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  1. Genidentity and Biological Processes.Thomas Pradeu - 2018 - In Daniel J. Nicholson & John Dupré (eds.), Everything Flows: Towards a Processual Philosophy of Biology. Oxford, United Kingdom: Oxford University Press.
    A crucial question for a process view of life is how to identify a process and how to follow it through time. The genidentity view can contribute decisively to this project. It says that the identity through time of an entity X is given by a well-identified series of continuous states of affairs. Genidentity helps address the problem of diachronic identity in the living world. This chapter describes the centrality of the concept of genidentity for David Hull and proposes an (...)
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  • Non-standard approaches to emergence: introduction to the special issue.Olivier Sartenaer & Umut Baysan - 2021 - Synthese 199 (3):7773-7776.
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  • Causal Explanation in Psychiatry.Tuomas K. Pernu - 2019 - In Bluhm Robyn & Tekin Serife (eds.), The Bloomsbury Companion to the Philosophy of Psychiatry. Bloomsbury.
  • Looking down, around, and up: Mechanistic explanation in psychology.William Bechtel - 2009 - Philosophical Psychology 22 (5):543-564.
    Accounts of mechanistic explanation have emphasized the importance of looking down—decomposing a mechanism into its parts and operations. Using research on visual processing as an exemplar, I illustrate how productive such research has been. But once multiple components of a mechanism have been identified, researchers also need to figure out how it is organized—they must look around and determine how to recompose the mechanism. Although researchers often begin by trying to recompose the mechanism in terms of sequential operations, they frequently (...)
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  • Part-whole science.Rasmus Grønfeldt Winther - 2011 - 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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  • Agents, Modeling Processes, and the Allure of Prophecy.William A. Griffin, Manfred D. Laubichler & Werner Callebaut - 2008 - Biological Theory 3 (1):73-78.
    Ioannidis [Why most published research findings are false. PLoS Med 2: e124 ] identifies six factors that contribute to explaining why most of the current published research findings are more likely to be false than true, and argues that for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this article, we argue that three “hot” areas in current biological research, viz., agent-based modeling, evolutionary developmental biology , and systems biology, are (...)
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  • Strong Emergence in Biological Systems: Is It Open to Mathematical Reasoning?Lars H. Wegner, Min Yu, Biao Wu, Jiayou Liu & Zhifeng Hao - 2021 - Acta Biotheoretica 69 (4):841-856.
    Complex, multigenic biological traits are shaped by the emergent interaction of proteins being the main functional units at the molecular scale. Based on a phenomenological approach, algorithms for quantifying two different aspects of emergence were introduced (Wegner and Hao in Progr Biophys Mol Biol 161:54–61, 2021) describing: (i) pairwise reciprocal interactions of proteins mutually modifying their contribution to a complex trait (denoted as weak emergence), and (ii) formation of a new, complex trait by a set of n ‘constitutive’ proteins at (...)
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  • Modelling Molecular Mechanisms: A Framework of Scientific Reasoning to Construct Molecular-Level Explanations for Cellular Behaviour.Marc H. W. van Mil, Dirk Jan Boerwinkel & Arend Jan Waarlo - 2013 - Science & Education 22 (1):93-118.
  • Towards a characterization of metaphysics of biology: metaphysics for and metaphysics in biology.Vanesa Triviño - 2022 - Synthese 200 (5):1-21.
    Since the last decades of the twentieth and the beginning of the twenty-first century, the use of metaphysics by philosophers when approaching conceptual problems in biology has increased. Some philosophers call this tendency in philosophy of biology ‘Metaphysics of Biology’. In this paper, I aim at characterizing Metaphysics of Biology by paying attention to the diverse ways philosophers use metaphysics when addressing conceptual problems in biology. I will claim that there are two different modes of doing Metaphysics of Biology, namely (...)
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  • Building Blocks in Search of a Theory: Primates and Philosophers: How Morality Evolved, Frans de Waal . Princeton, NJ: Princeton University Press, 2006, (209 pp; $22.95 hbk; ISBN 0691124477). [REVIEW]Tomislav Bracanović - 2007 - Biological Theory 2 (4):422-424.
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  • Complexity-based Theories of Emergence: Criticisms and Constraints.Kari L. Theurer - 2014 - International Studies in the Philosophy of Science 28 (3):277-301.
    In recent years, many philosophers of science have attempted to articulate a theory of non-epistemic emergence that is compatible with mechanistic explanation and incompatible with reductionism. The 2005 account of Fred C. Boogerd et al. has been particularly influential. They argued that a systemic property was emergent if it could not be predicted from the behaviour of less complex systems. Here, I argue that Boogerd et al.'s attempt to ground emergence in complexity guarantees that we will see emergence, but at (...)
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  • What is a hologenomic adaptation? Emergent individuality and inter-identity in multispecies systems.Javier Suárez & Vanessa Triviño - 2020 - Frontiers in Psychology 187 (11).
    Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...)
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  • Searching for General Principles in Cognitive Performance: Reply to Commentators.Damian G. Stephen & Guy Van Orden - 2012 - Topics in Cognitive Science 4 (1):94-102.
    The commentators expressed concerns regarding the relevance and value of non-computational non-symbolic explanations of cognitive performance. But what counts as an “explanation” depends on the pre-theoretical assumptions behind the scenes of empirical science regarding the kinds of variables and relationships that are sought out in the first place, and some of the present disagreements stem from incommensurate assumptions. Traditional cognitive science presumes cognition to be a decomposable system of components interacting according to computational rules to generate cognitive performances (i.e., component-dominant (...)
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  • Interactions dominate the dynamics of visual cognition.Damian G. Stephen & Daniel Mirman - 2010 - Cognition 115 (1):154-165.
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  • Emergence.Robert C. Richardson & Achim Stephan - 2007 - Biological Theory 2 (1):91-96.
  • Philosophy of biology, German styleReview of Ulrich Krohs and Georg Toepfer : Philosophie der Biologie: Eine Einführung [Philosophy of Biology: An Introduction].Thomas A. C. Reydon - 2007 - Biology and Philosophy 22 (4):619-626.
  • Towards a multi-level approach to the emergence of meaning processes in living systems.João Queiroz & Charbel Niño El-Hani - 2006 - Acta Biotheoretica 54 (3):179-206.
    Any description of the emergence and evolution of different types of meaning processes (semiosis, sensu C.S.Peirce) in living systems must be supported by a theoretical framework which makes it possible to understand the nature and dynamics of such processes. Here we propose that the emergence of semiosis of different kinds can be understood as resulting from fundamental interactions in a triadically-organized hierarchical process. To grasp these interactions, we develop a model grounded on Stanley Salthe's hierarchical structuralism. This model can be (...)
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  • The Limitations of Kim’s Reductive Physicalism in Accounting for Living Systems and an Alternative Nonreductionist Ontology.Slobodan Perovic - 2007 - Acta Biotheoretica 55 (3):243-267.
    Jaegwon Kim’s exclusion argument is a general ontological argument, applicable to any properties deemed supervenient on a microproperty basis, including biological properties. It implies that the causal power of any higher-level property must be reducible to the subset of the causal powers of its lower-level properties. Moreover, as Kim’s recent version of the argument indicates, a higher-level property can be causally efficient only to the extent of the efficiency of its micro-basis. In response, I argue that the ontology that aims (...)
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  • On Gene’s Action and Reciprocal Causation.Slobodan Perovic & Paul-Antoine Miquel - 2011 - Foundations of Science 16 (1):31-46.
    Advancing the reductionist conviction that biology must be in agreement with the assumptions of reductive physicalism (the upward hierarchy of causal powers, the upward fixing of facts concerning biological levels) A. Rosenberg argues that downward causation is ontologically incoherent and that it comes into play only when we are ignorant of the details of biological phenomena. Moreover, in his view, a careful look at relevant details of biological explanations will reveal the basic molecular level that characterizes biological systems, defined by (...)
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  • A Defense of Emergence.Jason Megill - 2013 - Axiomathes 23 (4):597-615.
    I defend a physicalistic version of ontological emergence; qualia emerge from the brain, but are physical properties nevertheless. First, I address the following questions: what are the central tenets of physicalistic ontological emergentism; what are the relationships between these tenets; what is the relationship between physicalistic ontological emergentism and non-reductive physicalism; and can there even be a physicalistic version of ontological emergentism? This discussion is merely an attempt to clarify exactly what a physicalistic version of ontological emergentism must claim, and (...)
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  • Mechanistic Explanation in Systems Biology: Cellular Networks.Dana Matthiessen - 2017 - British Journal for the Philosophy of Science 68 (1):1-25.
    It is argued that once biological systems reach a certain level of complexity, mechanistic explanations provide an inadequate account of many relevant phenomena. In this article, I evaluate such claims with respect to a representative programme in systems biological research: the study of regulatory networks within single-celled organisms. I argue that these networks are amenable to mechanistic philosophy without need to appeal to some alternate form of explanation. In particular, I claim that we can understand the mathematical modelling techniques of (...)
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  • Beyond free will: The embodied emergence of conscious agency.Michael F. Mascolo & Eeva Kallio - 2019 - Philosophical Psychology 32 (4):437-462.
    ABSTRACTIs it possible to reconcile the concept of conscious agency with the view that humans are biological creatures subject to material causality? The problem of conscious agency is complicated by the tendency to attribute autonomous powers of control to conscious processes. In this paper, we offer an embodied process model of conscious agency. We begin with the concept of embodied emergence – the idea that psychological processes are higher-order biological processes, albeit ones that exhibit emergent properties. Although consciousness, experience, and (...)
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  • Philosophies of particular biological research programs.Ulrich Krohs - 2006 - Biological Theory 1 (2):182-187.
    There is a trend within philosophy of biology to concentrate on questions that are strongly related to particular biological research programs rather than on the general scope of the field and its relation to other sciences. Projects of the latter kind, of course, are followed as well but will not be the topic of this review. Shifting the focus to particular research programs reflects philosophers’ increased interest in knowledge of, and contribution to, actual biological research, which is organized in such (...)
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  • In Search of Ontological Emergence: Diachronic, But Non-supervenient.Michael Kirchhoff - 2014 - Axiomathes 24 (1):89-116.
    Most philosophical accounts of emergence are based on supervenience, with supervenience being an ontologically synchronic relation of determination. This conception of emergence as a relation of supervenience, I will argue, is unable to make sense of the kinds of emergence that are widespread in self-organizing and nonlinear dynamical systems, including distributed cognitive systems. In these dynamical systems, an emergent property is ontological and diachronic.
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  • Toward Bridging the Mechanistic Gap Between Genes and Traits by Emphasizing the Role of Proteins in a Computational Environment.Michal Haskel-Ittah & Anat Yarden - 2017 - Science & Education 26 (10):1143-1160.
    Previous studies have shown that students often ignore molecular mechanisms when describing genetic phenomena. Specifically, students tend to directly link genes to their encoded traits, ignoring the role of proteins as mediators in this process. We tested the ability of 10th grade students to connect genes to traits through proteins, using concept maps and reasoning questions. The context of this study was a computational learning environment developed specifically to foster this ability. This environment presents proteins as the mechanism-mediating genetic phenomena. (...)
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  • Pluralization through epistemic competition: scientific change in times of data-intensive biology.Fridolin Gross, Nina Kranke & Robert Meunier - 2019 - History and Philosophy of the Life Sciences 41 (1):1.
    We present two case studies from contemporary biology in which we observe conflicts between established and emerging approaches. The first case study discusses the relation between molecular biology and systems biology regarding the explanation of cellular processes, while the second deals with phylogenetic systematics and the challenge posed by recent network approaches to established ideas of evolutionary processes. We show that the emergence of new fields is in both cases driven by the development of high-throughput data generation technologies and the (...)
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  • Equation or Algorithm: Differences and Choosing Between Them.C. Gaucherel & S. Bérard - 2010 - Acta Biotheoretica 59 (1):67-79.
    The issue of whether formal reasoning or a computing-intensive approach is the most efficient manner to address scientific questions is the subject of some considerable debate and pertains not only to the nature of the phenomena and processes investigated by scientists, but also the nature of the equation and algorithm objects they use. Although algorithms and equations both rely on a common background of mathematical language and logic, they nevertheless possess some critical differences. They do not refer to the same (...)
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  • Comments on William Bechtel's “Looking down, around, and up: Mechanistic explanation in psychology”.Denis Forest - 2009 - Philosophical Psychology 22 (5):565-573.
    The first part of this paper deals with the relations between mechanistic explanation and reduction. It is argued that there is no insuperable conflict between the two, but that the mechanistic framework adds requirements that are not acknowledged in the model of property reduction. The second part concerns the relations between organization and environmental factors. Internal organization may be so tightly linked to external context that both have to be considered together.
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  • The Causal Closure of Physics in Real World Contexts.George F. R. Ellis - 2020 - Foundations of Physics 50 (10):1057-1097.
    The causal closure of physics is usually discussed in a context free way. Here I discuss it in the context of engineering systems and biology, where strong emergence takes place due to a combination of upwards emergence and downwards causation. Firstly, I show that causal closure is strictly limited in terms of spatial interactions because these are cases that are of necessity strongly interacting with the environment. Effective Spatial Closure holds ceteris parabus, and can be violated by Black Swan Events. (...)
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  • Ins and outs of systems biology vis-à-vis molecular biology: Continuation or clear cut?Philippe De Backer, Danny De Waele & Linda Van Speybroeck - 2009 - Acta Biotheoretica 58 (1):15-49.
    The comprehension of living organisms in all their complexity poses a major challenge to the biological sciences. Recently, systems biology has been proposed as a new candidate in the development of such a comprehension. The main objective of this paper is to address what systems biology is and how it is practised. To this end, the basic tools of a systems biological approach are explored and illustrated. In addition, it is questioned whether systems biology ‘revolutionizes’ molecular biology and ‘transcends’ its (...)
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  • Toward a Philosophy of Systems Biology.Jonathan F. Davies & Maureen A. O’Malley - 2007 - Biological Theory 2 (4):420-422.
  • Top-down causation without top-down causes.Carl F. Craver & William Bechtel - 2007 - Biology and Philosophy 22 (4):547-563.
    We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...)
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  • Stuck in between. Phenomenology’s Explanatory Dilemma and its Role in Experimental Practice.Mark-Oliver Casper & Philipp Haueis - 2023 - Phenomenology and the Cognitive Sciences 22 (3):575-598.
    Questions about phenomenology’s role in non-philosophical disciplines gained renewed attention. While we claim that phenomenology makes indispensable, unique contributions to different domains of scientific practice such as concept formation, experimental design, and data collection, we also contend that when it comes to explanation, phenomenological approaches face a dilemma. Either phenomenological attempts to explain conscious phenomena do not satisfy a central constraint on explanations, i.e. the asymmetry between explanans and explanandum, or they satisfy this explanatory asymmetry only by largely merging with (...)
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  • Formalizing Biology.Werner Callebaut & Manfred D. Laubichler - 2008 - Biological Theory 3 (1):1-2.
    Ioannidis [Why most published research findings are false. PLoS Med 2: e124 ] identifies six factors that contribute to explaining why most of the current published research findings are more likely to be false than true, and argues that for many current scientific fields, claimed research findings may often be simply accurate measures of the prevailing bias. In this article, we argue that three “hot” areas in current biological research, viz., agent-based modeling, evolutionary developmental biology, and systems biology, are especially (...)
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  • Again, what the philosophy of biology is not.Werner Callebaut - 2005 - Acta Biotheoretica 53 (2):93-122.
    There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European (...)
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  • Getting over Atomism: Functional Decomposition in Complex Neural Systems.Daniel C. Burnston - 2021 - British Journal for the Philosophy of Science 72 (3):743-772.
    Functional decomposition is an important goal in the life sciences, and is central to mechanistic explanation and explanatory reduction. A growing literature in philosophy of science, however, has challenged decomposition-based notions of explanation. ‘Holists’ posit that complex systems exhibit context-sensitivity, dynamic interaction, and network dependence, and that these properties undermine decomposition. They then infer from the failure of decomposition to the failure of mechanistic explanation and reduction. I argue that complexity, so construed, is only incompatible with one notion of decomposition, (...)
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  • Systems biology and the integration of mechanistic explanation and mathematical explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):477-492.
    The paper discusses how systems biology is working toward complex accounts that integrate explanation in terms of mechanisms and explanation by mathematical models—which some philosophers have viewed as rival models of explanation. Systems biology is an integrative approach, and it strongly relies on mathematical modeling. Philosophical accounts of mechanisms capture integrative in the sense of multilevel and multifield explanations, yet accounts of mechanistic explanation have failed to address how a mathematical model could contribute to such explanations. I discuss how mathematical (...)
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  • Mechanistic Explanations and Models in Molecular Systems Biology.Fred C. Boogerd, Frank J. Bruggeman & Robert C. Richardson - 2013 - Foundations of Science 18 (4):725-744.
    Mechanistic models in molecular systems biology are generally mathematical models of the action of networks of biochemical reactions, involving metabolism, signal transduction, and/or gene expression. They can be either simulated numerically or analyzed analytically. Systems biology integrates quantitative molecular data acquisition with mathematical models to design new experiments, discriminate between alternative mechanisms and explain the molecular basis of cellular properties. At the heart of this approach are mechanistic models of molecular networks. We focus on the articulation and development of mechanistic (...)
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  • Uncoupling Mereology and Supervenience: A Dual Framework for Emergence and Downward Causation.Marta Bertolaso - 2017 - Axiomathes 27 (6):705-720.
    The philosophical discussion of emergence is often focused on properties of ‘wholes’ that are evaluated as emergent with respect to the properties of ‘parts’. Downward causation is, consequently, evaluated as some kind of causal influence of whole properties over parts properties. Yet, several important cases in scientific practice seem to be pursuing hypotheses of parts properties emerging from wholes properties, inverting the instinctive association of emergence with wholes. Furthermore, some areas of reflection which are very important for emergence, e.g., the (...)
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  • Philosophical and scientific perspectives on emergence.Hugues Bersini, Pasquale Stano, Pier Luigi Luisi & Mark A. Bedau - 2012 - Synthese 185 (2):165-169.
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  • Weak emergence drives the science, epistemology, and metaphysics of synthetic biology.Mark A. Bedau - 2013 - Biological Theory 8 (4):334-345.
    Top-down synthetic biology makes partly synthetic cells by redesigning simple natural forms of life, and bottom-up synthetic biology aims to make fully synthetic cells using only entirely nonliving components. Within synthetic biology the notions of complexity and emergence are quite controversial, but the imprecision of key notions makes the discussion inconclusive. I employ a precise notion of weak emergent property, which is a robust characteristic of the behavior of complex bottom-up causal webs, where a complex causal web is one that (...)
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  • Is weak emergence just in the mind?Mark A. Bedau - 2008 - Minds and Machines 18 (4):443-459.
    Weak emergence is the view that a system’s macro properties can be explained by its micro properties but only in an especially complicated way. This paper explains a version of weak emergence based on the notion of explanatory incompressibility and “crawling the causal web.” Then it examines three reasons why weak emergence might be thought to be just in the mind. The first reason is based on contrasting mere epistemological emergence with a form of ontological emergence that involves irreducible downward (...)
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  • Evo-devo: a science of dispositions.Christopher J. Austin - 2017 - European Journal for Philosophy of Science 7 (2):373-389.
    Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...)
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  • Evolutionary Developmental Biology and the Limits of Philosophical Accounts of Mechanistic Explanation.Ingo Brigandt - 2015 - In P.-A. Braillard & C. Malaterre (eds.), Explanation in Biology: An Enquiry into the Diversity of Explanatory Patterns in the Life Sciences. Springer. pp. 135-173.
    Evolutionary developmental biology (evo-devo) is considered a ‘mechanistic science,’ in that it causally explains morphological evolution in terms of changes in developmental mechanisms. Evo-devo is also an interdisciplinary and integrative approach, as its explanations use contributions from many fields and pertain to different levels of organismal organization. Philosophical accounts of mechanistic explanation are currently highly prominent, and have been particularly able to capture the integrative nature of multifield and multilevel explanations. However, I argue that evo-devo demonstrates the need for a (...)
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  • Strong Emergence and Freedom: Comment on A. Stephan.Max Kistler - 2010 - In Graham Macdonald & Cynthia Macdonald (eds.), Emergence in Mind. Oxford University Press. pp. 240--251.
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  • Complex biological mechanisms: Cyclic, oscillatory, and autonomous.William Bechtel & Adele Abrahamsen - unknown
    The mechanistic perspective has dominated biological disciplines such as biochemistry, physiology, cell and molecular biology, and neuroscience, especially during the 20th century. The primary strategy is reductionist: organisms are to be decomposed into component parts and operations at multiple levels. Researchers adopting this perspective have generated an enormous body of information about the mechanisms of life at scales ranging from the whole organism down to genetic and other molecular operations.
     
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  • Understanding Biological Mechanisms: Using Illustrations from Circadian Rhythm Research.William Bechtel - unknown
    In many fields of biology, researchers explain a phenomenon by characterizing the responsible mechanism. This requires identifying the candidate mechanism, decomposing it into its parts and operations, recomposing it so as to understand how it is organized and its operations orchestrated to generate the phenomenon, and situating it in its environment. Mechanistic researchers have developed sophisticated tools for decomposing mechanisms but new approaches, including modeling, are increasingly being invoked to recompose mechanisms when they involve nonsequential organization of nonlinear operations. The (...)
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  • Panpsychism and Causation: A New Argument and a Solution to the Combination Problem.Hedda Hassel Mørch - 2014 - Dissertation, Oslo
    Panpsychism is the view that every concrete and unified thing has some form of phenomenal consciousness or experience. It is an age-old doctrine, which, to the surprise of many, has recently taken on new life. In philosophy of mind, it has been put forth as a simple and radical solution to the mind–body problem (Chalmers 1996, 2003;Strawson 2006; Nagel 1979, 2012). In metaphysics and philosophy of science, it has been put forth as a solution to the problem of accounting for (...)
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  • 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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  • Downward determination.Charbel Niño El-Hani - 2005 - Abstracta 1 (2):162-192.
     
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