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  1. Classificatory Theory in Biology.Sabina Leonelli - 2013 - Biological Theory 7 (4):338-345.
    Scientific classification has long been recognized as involving a specific style of reasoning and doing research, and as occasionally affecting the development of scientific theories. However, the role played by classificatory activities in generating theories has not been closely investigated within the philosophy of science. I argue that classificatory systems can themselves become a form of theory, which I call classificatory theory, when they come to formalize and express the scientific significance of the elements being classified. This is particularly evident (...)
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  • Classificatory Theory in Data-intensive Science: The Case of Open Biomedical Ontologies.Sabina Leonelli - 2012 - International Studies in the Philosophy of Science 26 (1):47 - 65.
    Knowledge-making practices in biology are being strongly affected by the availability of data on an unprecedented scale, the insistence on systemic approaches and growing reliance on bioinformatics and digital infrastructures. What role does theory play within data-intensive science, and what does that tell us about scientific theories in general? To answer these questions, I focus on Open Biomedical Ontologies, digital classification tools that have become crucial to sharing results across research contexts in the biological and biomedical sciences, and argue that (...)
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  • An account of conserved functions and how biologists use them to integrate cell and evolutionary biology.Jeremy G. Wideman, Steve Elliott & Beckett Sterner - 2023 - Biology and Philosophy 38 (5):1-23.
    We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...)
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  • (1 other version)Data science and molecular biology: prediction and mechanistic explanation.Ezequiel López-Rubio & Emanuele Ratti - 2021 - Synthese 198 (4):3131-3156.
    In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...)
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  • Radiocarbon Dating in Archaeology: Triangulation and Traceability.Alison Wylie - 2020 - In Sabina Leonelli & Niccolò Tempini (eds.), Data Journeys in the Sciences. Springer. pp. 285-301.
    When radiocarbon dating techniques were applied to archaeological material in the 1950s they were hailed as a revolution. At last archaeologists could construct absolute chronologies anchored in temporal data backed by immutable laws of physics. This would make it possible to mobilize archaeological data across regions and time-periods on a global scale, rendering obsolete the local and relative chronologies on which archaeologists had long relied. As profound as the impact of 14C dating has been, it has had a long and (...)
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  • Scientific knowledge in the age of computation: Explicated, computable and manageable?Sophia Efstathiou, Rune Nydal, Astrid Laegreid & Martin Kuiper - 2019 - Theoria. An International Journal for Theory, History and Foundations of Science 34 (2):213.
    We have two theses about scientific knowledge in the age of computation. Our general claim is that scientific Knowledge Management practices emerge as second-order practices whose aim is to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data. Our specific thesis is that knowledge management practices are transforming biological research in at least three ways. We argue that scientific Knowledge Management a. operates with founded concepts of biological knowledge as explicated and computable, b. enables new outputs and (...)
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  • Scientific knowledge in the age of computation.Sophia Efstathiou, Rune Nydal, Astrid LÆgreid & Martin Kuiper - 2019 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 34 (2):213-236.
    With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...)
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  • Moving Past the Systematics Wars.Beckett Sterner & Scott Lidgard - 2018 - Journal of the History of Biology 51 (1):31-67.
    It is time to escape the constraints of the Systematics Wars narrative and pursue new questions that are better positioned to establish the relevance of the field in this time period to broader issues in the history of biology and history of science. To date, the underlying assumptions of the Systematics Wars narrative have led historians to prioritize theory over practice and the conflicts of a few leading theorists over the less-polarized interactions of systematists at large. We show how shifting (...)
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  • Taxonomy for Humans or Computers? Cognitive Pragmatics for Big Data.Beckett Sterner & Nico M. Franz - 2017 - Biological Theory 12 (2):99-111.
    Criticism of big data has focused on showing that more is not necessarily better, in the sense that data may lose their value when taken out of context and aggregated together. The next step is to incorporate an awareness of pitfalls for aggregation into the design of data infrastructure and institutions. A common strategy minimizes aggregation errors by increasing the precision of our conventions for identifying and classifying data. As a counterpoint, we argue that there are pragmatic trade-offs between precision (...)
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  • The Virtues of Scientific Practice: MacIntyre, Virtue Ethics, and the Historiography of Science.Daniel J. Hicks & Thomas A. Stapleford - 2016 - Isis 107 (3):499-72.
    “Practice” has become a ubiquitous term in the history of science, and yet historians have not always reflected on its philosophical import and especially on its potential connections with ethics. In this essay, we draw on the work of the virtue ethicist Alasdair MacIntyre to develop a theory of “communal practices” and explore how such an approach can inform the history of science, including allegations about the corruption of science by wealth or power; consideration of scientific ethics or “moral economies”; (...)
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  • The proactive historian: Methodological opportunities presented by the new archives documenting genomics.Miguel García-Sancho - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 55 (C):70-82.
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  • Too many numbers: Microarrays in clinical cancer research.Peter Keating & Alberto Cambrosio - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):37-51.
    In his highly regarded history of the rise of clinical trials in America, HarryMarks describes how their widespread adoption resulted largely fromthe efforts of ‘therapeutic reformers’ who sought to replace the individualexpertise of clinicians with the ‘science of controlled experiment’. Thetransition described by Marks resembles in many respects the transition fromthe ‘truth-to-nature’ objectivity of individual experts to a ‘mechanical’ formof objectivity portrayed by Daston and Galison. In particular,Marks details the passage from a regime of trust in expertise and experts to (...)
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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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  • The Comparative and the Exemplary: Revisiting the Early History of Molecular Biology.Bruno J. Strasser & Soraya de Chadarevian - 2011 - History of Science 49 (3):317-336.
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  • Modernizing Natural History: Berkeley’s Museum of Vertebrate Zoology in Transition. [REVIEW]Mary E. Sunderland - 2013 - Journal of the History of Biology 46 (3):369-400.
    Throughout the twentieth century calls to modernize natural history motivated a range of responses. It was unclear how research in natural history museums would participate in the significant technological and conceptual changes that were occurring in the life sciences. By the 1960s, the Museum of Vertebrate Zoology at the University of California, Berkeley, was among the few university-based natural history museums that were able to maintain their specimen collections and support active research. The MVZ therefore provides a window to the (...)
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  • Evo-Devo as a Trading Zone.Rasmus Grønfeldt Winther - 2014 - In Alan C. Love (ed.), Conceptual Change in Biology: Scientific and Philosophical Perspectives on Evolution and Development. Berlin: Springer Verlag, Boston Studies in the Philosophy of Science.
    Evo-Devo exhibits a plurality of scientific “cultures” of practice and theory. When are the cultures acting—individually or collectively—in ways that actually move research forward, empirically, theoretically, and ethically? When do they become imperialistic, in the sense of excluding and subordinating other cultures? This chapter identifies six cultures – three /styles/ (mathematical modeling, mechanism, and history) and three /paradigms/ (adaptationism, structuralism, and cladism). The key assumptions standing behind, under, or within each of these cultures are explored. Characterizing the internal structure of (...)
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  • Adjusting to precarity: how and why the Roslin Institute forged a leading role for itself in international networks of pig genomics research.James W. E. Lowe - 2021 - British Journal for the History of Science 54 (4):507-530.
    From the 1980s onwards, the Roslin Institute and its predecessor organizations faced budget cuts, organizational upheaval and considerable insecurity. Over the next few decades, it was transformed by the introduction of molecular biology and transgenic research, but remained a hub of animal geneticists conducting research aimed at the livestock-breeding industry. This paper explores how these animal geneticists embraced genomics in response to the many-faceted precarity that the Roslin Institute faced, establishing it as a global centre for pig genomics research through (...)
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  • Data Journeys in the Sciences.Sabina Leonelli & Niccolò Tempini (eds.) - 2020 - Springer.
    This groundbreaking, open access volume analyses and compares data practices across several fields through the analysis of specific cases of data journeys. It brings together leading scholars in the philosophy, history and social studies of science to achieve two goals: tracking the travel of data across different spaces, times and domains of research practice; and documenting how such journeys affect the use of data as evidence and the knowledge being produced. The volume captures the opportunities, challenges and concerns involved in (...)
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  • (1 other version)Data science and molecular biology: prediction and mechanistic explanation.Ezequiel López-Rubio & Emanuele Ratti - 2019 - Synthese (4):1-26.
    In the last few years, biologists and computer scientists have claimed that the introduction of data science techniques in molecular biology has changed the characteristics and the aims of typical outputs (i.e. models) of such a discipline. In this paper we will critically examine this claim. First, we identify the received view on models and their aims in molecular biology. Models in molecular biology are mechanistic and explanatory. Next, we identify the scope and aims of data science (machine learning in (...)
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  • Globalizing Genomics: The Origins of the International Nucleotide Sequence Database Collaboration.Hallam Stevens - 2017 - Journal of the History of Biology 51 (4):657-691.
    Genomics is increasingly considered a global enterprise – the fact that biological information can flow rapidly around the planet is taken to be important to what genomics is and what it can achieve. However, the large-scale international circulation of nucleotide sequence information did not begin with the Human Genome Project. Efforts to formalize and institutionalize the circulation of sequence information emerged concurrently with the development of centralized facilities for collecting that information. That is, the very first databases build for collecting (...)
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  • Unfolding epidemiological stories: How the WHO made frozen blood into a flexible resource for the future.Joanna Radin - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 47 (PA):62-73.
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  • Ontological Issues in the Life Sciences.James DiFrisco, Gaëlle Pontarotti, Federico Boem, Guillaume Schlaepfer, Ewelina Sokolowska & Eva Fernández-Labandera - 2015 - Biological Theory 10 (2):176-181.
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  • Towards “A Natural History of Data”: Evolving Practices and Epistemologies of Data in Paleontology, 1800–2000. [REVIEW]David Sepkoski - 2013 - Journal of the History of Biology 46 (3):401-444.
    The fossil record is paleontology’s great resource, telling us virtually everything we know about the past history of life. This record, which has been accumulating since the beginning of paleontology as a professional discipline in the early nineteenth century, is a collection of objects. The fossil record exists literally, in the specimen drawers where fossils are kept, and figuratively, in the illustrations and records of fossils compiled in paleontological atlases and compendia. However, as has become increasingly clear since the later (...)
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  • The Long and Winding Road of Molecular Data in Phylogenetic Analysis.Edna Suárez-Díaz - 2014 - Journal of the History of Biology 47 (3):443-478.
    The use of molecules and reactions as evidence, markers and/or traits for evolutionary processes has a history more than a century long. Molecules have been used in studies of intra-specific variation and studies of similarity among species that do not necessarily result in the analysis of phylogenetic relations. Promoters of the use of molecular data have sustained the need for quantification as the main argument to make use of them. Moreover, quantification has allowed intensive statistical analysis, as a condition and (...)
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  • Saving the gene pool for the future: Seed banks as archives.Sara Peres - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 55:96-104.
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  • The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project.Kathryn Maxson Jones, Rachel A. Ankeny & Robert Cook-Deegan - 2018 - Journal of the History of Biology 51 (4):693-805.
    The Bermuda Principles for DNA sequence data sharing are an enduring legacy of the Human Genome Project. They were adopted by the HGP at a strategy meeting in Bermuda in February of 1996 and implemented in formal policies by early 1998, mandating daily release of HGP-funded DNA sequences into the public domain. The idea of daily sharing, we argue, emanated directly from strategies for large, goal-directed molecular biology projects first tested within the “community” of C. elegans researchers, and were introduced (...)
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  • Managing the future: The Special Virus Leukemia Program and the acceleration of biomedical research.Robin Wolfe Scheffler - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 48 (PB):231-249.
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  • Integrating data to acquire new knowledge: Three modes of integration in plant science.Sabina Leonelli - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):503-514.
    This paper discusses what it means and what it takes to integrate data in order to acquire new knowledge about biological entities and processes. Maureen O’Malley and Orkun Soyer have pointed to the scientific work involved in data integration as important and distinct from the work required by other forms of integration, such as methodological and explanatory integration, which have been more successful in captivating the attention of philosophers of science. Here I explore what data integration involves in more detail (...)
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  • Openness and trust in data-intensive science: the case of biocuration.Ane Møller Gabrielsen - 2020 - Medicine, Health Care and Philosophy 23 (3):497-504.
    Data-intensive science comes with increased risks concerning quality and reliability of data, and while trust in science has traditionally been framed as a matter of scientists being expected to adhere to certain technical and moral norms for behaviour, emerging discourses of open science present openness and transparency as substitutes for established trust mechanisms. By ensuring access to all available information, quality becomes a matter of informed judgement by the users, and trust no longer seems necessary. This strategy does not, however, (...)
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  • The Scientific Life in the Alpine: Recreation and Moral Life in the Field.Danielle K. Inkpen - 2018 - Isis 109 (3):515-537.
    Historians of science have long recognized the field as a socially heterogeneous space wherein different groups jostle for access and to assert the priority of their activities. This essay offers a new take on this heterogeneity by considering recreation as a form of moralized social belonging that scientists bring to the field. In the 1940s, when North American glaciology was emerging as a military-supported geophysical science, many glaciologists were also mountaineers. The essay analyzes a dispute between a mountaineer and a (...)
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  • Practice and Place in Twentieth-Century Field Biology: A Comment. [REVIEW]Robert E. Kohler - 2012 - Journal of the History of Biology 45 (4):579 - 586.
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  • Data-driven sciences: From wonder cabinets to electronic databases.Bruno J. Strasser - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):85-87.
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  • Valuing Shorebirds: Bureaucracy, Natural History, and Expertise in North American Conservation.Kristoffer Whitney - 2020 - Journal of the History of Biology 53 (4):631-652.
    This article follows shorebirds—migratory animals that have gone from game to nongame animals over the course of the past century in North America—as a way to track modern field biology, bureaucratic institutions, and the valuation of wildlife. Doing so allows me to make interrelated arguments about the history of wildlife management and science. The first is to note the endurance of observation-based natural history methods in field biology over the long twentieth century and the importance of these methods for the (...)
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  • Filling China’s Gaps. Viral Banks and Bird Collections as Museums for Pandemics.Frédéric Keck - 2023 - Centaurus 65 (2):313-335.
    Two different kinds of collections have been used to anticipate influenza pandemics: viral strains and bird specimens. These collections have been organized in museums and data banks to fill the gaps when specimens were decaying or when viral strains were missing. This article asks how collecting practices changed when such collections integrated specimens from China, considered a reservoir of influenza viruses and bird species, following a recurrent critical trope that Chinese specimens were missing. The article shows that techniques for hunting (...)
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  • Who Owns What? Private Ownership and the Public Interest in Recombinant DNA Technology in the 1970s.Doogab Yi - 2011 - Isis 102 (3):446-474.
    ABSTRACT This essay analyzes how academic institutions, government agencies, and the nascent biotech industry contested the legal ownership of recombinant DNA technology in the name of the public interest. It reconstructs the way a small but influential group of government officials and university research administrators introduced a new framework for the commercialization of academic research in the context of a national debate over scientific research's contributions to American economic prosperity and public health. They claimed that private ownership of inventions arising (...)
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  • Computerizing Diagnosis: Keeve Brodman and the Medical Data Screen.Andrew Lea - 2019 - Isis 110 (2):228-249.
    In 1947, the Cornell psychiatrist Keeve Brodman and a handful of colleagues began developing what would become one of the most widely used health questionnaires of its time—the Cornell Medical Index (CMI). A rigidly standardized form, the CMI presented 195 yes-no questions designed to capture the health status of “the total patient.” Over the following decades, Brodman’s project of standardizing medical history taking gradually evolved into a project of mathematizing and computerizing diagnosis: out of the CMI grew the Medical Data (...)
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  • From garden biotech to garage biotech: amateur experimental biology in historical perspective.Helen Anne Curry - 2014 - British Journal for the History of Science 47 (3):539-565.
    This paper describes the activities of amateur plant breeders and their application of various methods and technologies derived from genetics research over the course of the twentieth century. These ranged from selection and hybridization to more interventionist approaches such as radiation treatment to induce genetic mutations and chemical manipulation of chromosomes. I argue that these activities share characteristics with twenty-first-century do-it-yourself (DIY) biology (a recent upswing in amateur experimental biology) as well as other amateur science and technology of the twentieth (...)
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