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  1. Re-engineering philosophy for limited beings: piecewise approximations to reality.William C. Wimsatt - 2007 - Cambridge: Harvard University Press.
    This book offers a philosophy for error-prone humans trying to understand messy systems in the real world.
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  • (1 other version)Explaining the brain: mechanisms and the mosaic unity of neuroscience.Carl F. Craver - 2007 - New York : Oxford University Press,: Oxford University Press, Clarendon Press.
    Carl Craver investigates what we are doing when we sue neuroscience to explain what's going on in the brain.
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  • Beyond reduction and pluralism: Toward an epistemology of explanatory integration in biology.Ingo Brigandt - 2010 - Erkenntnis 73 (3):295-311.
    The paper works towards an account of explanatory integration in biology, using as a case study explanations of the evolutionary origin of novelties-a problem requiring the integration of several biological fields and approaches. In contrast to the idea that fields studying lower level phenomena are always more fundamental in explanations, I argue that the particular combination of disciplines and theoretical approaches needed to address a complex biological problem and which among them is explanatorily more fundamental varies with the problem pursued. (...)
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  • Reductionism in Biology.Ingo Brigandt & Alan Love - 2008 - The Stanford Encyclopedia of Philosophy.
    Reductionism encompasses a set of ontological, epistemological, and methodological claims about the relation of different scientific domains. The basic question of reduction is whether the properties, concepts, explanations, or methods from one scientific domain (typically at higher levels of organization) can be deduced from or explained by the properties, concepts, explanations, or methods from another domain of science (typically one about lower levels of organization). Reduction is germane to a variety of issues in philosophy of science, including the structure of (...)
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  • Beyond the genome: community-level analysis of the microbial world.Iratxe Zarraonaindia, Daniel P. Smith & Jack A. Gilbert - 2013 - Biology and Philosophy 28 (2):261-282.
    The development of culture-independent strategies to study microbial diversity and function has led to a revolution in microbial ecology, enabling us to address fundamental questions about the distribution of microbes and their influence on Earth’s biogeochemical cycles. This article discusses some of the progress that scientists have made with the use of so-called “omic” techniques (metagenomics, metatranscriptomics, and metaproteomics) and the limitations and major challenges these approaches are currently facing. These ‘omic methods have been used to describe the taxonomic structure (...)
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  • Mechanism and Biological Explanation.William Bechtel - 2011 - Philosophy of Science 78 (4):533-557.
    This article argues that the basic account of mechanism and mechanistic explanation, involving sequential execution of qualitatively characterized operations, is itself insufficient to explain biological phenomena such as the capacity of living organisms to maintain themselves as systems distinct from their environment. This capacity depends on cyclic organization, including positive and negative feedback loops, which can generate complex dynamics. Understanding cyclically organized mechanisms with complex dynamics requires coordinating research directed at decomposing mechanisms into parts and operations with research using computational (...)
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  • Local Ecological Communities.Kim Sterelny - 2006 - Philosophy of Science 73 (2):215-231.
    A phenomenological community is an identifiable assemblage of organisms in a local habitat patch: a local wetland or mudflat are typical examples. Such communities are typically persistent: membership and abundance stay fairly constant over time. In this paper I discuss whether phenomenological communities are functionally structured, causal systems that play a role in determining the presence and abundance of organisms in a local habitat patch. I argue they are not, if individualist models of community assembly are vindicated; i.e., if the (...)
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  • Explaining evolutionary innovations and novelties: Criteria of explanatory adequacy and epistemological prerequisites.Alan C. Love - 2008 - Philosophy of Science 75 (5):874-886.
    It is a common complaint that antireductionist arguments are primarily negative. Here I describe an alternative nonreductionist epistemology based on considerations taken from multidisciplinary research in biology. The core of this framework consists in seeing investigation as coordinated around sets of problems (problem agendas) that have associated criteria of explanatory adequacy. These ideas are developed in a case study, the explanation of evolutionary innovations and novelties, which demonstrates the applicability and fruitfulness of this nonreductionist epistemological perspective. This account also bears (...)
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  • Integrative pluralism.Sandra D. Mitchell - 2002 - Biology and Philosophy 17 (1):55-70.
    The `fact' of pluralism in science is nosurprise. Yet, if science is representing andexplaining the structure of the oneworld, why is there such a diversity ofrepresentations and explanations in somedomains? In this paper I consider severalphilosophical accounts of scientific pluralismthat explain the persistence of bothcompetitive and compatible alternatives. PaulSherman's `Levels of Analysis' account suggeststhat in biology competition betweenexplanations can be partitioned by the type ofquestion being investigated. I argue that thisaccount does not locate competition andcompatibility correctly. I then defend anintegrative (...)
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  • Simulation and Similarity: Using Models to Understand the World.Michael Weisberg - 2013 - New York, US: Oxford University Press.
    one takes to be the most salient, any pair could be judged more similar to each other than to the third. Goodman uses this second problem to showthat there can be no context-free similarity metric, either in the trivial case or in a scientifically ...
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  • Aspects of Reductive Explanation in Biological Science: Intrinsicality, Fundamentality, and Temporality.Andreas Hüttemann & Alan C. Love - 2011 - British Journal for the Philosophy of Science 62 (3):519-549.
    The inapplicability of variations on theory reduction in the context of genetics and their irrelevance to ongoing research has led to an anti-reductionist consensus in philosophy of biology. One response to this situation is to focus on forms of reductive explanation that better correspond to actual scientific reasoning (e.g. part–whole relations). Working from this perspective, we explore three different aspects (intrinsicality, fundamentality, and temporality) that arise from distinct facets of reductive explanation: composition and causation. Concentrating on these aspects generates new (...)
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  • The Downs and Ups of Mechanistic Research: Circadian Rhythm Research as an Exemplar. [REVIEW]William Bechtel - 2010 - Erkenntnis 73 (3):313 - 328.
    In the context of mechanistic explanation, reductionistic research pursues a decomposition of complex systems into their component parts and operations. Using research on the mechanisms responsible for circadian rhythms, I consider both the gains that have been made by discovering genes and proteins that figure in these intracellular oscillators and also highlight the increasingly recognized need to understand higher-level integration, both between cells in the central oscillator and between the central and peripheral oscillators. This history illustrates a common need to (...)
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  • When one model is not enough: Combining epistemic tools in systems biology.Sara Green - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (2):170-180.
    In recent years, the philosophical focus of the modeling literature has shifted from descriptions of general properties of models to an interest in different model functions. It has been argued that the diversity of models and their correspondingly different epistemic goals are important for developing intelligible scientific theories. However, more knowledge is needed on how a combination of different epistemic means can generate and stabilize new entities in science. This paper will draw on Rheinberger’s practice-oriented account of knowledge production. The (...)
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  • Microbes modeling ontogeny.Alan C. Love & Michael Travisano - 2013 - Biology and Philosophy 28 (2):161-188.
    Model organisms are central to contemporary biology and studies of embryogenesis in particular. Biologists utilize only a small number of species to experimentally elucidate the phenomena and mechanisms of development. Critics have questioned whether these experimental models are good representatives of their targets because of the inherent biases involved in their selection (e.g., rapid development and short generation time). A standard response is that the manipulative molecular techniques available for experimental analysis mitigate, if not counterbalance, this concern. But the most (...)
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  • Understanding endogenously active mechanisms: A scientific and philosophical challenge. [REVIEW]William Bechtel - 2012 - European Journal for Philosophy of Science 2 (2):233-248.
    Abstract Although noting the importance of organization in mechanisms, the new mechanistic philosophers of science have followed most biologists in focusing primarily on only the simplest mode of organization in which operations are envisaged as occurring sequentially. Increasingly, though, biologists are recognizing that the mechanisms they confront are non-sequential and the operations nonlinear. To understand how such mechanisms function through time, they are turning to computational models and tools of dynamical systems theory. Recent research on circadian rhythms addressing both intracellular (...)
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  • Systems biology and the integration of mechanistic explanation and mathematical explanation.Ingo Brigandt - 2013 - Studies in History and Philosophy of Science Part C: 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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  • Re-Engineering Philosophy for Limited Beings. Piecewise Approximations to Reality.William C. Wimsatt - 2010 - Critica 42 (124):108-117.
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  • The roles of integration in molecular systems biology.Maureen A. O’Malley & Orkun S. Soyer - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):58-68.
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  • Integration in biology: Philosophical perspectives on the dynamics of interdisciplinarity.Ingo Brigandt - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):461-465.
    This introduction to the special section on integration in biology provides an overview of the different contributions. In addition to motivating the philosophical significance of analyzing integration and interdisciplinary research, I lay out common themes and novel insights found among the special section contributions, and indicate how they exhibit current trends in the philosophical study of integration. One upshot of the contributed papers is that there are different aspects to and kinds of integration, so that rather than attempting to offer (...)
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  • Explanation in Biology: Reduction, Pluralism, and Explanatory Aims.Ingo Brigandt - 2011 - Science & Education 22 (1):69-91.
    This essay analyzes and develops recent views about explanation in biology. Philosophers of biology have parted with the received deductive-nomological model of scientific explanation primarily by attempting to capture actual biological theorizing and practice. This includes an endorsement of different kinds of explanation (e.g., mathematical and causal-mechanistic), a joint study of discovery and explanation, and an abandonment of models of theory reduction in favor of accounts of explanatory reduction. Of particular current interest are philosophical accounts of complex explanations that appeal (...)
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  • Relations among fields: Mendelian, cytological and molecular mechanisms.Lindley Darden - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (2):349-371.
    Philosophers have proposed various kinds of relations between Mendelian genetics and molecular biology: reduction, replacement, explanatory extension. This paper argues that the two fields are best characterized as investigating different, serially integrated, hereditary mechanisms. The mechanisms operate at different times and contain different working entities. The working entities of the mechanisms of Mendelian heredity are chromosomes, whose movements serve to segregate alleles and independently assort genes in different linkage groups. The working entities of numerous mechanisms of molecular biology are larger (...)
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  • Towards philosophical foundations of Systems Biology: introduction.Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff - 2007 - In Fred C. Boogerd, Frank J. Bruggeman, Jan-Hendrik S. Hofmeyr & Hans V. Westerhoff (eds.), Systems Biology: Philosophical Foundations. Boston: Elsevier.
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  • Calibrating and constructing models of protein folding.Jeffry L. Ramsey - 2007 - Synthese 155 (3):307-320.
    Prediction is more than testing established theory by examining whether the prediction matches the data. To show this, I examine the practices of a community of scientists, known as threaders, who are attempting to predict the final, folded structure of a protein from its primary structure, i.e., its amino acid sequence. These scientists employ a careful and deliberate methodology of prediction. A key feature of the methodology is calibration. They calibrate in order to construct better models. The construction leads to (...)
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  • Viral information.Forest Rohwer & Katie Barott - 2013 - Biology and Philosophy 28 (2):283-297.
    Viruses are major drivers of global biogeochemistry and the etiological agents of many diseases. They are also the winners in the game of life: there are more viruses on the planet than cellular organisms and they encode most of the genetic diversity on the planet. In fact, it is reasonable to view life as a viral incubator. Nevertheless, most ecological and evolutionary theories were developed, and continue to be developed, without considering the virosphere. This means these theories need to be (...)
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  • From molecules to dynamic biological communities.Daniel McDonald, Yoshiki Vázquez-Baeza, William A. Walters, J. Gregory Caporaso & Rob Knight - 2013 - Biology and Philosophy 28 (2):241-259.
    Microbial ecology is flourishing, and in the process, is making contributions to how the ecology and biology of large organisms is understood. Ongoing advances in sequencing technology and computational methods have enabled the collection and analysis of vast amounts of molecular data from diverse biological communities. While early studies focused on cataloguing microbial biodiversity in environments ranging from simple marine ecosystems to complex soil ecologies, more recent research is concerned with community functions and their dynamics over time. Models and concepts (...)
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