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  1. Systems Biology, Systems Medicine, Systems Pharmacology: The What and The Why.Angélique Stéphanou, Eric Fanchon, Pasquale F. Innominato & Annabelle Ballesta - 2018 - Acta Biotheoretica 66 (4):345-365.
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  2. “A Temporary Oversimplification”: Mayr, Simpson, Dobzhansky, and the Origins of the Typology/Population Dichotomy.Joeri Witteveen - 2015 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 55:20-33.
    The dichotomy between ‘typological thinking’ and ‘population thinking’ features in a range of debates in contemporary and historical biology. The origins of this dichotomy are often traced to Ernst Mayr, who is said to have coined it in the 1950s as a rhetorical device that could be used to shield the Modern Synthesis from attacks by the opponents of population biology. In this two-part essay, I argue that the origins of the typology/population dichotomy are considerably more complicated and more interesting (...)
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  3. What the Philosophy of Biology Is: Essays Dedicated to David Hull.Michael Ruse (ed.) - 1989 - Dordrecht: Kluwer Academic Publishers.
    Philosophers of science frequently bemoan (or cheer) the fact that today, with the supposed collapse of logical empiricism, there are now ;;10 grand systems. However, although this mayor may not be true, and if true mayor may not be a cause for delight, no one should conclude that the philosophy of science has ground to a halt, its problems exhausted and its practioners dispirited. In fact, in this post­ Kuhnian age the subject has never been more alive, as we work (...)
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  4. Toward a Philosophy of Systems Biology.Jonathan F. Davies & Maureen A. O’Malley - 2007 - Biological Theory 2 (4):420-422.
  5. Fifty Shades of Cladism.Andrew V. Z. Brower - 2018 - Biology and Philosophy 33 (1-2):8.
    Quinn offered seven definitions of “cladist” and discussed the context in which they are used in relation to historical and current debates in systematics. As a member of her study taxon, I offer some contextual color commentary, clarifications on the views of “pattern cladists” regarding monophyly, ancestors, synapomorphy and other concepts, a definition of “syncretist”, and some thoughts on cladistics and philosophy in the twenty first century.
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  6. The Manipulability of What? The History of G-Protein Coupled Receptors.Ann-Sophie Barwich & Karim Bschir - 2017 - Biology and Philosophy 32 (6):1317-1339.
    This paper tells the story of G-protein coupled receptors, one of the most important scientific objects in contemporary biochemistry and molecular biology. By looking at how cell membrane receptors turned from a speculative concept into a central element in modern biochemistry over the past 40 years, we revisit the role of manipulability as a criterion for entity realism in wet-lab research. The central argument is that manipulability as a condition for reality becomes meaningful only once scientists have decided how to (...)
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  7. Thirty-One Years of Systematic Zoology.David L. Hull - 1983 - Systematic Zoology 32 (4):315-342.
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  8. Contemporary Logic and Evolutionary Taxonomy: A Reply to Gregg.David L. Hull & D. Paul Snyder - 1969 - Systematic Zoology 18 (3):347-354.
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  9. Definitions of Taxa.David L. Hull & Roger Buck - 1967 - Systematic Zoology 16 (4):349.
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  10. Reply to Gregg.Roger C. Buck & David L. Hull - 1969 - Systematic Zoology 18 (3):354-357.
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  11. Contemporary Systematic Philosophies.David L. Hull - 1970 - Annual Review of Ecology and Systematics 1:19-54.
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  12. Reply to Randal and Scott.David L. Hull - 1969 - Systematic Zoology 18 (4):468-469.
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  13. The Syntax of Numericlature.David L. Hull - 1968 - Systematic Zoology 17 (4):472-474.
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  14. Phylogenetic Numericlature.David L. Hull - 1966 - Systematic Zoology 15 (1):14-17.
    The author proposes a system of identification, positional, and phyletic numbers for taxa that makes possible a significant relationship between numerical classification and phylogeny.
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  15. The Limits of Cladism.David L. Hull - 1979 - Systematic Zoology 28 (4):416-440.
    The goal of cladistic systematics is to discern sister-group relations (cladistic relations) by the methods of cladistic analysis and to represent them explicitly and unambiguously in cladograms and cladistic classifications. Cladists have selected cladistic relations to represent for two reasons: cladistic relations can be discerned with reasonable certainty by the methods of cladistic analysis and they can be represented with relative ease in cladograms and classifications. Cladists argue that features of phylogeny other than cladistic relations cannot be discerned with sufficient (...)
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  16. Frédéric Bouchard and Philippe Huneman, Eds.: From Groups to Individuals. Evolution and Emerging Individuality.J. Ayala Francisco - 2014 - History and Philosophy of the Life Sciences 36 (1):136-138.
  17. Frédéric Bouchard and Philippe Huneman, Eds.: From Groups to Individuals. Evolution and Emerging Individuality.J. Ayala Francisco - 2014 - History and Philosophy of the Life Sciences 36 (1):136-138.
  18. Structural Powers and the Homeodynamic Unity of Organisms.Christopher J. Austin & Anna Marmodoro - 2017 - In William M. R. Simpson, Robert C. Koons & Nicholas J. Teh (eds.), Neo-Aristotelian Perspectives on Contemporary Science. Routledge. pp. 169-184.
    Although they are continually compositionally reconstituted and reconfigured, organisms nonetheless persist as ontologically unified beings over time – but in virtue of what? A common answer is: in virtue of their continued possession of the capacity for morphological invariance which persists through, and in spite of, their mereological alteration. While we acknowledge that organisms‟ capacity for the “stability of form” – homeostasis - is an important aspect of their diachronic unity, we argue that this capacity is derived from, and grounded (...)
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  19. A Biologically Informed Hylomorphism.Christopher J. Austin - 2017 - In William M. R. Simpson, Robert C. Koons & Nicholas J. Teh (eds.), Neo-Aristotelian Perspectives on Contemporary Science. Routledge. pp. 185-210.
    Although contemporary metaphysics has recently undergone a neo-Aristotelian revival wherein dispositions, or capacities are now commonplace in empirically grounded ontologies, being routinely utilised in theories of causality and modality, a central Aristotelian concept has yet to be given serious attention – the doctrine of hylomorphism. The reason for this is clear: while the Aristotelian ontological distinction between actuality and potentiality has proven to be a fruitful conceptual framework with which to model the operation of the natural world, the distinction between (...)
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  20. Using the Hierarchy of Biological Ontologies to Identify Mechanisms in Flat Networks.William Bechtel - 2017 - Biology and Philosophy 32 (5):627-649.
    Systems biology has provided new resources for discovering and reasoning about mechanisms. In addition to generating databases of large bodies of data, systems biologists have introduced platforms such as Cytoscape to represent protein–protein interactions, gene interactions, and other data in networks. Networks are inherently flat structures. One can identify clusters of highly connected nodes, but network representations do not represent these clusters as at a higher level than their constituents. Mechanisms, however, are hierarchically organized: they can be decomposed into their (...)
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  21. A New Cladistics of Cladists.Malte Ebach, Juan Morrone & David Williams - 2008 - Biology and Philosophy 23 (1):153-156.
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  22. Two Sides of the Same Coin? The Epistemic Cultures of Systems and Synthetic Biology.Karen Kastenhofer - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):130-140.
    Systems and synthetic biology both emerged around the turn of this century as labels for new research approaches. Although their disciplinary status as well as their relation to each other is rarely discussed in depth, now and again the idea is invoked that both approaches represent ‘two sides of the same coin’. The following paper focuses on this general notion and compares it with empirical findings concerning the epistemic cultures prevalent in the two contexts. Drawing on interviews with researchers from (...)
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  23. Evidence, Content and Corroboration and the Tree of Life. E. Lienau & Rob Desalle - 2009 - Acta Biotheoretica 57 (1-2):187-199.
    We examine three critical aspects of Popper’s formulation of the ‘Logic of Scientific Discovery’—evidence, content and degree of corroboration—and place these concepts in the context of the Tree of Life problem with particular reference to molecular systematics. Content, in the sense discussed by Popper, refers to the breadth and scope of existence that a hypothesis purports to explain. Content, in conjunction with the amount of available and relevant evidence, determines the testability, or potential degree of corroboration, of a statement; content (...)
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  24. Holobionts and the Ecology of Organisms: Multi-Species Communities or Integrated Individuals?Derek Skillings - 2016 - Biology and Philosophy 31 (6):875-892.
    It is now widely accepted that microorganisms play many important roles in the lives of plants and animals. Every macroorganism has been shaped in some way by microorganisms. The recognition of the ubiquity and importance of microorganisms has led some to argue for a revolution in how we understand biological individuality and the primary units of natural selection. The term “holobiont” was introduced as a name for the biological unit made up by a host and all of its associated microorganisms, (...)
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  25. The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher J. Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...)
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  26. “Man-Machines and Embodiment: From Cartesian Physiology to Claude Bernard’s ‘Living Machine’”.Charles T. Wolfe & Philippe Huneman - forthcoming - In Justin E. H. Smith (ed.), Embodiment, Oxford Philosophical Concepts. Oxford University Press.
    A common and enduring early modern intuition is that materialists reduce organisms in general and human beings in particular to automata. Wasn’t a famous book of the time entitled L’Homme-Machine? In fact, the machine is employed as an analogy, and there was a specifically materialist form of embodiment, in which the body is not reduced to an inanimate machine, but is conceived as an affective, flesh-and-blood entity. We discuss how mechanist and vitalist models of organism exist in a more complementary (...)
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  27. The Organism in Interdisciplinary Context: Proceedings of the STOQ Research Group on Organisms Edited by Pietro Ramellini.Nicanor Pier Giorgio Austriaco - 2008 - The National Catholic Bioethics Quarterly 8 (3):599-602.
  28. 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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  29. SMT and TOFT: Why and How They Are Opposite and Incompatible Paradigms.Mariano Bizzarri & Alessandra Cucina - forthcoming - Acta Biotheoretica.
  30. Sequence Data, Phylogenetic Inference, and Implications of Downward Causation.Kirk Fitzhugh - 2016 - Acta Biotheoretica 64 (2):133-160.
    Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain ‘morphological’ characters but selection cannot be causally (...)
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  31. Rational Disagreements in Phylogenetics.Fabrizzio Guerrero Mc Manus - 2009 - Acta Biotheoretica 57 (1-2):99-127.
    This paper addresses the general problem of how to rationally choose an algorithm for phylogenetic inference. Specifically, the controversy between maximum likelihood (ML) and maximum parsimony (MP) perspectives is reframed within the philosophical issue of theory choice. A Kuhnian approach in which rationality is bounded and value-laden is offered and construed through the notion of a Style of Modeling. A Style is divided into four stages: collecting remnant models, constructing models of taxonomical identity, implementing modeling algorithms, and finally inferring and (...)
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  32. Biology as History: Papers From International Conferences Sponsored by the California Academy of Sciences in San Francisco and the Museo Civico di Storia Naturale in Milan. Vol. 1: Systematic Biology as an Historical Science. Giovanni Pinna, Michael T. GhiselinBiology as History: Papers From International Conferences Sponsored by the California Academy of Sciences in San Francisco and the Museo Civico di Storia Naturale in Milan. Vol. 2: New Perspectives on the History of Life: Essays on Systematic Biology as Historical Narrative. Michael T. Ghiselin, Giovanni Pinna. [REVIEW]Kraig Adler - 1998 - Isis 89 (3):584-585.
  33. Biological Classification: A Philosophical Introduction.Richard A. Richards - 2016 - Cambridge University Press.
    Modern biological classification is based on the system developed by Linnaeus, and interpreted by Darwin as representing the tree of life. But despite its widespread acceptance, the evolutionary interpretation has some problems and limitations. This comprehensive book provides a single resource for understanding all the main philosophical issues and controversies about biological classification. It surveys the history of biological classification from Aristotle to contemporary phylogenetics and shows how modern biological classification has developed and changed over time. Readers will also be (...)
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  34. The Role of Theories in Biological Systematics.David L. Hull - 2001 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 32 (2):221-238.
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  35. Linnaean Ranks: Vestiges of a Bygone Era.Marc Ereshefsky - 2002 - Philosophy of Science 69 (S3):S305-S315.
    We tend to think that there are different types of biological taxa: some taxa are species, others are genera, while others are families. Linnaeus gave us his ranks in 1731. Biological theory has changed since Linnaeus’s time. Nevertheless, the vast majority of biologists still assign Linnaean ranks to taxa, even though that practice is at odds with evolutionary theory and even though it causes a number of practical problems. The Linnaean ranks should be abandoned and alternative methods for displaying the (...)
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  36. Structuralism in Phylogenetic Systematics.Richard H. Zander - 2010 - Biological Theory 5 (4):383-394.
    Systematics based solely on structuralist principles is non-science because it is derived from first principles that are inconsistent in dealing with both synchronic and diachronic aspects of evolution, and its evolutionary models involve hidden causes, and unnameable and unobservable entities. Structuralist phylogenetics emulates axiomatic mathematics through emphasis on deduction, and “hypotheses” and “mapped trait changes” that are actually lemmas and theorems. Sister-group-only evolutionary trees have no caulistic element of scientific realism. This results in a degenerate systematics based on patterns of (...)
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  37. Possible Similar Role of Cytochrome P450 in Primordial Evolution of Species and in Chemical Carcinogenesis.Rohan H. Wickramasinghe & Claude A. Villee - 1976 - Perspectives in Biology and Medicine 19 (4):473-475.
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  38. Annual Meeting of the EpiGeneSys Network of Excellence - Advancing Epigenetics Towards Systems Biology.Jon Houseley, Caroline S. Hill & Peter J. Rugg-Gunn - 2015 - Bioessays 37 (6):592-595.
  39. How Discordant Morphological and Molecular Evolution Among Microorganisms Can Revise Our Notions of Biodiversity on Earth.Daniel J. G. Lahr, Haywood Dail Laughinghouse, Angela M. Oliverio, Feng Gao & Laura A. Katz - 2014 - Bioessays 36 (10):950-959.
    Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular (...)
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  40. Revisiting Generality in Biology: Systems Biology and the Quest for Design Principles.Sara Green - 2015 - Biology and Philosophy 30 (5):629-652.
    Due to the variation, contingency and complexity of living systems, biology is often taken to be a science without fundamental theories, laws or general principles. I revisit this question in light of the quest for design principles in systems biology and show that different views can be reconciled if we distinguish between different types of generality. The philosophical literature has primarily focused on generality of specific models or explanations, or on the heuristic role of abstraction. This paper takes a different (...)
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  41. The History of Systematics: A Working Bibliography, 1965–1996.Robert J. O'Hara - 1998 - SSRN Electronic Journal 2541429.
    80 titles published between 1965 and 1996 in multiple languages attest to an increase in scholarly interest in the history of systematic biology, both among scientific practitioners and also among historians and philosophers of science. Topics studied have included the early history of the field (Ray, Linnaeus, Buffon), the influence of essentialism on systematics, the history of systematic diagrams, the development of cladistic analysis, the nature of species, and the growth of phylogenetic thinking.
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  42. Trees of History in Systematics, Historical Linguistics, and Stemmatics: A Working Interdisciplinary Bibliography.Robert J. O'Hara - 2006 - SSRN Electronic Journal 2540351.
    138 titles across a wide range of scholarly publications illustrate the conceptual affinities that connect the palaetiological sciences of biological systematics, historical linguistics, and stemmatics. These three fields all have as their central objective the reconstruction of evolutionary "trees of history" that depict phylogenetic patterns of descent with modification among species, languages, and manuscripts. All three fields flourished in the nineteenth century, underwent parallel periods of quiescence in the early twentieth century, and in recent decades have seen widespread parallel revivals. (...)
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  43. Diagrammatic Classifications of Birds, 1819–1901: Views of the Natural System in 19th-Century British Ornithology.Robert J. O'Hara - 1988 - Acta XIX Congressus Internationalis Ornithologici: pp. 2746–2759.
    Classifications of animals and plants have long been represented by hierarchical lists of taxa, but occasional authors have drawn diagrammatic versions of their classifications in an attempt to better depict the "natural relationships" of their organisms. Ornithologists in 19th-century Britain produced and pioneered many types of classificatory diagrams, and these fall into three groups: (a) the quinarian systems of Vigors and Swainson (1820s and 1830s); (b) the "maps" of Strickland and Wallace (1840s and 1850s); and (c) the evolutionary diagrams of (...)
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  44. Review of Atran's 'Cognitive Foundations of Natural History: Towards an Anthropology of Science'. [REVIEW]Robert J. O'Hara - 1993 - Forest and Conservation History 37 (1): 43.
  45. Population Thinking and Tree Thinking in Systematics.Robert J. O'Hara - 1997 - Zoologica Scripta 26 (4): 323–329.
    Two new modes of thinking have spread through systematics in the twentieth century. Both have deep historical roots, but they have been widely accepted only during this century. Population thinking overtook the field in the early part of the century, culminating in the full development of population systematics in the 1930s and 1940s, and the subsequent growth of the entire field of population biology. Population thinking rejects the idea that each species has a natural type (as the earlier essentialist view (...)
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  46. Mapping the Space of Time: Temporal Representation in the Historical Sciences.Robert J. O'Hara - 1996 - Memoirs of the California Academy of Sciences 20: 7–17.
    William Whewell (1794–1866), polymathic Victorian scientist, philosopher, historian, and educator, was one of the great neologists of the nineteenth century. Although Whewell's name is little remembered today except by professional historians and philosophers of science, researchers in many scientific fields work each day in a world that Whewell named. "Miocene" and "Pliocene," "uniformitarian" and "catastrophist," "anode" and "cathode," even the word "scientist" itself—all of these were Whewell coinages. Whewell is particularly important to students of the historical sciences for another word (...)
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  47. Trees of History in Systematics and Philology.Robert J. O'Hara - 1996 - Memorie Della Società Italiana di Scienze Naturali E Del Museo Civico di Storia Naturale di Milano 27 (1): 81–88.
    "The Natural System" is the name given to the underlying arrangement present in the diversity of life. Unlike a classification, which is made up of classes and members, a system or arrangement is an integrated whole made up of connected parts. In the pre-evolutionary period a variety of forms were proposed for the Natural System, including maps, circles, stars, and abstract multidimensional objects. The trees sketched by Darwin in the 1830s should probably be considered the first genuine evolutionary diagrams of (...)
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  48. Evolutionary History and the Species Problem.Robert J. O'Hara - 1994 - American Zoologist 34 (1): 12–22.
    In the last thirty years systematics has transformed itself from a discipline concerned with classification into a discipline concerned with reconstructing the evolutionary history of life. This transformation has been driven by cladistic analysis, a set of techniques for reconstructing evolutionary trees. Long interested in the large-scale structure of evolutionary history, cladistically oriented systematists have recently begun to apply "tree thinking" to problems near the species level. ¶ In any local ("non-dimensional") situation species are usually well-defined, but across space and (...)
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  49. Homage to Clio, or, Toward an Historical Philosophy for Evolutionary Biology.Robert J. O'Hara - 1988 - Systematic Zoology 37 (2): 142–155.
    Discussions of the theory and practice of systematics and evolutionary biology have heretofore revolved around the views of philosophers of science. I reexamine these issues from the different perspective of the philosophy of history. Just as philosophers of history distinguish between chronicle (non-interpretive or non-explanatory writing) and narrative history (interpretive or explanatory writing), I distinguish between evolutionary chronicle (cladograms, broadly construed) and narrative evolutionary history. Systematics is the discipline which estimates the evolutionary chronicle. ¶ Explanations of the events described in (...)
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  50. Problems of Classification and Individuation with Examples From Nineteenth Century Biology.Berent Enç - 1967
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