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  1. Causal Concepts in Biology: How Pathways Differ from Mechanisms and Why It Matters.Lauren N. Ross - 2021 - British Journal for the Philosophy of Science 72 (1):131-158.
    In the last two decades few topics in philosophy of science have received as much attention as mechanistic explanation. A significant motivation for these accounts is that scientists frequently use the term “mechanism” in their explanations of biological phenomena. While scientists appeal to a variety of causal concepts in their explanations, many philosophers argue or assume that all of these concepts are well understood with the single notion of mechanism. This reveals a significant problem with mainstream mechanistic accounts– although philosophers (...)
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  • Molecular pathways and the contextual explanation of molecular functions.Giovanni Boniolo & Raffaella Campaner - 2018 - Biology and Philosophy 33 (3-4):24.
    Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...)
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  • What was Hodgkin and Huxley’s Achievement?Arnon Levy - 2013 - British Journal for the Philosophy of Science 65 (3):469-492.
    The Hodgkin–Huxley (HH) model of the action potential is a theoretical pillar of modern neurobiology. In a number of recent publications, Carl Craver ([2006], [2007], [2008]) has argued that the model is explanatorily deficient because it does not reveal enough about underlying molecular mechanisms. I offer an alternative picture of the HH model, according to which it deliberately abstracts from molecular specifics. By doing so, the model explains whole-cell behaviour as the product of a mass of underlying low-level events. The (...)
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  • The Experimenter's Museum: GenBank, Natural History, and the Moral Economies of Biomedicine.Bruno J. Strasser - 2011 - Isis 102 (1):60-96.
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  • Towards a Notion of Intervention in Big-Data Biology and Molecular Medicine.Emanuele Ratti & Federico Boem - 2016 - In Marco Nathan & Giovanni Boniolo (eds.), Foundational Issues in Molecular Medicine. Routledge.
    We claim that in contemporary studies in molecular biology and biomedicine, the nature of ‘manipulation’ and ‘intervention’ has changed. Traditionally, molecular biology and molecular studies in medicine are considered experimental sciences, whereas experiments take the form of material manipulation and intervention. On the contrary “big science” projects in biology focus on the practice of data mining of biological databases. We argue that the practice of data mining is a form of intervention although it does not require material manipulation. We also (...)
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  • A History of Molecular Biology.Michel Morange & Matthew Cobb - 1999 - Journal of the History of Biology 32 (3):568-570.
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  • Scientific understanding: truth or dare?Henk W. de Regt - 2015 - Synthese 192 (12):3781-3797.
    It is often claimed—especially by scientific realists—that science provides understanding of the world only if its theories are (at least approximately) true descriptions of reality, in its observable as well as unobservable aspects. This paper critically examines this ‘realist thesis’ concerning understanding. A crucial problem for the realist thesis is that (as study of the history and practice of science reveals) understanding is frequently obtained via theories and models that appear to be highly unrealistic or even completely fictional. So we (...)
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  • State of the Field: Why novel prediction matters.Heather Douglas & P. D. Magnus - 2013 - Studies in History and Philosophy of Science Part A 44 (4):580-589.
    There is considerable disagreement about the epistemic value of novel predictive success, i.e. when a scientist predicts an unexpected phenomenon, experiments are conducted, and the prediction proves to be accurate. We survey the field on this question, noting both fully articulated views such as weak and strong predictivism, and more nascent views, such as pluralist reasons for the instrumental value of prediction. By examining the various reasons offered for the value of prediction across a range of inferential contexts , we (...)
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  • The Instrumental Value of Explanations.Tania Lombrozo - 2011 - Philosophy Compass 6 (8):539-551.
    Scientific and ‘intuitive’ or ‘folk’ theories are typically characterized as serving three critical functions: prediction, explanation, and control. While prediction and control have clear instrumental value, the value of explanation is less transparent. This paper reviews an emerging body of research from the cognitive sciences suggesting that the process of seeking, generating, and evaluating explanations in fact contributes to future prediction and control, albeit indirectly by facilitating the discovery and confirmation of instrumentally valuable theories. Theoretical and empirical considerations also suggest (...)
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  • The epistemic value of understanding.Henk W. de Regt - 2009 - Philosophy of Science 76 (5):585-597.
    This article analyzes the epistemic value of understanding and offers an account of the role of understanding in science. First, I discuss the objectivist view of the relation between explanation and understanding, defended by Carl Hempel and J. D. Trout. I challenge this view by arguing that pragmatic aspects of explanation are crucial for achieving the epistemic aims of science. Subsequently, I present an analysis of these pragmatic aspects in terms of ‘intelligibility’ and a contextual account of scientific understanding based (...)
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  • Reintroducing prediction to explanation.Heather E. Douglas - 2009 - Philosophy of Science 76 (4):444-463.
    Although prediction has been largely absent from discussions of explanation for the past 40 years, theories of explanation can gain much from a reintroduction. I review the history that divorced prediction from explanation, examine the proliferation of models of explanation that followed, and argue that accounts of explanation have been impoverished by the neglect of prediction. Instead of a revival of the symmetry thesis, I suggest that explanation should be understood as a cognitive tool that assists us in generating new (...)
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  • The Structure of Tradeoffs in Model Building.John Matthewson & Michael Weisberg - 2009 - Synthese 170 (1):169 - 190.
    Despite their best efforts, scientists may be unable to construct models that simultaneously exemplify every theoretical virtue. One explanation for this is the existence of tradeoffs: relationships of attenuation that constrain the extent to which models can have such desirable qualities. In this paper, we characterize three types of tradeoffs theorists may confront. These characterizations are then used to examine the relationships between parameter precision and two types of generality. We show that several of these relationships exhibit tradeoffs and discuss (...)
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  • Forty years of 'the strategy': Levins on model building and idealization.Michael Weisberg - 2006 - Biology and Philosophy 21 (5):623-645.
    This paper is an interpretation and defense of Richard Levins’ “The Strategy of Model Building in Population Biology,” which has been extremely influential among biologists since its publication 40 years ago. In this article, Levins confronted some of the deepest philosophical issues surrounding modeling and theory construction. By way of interpretation, I discuss each of Levins’ major philosophical themes: the problem of complexity, the brute-force approach, the existence and consequence of tradeoffs, and robustness analysis. I argue that Levins’ article is (...)
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  • (1 other version)Studies in the logic of explanation.Carl Gustav Hempel & Paul Oppenheim - 1948 - Philosophy of Science 15 (2):135-175.
    To explain the phenomena in the world of our experience, to answer the question “why?” rather than only the question “what?”, is one of the foremost objectives of all rational inquiry; and especially, scientific research in its various branches strives to go beyond a mere description of its subject matter by providing an explanation of the phenomena it investigates. While there is rather general agreement about this chief objective of science, there exists considerable difference of opinion as to the function (...)
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  • When mechanistic models explain.Carl F. Craver - 2006 - Synthese 153 (3):355-376.
    Not all models are explanatory. Some models are data summaries. Some models sketch explanations but leave crucial details unspecified or hidden behind filler terms. Some models are used to conjecture a how-possibly explanation without regard to whether it is a how-actually explanation. I use the Hodgkin and Huxley model of the action potential to illustrate these ways that models can be useful without explaining. I then use the subsequent development of the explanation of the action potential to show what is (...)
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  • Thinking about mechanisms.Peter Machamer, Lindley Darden & Carl F. Craver - 2000 - Philosophy of Science 67 (1):1-25.
    The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.
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  • Explanation: a mechanist alternative.William Bechtel & Adele Abrahamsen - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (2):421-441.
    Explanations in the life sciences frequently involve presenting a model of the mechanism taken to be responsible for a given phenomenon. Such explanations depart in numerous ways from nomological explanations commonly presented in philosophy of science. This paper focuses on three sorts of differences. First, scientists who develop mechanistic explanations are not limited to linguistic representations and logical inference; they frequently employ diagrams to characterize mechanisms and simulations to reason about them. Thus, the epistemic resources for presenting mechanistic explanations are (...)
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  • Scientific perspectivism: A philosopher of science’s response to the challenge of big data biology.Werner Callebaut - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):69-80.
    Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science to slip into (...)
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  • The Idealization of Causation in Mechanistic Explanation.Alan C. Love & Marco J. Nathan - 2015 - Philosophy of Science 82 (5):761-774.
    Causal relations among components and activities are intentionally misrepresented in mechanistic explanations found routinely across the life sciences. Since several mechanists explicitly advocate accurately representing factors that make a difference to the outcome, these idealizations conflict with the stated rationale for mechanistic explanation. We argue that these idealizations signal an overlooked feature of reasoning in molecular and cell biology—mechanistic explanations do not occur in isolation—and suggest that explanatory practices within the mechanistic tradition share commonalities with model-based approaches prevalent in population (...)
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  • Big Data Biology: Between Eliminative Inferences and Exploratory Experiments.Emanuele Ratti - 2015 - Philosophy of Science 82 (2):198-218.
    Recently, biologists have argued that data - driven biology fosters a new scientific methodology; namely, one that is irreducible to traditional methodologies of molecular biology defined as the discovery strategies elucidated by mechanistic philosophy. Here I show how data - driven studies can be included into the traditional mechanistic approach in two respects. On the one hand, some studies provide eliminative inferential procedures to prioritize and develop mechanistic hypotheses. On the other, different studies play an exploratory role in providing useful (...)
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  • Abstraction and the Organization of Mechanisms.Arnon Levy & William Bechtel - 2013 - Philosophy of Science 80 (2):241-261.
    Proponents of mechanistic explanation all acknowledge the importance of organization. But they have also tended to emphasize specificity with respect to parts and operations in mechanisms. We argue that in understanding one important mode of organization—patterns of causal connectivity—a successful explanatory strategy abstracts from the specifics of the mechanism and invokes tools such as those of graph theory to explain how mechanisms with a particular mode of connectivity will behave. We discuss the connection between organization, abstraction, and mechanistic explanation and (...)
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  • Introduction: Making sense of data-driven research in the biological and biomedical sciences.S. Leonelli - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):1-3.
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  • The Explanatory Force of Dynamical and Mathematical Models in Neuroscience: A Mechanistic Perspective.David Michael Kaplan & Carl F. Craver - 2011 - Philosophy of Science 78 (4):601-627.
    We argue that dynamical and mathematical models in systems and cognitive neuro- science explain (rather than redescribe) a phenomenon only if there is a plausible mapping between elements in the model and elements in the mechanism for the phe- nomenon. We demonstrate how this model-to-mechanism-mapping constraint, when satisfied, endows a model with explanatory force with respect to the phenomenon to be explained. Several paradigmatic models including the Haken-Kelso-Bunz model of bimanual coordination and the difference-of-Gaussians model of visual receptive fields are (...)
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  • Mechanistic Models and the Explanatory Limits of Machine Learning.Emanuele Ratti & Ezequiel López-Rubio - unknown
    We argue that mechanistic models elaborated by machine learning cannot be explanatory by discussing the relation between mechanistic models, explanation and the notion of intelligibility of models. We show that the ability of biologists to understand the model that they work with severely constrains their capacity of turning the model into an explanatory model. The more a mechanistic model is complex, the less explanatory it will be. Since machine learning increases its performances when more components are added, then it generates (...)
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  • Prediction in context: On the comparative epistemic merit of predictive success.Martin Carrier - 2014 - Studies in History and Philosophy of Science Part A 45:97-102.
    The considerations set out in the paper are intended to suggest that in practical contexts predictive power does not play the outstanding roles sometimes accredited to it in an epistemic framework. Rather, predictive power is part of a network of other merits and achievements. Predictive power needs to be judged differently according to the specific conditions that apply. First, predictions need to be part of an explanatory framework if they are supposed to guide actions reliably. Second, in scientific expertise, the (...)
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  • Factive scientific understanding without accurate representation.Collin C. Rice - 2016 - Biology and Philosophy 31 (1):81-102.
    This paper analyzes two ways idealized biological models produce factive scientific understanding. I then argue that models can provide factive scientific understanding of a phenomenon without providing an accurate representation of the features of their real-world target system. My analysis of these cases also suggests that the debate over scientific realism needs to investigate the factive scientific understanding produced by scientists’ use of idealized models rather than the accuracy of scientific models themselves.
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  • Aspects of Theory-Ladenness in Data-Intensive Science.Wolfgang Pietsch - 2015 - Philosophy of Science 82 (5):905-916.
    Recent claims, mainly from computer scientists, concerning a largely automated and model-free data-intensive science have been countered by critical reactions from a number of philosophers of science. The debate suffers from a lack of detail in two respects, regarding the actual methods used in data-intensive science and the specific ways in which these methods presuppose theoretical assumptions. I examine two widely-used algorithms, classificatory trees and non-parametric regression, and argue that these are theory-laden in an external sense, regarding the framing of (...)
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  • The End of 'Small Biology'? Some Thoughts About Biomedicine and Big Science.Emanuele Ratti - 2016 - Big Data and Society:1-6.
    In biology—as in other scientific fields—there is a lively opposition between big and small science projects. In this commentary, I try to contextualize this opposition in the field of biomedicine, and I argue that, at least in this context, big science projects should come first.
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