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53Out of our skull, in our skin: the Microbiota-Gut-Brain axis and the Extended Cognition ThesisBiology and Philosophy 36 (2): 1-32. 2021.According to a shared functionalist view in philosophy of mind, a cognitive system, and cognitive function thereof, is based on the components of the organism it is realized by which, indeed, play a causal role in regulating our cognitive processes. This led philosophers to suggest also that, thus, cognition could be seen as an extended process, whose vehicle can extend not only outside the brain but also beyond bodily boundaries, on different kinds of devices. This is what we call the ‘External…Read more
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11Epistemic misalignments in microbiome researchBioessays 46 (4): 2300220. 2024.We argue that microbiome research should be more reflective on the methods that it relies on to build its datasets due to the danger of facing a methodological problem which we call “epistemic misalignment.” An epistemic misalignment occurs when the method used to answer specific scientific questions does not track justified answers, due to the material constraints imposed by the very method. For example, relying on 16S rRNA to answer questions about the function of the microbiome generates epis…Read more
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119“Microbiota, symbiosis and individuality summer school” meeting reportMicrobiome 8 117. 2020.How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and hum…Read more
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103Why genes are like lemonsStudies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 57 (June): 88-95. 2016.In the last few years, the lack of a unitary notion of gene across biological sciences has troubled the philosophy of biology community. However, the debate on this concept has remained largely historical or focused on particular cases presented by the scientific empirical advancements. Moreover, in the literature there are no explicit and reasonable arguments about why a philosophical clarification of the concept of gene is needed. In our paper, we claim that a philosophical clarification of th…Read more
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17Technology-driven surrogates and the perils of epistemic misalignment: an analysis in contemporary microbiome scienceSynthese 200 (6): 1-28. 2022.A general view in philosophy of science says that the appropriateness of an object to act as a surrogate depends on the user’s decision to utilize it as such. This paper challenges this claim by examining the role of surrogative reasoning in high-throughput sequencing technologies as they are used in contemporary microbiome science. Drawing on this, we argue that, in technology-driven surrogates, knowledge about the type of inference practically permitted and epistemically justified by the surro…Read more
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8A Logic for a Critical Attitude?Logic and Logical Philosophy 1-28. forthcoming.Individuating the logic of scientific discovery appears a hopeless enterprise. Less hopeless is trying to figure out a logical way to model the epistemic attitude distinguishing the practice of scientists. In this paper, we claim that classical logic cannot play such a descriptive role. We propose, instead, one of the three-valued logics in the Kleene family that is often classified as the less attractive one, namely Hallden’s logic. By providing it with an appropriate epistemic interpretation, …Read more
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25Science and Politics in a Time of Pandemic: Some Epistemological and Political Lessons from the Italian StoryHumana Mente 14 (40). 2021.Making public policy choices based on available scientific evidence is an ideal condition for any policy making. However, the mechanisms governing these scenarios are complex, non-linear, and, alongside the medical-health and epidemiological issues, involve socio-economic, political, communicative, informational, ethical and epistemological aspects. In this article we analyze the role of scientific evidence when implementing political decisions that strictly depend on it, as in the case of the C…Read more
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26Public Health Policies: Philosophical Perspectives Between Science and DemocracyHumana Mente 14 (40). 2021.COVID19 pandemic has clarified that public health policies are central for the future of human societies from several perspectives. As a matter of fact, they are based on certain premises that are practical-political (e.g., ensuring the health of citizens), moral (e.g., health is a value), or epistemological (e.g., certain ideas concerning expertise and shared knowledge). Indeed, effective policies require first and foremost not only to be based on reliable data and models (i.e., so-called evide…Read more
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13La mente estesa ma individuata: una prospettiva simbioticaRivista Internazionale di Filosofia e Psicologia 12 (3): 254-270. 2021.Riassunto: Nell’ambito delle associazioni simbiotiche ha acquisito credito crescente la cosiddetta prospettiva “olobiontica”, secondo cui animali e piante non dovrebbero più essere considerati entità autonome, con confini chiaramente delimitati, ma li si dovrebbe vedere come unità funzionali che consistono di reti inter-relazionali tra specie diverse. In quest’ottica le funzioni precedentemente attribuite a un singolo componente devono essere riviste alla luce della prospettiva relazionale e con…Read more
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16The experimental practice in contemporary molecular biology oscillates between the creativity of the researcher in tinkering with the experimental system, and the necessity of standardization of methods of inquiry. Experimental procedures, when standardized in lab protocols, might definitely be seen as actual recipes. Considering these protocols as recipes can help us understand some epistemological characteristics of current practice in molecular biology. On the one hand, protocols represent a …Read more
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38The Cochrane Case: An Epistemic Analysis on Decision-Making and Trust in Science in the Age of InformationFoundations of Science 28 (1): 143-158. 2020.In this study we analyze a recent controversy within the biomedical world, concerning the evaluation of safety of certain vaccines. This specific struggle took place among experts: the Danish epidemiologist Peter Gøtzsche on one side and a respected scientific institution, the Cochrane, on the other. However, given its relevance, the consequences of such a conflict invest a much larger spectrum of actors, last but not least the public itself. Our work is aimed at dissecting a specific aspect hap…Read more
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10A ngela P otochnik, Idealization and the aims of science, Chicago: University of Chicago Press, 2017, 252 pp., $45.00, ISBN 9780226507057 (review)History and Philosophy of the Life Sciences 41 (4): 44. 2019.
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8A ngela P otochnik, Idealization and the aims of science, Chicago: University of Chicago Press, 2017, 252 pp., $45.00, ISBN 9780226507057 (review)History and Philosophy of the Life Sciences 41 (4): 44. 2019.
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16A ngela P otochnik, Idealization and the aims of science, Chicago: University of Chicago Press, 2017, 252 pp., $45.00, ISBN 9780226507057 (review)History and Philosophy of the Life Sciences 41 (4): 44. 2019.
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13Orienteering Tools: Biomedical Research with OntologiesHumana Mente 9 (30). 2016.Biomedical ontologies are considered a serious innovation for biomedical research and clinical practice. They promise to integrate information coming from different biological databases thus creating a common ground for the representation of knowledge in all the life sciences. Such a tool has potentially many implications for both basic biomedical research and clinical practice. Here I discuss how this tool has been generated and thought. Due to the analysis of some empirical cases I try to elab…Read more
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70Diverse perspectives on ontology: A joint report on the First IAOA Interdisciplinary Summer School on Ontological AnalysisApplied ontology 8 (1): 59-71. 2013.
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33The Main Faces of RobustnessDialogue and Universalism 27 (3): 157-172. 2017.In the last decade, robustness has been extensively mentioned and discussed in biology as well as in the philosophy of the life sciences. Nevertheless, from both fields, someone has affirmed that this debate has resulted in more semantic confusion than in semantic clearness. Starting from this claim, we wish to offer a sort of prima facie map of the different usages of the term. In this manner we would intend to predispose a sort of “semantic platform” which could be exploited by those who wish …Read more
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92Junk or functional DNA? ENCODE and the function controversyBiology and Philosophy 29 (6): 807-831. 2014.In its last round of publications in September 2012, the Encyclopedia Of DNA Elements (ENCODE) assigned a biochemical function to most of the human genome, which was taken up by the media as meaning the end of ‘Junk DNA’. This provoked a heated reaction from evolutionary biologists, who among other things claimed that ENCODE adopted a wrong and much too inclusive notion of function, making its dismissal of junk DNA merely rhetorical. We argue that this criticism rests on misunderstandings concer…Read more
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4Towards a Notion of Intervention in Big-Data Biology and Molecular MedicineIn Marco Nathan & Giovanni Boniolo (eds.), Foundational Issues in Molecular Medicine, Routledge. 2016.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 a…Read more
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