed for the production of the (...)
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  8. Developmental Causation and the Problem of Homology.David A. Baum - 2013 - Philosophy and Theory in Biology 5 (20160629).
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  9. Developmental Genetics and Traditional Homology.Jessica A. Bolker & Rudolf A. Raff - 1996 - Bioessays 18 (6):489-494.
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  10. Helicase Homologues Maintain Cytosine Methylation in Plants and Mammals.Déborah Bourc'his & Timothy H. Bestor - 2002 - Bioessays 24 (4):297-299.
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  11. Reference Determination and Conceptual Change.Ingo Brigandt - manuscript
    The paper discusses reference determination from the point of view of conceptual change in science. The first part of the discussion uses the homology concept, a natural kind term from biology, as an example. It is argued that the causal theory of reference gives an incomplete account of reference determination even in the case of natural kind terms. Moreover, even if descriptions of the referent are taken into account, this does not yield a satisfactory account of reference in the case (...)
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  12. Scientific Practice, Conceptual Change, and the Nature of Concepts.Ingo Brigandt - manuscript
    The theory of concepts advanced in the present discussion aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. To this end, I suggest that each scientific concept consists of three components of content: 1) the concept.
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  13. The Role a Concept Plays in Science: The Case of Homology.Ingo Brigandt - manuscript
    The present paper gives a philosophical analysis of the conceptual variation in the homology concept. It is argued that different homology concepts are used in evolutionary and comparative biology, in evolutionary developmental biology, and in molecular biology. The study uses conceptual role semantics, focusing on the inferences and explanations supported by concepts, as a heuristic tool to explain conceptual change. The differences between homology concepts are due to the fact that these concepts play different theoretical roles for different biological fields. (...)
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  14. Bodily Parts in the Structure-Function Dialectic.Ingo Brigandt - forthcoming - In Scott Lidgard & Lynn K. Nyhart (eds.), Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives. University of Chicago Press.
    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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  15. Essay: Homology.Ingo Brigandt - 2011 - The Embryo Project Encyclopedia.
    Homology is a central concept of comparative and evolutionary biology, referring to the presence of the same bodily parts (e.g., morphological structures) in different species. The existence of homologies is explained by common ancestry, and according to modern definitions of homology, two structures in different species are homologous if they are derived from the same structure in the common ancestor. Homology has traditionally been contrasted with analogy, the presence of similar traits in different species not necessarily due to common ancestry (...)
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  16. Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations.Ingo Brigandt - 2009 - Acta Biotheoretica 57 (1-2):77-97.
    Despite the traditional focus on metaphysical issues in discussions of natural kinds in biology, epistemological considerations are at least as important. By revisiting the debate as to whether taxa are kinds or individuals, I argue that both accounts are metaphysically compatible, but that one or the other approach can be pragmatically preferable depending on the epistemic context. Recent objections against construing species as homeostatic property cluster kinds are also addressed. The second part of the paper broadens the perspective by considering (...)
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  17. Accounting for Vertebrate Limbs: From Owen's Homology to Novelty in Evo-Devo.Ingo Brigandt - 2009 - Philosophy & Theory in Biology 1 (20130604):e004.
    This article reviews the recent reissuing of Richard Owen’s On the Nature of Limbs and its three novel, introductory essays. These essays make Owen’s 1849 text very accessible by discussing the historical context of his work and explaining how Owen’s ideas relate to his larger intellectual framework. In addition to the ways in which the essays point to Owen’s relevance for contemporary biology, I discuss how Owen’s unity of type theory and his homology claims about fins and limbs compare with (...)
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  18. Typology Now: Homology and Developmental Constraints Explain Evolvability.Ingo Brigandt - 2007 - Biology and Philosophy 22 (5):709-725.
    By linking the concepts of homology and morphological organization to evolvability, this paper attempts to (1) bridge the gap between developmental and phylogenetic approaches to homology and to (2) show that developmental constraints and natural selection are compatible and in fact complementary. I conceive of a homologue as a unit of morphological evolvability, i.e., as a part of an organism that can exhibit heritable phenotypic variation independently of the organism’s other homologues. An account of homology therefore consists in explaining how (...)
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  19. A Theory of Conceptual Advance: Explaining Conceptual Change in Evolutionary, Molecular, and Evolutionary Developmental Biology.Ingo Brigandt - 2006 - Dissertation, University of Pittsburgh
    The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...)
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  20. Homology and Heterochrony: The Evolutionary Embryologist Gavin Rylands de Beer (1899-1972).Ingo Brigandt - 2006 - Journal of Experimental Zoology (Molecular and Developmental Evolution) 306:317–328.
    The evolutionary embryologist Gavin Rylands de Beer can be viewed as one of the forerunners of modern evolutionary developmental biology in that he posed crucial questions and proposed relevant answers about the causal relationship between ontogeny and phylogeny. In his developmental approach to the phylogenetic phenomenon of homology, he emphasized that homology of morphological structures is to be identified neither with the sameness of the underlying developmental processes nor with the homology of the genes that are in involved in the (...)
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  21. Biological Kinds and the Causal Theory of Reference.Ingo Brigandt - 2004 - In J. C. Marek & M. E. Reicher (eds.), Experience and Analysis: Papers of the 27th International Wittgenstein Symposium. Kirchberg am Wechsel: Austrian Ludwig Wittgenstein Society. pp. 58–60.
    This paper uses an example from biology, the homology concept, to argue that current versions of the causal theory of reference give an incomplete account of reference determination. It is suggested that in addition to samples and stereotypical properties, the scientific use of concepts and the epistemic interests pursued with concepts are important factors in determining the reference of natural kind terms.
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  22. Homology in Comparative, Molecular, and Evolutionary Developmental Biology: The Radiation of a Concept.Ingo Brigandt - 2003 - Journal of Experimental Zoology (Molecular and Developmental Evolution) 299:9-17.
    The present paper analyzes the use and understanding of the homology concept across different biological disciplines. It is argued that in its history, the homology concept underwent a sort of adaptive radiation. Once it migrated from comparative anatomy into new biological fields, the homology concept changed in accordance with the theoretical aims and interests of these disciplines. The paper gives a case study of the theoretical role that homology plays in comparative and evolutionary biology, in molecular biology, and in evolutionary (...)
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  23. Homology and the Origin of Correspondence.Ingo Brigandt - 2002 - Biology and Philosophy 17 (3):389–407.
    Homology is a natural kind term and a precise account of what homologyis has to come out of theories about the role of homologues in evolution anddevelopment. Definitions of homology are discussed with respect to the questionas to whether they are able to give a non-circular account of thecorrespondenceor sameness referred to by homology. It is argued that standard accounts tiehomology to operational criteria or specific research projects, but are not yetable to offer a concept of homology that does not (...)
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  24. The Importance of Homology for Biology and Philosophy.Ingo Brigandt & Paul Griffiths - 2007 - Biology and Philosophy 22 (5):633-641.
    Editors' introduction to the special issue on homology (Biology and Philosophy Vol. 22, Issue 5, 2007).
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  25. Why Development Matters.Rachael L. Brown - 2015 - Biology and Philosophy 30 (6):889-899.
    Günter Wagner’s Homology, Genes, and Evolutionary Innovation is a compelling, and empirically well-supported account of the evolution of character identity and character origination which emphasizes the importance of homology and novelty as central explananda for 21st century evolutionary biology. In this essay review, I focus on the similarities and differences between the structuralist picture of evolutionary biology advocated by Wagner, and that presented by standard evolutionary theory. First, I outline the ways in which Wagner’s genetic theory of homology diverges from (...)
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  26. Defining Sameness: Historical, Biological, and Generative Homology.Ann B. Butler & William M. Saidel - 2000 - Bioessays 22 (9):846-853.
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  27. Homologies in the Fossil Record: The Middle Ear as a Test Case.J. A. Clack - 1993 - Acta Biotheoretica 41 (4):391-409.
    This paper examines the middle ear of fossil living animals in terms of the homologies which have been drawn between its parts in different vertebrate groups. Seven homologies are considered: 1, the middle ear cavity/spiracular pouch; 2, the stapes/hyomandibula; 3, the stapedial/hyomandibular processes; 4 the tympanic membrane; 5, the otic notch; 6, the fenestra ovalis; 7, and the stapedial/hyomandibular foramen. The reasons leading to assessments of homology are reviewed. Homologies 1 and 2, based largely on embryological evidence, are fairly robust, (...)
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  28. Relations of Homology Between Higher Cognitive Emotions and Basic Emotions.Jason A. Clark - 2010 - Biology and Philosophy 25 (1):75-94.
    In the last 10 years, several authors including Griffiths and Matthen have employed classificatory principles from biology to argue for a radical revision in the way that we individuate psychological traits. Arguing that the fundamental basis for classification of traits in biology is that of ‘homology’ (similarity due to common descent) rather than ‘analogy’, or ‘shared function’, and that psychological traits are a special case of biological traits, they maintain that psychological categories should be individuated primarily by relations of homology (...)
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  29. Ancestors and Homology.M. I. Coates - 1993 - Acta Biotheoretica 41 (4):411-424.
    Current issues concerning the nature of ancestry and homology are discussed with reference to the evolutionary origin of the tetrapod limb. Homologies are argued to be complex conjectural inferences dependant upon a pre-existing phylogenetic analysisand a theoretical model of the evolutionary development of ontogenetic information. Ancestral conditions are inferred primarily from character (synapomorphy/homology) distributions within phylogeny, because of the deficiencies of palaeontological data. Recent analyses of tetrapod limb ontogeny, and the diverse, earliest morphologies known from the fossil record, are inconsistent (...)
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  30. Convergence as Evidence.A. Currie - 2013 - British Journal for the Philosophy of Science 64 (4):763-786.
    The comparative method grants epistemic access to the biological past. Comparing lineages provides empirical traction on both hypotheses about particular lineages and models of trait evolution. Understanding this evidential role is important. Although philosophers have recently turned their attention to relations of descent, little work exists exploring the status of evidence from convergences. I argue that, where they exist, convergences play a central role in the confirmation of adaptive hypotheses. I focus on ‘analogous inferences’, show how such inferences ought to (...)
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  31. Venomous Dinosaurs and Rear-Fanged Snakes: Homology and Homoplasy Characterized. [REVIEW]Adrian Mitchell Currie - 2014 - Erkenntnis 79 (3):701-727.
    I develop an account of homology and homoplasy drawing on their use in biological inference and explanation. Biologists call on homology and homoplasy to infer character states, support adaptationist explanations, identify evolutionary novelties and hypothesize phylogenetic relationships. In these contexts, the concepts must be understood phylogenetically and kept separate: as they play divergent roles, overlap between the two ought to be avoided. I use these considerations to criticize an otherwise attractive view defended by Gould, Hall, and Ramsey & Peterson. By (...)
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  32. An Oxymoric Homology — Homosexuality and Cultural Homologie.Paul Egan - 2003 - Semiotics:193-199.
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  33. Homology Thinking.Marc Ereshefsky - 2012 - Biology and Philosophy 27 (3):381-400.
    This paper explores an important type of biological explanation called ‘homology thinking.’ Homology thinking explains the properties of a homologue by citing the history of a homologue. Homology thinking is significant in several ways. First, it offers more detailed explanations of biological phenomena than corresponding analogy explanations. Second, it provides an important explanation of character similarity and difference. Third, homology thinking offers a promising account of multiple realizability in biology.
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  34. Homology: Integrating Phylogeny and Development.Marc Ereshefsky - 2009 - Biological Theory 4 (3):225-229.
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  35. Psychological Categories as Homologies: Lessons From Ethology.Mark Ereshefsky - 2007 - Biology and Philosophy 22 (5):659-674.
    Biology and Philosophy, forthcoming 2007.
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  36. Forever Beyond Our Grasp?Patrick Forber - 2007 - Biology and Philosophy 23 (1):135-141.
    Does science successfully uncover the deep structure of the natural world? Or are the depths forever beyond our epistemic grasp? Since the decline of logical positivism and logical empiricism, scientific realism has become the consensus view: of course our scientific theories apprehend the deep structure of the world. What else could explain the remarkable success of science? This is the explanationist defense of scientific realism, the “ultimate argument.” Kyle Stanford starts here and, using the history of theorizing about biological inheritance (...)
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  37. A History of Character Concepts in Evolutionary Biology.Kurt M. Fristrup - 2001 - In G. P. Wagner (ed.), The Character Concept in Evolutionary Biology. Academic Press. pp. 15--37.
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  38. Functional Homology and Functional Variation in Evolutionary Cognitive Science.Claudia García - 2010 - Biological Theory 5 (2):124-135.
    Most cognitive scientists nowadays tend to think that at least some of the mind’s capacities are the product of biological evolution, yet important conceptual problems remain for all scientists in order to be able to speak coherently of mental or cognitive systems as having evolved naturally. Two of these important problems concern the articulation of adequate, interesting, and empirically useful concepts of homology and variation as applied to cognitive systems. However, systems in cognitive science are usually understood as functional systems (...)
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  39. Homology and a Generative Theory of Biological Form.Brian Goodwin - 1993 - Acta Biotheoretica 41 (4):305-314.
    Homology continues to be a concept of central importance in the study of phylogenetic relations, but its relation to ontogenetic processes remains problematical. A definition of homology in terms of equivalent morphogenetic processes is defined and applied to the comparative study of tetrapod limbs. This allows for a consistent treatment of relations of similarity and difference of appendage structure in vertebrates, and the distinction between fishes fins and tetrapod limbs in terms of the concept of equivalence is described. The role (...)
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  40. The Phenomena of Homology.Paul E. Griffiths - 2007 - Biology and Philosophy 22 (5):643-658.
    Philosophical discussions of biological classification have failed to recognise the central role of homology in the classification of biological parts and processes. One reason for this is a misunderstanding of the relationship between judgments of homology and the core explanatory theories of biology. The textbook characterisation of homology as identity by descent is commonly regarded as a definition. I suggest instead that it is one of several attempts to explain the phenomena of homology. Twenty years ago the ‘new experimentalist’ movement (...)
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  41. Function, Homology, and Character Individuation.Paul E. Griffiths - 2006 - Philosophy of Science 73 (1):1-25.
    I defend the view that many biological categories are defined by homology against a series of arguments designed to show that all biological categories are defined, at least in part, by selected function. I show that categories of homology are `abnormality inclusive'—something often alleged to be unique to selected function categories. I show that classifications by selected function are logically dependent on classifications by homology, but not vice-versa. Finally, I reject the view that biologists must use considerations of selected function (...)
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  42. Occam's Razor and the Collothalamic Projection.Onur Güntürkün - 2003 - Behavioral and Brain Sciences 26 (5):558-559.
    Aboitiz and colleagues propose that the tectorotundal pathway of birds and reptiles is homologous not to the mammalian colliculopulvinar system but to the posterior complex/intralaminar nuclei. However, as outlined below, a large amount of strong evidence points to a homology of the tectorotundal and the colliculopulvinar system. This makes it likely that DVR and isocortex might be in part homologous.
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  43. A Recapitulation of the Rise and Fall of the Cell Lineage Research Program: The Evolutionary-Developmental Relationship of Cleavage to Homology, Body Plans and Life History. [REVIEW]Robert Guralnick - 2002 - Journal of the History of Biology 35 (3):537 - 567.
    American biologists in the late nineteenth century pioneered the descriptive-comparative study of all cell divisions from zygote to gastrulation -- the cell lineage. Data from cell lineages were crucial to evolutionary and developmental questions of the day. One of the main questions was the ultimate causation of developmental patterns -- historical or mechanical. E. B. Wilson's groundbreaking lineage work on the polychaete worm Nereis in 1892 set the stage for (1) an attack on Haeckel's phylogenetic-historical notion of recapitulation and (2) (...)
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  44. CARO: The Common Anatomy Reference Ontology.Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith - 2008 - In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer.
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...)
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  45. Steven Rose's Alternative to Ultra-Darwinism.David L. Hull - 1999 - Behavioral and Brain Sciences 22 (5):896-896.
    Stephen Rose's formulation of evolutionary theory is too scattered and impressionistic to serve as a genuine alternative to ultra- Darwinism. In addition, he has muddied a distinction that is crucial to our understanding of evolutionary phenomenona – the distinction between homologies and homoplasies.
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  46. Biological Pluralism and Homology.Heather A. Jamniczky - 2005 - Philosophy of Science 72 (5):687-698.
    The study of similarity is fundamental to biological inquiry. Many homology concepts have been formulated that function successfully to explain similarity in their native domains, but fail to provide an overarching account applicable to variably interconnected and independent areas of biological research despite the monistic standpoint from which they originate. The use of multiple, explicitly articulated homology concepts, applicable at different levels of the biological hierarchy, allows a more thorough investigation of the nature of biological similarity. Responsible epistemological pluralism as (...)
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  47. The Concept of Homology in Biology.N. Jardine - 1967 - British Journal for the Philosophy of Science 18 (2):125-139.
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  48. Analogy and Homology as an Instrument of Understanding and Error.J. Kamaryt - 1995 - Filosoficky Casopis 43 (4):565-583.
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  49. Homologizing as Kinding.Catherine Kendig - 2016 - In C. Kendig (ed.), Natural Kinds and Classification in Scientific Practice. Routledge.
    Homology is a natural kind concept, but one that has been notoriously elusive to pin down. There has been sustained debate over the nature of correspondence and the units of comparison. But this continued debate over its meaning has focused on defining homology rather than on its use in practice. The aim of this chapter is to concentrate on the practices of homologizing. I define “homologizing” to be a concept-in-use. Practices of homologizing are kinds of rule following, the satisfaction of (...)
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  50. Natural Kinds and Classification in Scientific Practice.Catherine Kendig (ed.) - 2016 - Routledge.
    This edited volume of 13 new essays aims to turn past discussions of natural kinds on their head. Instead of presenting a metaphysical view of kinds based largely on an unempirical vantage point, it pursues questions of kindedness which take the use of kinds and activities of kinding in practice as significant in the articulation of them as kinds. The book brings philosophical study of current and historical episodes and case studies from various scientific disciplines to bear on natural kinds (...)
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