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  1. W. E. Agar (1948). The Wholeness of the Living Organism. Philosophy of Science 15 (3):179-191.
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  2. Thomas R. Alley (1985). Organism-Environment Mutuality Epistemics, and the Concept of an Ecological Niche. Synthese 65 (3):411 - 444.
    The concept of an ecological niche (econiche) has been used in a variety of ways, some of which are incompatible with a relational or functional interpretation of the term. This essay seeks to standardize usage by limiting the concept to functional relations between organisms and their surroundings, and to revise the concept to include epistemic relations. For most organisms, epistemics are a vital aspect of their functional relationships to their surroundings and, hence, a major determinant of their econiche. Rejecting the (...)
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  3. Rachel A. Ankeny (forthcoming). Historiographic Reflections on Model Organisms: Or How the Mureaucracy May Be Limiting Our Understanding of Contemporary Genetics and Genomics. History and Philosophy of the Life Sciences.
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  4. Argyris Arnellos, Alvaro Moreno & Kepa Ruiz-Mirazo (forthcoming). Organizational Requirements for Multicellular Autonomy: Insights From a Comparative Case Study. Biology and Philosophy:1-34.
    In this paper we explore the organizational conditions underlying the emergence of organisms at the multicellular level. More specifically, we shall propose a general theoretical scheme according to which a multicellular organism is an ensemble of cells that effectively regulates its own development through collective (meta-cellular) mechanisms of control of cell differentiation and cell division processes. This theoretical result derives from the detailed study of the ontogenetic development of three multicellular systems (Nostoc punctiforme, Volvox carteri and Strongylocentrotus purpuratus) and, in (...)
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  5. Robin Attfield (2007). Is the Concept of Nature Dispensable? The Proceedings of the Twenty-First World Congress of Philosophy 5 (25):59-63.
    In response to the arguments of Bill McKibben and of Stephen Vogel that nature is at an end and that the very concept of nature should be discarded, I argue that, far from this being the case, the concept of nature is indispensable. A third sense of 'nature' besides the two distinguished by Vogel, that of the nature of an organism, is brought to attention and shown, through five arguments, to be indispensable for environmental philosophy and ethics, and for ethics (...)
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  6. G. F. Azzone (2001). The Case and the Need: The Double Identity of Living Organisms. History and Philosophy of the Life Sciences 23 (1):163-184.
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  7. G. F. Azzone (2000). [Necessary Sites: Identical Duplication of Living Organisms]. History and Philosophy of the Life Sciences 23 (1):163-184.
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  8. Giovanni Felice Azzone (2001). Il caso e la necessità: la duplice identità degli organismi viventi. History and Philosophy of the Life Sciences 23 (1):163 - 184.
    The paper deals with the concept of the identity of living organisms, a concept used up until now very ambiguously. The discussion rests on the combination of two concepts, one proposed by Munzer (1993) and another derived from the considerations of Riedl (1975). The first is the proposal that the identity of living organisms depends on the properties of their elementary constituents, such as cells and tissues, and that these properties, in turn, depend on those of their DNA and RNA. (...)
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  9. Eric Bapteste & John Dupré (2013). Towards a Processual Microbial Ontology. 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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  10. Maarten Boudry & Massimo Pigliucci (2013). The Mismeasure of Machine: Synthetic Biology and the Trouble with Engineering Metaphors. Studies in History and Philosophy of Biological and Biomedical Sciences (4):660-668.
    The scientific study of living organisms is permeated by machine and design metaphors. Genes are thought of as the ‘‘blueprint’’ of an organism, organisms are ‘‘reverse engineered’’ to discover their func- tionality, and living cells are compared to biochemical factories, complete with assembly lines, transport systems, messenger circuits, etc. Although the notion of design is indispensable to think about adapta- tions, and engineering analogies have considerable heuristic value (e.g., optimality assumptions), we argue they are limited in several important respects. In (...)
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  11. Ingo Brigandt (2005). The Instinct Concept of the Early Konrad Lorenz. Journal of the History of Biology 38 (3):571–608..
    Peculiar to Konrad Lorenz’s view of instinctive behavior is his strong innate-learned dichotomy. He claimed that there are neither ontogenetic nor phylogenetic transitions between instinctive and experience-based behavior components, thus contradicting all former accounts of instinct. The present study discusses how Lorenz came to hold this controversial position by examining the history of Lorenz’s early theoretical development in the crucial period from 1931 to 1937, taking relevant influences into account. Lorenz’s intellectual development is viewed as being guided by four theoretical (...)
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  12. Ingo Brigandt (2005). The Early Theoretical Development of Konrad Lorenz and the Motivating Factors Behind His Instinct Concept [La Prima Fase Dello Sviluppo Teorico di Konrad Lorenz E I Fattori Motivanti Del Suo Concetto di Istinto]. In M. Celentano & M. Stanzione (eds.), Konrad Lorenz cent'anni dopo: L'eredità scientifica del padre dell'etologia.
    The present study discusses the early theoretical development of Konrad Lorenz in the period from 1930 to 1937. In this period Lorenz developed his position on instinct in the first place, and thus his theoretical views were subject to change. Despite this change, the paper points to relatively stable features of Lorenz’s approach, which emerged relatively soon in his scientific career and guided his theoretical development in this and beyond this early phase.
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  13. Richard M. Burian (1993). How the Choice of Experimental Organism Matters: Epistemological Reflections on an Aspect of Biological Practice. [REVIEW] Journal of the History of Biology 26 (2):351 - 367.
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  14. Werner Callebaut (2007). Modeling Organisms. Biological Theory 2 (2):209-210.
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  15. Tobias Cheung (forthcoming). What is an" Organism"? On the Occurrence of a New Term and Its Conceptual Transformations 1680-1850. History and Philosophy of the Life Sciences.
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  16. Laura Nuño de la Rosa (forthcoming). Becoming Organisms: The Organisation of Development and the Development of Organisation. History and Philosophy of the Life Sciences.
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  17. John Dupré (2006). Humans and Other Animals. Clarendon Press.
    John Dupré explores the ways in which we categorize animals, including humans, and comes to surprisingly radical conclusions. He opposes the idea that there is only one legitimate way of classifying things in the natural world, the 'scientific' way. The lesson we should learn from Darwin is to reject the idea that each organism has an essence that determines its necessary place in the unique hierarchy of things. Nature is not like that: it is not organized in a single system. (...)
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  18. Walter M. Elsasser (1987/1998). Reflections on a Theory of Organisms: Holism in Biology. Published for the Johns Hopkins Dept. Of Earth and Planetary Sciences by the Johns Hopkins University Press.
    Are living organisms--as Descartes argued--just machines? Or is the nature of life such that it can never be fully explained by mechanistic models? In this thought-provoking and controversial book, eminent geophysicist Walter M. Elsasser argues that the behavior of living organisms cannot be reduced to physico-chemical causality. Suggesting that molecular biology today is at the same point as Newtonian physics on the eve of the quantum revolution, Elsasser lays the foundation for a theoretical biology that points the way toward a (...)
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  19. Michael T. Ghiselin (2007). Is the Pope a Catholic? Biology and Philosophy 22 (2):283-291.
    The whole-part relationship is generally considered transitive, but there are some apparent exceptions. Componential sortals create some apparent problems. Homo sapiens, the Pope, and his heart are all individuals. A human being, such as the Pope, is an organism-level component of Homo sapiens. The Pope’s heart is an organ-level component of both Homo sapiens and the Pope. Although the Pope is a part, and not an instance, of the Roman Catholic Church, it seems odd to say that his heart is (...)
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  20. Root Gorelick (2012). Mitosis Circumscribes Individuals; Sex Creates New Individuals. Biology and Philosophy 27 (6):871-890.
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  21. David Haig (2014). Genetic Dissent and Individual Compromise. Biology and Philosophy 29 (2):233-239.
    Organisms can be treated as optimizers when there is consensus among their genes about what is best to be done, but genomic consensus is often lacking, especially in interactions among kin because kin share some genes but not others. Grafen adopts a majoritarian perspective in which an individual’s interests are identified with the interests of the largest coreplicon of its genome, but genomic imprinting and recombination factionalize the genome so that no faction may predominate in some interactions among kin. Once (...)
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  22. Christopher D. Horvath (1997). Some Questions About Identifying Individuals: Failed Intuitions About Organisms and Species. Philosophy of Science 64 (4):654-668.
    Treating species as individuals and not classes has been crucial to the integration of evolutionary theory with modern systematics. Despite the theoretically important role the concept of individuality plays in modern phylogenetic systematics and in evolutionary theory more generally, many have been content to rely on common-sense intuitions about what counts as an individual. One of the most often cited intuitions is that individuals should be defined intrinsically. Unfortunately, common-sense intuitions like this one have proven to be inadequate for identifying (...)
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  23. Philippe Huneman (forthcoming). Assessing the Prospects for a Return of Organisms in Evolutionary Biology. History and Philosophy of the Life Sciences.
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  24. Phillipe Huneman & Charles T. Wolfe (2010). The Concept of Organism: Historical Philosophical, Scientific Perspectives. History and Philosophy of the Life Sciences 32 (2-3):147.
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  25. Catherine Kendig (2013). Integrating History and Philosophy of the Life Sciences in Practice to Enhance Science Education: Swammerdam's Historia Insectorum Generalis and the Case of the Water Flea. Science and Education 22 (8):1939-1961.
    Hasok Chang (Science & Education 20:317–341, 2011) shows how the recovery of past experimental knowledge, the physical replication of historical experiments, and the extension of recovered knowledge can increase scientific understanding. These activities can also play an important role in both science and history and philosophy of science education. In this paper I describe the implementation of an integrated learning project that I initiated, organized, and structured to complement a course in history and philosophy of the life sciences (HPLS). The (...)
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  26. Elias L. Khalil (1996). Organism and Organization. Biology and Philosophy 12 (1):119-126.
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  27. Nikolay P. Kolomiytsev & Nadezhda Ya Poddubnaya (2010). The Diffuse Organism as the First Biological System. Biological Theory 5 (1):67-78.
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  28. Dietmar Kültz, David F. Clayton, Gene E. Robinson, Craig Albertson, Hannah V. Carey, Molly E. Cummings, Ken Dewar, Scott V. Edwards, Hans A. Hofmann & Louis J. Gross (2013). New Frontiers for Organismal Biology. Bioscience 63 (6).
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  29. Manfred D. Laubichler & Gunter P. Wagner (2000). Organism and Character Decomposition: Steps Towards an Integrative Theory of Biology. Philosophy of Science 67 (3):300.
    In this paper we argue that an operational organism concept can help to overcome the structural deficiency of mathematical models in biology. In our opinion, the structural deficiency of mathematical models lies mainly in our inability to identify functionally relevant biological characters in biological systems, and not so much in a lack of adequate mathematical representations of biological processes. We argue that the problem of character identification in biological systems is linked to the question of a properly formulated organism concept. (...)
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  30. Ralph S. Lillie (1945). General Biology and Philosophy of Organism. Chicago, Ill.,University of Chicago Press.
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  31. James A. Marcum & Geert M. N. Verschuuren (1986). Hemostatic Regulation and Whitehead's Philosophy of Organism. Acta Biotheoretica 35 (1-2).
    Biology as a scientific discipline has relied heavily upon advances in chemistry and physics. An inherent danger in this relationship is the reduction of living phenomena to physico-chemical terms. Whitehead's Philosophy of Organism is utilized to examine current methodologies within biology and to evaluate their appropriateness for future research. Hemostatic regulation is employed to illustrate the applications of organistic concepts to biological research. It is concluded that understanding of living entities and their properties as well as possibly life itself will (...)
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  32. Johannes Martens (forthcoming). Organisms in Evolution. History and Philosophy of the Life Sciences.
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  33. Adolf Meyer-Abich (1955). Organismen AlS Holismen. Acta Biotheoretica 11 (2).
  34. Matteo Mossio & Alvaro Moreno (forthcoming). Organisational Closure in Biological Organisms. History and Philosophy of the Life Sciences.
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  35. Antonio Nunziante (2011). Continuity or Discontinuity? Some Remarks on Leibniz’s Concepts of ‘Substantia Vivens‘ and ‘Organism‘. In Ohad Nachtomy & Justin Smith (eds.), Corporeal Substances and Machines of Nature in Leibniz. springer.
    The doctrine of natural machines, of organisms, of composite substances, assumes a marked consistency in Leibniz starting from his mature years (let us say, from the publishing of New System in 1965 onwards). There is no doubt, therefore, that for a full explanation of the conceptual content of the reflection of Leibniz on the nature of living substances we must turn to the “classic” places in which it took form: from the letters to De Volder and Lady Masham of the (...)
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  36. Dieter Stefan Peters, Michael Weingarten & Michael T. Ghiselin (2000). Book Reviews-Organisms, Genes and Evolution. Evolutionary Theory at the Crossroads. History and Philosophy of the Life Sciences 22 (3):439-440.
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  37. Thomas Pradeu (2010). What is an Organism? An Immunological Answer. History and Philosophy of the Life Sciences 32.
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  38. Thomas Pradeu, What is an Organism?
    The question ‘What is an organism?’, formerly considered as essential in biology, has now been increasingly replaced by a larger question, ‘What is a biological individual?’. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...)
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  39. G. Ramsey (2013). Organisms, Traits, and Population Subdivisions: Two Arguments Against the Causal Conception of Fitness? British Journal for the Philosophy of Science 64 (3):589-608.
    A major debate in the philosophy of biology centers on the question of how we should understand the causal structure of natural selection. This debate is polarized into the causal and statistical positions. The main arguments from the statistical side are that a causal construal of the theory of natural selection's central concept, fitness, either (i) leads to inaccurate predictions about population dynamics, or (ii) leads to an incoherent set of causal commitments. In this essay, I argue that neither the (...)
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  40. Adam M. Reitzel, Joseph F. Ryan & Ann M. Tarrant (2012). Establishing a Model Organism: A Report From the First Annual Nematostella Meeting. Bioessays 34 (2):158-161.
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  41. Andrew Reynolds (2008). Amoebae as Exemplary Cells: The Protean Nature of an Elementary Organism. [REVIEW] Journal of the History of Biology 41 (2):307 - 337.
    In the nineteenth century protozoology and early cell biology intersected through the nexus of Darwin's theory of evolution. As single-celled organisms, amoebae offered an attractive focus of study for researchers seeking evolutionary relationships between the cells of humans and other animals, and their primitive appearance made them a favourite model for the ancient ancestor of all living things. Their resemblance to human and other metazoan cells made them popular objects of study among morphologists, physiologists, and even those investigating animal behaviour. (...)
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  42. Ruth G. Rinard (1981). The Problem of the Organic Individual: Ernst Haeckel and the Development of the Biogenetic Law. [REVIEW] Journal of the History of Biology 14 (2):249 - 275.
  43. A. Ritterbusch (1981). Komparative Aussagemuster in Bezug Zu Komplementären Und Enkaptischen Modellen der Morphologie. Acta Biotheoretica 30 (1).
    The unity of organisms can be viewed in terms of the concepts of enkapsis and complementarity. A model (or a type) represents those properties (of elements, structure, and system) which renders cases - the organisms under consideration — comparable. Comparability is established by operations (or metamorphoses) which relate a case to a model. Therefore, the model and the operations must be enumerated together, if a certain morphology is to be established and applied. Two models, which in some way are related, (...)
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  44. Chris Sinha (2006). Epigenetics, Semiotics, and the Mysteries of the Organism. Biological Theory 1 (2):112-115.
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  45. John Symons (2010). The Individuality of Artifacts and Organisms. History and Philosophy of the Life Sciences 32.
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  46. Alfred I. Tauber & Elias L. Khalil (1994). Organism and the Origins of Self. History and Philosophy of the Life Sciences 16 (2):355.
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  47. Georg Toepfer (2004). Zweckbegriff Und Organismus: Über Die Teleologische Beurteilung Biologischer Systeme. Königshausen & Neumann.
    Welche Rolle spielen die Begriffe des Zwecks und der Funktion für die Biologie und die Bestimmung ihres Grundbegriffs, des Organismus?
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  48. José-Leonel Torres & Lynn Trainor (2008). On Organism: Environment Buffers and Their Ecological Significance. Biology and Philosophy 23 (3):403-416.
    We consider, from a physical perspective, the case where the interface between an organism and its environment becomes large enough that it acts as a buffer regulating their matter and energy exchanges. We illustrate the physiological and evolutionary role of buffers through the example of lungfish estivation. Then we ponder the relevance of buffers of this kind to the quest for a general definition of concepts like niche construction, the extended phenotype, and related ones, whose meaning is conveyed at present (...)
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  49. Jack A. Wilson (2000). Ontological Butchery: Organism Concepts and Biological Generalizations. Philosophy of Science 67 (3):311.
    Biology lacks a central organism concept that unambiguously marks the distinction between organism and non-organism because the most important questions about organisms do not depend on this concept. I argue that the two main ways to discover useful biological generalizations about multicellular organization--the study of homology within multicellular lineages and of convergent evolution across lineages in which multicellularity has been independently established--do not require what would have to be a stipulative sharpening of an organism concept.
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  50. Charles T. Wolfe (2012). Chance Between Holism and Reductionism: Tensions in the Conceptualisation of Life. Progress in Biophysics and Molecular Biology.
    In debates between holism and reductionism in biology, from the early 20th century to more recent re-enactments involving genetic reductionism, developmental systems theory, or systems biology, the role of chance – the presence of theories invoking chance as a strong explanatory principle – is hardly ever acknowledged. Conversely, Darwinian models of chance and selection (Dennett 1995, Kupiec 1996, Kupiec 2009) sit awkwardly with reductionist and holistic concepts, which they alternately challenge or approve of. I suggest that the juxtaposition of chance (...)
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