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  1. Alexey Alyushin (2010). Time Scales of Observation and Ontological Levels of Reality. Axiomathes 20 (4):439-460.
    My goal is to conceive how the reality would look like for hypothetical creatures that supposedly perceive on time scales much faster or much slower than that of us humans. To attain the goal, I propose modelling in two steps. At step one, we have to single out a unified parameter that sets time scale of perception. Changing substantially the value of the parameter would mean changing scale. I argue that the required parameter is duration of discrete perceptive frames, or (...)
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  2. Kevin S. Amidon (2008). Adolf Meyer-Abich, Holism, and the Negotiation of Theoretical Biology. Biological Theory 3 (4):357-370.
  3. Larry Arnhart (2007). The Behavioral Sciences Are Historical Sciences of Emergent Complexity. Behavioral and Brain Sciences 30 (1):18-19.
    Unlike physics and chemistry, the behavioral sciences are historical sciences that explain the fuzzy complexity of social life through historical narratives. Unifying the behavioral sciences through evolutionary game theory would require a nested hierarchy of three kinds of historical narratives: natural history, cultural history, and biographical history. (Published Online April 27 2007).
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  4. Pierre Auger & Jean-Christophe Poggiale (1996). Aggregation and Emergence in Hierarchically Organized Systems: Population Dynamics. Acta Biotheoretica 44 (3-4).
    The aim of this work is to present aggregation methods of hierarchically organized systems allowing one to replace the initial micro-system by a macro-system described by a few global variables. We also study the relations between the fast micro-dynamics and the slow macro-dynamics which can produce global properties. Emergence corresponds to a bottom-up coupling that is the result effected by a micro-level at a macro-level. As an example, we present prey-predator models with different time scales in an heterogeneous environment. A (...)
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  5. 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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  6. E. Bernard-Weil (1995). Self-Organization and Emergence Are Some Irrelevant Concepts Without Their Association with the Concepts of Hetero-Organization and Immergence. Acta Biotheoretica 43 (4).
    There are many reasons for questioning the relevance of the concepts of self-organization (SO) and emergence. By studying three types of SO, respectively related to ontogeny, phylogeny and formalized models, we show that we always have to suppose an associated hetero-organization and preconceived immergence, unconsciously present in the authors mind. In order to understand how these unusual couples are working, they must be considered as agonistic antagonistic couples. Heteroorganization and immergence put constraints on the system so that SO and emergence (...)
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  7. F. C. Boogerd, F. J. Bruggeman, Robert C. Richardson, Achim Stephan & H. Westerhoff (2005). Emergence and Its Place in Nature: A Case Study of Biochemical Networks. Synthese 145 (1):131 - 164.
    We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...)
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  8. Jerry L. R. Chandler & Gertrudis van de Vijver (eds.) (2000). Closure: Emergent Organizations and Their Dynamics. New York Academy of Sciences.
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  9. Bernard Feltz (ed.) (2006). Self-Organization and Emergence in Life Sciences (Synthese Library, Volume 331). Dordrecht: Springer.
    Historical aspects of the issue are also broached. Intuitions relative to self-organization can be found in the works of such key Western philosophical figures as Aristotle, Leibniz and Kant. Interacting with more recent authors and cybernetics, self-organization represents a notion in keeping with the modern world’s discovery of radical complexity. The themes of teleology and emergence are analyzed by philosophers of sciences with regards to the issues of modelization and scientific explanation. (publisher, edited).
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  10. Amit Hagar, Review of M. Thalos' "Without Hierarchy" (OUP 2012).
  11. Oren Harman & Stephen Grand (2013). On Modeling Emergence. Biological Theory 8 (1):7-14.
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  12. Philippe Huneman, Review Of: Biological Emergences. Evolution by Natural Experiment. [REVIEW]
    This extensive book may be the most complete synthesis of various criticisms of neo-Darwinian ideas stemming from distinct research traditions that, although steeped in the past, have received new attention in the last decade. The criticisms are used to build an alternative to neo-Darwinism by contesting its core claim; that is, natural selection is the cause of evolution.
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  13. Christophe Malaterre (2011). Making Sense of Downward Causation in Manipulationism (with Illustrations From Cancer Research). History and Philosophy of the Life Sciences (33):537-562.
    Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998). For others, the causes of cancer are to be found not at the molecular level but at the tissue level where carcinogenesis consists of disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein and Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. Adopting a manipulationist account of causation (...)
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  14. Christophe Malaterre (2010). Les origines de la vie : émergence ou explication réductive ? Hermann.
    La vie est-elle un phénomène émergent ? Traduit-elle l'apparition de propriétés nouvelles au niveau d'un tout, qui seraient irréductibles aux propriétés et à l'organisation des composants de ce tout, ou encore imprédictibles à partir de ces mêmes éléments ? Développées à la charnière des XIXe et XXe siècles comme alternative aux deux approches antinomiques du vivant que sont le vitalisme et le mécanisme, la notion philosophique d'émergence connait aujourd'hui de nouveaux développements : avec la prise de conscience de la complexité (...)
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  15. Christophe Malaterre (2009). Are Self-Organizing Biochemical Networks Emergent? In Maryvonne Gérin & Marie-Christine Maurel (eds.), Origins of Life: Self-Organization and/or Biological Evolution? EDP Sciences. 117--123.
    Biochemical networks are often called upon to illustrate emergent properties of living systems. In this contribution, I question such emergentist claims by means of theoretical work on genetic regulatory models and random Boolean networks. If the existence of a critical connectivity Kc of such networks has often been coined “emergent” or “irreducible”, I propose on the contrary that the existence of a critical connectivity Kc is indeed mathematically explainable in network theory. This conclusion also applies to many other types of (...)
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  16. Alfredo Pérez Martínez (2009). Emergence : Between Reductive and Non Reductive Explanations : Does It Make Sense? In González Recio & José Luis (eds.), Philosophical Essays on Physics and Biology. G. Olms.
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  17. Addy Pross (2012). What is Life?: How Chemistry Becomes Biology. Oxford University Press.
    Livings things are so very strange -- The quest for a theory of life -- Understanding 'understanding' -- Stability and instability -- The knotty origin of life problem -- Biology's crisis of identity -- Biology is chemistry -- What is life?
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  18. Robert C. Richardson & Achim Stephan (2007). Emergence. Biological Theory 2 (1):91-96.
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  19. Lynn Rothschild (2006). The Role of Emergence in Biology. In Philip Clayton & Paul Sheldon Davies (eds.), The Re-Emergence of Emergence. Oxford University Press. 151--165.
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  20. Benton M. Stidd & David L. Wade (1995). Is Species Selection Dependent Upon Emergent Characters? Biology and Philosophy 10 (1):55-76.
    The architects of punctuated equilibrium and species selection as well as more recent workers (Vrba) have narrowed the original formulation of species selection and made it dependent upon so-called emergent characters. One criticism of this narrow version is the dearth of emergent characters with a consequent diminution in the robustness of species selection as an important evolutionary process. We argue that monomorphic species characters may at times be the focus of selection and that under these circumstances selection at the organism (...)
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  21. Paul Thompson (2003). The Revival of 'Emergence' in Biology. Croatian Journal of Philosophy 3 (3):217-229.
    Holism and emergence are coherent notions. The paper points to the classes of emergent phenomena -- such as autocatalysis -- that are taken as commonplace phenomena in biological sciences. Thus it questions the Democritean credo, “wholes are completely determined by their parts” (in some of its forms, called mereological determinism), that has become a dogma of contemporary philosophy. A living thing requires the ability to initiate, mediate and terminate processes that produce products that make up the whole. Autocatalysis is one (...)
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  22. Franck Varenne (2008). Émergences par les règles sans « formes de vie » une relecture de Kripke (1982) pour la simulation informatique du vivant. Noesis 14:201-236.
    Cet article ne se veut pas un commentaire suivi de la réflexion de Wittgenstein sur les règles. Ce ne sera pas non plus un commentaire de l’interprétation que Kripke fait du « suivi de la règle » chez Wittgenstein. Il ne sera pas davantage une application des thèses de Wittgenstein ni une tentative d’application directe d’une interprétation de ces thèses à l’épistémologie de la simulation du vivant ; ce qui serait, en soi, d’ailleurs contestable. Ce travail vise seulement à approfondir (...)
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  23. Agustin Vicente (2013). Where to Look for Emergent Properties. International Studies in the Philosophy of Science 27 (137):156.
    Recent years have seen renewed interest in the emergence issue. The contemporary debate, in contrast with that of past times, has to do not so much with the mind–body problem as with the relationship between the physical and other domains; mostly with the biological domain. One of the main sources of this renewed interest is the study of complex and, in general, far-from-equilibrium self-preserving systems, which seem to fulfil one of the necessary conditions for an entity to be emergent; namely, (...)
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  24. Bruce H. Weber (1999). Irreducible Complexity and the Problem of Biochemical Emergence. Biology and Philosophy 14 (4):593-605.
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  25. Rasmus Grønfeldt Winther (2013). Evo-Devo as a Trading Zone. In Alan Love (ed.), Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Springer Verlag, Boston Studies in the Philosophy of Science.
    Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...)
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  26. Rasmus Grønfeldt Winther (2011). Part-Whole Science. Synthese 178 (3):397-427.
    A scientific explanatory project, part-whole explanation, and a kind of science, part-whole science are premised on identifying, investigating, and using parts and wholes. In the biological sciences, mechanistic, structuralist, and historical explanations are part-whole explanations. Each expresses different norms, explananda, and aims. Each is associated with a distinct partitioning frame for abstracting kinds of parts. These three explanatory projects can be complemented in order to provide an integrative vision of the whole system, as is shown for a detailed case study: (...)
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  27. Rasmus Grønfeldt Winther (2008). Systemic Darwinism. Proceedings of the National Academy of Sciences 105 (33):11833-11838.
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