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  1. Coordinating Dissent as an Alternative to Consensus Classification: Insights From Systematics for Bio-Ontologies.Beckett Sterner, Joeri Witteveen & Nico Franz - 2020 - History and Philosophy of the Life Sciences 42 (1):1-25.
    The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on (...)
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  • Integrative Pluralism for Biological Function.Beckett Sterner & Samuel Cusimano - 2019 - Biology and Philosophy 34 (6):1-21.
    We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...)
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  • “Location” Incommensurability and “Replication” Indeterminacy: Clarifying an Entrenched Conflation by Using an Involved Approach.Ayelet Shavit - 2016 - Perspectives on Science 24 (4):425-442.
    This paper emerged from a decade of involvement in long-term bio-diversity surveys in places such as Yosemite Valley, Lassen National Park, New England Harvard Forest, and the Israeli Negev Desert. While actively engaged in the scientific work it was impossible not to notice the reoccurring discussions over how to replicate a survey to the same location. These two terms—“replication” and “location”—were necessary and basic for the scientists yet marginal in philosophical literature. The first two sections of this paper analyze the (...)
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  • Interdisciplinarities in Action: Cognitive Ethnography of Bioengineering Sciences Research Laboratories.Nancy J. Nersessian - 2019 - Perspectives on Science 27 (4):553-581.
    The paper frames interdisciplinary research as creating complex, distributed cognitive-cultural systems. It introduces and elaborates on the method of cognitive ethnography as a primary means for investigating interdisciplinary cognitive and learning practices in situ. The analysis draws from findings of nearly 20 years of investigating such practices in research laboratories in pioneering bioengineering sciences. It examines goals and challenges of two quite different kinds of integrative problem-solving practices: biomedical engineering and integrative systems biology. Practical lessons for facilitating research and learning (...)
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  • A Roadmap to Explanatory Pluralism: Introduction to the Topical Collection The Biology of Behaviour.Eric Muszynski & Christophe Malaterre - forthcoming - Synthese.
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  • Coordination Instead of Consensus Classification: Insights From Systematics for Bio-Ontologies.Beckett Sterner, Joeri Witteveen & Nico Franz - forthcoming - History and Philosophy of the Life Sciences.
    Big data is opening new angles on old questions about scientific progress. Is scientific knowledge cumulative? If yes, how does it make progress? In the life sciences, what we call the Consensus Principle has dominated the design of data discovery and integration tools: the design of a formal classificatory system for expressing a body of data should be grounded in consensus. Based on current approaches in biomedicine and systematic biology, we formulate and compare three types of the Consensus Principle: realist, (...)
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  • Information Quality, Data and Philosophy.Luciano Floridi & Phyllis Illari - 2014 - In Phyllis Illari & Luciano Floridi (eds.), The Philosophy of Information Quality. Switzerland: Springer International Publishing. pp. 5–23.
    In this opening chapter, we review the literature on information quality. Our major aim is to introduce the issues, and trace some of the history of the debates, with a view to situating the chapters in this volume – whose authors come from different disciplines – to help make them accessible to readers with different backgrounds and expertise. We begin in this section by tracing some influential analyses of IQ in computer science. This is a useful basis for examining some (...)
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  • Computational Construction of the Reality: Abstraction and Exploration-Driven Strategies in Constructing Protein–Protein Interfaces.Sim-Hui Tee - 2019 - Axiomathes 29 (3):311-328.
    Computational modeling is one of the primary approaches to constructing protein–protein interfaces in the laboratory. The algorithm-driven computational protein design has been successfully applied to the construction of functional proteins with improved binding affinity and increased thermostability. It is intriguing how a computational protein modeling approach can construct and shape the reality of new functional proteins from scratch. I articulate an account of abstraction and exploration-driven strategies in this computational endeavor. I aim to show that how a computational modelling approach, (...)
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  • Interdisciplinary Problem- Solving: Emerging Modes in Integrative Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2016 - European Journal for Philosophy of Science 6 (3):401-418.
    Integrative systems biology is an emerging field that attempts to integrate computation, applied mathematics, engineering concepts and methods, and biological experimentation in order to model large-scale complex biochemical networks. The field is thus an important contemporary instance of an interdisciplinary approach to solving complex problems. Interdisciplinary science is a recent topic in the philosophy of science. Determining what is philosophically important and distinct about interdisciplinary practices requires detailed accounts of problem-solving practices that attempt to understand how specific practices address the (...)
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  • Data Interpretation in the Digital Age.Sabina Leonelli - 2014 - Perspectives on Science 22 (3):397-417.
    Scientific knowledge production is currently affected by the dissemination of data on an unprecedented scale. Technologies for the automated production and sharing of vast amounts of data have changed the way in which data are handled and interpreted in several scientific domains, most notably molecular biology and biomedicine. In these fields, the activity of data gathering has become increasingly technology-driven, with machines such as next generation genome sequencers and mass spectrometers generating billions of data points within hours, and with little (...)
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  • Putting multidisciplinarity (back) on the map.Julie Mennes - 2020 - European Journal for Philosophy of Science 10 (2):1-23.
    The dominant theory of cross-disciplinarity represents multidisciplinarity as ‘lower’ or ‘less interesting’ than interdisciplinarity. In this paper, it is argued that this unfavorable representation of multidisciplinarity is ungrounded because it is an effect of the theory being incomplete. It is also explained that the unfavorable, ungrounded representation of multidisciplinarity is problematic: when someone adopts the dominant theory of cross-disciplinarity, the unfavorable representation supports the development of a preference for interdisciplinarity over multidisciplinarity. However, being ungrounded, the support the representation provides for (...)
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  • Unificatory Explanation.Marco J. Nathan - 2017 - British Journal for the Philosophy of Science 68 (1).
    Philosophers have traditionally addressed the issue of scientific unification in terms of theoretical reduction. Reductive models, however, cannot explain the occurrence of unification in areas of science where successful reductions are hard to find. The goal of this essay is to analyse a concrete example of integration in biology—the developmental synthesis—and to generalize it into a model of scientific unification, according to which two fields are in the process of being unified when they become explanatorily relevant to each other. I (...)
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  • Why the Current Insistence on Open Access to Scientific Data? Big Data, Knowledge Production, and the Political Economy of Contemporary Biology.Sabina Leonelli - 2013 - Bulletin of Science, Technology and Society 33 (1-2):6-11.
    The collection and dissemination of data on human and nonhuman organisms has become a central feature of 21st-century biology and has been endorsed by funding agencies in the United States and Europe as crucial to translating biological research into therapeutic and agricultural innovation. Large molecular data sets, often referred to as “big data,” are increasingly incorporated into digital databases, many of which are freely accessible online. These data have come to be seen as resources that play a key role in (...)
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  • The Causal Nature of Modeling with Big Data.Wolfgang Pietsch - 2016 - Philosophy and Technology 29 (2):137-171.
    I argue for the causal character of modeling in data-intensive science, contrary to widespread claims that big data is only concerned with the search for correlations. After discussing the concept of data-intensive science and introducing two examples as illustration, several algorithms are examined. It is shown how they are able to identify causal relevance on the basis of eliminative induction and a related difference-making account of causation. I then situate data-intensive modeling within a broader framework of an epistemology of scientific (...)
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  • Wprowadzenie: Ontologie poznawcze i jednorodność nauk poznawczych.Przemysław Nowakowski - 2016 - Avant: Trends in Interdisciplinary Studies 7 (3):71-73.
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  • Grand Challenges and Small Steps. Introduction to the Special Issue 'Interdisciplinary Integration: The Real Grand Challenge for the Life Sciences?'.Giovanni De Grandis & Sophia Efstathiou - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 56:39-47.
    This collection addresses two different audiences: 1) historians and philosophers of the life sciences reflecting on collaborations across disciplines, especially as regards defining and addressing Grand Challenges; 2) researchers and other stakeholders involved in cross-disciplinary collaborations aimed at tackling Grand Challenges in the life and medical sciences. The essays collected here offer ideas and resources both for the study and for the practice of goal-driven cross-disciplinary research in the life and medical sciences. We organise this introduction in three sections. The (...)
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  • Robustness, Evidence, and Uncertainty: An Exploration of Policy Applications of Robustness Analysis.Nicolas Wüthrich - unknown
    Policy-makers face an uncertain world. One way of getting a handle on decision-making in such an environment is to rely on evidence. Despite the recent increase in post-fact figures in politics, evidence-based policymaking takes centre stage in policy-setting institutions. Often, however, policy-makers face large volumes of evidence from different sources. Robustness analysis can, prima facie, handle this evidential diversity. Roughly, a hypothesis is supported by robust evidence if the different evidential sources are in agreement. In this thesis, I strengthen the (...)
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  • Practical Integration: The Art of Balancing Values, Institutions and Knowledge. Lessons From the History of British Public Health and Town Planning.Giovanni De Grandis - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 56:92-105.
    The paper uses two historical examples, public health (1840-1880) and town planning (1945-1975) in Britain, to analyse the challenges faced by goal-driven research, an increasingly important trend in science policy, as exemplified by the prominence of calls for addressing Grand Challenges. Two key points are argued. (1) Given that the aim of research addressing social or global problems is to contribute to improving things, this research should include all the steps necessary to bring science and technology to fruition. This need (...)
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  • The Resisted Rise of Randomisation in Experimental Design: British Agricultural Science, C.1910–1930.Dominic Berry - 2015 - History and Philosophy of the Life Sciences 37 (3):242-260.
    The most conspicuous form of agricultural experiment is the field trial, and within the history of such trials, the arrival of the randomised control trial is considered revolutionary. Originating with R.A. Fisher within British agricultural science in the 1920s and 30s, the RCT has since become one of the most prodigiously used experimental techniques throughout the natural and social sciences. Philosophers of science have already scrutinised the epistemological uniqueness of RCTs, undermining their status as the ‘gold standard’ in experimental design. (...)
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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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  • EvoDevo as a Motley Aggregation: Local Integration and Conflicting Views of Genes During the 1980s.Yoshinari Yoshida & Hisashi Nakao - 2015 - Biological Theory 10 (2):156-166.
    Although there are many historical and philosophical analyses of evolutionary developmental biology (EvoDevo), its development in the 1980s, when many individual or collective attempts to synthesize evolution and development were made, has not been examined in detail. This article focuses on some interdisciplinary studies during the 1980s and argues that they had important characteristics that previous historical and philosophical work has not recognized. First, we clarify how each set of studies from the 1980s integrated the results or approaches from different (...)
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  • Coordinated Pluralism as a Means to Facilitate Integrative Taxonomies of Cognition.Jacqueline Anne Sullivan - 2017 - Philosophical Explorations 20 (2):129-145.
    The past decade has witnessed a growing awareness of conceptual and methodological hurdles within psychology and neuroscience that must be addressed for taxonomic and explanatory progress in understanding psychological functions to be possible. In this paper, I evaluate several recent knowledge-building initiatives aimed at overcoming these obstacles. I argue that while each initiative offers important insights about how to facilitate taxonomic and explanatory progress in psychology and neuroscience, only a “coordinated pluralism” that incorporates positive aspects of each initiative will have (...)
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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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  • On the Nature of Cross-Disciplinary Integration: A Philosophical Framework.Michael O'Rourke, Stephen Crowley & Chad Gonnerman - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 56:62-70.
    Meeting grand challenges requires responses that constructively combine multiple forms of expertise, both academic and non-academic; that is, it requires cross-disciplinary integration. But just what is cross-disciplinary integration? In this paper, we supply a preliminary answer by reviewing prominent accounts of cross-disciplinary integration from two literatures that are rarely brought together: cross-disciplinarity and philosophy of biology. Reflecting on similarities and differences in these accounts, we develop a framework that integrates their insights—integration as a generic combination process the details of which (...)
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