•  4
    The central role of such epistemic concepts as theory, explanation, model, or mechanism is rarely questioned in philosophy of science. Yet, what is their actual use in the practice of science? In this philosophy of science project, we deploy text-mining methods to investigate the usage of 61 epistemic notions in a corpus of full-text articles from the biological and biomedical sciences (N=73,771). The influence of disciplinary context is also examined by splitting the corpus into sub-disciplinar…Read more
  •  6
    This release includes the data and code used in: Malaterre, C., F. Lareau (2023) Inferring social networks from unstructured text data: A proof of concept detection of “hidden communities of interest”. Text and Data Analytics for Policy.
  •  17
    Misconceptions in Science
    with Emmanuelle J. Javaux and Purificación López-García
    Perspectives on Science 31 (6): 717-743. 2023.
    Disagreement in science exists in a variety of strengths, from doubt-raising articles and issues of non-reproducibility up to raging disputes and major controversies. An often-latent form of disagreement consists of misconceptions whereby false ideas are held that run contrary to what is commonly accepted as knowledge. Misconceptions have been the focus of much research in education science and psychology. Here we draw attention to misconceptions that may arise in the very practice of science. W…Read more
  •  13
    This release includes the code and supplementary information mentioned in: Malaterre, Christophe & Martin Léonard. 2023. "Charting the Territories of Epistemic Concepts in the Practice of Science: A Text-Mining Approach", British Journal for the Philosophy of Science.
  •  16
    Scientific networks are often investigated by means of citation analyses. Yet, interpretation of such networks in terms of semantic (and often disciplinary) content heavily depends on supplementary knowledge, notably about author research specialties. Similar situations arise more generally in many types of social networks whose semantic interpretation relies on supplementary information. Here, author community net-works are inferred from a topic model which provides direct insights into the sem…Read more
  •  16
    Topic model is a well proven tool to investigate the semantic content of textual corpora. Yet corpora sometimes include texts in several languages, making it impossible to apply language-specific computational approaches over their entire content. This is the problem we encountered when setting to analyze a philosophy of science corpus spanning over eight decades and including original articles in Dutch, German and French, on top of a large majority of articles in English. To circumvent this mul…Read more
  •  23
    Natural Selection beyond Life? A Workshop Report
    with Sylvain Charlat, André Ariew, Pierrick Bourrat, María Ferreira Ruiz, Thomas Heams, Philippe Huneman, Sandeep Krishna, Michael Lachmann, Nicolas Lartillot, Louis Le Sergeant D'Hendecourt, Philippe Nghe, Etienne Rajon, Olivier Rivoire, Matteo Smerlak, and Zorana Zeravcic
    Life 11 (10): 1051. 2021.
    Natural selection is commonly seen not just as an explanation for adaptive evolution, but as the inevitable consequence of “heritable variation in fitness among individuals”. Although it remains embedded in biological concepts, such a formalisation makes it tempting to explore whether this precondition may be met not only in life as we know it, but also in other physical systems. This would imply that these systems are subject to natural selection and may perhaps be investigated in a biological …Read more
  •  44
    Pluralism is widely appealed to in many areas of philosophy of science, though what is meant by ‘pluralism’ may profoundly vary. Because explanations of behaviour have been a favoured target for pluralistic theses, the sciences of behaviour offer a rich context in which to further investigate pluralism. This is what the topical collection The Biology of Behaviour: Explanatory pluralism across the life sciences is about. In the present introduction, we briefly review major strands of pluralist th…Read more
  •  47
    Eight journals over eight decades: a computational topic-modeling approach to contemporary philosophy of science
    with Francis Lareau, Davide Pulizzotto, and Jonathan St-Onge
    Synthese 199 (1-2): 2883-2923. 2020.
    As a discipline of its own, the philosophy of science can be traced back to the founding of its academic journals, some of which go back to the first half of the twentieth century. While the discipline has been the object of many historical studies, notably focusing on specific schools or major figures of the field, little work has focused on the journals themselves. Here, we investigate contemporary philosophy of science by means of computational text-mining approaches: we apply topic-modeling …Read more
  •  12
    The history and philosophy of the Origin of Life
    with David Dunér and Wolf Geppert
    International Journal of Astrobiology 15 (S4). 2016.
  •  26
    Revisiting three decades of Biology and Philosophy: a computational topic-modeling perspective
    with Davide Pulizzotto and Francis Lareau
    Biology and Philosophy 35 (1): 5. 2020.
    Though only established as a discipline since the 1970s, philosophy of biology has already triggered investigations about its own history The Oxford handbook of philosophy of biology, Oxford University Press, New York, pp 11–33, 2008). When it comes to assessing the road since travelled—the research questions that have been pursued—manuals and ontologies also offer specific viewpoints, highlighting dedicated domains of inquiry and select work. In this article, we propose to approach the history …Read more
  •  18
    Revisiting three decades of Biology and Philosophy : a computational topic-modeling perspective
    with Davide Pulizzotto and Francis Lareau
    Biology and Philosophy 35 (1): 5. 2020.
    Though only established as a discipline since the 1970s, philosophy of biology has already triggered investigations about its own history The Oxford handbook of philosophy of biology, Oxford University Press, New York, pp 11–33, 2008). When it comes to assessing the road since travelled—the research questions that have been pursued—manuals and ontologies also offer specific viewpoints, highlighting dedicated domains of inquiry and select work. In this article, we propose to approach the history …Read more
  •  17
    Best behaviour: A proposal for a non-binary conceptualization of behaviour in biology
    Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 79 101222. 2020.
  •  191
    Making Sense of Downward Causation in Manipulationism. Illustrations from Cancer Research
    History and Philosophy of the Life Sciences 4 (33): 537-562. 2011.
    Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998); yet for others, the causes of cancer are to be found not at the molecular level but at the tissue level and carcinogenesis would consist in a disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein & Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. A…Read more
  •  11
    La vie est-elle un phénomène émergent ? Traduit-elle l'apparition de propriétés nouvelles au niveau d'un tout, qui seraient irréductibles aux propriétés et à l'organisation des composants de ce tout, ou encore imprédictibles à partir de ces mêmes éléments ? Développée à la charnière des XIXe et XXe siècles comme alternative aux deux approches antinomiques du vivant que sont le vitalisme et le mécanisme, la notion philosophique d'émergence connaît aujourd'hui de nouveaux développements : avec la …Read more
  •  512
    Making Sense of Downward Causation in Manipulationism (with illustrations from cancer research)
    History and Philosophy of the Life Sciences (33): 537-562. 2011.
    Many researchers consider cancer to have molecular causes, namely mutated genes that result in abnormal cell proliferation (e.g. Weinberg 1998). For others, the causes of cancer are to be found not at the molecular level but at the tissue level where carcinogenesis consists of disrupted tissue organization with downward causation effects on cells and cellular components (e.g. Sonnenschein and Soto 2008). In this contribution, I ponder how to make sense of such downward causation claims. Adopting…Read more
  •  823
    Synthetic Biology and Synthetic Knowledge
    Biological Theory (8). 2013.
    Probably the most distinctive feature of synthetic biology is its being “synthetic” in some sense or another. For some, synthesis plays a unique role in the production of knowledge that is most distinct from that played by analysis: it is claimed to deliver knowledge that would otherwise not be attained. In this contribution, my aim is to explore how synthetic biology delivers knowledge via synthesis, and to assess the extent to which this knowledge is distinctly synthetic. On the basis of disti…Read more
  •  47
    La vie est-elle un phénomène émergent ? Traduit-elle l'apparition de propriétés nouvelles au niveau d'un tout, qui seraient irréductibles aux propriétés et à l'organisation des composants de ce tout, ou encore imprédictibles à partir de ces mêmes éléments ? Développées à la charnière des XIXe et XXe siècles comme alternative aux deux approches antinomiques du vivant que sont le vitalisme et le mécanisme, la notion philosophique d'émergence connait aujourd'hui de nouveaux développements : avec la…Read more