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  1. Francisco Aboitiz (1988). Homology: A Comparative or a Historical Concept? Acta Biotheoretica 37 (1).
    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. Ron Amundson, Accounting For Vertebrate Limbs: From Owen's Homology To Novelty In Evo-Devo.
    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. Christopher Arthur (2003). Once More on the Homology Thesis: A Response to Smith's Reply. Historical Materialism 11 (1):195-198.
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  4. Leandro Assis & Ingo Brigandt (2009). Homology: Homeostatic Property Cluster Kinds in Systematics and Evolution. 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. Denis Barabé (1991). Chaos in Plant Morphology. Acta Biotheoretica 39 (2).
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  6. Denis Barabé, Stéphane Daigle & Luc Brouillet (1992). On the Interpretation of the Asymmetrical Leaf of Begonia by D'Arcy Thompson. Acta Biotheoretica 40 (4).
  7. David A. Baum (2013). Developmental Causation and the Problem of Homology. Philosophy and Theory in Biology 5.
    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. Jessica A. Bolker & Rudolf A. Raff (1996). Developmental Genetics and Traditional Homology. Bioessays 18 (6):489-494.
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  9. Déborah Bourc'his & Timothy H. Bestor (2002). Helicase Homologues Maintain Cytosine Methylation in Plants and Mammals. Bioessays 24 (4):297-299.
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  10. Ingo Brigandt, Scientific Practice, Conceptual Change, and the Nature of Concepts.
    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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  11. Ingo Brigandt, The Role a Concept Plays in Science: The Case of Homology.
    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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  12. Ingo Brigandt, Reference Determination and Conceptual Change.
    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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  13. Ingo Brigandt (2009). Accounting for Vertebrate Limbs: From Owen's Homology to Novelty in Evo-Devo. [REVIEW] 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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  14. Ingo Brigandt (2009). Accounting for Vertebrate Limbs: From Owen's Homology to Novelty in Evo-Devo. Philosophy and 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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  15. Ingo Brigandt (2009). Natural Kinds in Evolution and Systematics: Metaphysical and Epistemological Considerations. Acta Biotheoretica 57:77-97.
    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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  16. Ingo Brigandt (2007). Typology Now: Homology and Developmental Constraints Explain Evolvability. [REVIEW] 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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  17. Ingo Brigandt (2006). Homology and Heterochrony: The Evolutionary Embryologist Gavin Rylands de Beer (1899-1972). 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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  18. Ingo Brigandt (2004). Biological Kinds and the Causal Theory of Reference. In J. C. Marek & M. E. Reicher (eds.), Experience and Analysis: Papers of the 27th International Wittgenstein Symposium. Austrian Ludwig Wittgenstein Society.
    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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  19. Ingo Brigandt (2003). Homology in Comparative, Molecular, and Evolutionary Developmental Biology: The Radiation of a Concept. 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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  20. Ingo Brigandt (2002). Homology and the Origin of Correspondence. 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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  21. Ingo Brigandt & Paul Griffiths (2007). The Importance of Homology for Biology and Philosophy. 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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  22. Ann B. Butler & William M. Saidel (2000). Defining Sameness: Historical, Biological, and Generative Homology. Bioessays 22 (9):846-853.
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  23. J. A. Clack (1993). Homologies in the Fossil Record: The Middle Ear as a Test Case. Acta Biotheoretica 41 (4).
    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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  24. Jason A. Clark (2010). Relations of Homology Between Higher Cognitive Emotions and Basic Emotions. 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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  25. M. I. Coates (1993). Ancestors and Homology. Acta Biotheoretica 41 (4).
    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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  26. A. Currie (2012). Convergence as Evidence. British Journal for the Philosophy of Science 64 (4):axs027.
    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 (homology), little work exists exploring the status of evidence from convergences (analogy). I argue that, where they exist, convergences play a central role in the confirmation of adaptive hypotheses. I focus on ‘analogous inferences’ (inferences that take a (...)
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  27. Adrian Mitchell Currie (2014). Venomous Dinosaurs and Rear-Fanged Snakes: Homology and Homoplasy Characterized. [REVIEW] 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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  28. Paul Egan (2003). An Oxymoric Homology — Homosexuality and Cultural Homologie. Semiotics:193-199.
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  29. Marc Ereshefsky (2012). Homology Thinking. 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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  30. Marc Ereshefsky (2009). Homology: Integrating Phylogeny and Development. Biological Theory 4 (3):225-229.
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  31. Mark Ereshefsky (2007). Psychological Categories as Homologies: Lessons From Ethology. Biology and Philosophy 22 (5):659-674.
    Biology and Philosophy, forthcoming 2007.
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  32. Claudia Lorena García (2010). Functional Homology and Functional Variation in Evolutionary Cognitive Science. 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 of them 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 (...)
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  33. Brian Goodwin (1993). Homology and a Generative Theory of Biological Form. Acta Biotheoretica 41 (4).
    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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  34. Paul E. Griffiths (2007). The Phenomena of Homology. 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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  35. Paul Edmund Griffiths (2006). Function, Homology, and Character Individuation. Philosophy of Science 73 (1):1-25.
    Many philosophers believe that 1) most uses of functional language in biology make implicit reference to natural selection and 2) the fundamental way in which biologists identify parts and processes in organisms is by their selected function(s). Both these claims are mistaken. Much functional language in biology refers to actual causal roles, and if this were not so, biology would be impossible. The extensive biological literature on the ‘character concept’ focuses on another principle of biological identity, namely homology. I outline (...)
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  36. Paul E. Griffiths (2006). Function, Homology, and Character Individuation. 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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  37. Onur Güntürkün (2003). Occam's Razor and the Collothalamic Projection. 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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  38. Robert Guralnick (2002). 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] 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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  39. Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith (2008). CARO: The Common Anatomy Reference Ontology. 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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  40. David L. Hull (1999). Steven Rose's Alternative to Ultra-Darwinism. 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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  41. Heather Jamniczky (2005). Biological Pluralism and Homology. Philosophy of Science 72 (5):687-698.
    Homology concepts are fundamental to the study of biological similarity. Monistic attempts to articulate an overarching homology concept, applicable to all areas of biology, have yet to succeed. Biology is fundamentally pluralistic, and multiple homology concepts, applicable at different levels of the biological hierarchy, allow a more thorough investigation of the nature of biological similarity. Articulating the definition and causes associated with any homology concept ensures that the pluralistic approach advocated here is neither relativistic nor defeatist, but generative of fruitful (...)
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  42. Heather A. Jamniczky (2005). Biological Pluralism and Homology. 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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  43. N. Jardine (1967). The Concept of Homology in Biology. British Journal for the Philosophy of Science 18 (2):125-139.
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  44. Catherine Kendig, Reconstructing the Concept of Homology for Genomics. Pittsburgh/London Colloquium on Philosophy of Biology and Neuroscience, University of London. Online at PhilSci Archive.
    Homology has been one of, if not the most, fecund concepts which has been used towards the understanding of the genomes of the model organisms. The evidence for this claim can be supported best with an examination of current research in comparative genomics. In comparative genomics, the information of genes or segments of the genome, and their location and sequence, are used to search for genes similar to them, known as 'homologues'. Homologues can be either within that same organism (paralogues), (...)
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  45. Karel Kleisner (2007). The Formation of the Theory of Homology in Biological Sciences. Acta Biotheoretica 55 (4).
    Homology is among the most important comparative concepts in biology. Today, the evolutionary reinterpretation of homology is usually conceived of as the most important event in the development of the concept. This paradigmatic turning point, however important for the historical explanation of life, is not of crucial importance for the development of the concept of homology itself. In the broadest sense, homology can be understood as sameness in reference to the universal guarantor so that in this sense the different concepts (...)
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  46. Dean J. Lee (2013). Homology, Female Orgasm and the Forgotten Argument of Donald Symons. Biology and Philosophy 28 (6):1021-1027.
    The ‘byproduct account’ of female orgasm, a subject of renewed debate since Lloyd (The case of the female orgasm, Harvard University Press, Cambridge, 2005), is universally attributed to Symons (The evolution of human sexuality, Oxford University Press, Oxford, 1979). While this is correct to the extent that he linked it to the adaptive value of male orgasm, I argue that the attribution of the theory as we understand it to Symons is based on a serious and hitherto unrecognised misinterpretation. Symons (...)
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  47. Alan C. Love (2007). Functional Homology and Homology of Function: Biological Concepts and Philosophical Consequences. Biology and Philosophy 22 (5):691-708.
    “Functional homology” appears regularly in different areas of biological research and yet it is apparently a contradiction in terms—homology concerns identity of structure regardless of form and function. I argue that despite this conceptual tension there is a legitimate conception of ‘homology of function’, which can be recovered by utilizing a distinction from pre-Darwinian physiology (use versus activity) to identify an appropriate meaning of ‘function’. This account is directly applicable to molecular developmental biology and shares a connection to the theme (...)
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  48. Miles MacLeod (2013). Limitations of Natural Kind Talk in the Life Sciences: Homology and Other Cases. [REVIEW] Biological Theory 7 (2):109-120.
    The aim of this article is to detail some reservations against the beliefs, claims, or presuppositions that current essentialist natural kind concepts (including homeostatic property cluster kinds) model grouping practices in the life sciences accurately and generally. Such concepts fit reasoning into particular preconceived epistemic and semantic patterns. The ability of these patterns to fit scientific practice is often argued in support of homeostatic property cluster accounts, yet there are reasons to think that in the life sciences kind concepts exhibit (...)
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  49. Miles MacLeod (2011). How to Compare Homology Concepts: Class Reasoning About Evolution and Morphology in Phylogenetics and Developmental Biology. Biological Theory 6 (2):141-153.
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  50. Mohan Matthen (2007). Defining Vision: What Homology Thinking Contributes. Biology and Philosophy 22 (5):675-689.
    The specialization of visual function within biological function is reason for introducing “homology thinking” into explanations of the visual system. It is argued that such specialization arises when organisms evolve by differentiation from their predecessors. Thus, it is essentially historical, and visual function should be regarded as a lineage property. The colour vision of birds and mammals do not function the same way as one another, on this account, because each is an adaptation to special needs of the visual functions (...)
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