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  1. Exploratory Experimentation and Scientific Practice: Metagenomics and the Proteorhodopsin Case.Maureen O'Malley - 2007 - History and Philosophy of the Life Sciences 29 (3):337 - 360.
    Exploratory experimentation and high-throughput molecular biology appear to have considerable affinity for each other. Included in the latter category is metagenomics, which is the DNA-based study of diverse microbial communities from a vast range of non-laboratory environments. Metagenomics has already made numerous discoveries and these have led to reinterpretations of fundamental concepts of microbial organization, evolution, and ecology. The most outstanding success story of metagenomics to date involves the discovery of a rhodopsin gene, named proteorhodopsin, in marine bacteria that were (...)
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  • The philosophy of information.Luciano Floridi - 2011 - New York: Oxford University Press.
    Luciano Floridi presents a book that will set the agenda for the philosophy of information. PI is the philosophical field concerned with the critical investigation of the conceptual nature and basic principles of information, including its dynamics, utilisation, and sciences, and the elaboration and application of information-theoretic and computational methodologies to philosophical problems. This book lays down, for the first time, the conceptual foundations for this new area of research. It does so systematically, by pursuing three goals. Its metatheoretical goal (...)
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  • Models in Science (2nd edition).Roman Frigg & Stephan Hartmann - 2021 - The Stanford Encyclopedia of Philosophy.
    Models are of central importance in many scientific contexts. The centrality of models such as inflationary models in cosmology, general-circulation models of the global climate, the double-helix model of DNA, evolutionary models in biology, agent-based models in the social sciences, and general-equilibrium models of markets in their respective domains is a case in point (the Other Internet Resources section at the end of this entry contains links to online resources that discuss these models). Scientists spend significant amounts of time building, (...)
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  • Data-Centric Biology: A Philosophical Study.Sabina Leonelli - 2016 - London: University of Chicago Press.
  • Evidential Reasoning in Archaeology.Robert Chapman & Alison Wylie - 2016 - London: Bloomsbury Academic Publishing.
    Material traces of the past are notoriously inscrutable; they rarely speak with one voice, and what they say is never unmediated. They stand as evidence only given a rich scaffolding of interpretation which is, itself, always open to challenge and revision. And yet archaeological evidence has dramatically expanded what we know of the cultural past, sometimes demonstrating a striking capacity to disrupt settled assumptions. The questions we address in Evidential Reasoning are: How are these successes realized? What gives us confidence (...)
  • Data, phenomena, and reliability.James Woodward - 2000 - Philosophy of Science 67 (3):179.
    This paper explores how data serve as evidence for phenomena. In contrast to standard philosophical models which invite us to think of evidential relationships as logical relationships, I argue that evidential relationships in the context of data-to-phenomena reasoning are empirical relationships that depend on holding the right sort of pattern of counterfactual dependence between the data and the conclusions investigators reach on the phenomena themselves.
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  • The Uses of Argument.Frederick L. Will & Stephen Toulmin - 1960 - Philosophical Review 69 (3):399.
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  • The Nature and Context of Exploratory Experimentation: An Introduction to Three Case Studies of Exploratory Research.C. Kenneth Waters - 2007 - History and Philosophy of the Life Sciences 29 (3):275 - 284.
    My aim in this article is to introduce readers to the topic of exploratory experimentation and briefly explain how the three articles that follow, by Richard Burian, Kevin Elliott, and Maureen O'Malley, advance our understanding of the nature and significance of exploratory research. I suggest that the distinction between exploratory and theory-driven experimentation is multidimensional and that some of the dimensions are continuums. I point out that exploratory experiments are typically theory-informed even if they are not theory-driven. I also distinguish (...)
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  • Scientific Representation: Paradoxes of Perspective.B. C. van Fraassen - 2010 - Analysis 70 (3):511-514.
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  • Scientific Representation: Paradoxes of Perspective.Bas C. Van Fraassen - 2008 - Oxford, GB: Oxford University Press UK.
  • Infra-experimentality: from traces to data, from data to patterning facts.Hans-Jörg Rheinberger - 2011 - History of Science 49 (3):337-348.
  • “Saving the Phenomena” Today.Paul Teller - 2010 - Philosophy of Science 77 (5):815-826.
    Bogen and Woodward argued the indirect connection between data and theory in terms of their conception of “phenomena.” I outline and elaborate on their presentation. To illuminate the connection with contemporary thinking in terms of models, I distinguish between phenomena tokens, representations of which can be identified with data models, and phenomena types that can be identified with relatively low-lying models or aspects of models in the model hierarchy. Throughout I stress the role of idealization in these considerations.
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  • Old and New Problems in Philosophy of Measurement.Eran Tal - 2013 - Philosophy Compass 8 (12):1159-1173.
    The philosophy of measurement studies the conceptual, ontological, epistemic, and technological conditions that make measurement possible and reliable. A new wave of philosophical scholarship has emerged in the last decade that emphasizes the material and historical dimensions of measurement and the relationships between measurement and theoretical modeling. This essay surveys these developments and contrasts them with earlier work on the semantics of quantity terms and the representational character of measurement. The conclusions highlight four characteristics of the emerging research program in (...)
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  • An inferential conception of scientific representation.Mauricio Suárez - 2004 - Philosophy of Science 71 (5):767-779.
    This paper defends an inferential conception of scientific representation. It approaches the notion of representation in a deflationary spirit, and minimally characterizes the concept as it appears in science by means of two necessary conditions: its essential directionality and its capacity to allow surrogate reasoning and inference. The conception is defended by showing that it successfully meets the objections that make its competitors, such as isomorphism and similarity, untenable. In addition the inferential conception captures the objectivity of the cognitive representations (...)
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  • Statistical concepts in philosophy of science.Patrick Suppes - 2007 - Synthese 154 (3):485--496.
    This article focuses on the role of statistical concepts in both experiment and theory in various scientific disciplines, especially physics, including astronomy, and psychology. In Sect. 1 the concept of uncertainty in astronomy is analyzed from Ptolemy to Laplace and Gauss. In Sect. 2 theoretical uses of probability and statistics in science are surveyed. Attention is focused on the historically important example of radioactive decay. In Sect. 3 the use of statistics in biology and the social sciences is examined, with (...)
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  • Entering new fields: Exploratory uses of experimentation.Friedrich Steinle - 1997 - Philosophy of Science 64 (4):74.
    Starting with some illustrative examples, I develop a systematic account of a specific type of experimentation--an experimentation which is not, as in the "standard view", driven by specific theories. It is typically practiced in periods in which no theory or--even more fundamentally--no conceptual framework is readily available. I call it exploratory experimentation and I explicate its systematic guidelines. From the historical examples I argue furthermore that exploratory experimentation may have an immense, but hitherto widely neglected, epistemic significance.
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  • Preparations, models, and simulations.Hans-Jörg Rheinberger - 2015 - History and Philosophy of the Life Sciences 36 (3):321-334.
    This paper proposes an outline for a typology of the different forms that scientific objects can take in the life sciences. The first section discusses preparations (or specimens)—a form of scientific object that accompanied the development of modern biology in different guises from the seventeenth century to the present: as anatomical–morphological specimens, as microscopic cuts, and as biochemical preparations. In the second section, the characteristics of models in biology are discussed. They became prominent from the end of the nineteenth century (...)
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  • Computer Simulation, Measurement, and Data Assimilation.Wendy S. Parker - 2017 - British Journal for the Philosophy of Science 68 (1):273-304.
    This article explores some of the roles of computer simulation in measurement. A model-based view of measurement is adopted and three types of measurement—direct, derived, and complex—are distinguished. It is argued that while computer simulations on their own are not measurement processes, in principle they can be embedded in direct, derived, and complex measurement practices in such a way that simulation results constitute measurement outcomes. Atmospheric data assimilation is then considered as a case study. This practice, which involves combining information (...)
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  • There Are No Universal Rules for Induction.John D. Norton - 2010 - Philosophy of Science 77 (5):765-777.
    In a material theory of induction, inductive inferences are warranted by facts that prevail locally. This approach, it is urged, is preferable to formal theories of induction in which the good inductive inferences are delineated as those conforming to some universal schema. An inductive inference problem concerning indeterministic, non-probabilistic systems in physics is posed and it is argued that Bayesians cannot responsibly analyze it, thereby demonstrating that the probability calculus is not the universal logic of induction.
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  • Models, measurement and computer simulation: the changing face of experimentation.Margaret Morrison - 2009 - Philosophical Studies 143 (1):33-57.
    The paper presents an argument for treating certain types of computer simulation as having the same epistemic status as experimental measurement. While this may seem a rather counterintuitive view it becomes less so when one looks carefully at the role that models play in experimental activity, particularly measurement. I begin by discussing how models function as “measuring instruments” and go on to examine the ways in which simulation can be said to constitute an experimental activity. By focussing on the connections (...)
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  • The Ontology of Patterns in Empirical Data.James W. McAllister - 2010 - Philosophy of Science 77 (5):804-814.
    This article defends the following claims. First, for patterns exhibited in empirical data, there is no criterion on which to demarcate patterns that are physically significant and patterns that are not physically significant. I call a pattern physically significant if it corresponds to a structure in the world. Second, all patterns must be regarded as physically significant. Third, distinct patterns must be regarded as providing evidence for distinct structures in the world. Fourth, in consequence, the world must be conceived as (...)
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  • From data to phenomena: a Kantian stance.Michela Massimi - 2011 - Synthese 182 (1):101-116.
    This paper investigates some metaphysical and epistemological assumptions behind Bogen and Woodward’s data-to-phenomena inferences. I raise a series of points and suggest an alternative possible Kantian stance about data-to-phenomena inferences. I clarify the nature of the suggested Kantian stance by contrasting it with McAllister’s view about phenomena as patterns in data sets.
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  • Building Simulations from the Ground Up: Modeling and Theory in Systems Biology.Miles MacLeod & Nancy J. Nersessian - 2013 - Philosophy of Science 80 (4):533-556.
    In this article, we provide a case study examining how integrative systems biologists build simulation models in the absence of a theoretical base. Lacking theoretical starting points, integrative systems biology researchers rely cognitively on the model-building process to disentangle and understand complex biochemical systems. They build simulations from the ground up in a nest-like fashion, by pulling together information and techniques from a variety of possible sources and experimenting with different structures in order to discover a stable, robust result. Finally, (...)
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  • Performing abstraction: Two ways of modelling arabidopsis thaliana.Sabina Leonelli - 2008 - Biology and Philosophy 23 (4):509-528.
    What is the best way to analyse abstraction in scientific modelling? I propose to focus on abstracting as an epistemic activity, which is achieved in different ways and for different purposes depending on the actual circumstances of modelling and the features of the models in question. This is in contrast to a more conventional use of the term ‘abstract’ as an attribute of models, which I characterise as black-boxing the ways in which abstraction is performed and to which epistemological advantage. (...)
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  • Modelling and representing: An artefactual approach to model-based representation.Tarja Knuuttila - 2011 - Studies in History and Philosophy of Science Part A 42 (2):262-271.
    The recent discussion on scientific representation has focused on models and their relationship to the real world. It has been assumed that models give us knowledge because they represent their supposed real target systems. However, here agreement among philosophers of science has tended to end as they have presented widely different views on how representation should be understood. I will argue that the traditional representational approach is too limiting as regards the epistemic value of modelling given the focus on the (...)
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  • Lessons from the Large Hadron Collider for model-based experimentation: the concept of a model of data acquisition and the scope of the hierarchy of models.Koray Karaca - 2018 - Synthese 195 (12):1-22.
    According to the hierarchy of models account of scientific experimentation developed by Patrick Suppes and elaborated by Deborah Mayo, theoretical considerations about the phenomena of interest are involved in an experiment through theoretical models that in turn relate to experimental data through data models, via the linkage of experimental models. In this paper, I dispute the HoM account in the context of present-day high-energy physics experiments. I argue that even though the HoM account aims to characterize experimentation as a model-based (...)
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  • Lessons from the Large Hadron Collider for model-based experimentation: the concept of a model of data acquisition and the scope of the hierarchy of models.Koray Karaca - 2018 - Synthese 195 (12):5431-5452.
    According to the hierarchy of models (HoM) account of scientific experimentation developed by Patrick Suppes and elaborated by Deborah Mayo, theoretical considerations about the phenomena of interest are involved in an experiment through theoretical models that in turn relate to experimental data through data models, via the linkage of experimental models. In this paper, I dispute the HoM account in the context of present-day high-energy physics (HEP) experiments. I argue that even though the HoM account aims to characterize experimentation as (...)
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  • Data models and the acquisition and manipulation of data.Todd Harris - 2003 - Philosophy of Science 70 (5):1508-1517.
    This paper offers an account of data manipulation in scientific experiments. It will be shown that in many cases raw, unprocessed data is not produced, but rather a form of processed data that will be referred to as a data model. The language of data models will be used to provide a framework within which to understand a recent debate about the status of data and data manipulation. It will be seen that a description in terms of data models allows (...)
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  • The turn of the valve: representing with material models.Roman Frigg & James Nguyen - 2018 - European Journal for Philosophy of Science 8 (2):205-224.
    Many scientific models are representations. Building on Goodman and Elgin’s notion of representation-as we analyse what this claim involves by providing a general definition of what makes something a scientific model, and formulating a novel account of how they represent. We call the result the DEKI account of representation, which offers a complex kind of representation involving an interplay of, denotation, exemplification, keying up of properties, and imputation. Throughout we focus on material models, and we illustrate our claims with the (...)
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  • What exactly is stabilized when phenomena are stabilized?Uljana Feest - 2011 - Synthese 182 (1):57-71.
    The last two decades have seen a rising interest in (a) the notion of a scientific phenomenon as distinct from theories and data, and (b) the intricacies of experimentally producing and stabilizing phenomena. This paper develops an analysis of the stabilization of phenomena that integrates two aspects that have largely been treated separately in the literature: one concerns the skills required for empirical work; the other concerns the strategies by which claims about phenomena are validated. I argue that in order (...)
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  • Saving the phenomena.James Bogen & James Woodward - 1988 - Philosophical Review 97 (3):303-352.
  • Logic, Methodology and Philosophy of Science.Max Black, Ernest Nagel, Patrick Suppes & Alfred Tarski - 1963 - Philosophical Review 72 (4):538.
  • Explaining features of fine-grained phenomena using abstract analyses of phenomena and mechanisms: two examples from chronobiology.William Bechtel - 2017 - Synthese 198 (Suppl 24):1-23.
    Explanations of biological phenomena such as cell division, protein synthesis or circadian rhythms commonly take the form of models of the responsible mechanisms. Recently philosophers of science have attempted to analyze this practice, presenting mechanisms as organized collections of parts performing operations that together produce the phenomenon. But in some cases what researchers seek to explain is not a general phenomenon, but a specific feature of a more fine-grained phenomenon. In some of these cases, it is not the model of (...)
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  • The World in the Model: How Economists Work and Think.Mary S. Morgan - 2012 - Cambridge University Press: Cambridge.
    During the last two centuries, the way economic science is done has changed radically: it has become a social science based on mathematical models in place of words. This book describes and analyses that change - both historically and philosophically - using a series of case studies to illuminate the nature and the implications of these changes. It is not a technical book; it is written for the intelligent person who wants to understand how economics works from the inside out. (...)
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  • Causation, Evidence, and Inference.Julian Reiss - 2015 - New York: Routledge.
    In this book, Reiss argues in favor of a tight fit between evidence, concept and purpose in our causal investigations in the sciences. There is no doubt that the sciences employ a vast array of techniques to address causal questions such as controlled experiments, randomized trials, statistical and econometric tools, causal modeling and thought experiments. But how do these different methods relate to each other and to the causal inquiry at hand? Reiss argues that there is no "gold standard" in (...)
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  • How to Do Science with Models: A Philosophical Primer.Axel Gelfert - 2016 - Cham: Springer.
    Taking scientific practice as its starting point, this book charts the complex territory of models used in science. It examines what scientific models are and what their function is. Reliance on models is pervasive in science, and scientists often need to construct models in order to explain or predict anything of interest at all. The diversity of kinds of models one finds in science – ranging from toy models and scale models to theoretical and mathematical models – has attracted attention (...)
  • Scientific Models in Philosophy of Science.Daniela M. Bailer-Jones - 2009 - University of Pittsburgh Press.
    Scientists have used models for hundreds of years as a means of describing phenomena and as a basis for further analogy. In Scientific Models in Philosophy of Science, Daniela Bailer-Jones assembles an original and comprehensive philosophical analysis of how models have been used and interpreted in both historical and contemporary contexts. Bailer-Jones delineates the many forms models can take (ranging from equations to animals; from physical objects to theoretical constructs), and how they are put to use. She examines early mechanical (...)
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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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  • Inventing Temperature: Measurement and Scientific Progress.Hasok Chang - 2004 - New York, US: OUP Usa.
    This book presents the concept of “complementary science” which contributes to scientific knowledge through historical and philosophical investigations. It emphasizes the fact that many simple items of knowledge that we take for granted were actually spectacular achievements obtained only after a great deal of innovative thinking, painstaking experiments, bold conjectures, and serious controversies. Each chapter in the book consists of two parts: a narrative part that states the philosophical puzzle and gives a problem-centred narrative on the historical attempts to solve (...)
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  • Re-engineering philosophy for limited beings: piecewise approximations to reality.William C. Wimsatt - 2007 - Cambridge, Mass.: 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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  • Using models to represent reality.Ronald N. Giere - 1999 - In L. Magnani, N. J. Nersessian & P. Thagard (eds.), Model-Based Reasoning in Scientific Discovery. Kluwer/Plenum. pp. 41--57.
  • The philosophy of information.Luciano Floridi - 2010 - The Philosophers' Magazine 50:42-43.
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  • Error and the growth of experimental knowledge.Deborah Mayo - 1996 - International Studies in the Philosophy of Science 15 (1):455-459.
  • Fiction and scientific representation.Roman Frigg - 2010 - In Roman Frigg & Matthew Hunter (eds.), Beyond Mimesis and Convention: Representation in Art and Science. pp. 97-138.
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  • The genotype/phenotype distinction.Richard Lewontin - 2008 - Stanford Encyclopedia of Philosophy.
    The distinction between phenotype and genotype is fundamental to the understanding of heredity and development of organisms. The genotype of an organism is the class to which that organism belongs as determined by the description of the actual physical material made up of DNA that was passed to the organism by its parents at the organism's conception. For sexually reproducing organisms that physical material consists of the DNA contributed to the fertilized egg by the sperm and egg of its two (...)
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  • Scientific representation.Roman Frigg & James Nguyen - 2016 - Stanford Encyclopedia of Philosophy.
    Science provides us with representations of atoms, elementary particles, polymers, populations, genetic trees, economies, rational decisions, aeroplanes, earthquakes, forest fires, irrigation systems, and the world’s climate. It's through these representations that we learn about the world. This entry explores various different accounts of scientific representation, with a particular focus on how scientific models represent their target systems. As philosophers of science are increasingly acknowledging the importance, if not the primacy, of scientific models as representational units of science, it's important to (...)
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  • Fiction and scientific representation.Roman Frigg - 2010 - In .
    Understanding scientific modelling can be divided into two sub-projects: analysing what model-systems are, and understanding how they are used to represent something beyond themselves. The first is a prerequisite for the second: we can only start analysing how representation works once we understand the intrinsic character of the vehicle that does the representing. Coming to terms with this issue is the project of the first half of this chapter. My central contention is that models are akin to places and characters (...)
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  • The self-vindication of the laboratory sciences.Ian Hacking - 1992 - In Andrew Pickering (ed.), Science as Practice and Culture. University of Chicago Press. pp. 29--64.
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  • Exploratory Experimentation and the Role of Histochemical Techniques in the Work of Jean Brachet, 1938-1952.Richard M. Burian - 1997 - History and Philosophy of the Life Sciences 19 (1):27 - 45.
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  • The Uses of Argument.Stephen E. Toulmin - 1958 - Philosophy 34 (130):244-245.
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