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Taking a Naturalistic Turn in the Health and Disease Debate by Jonathan Sholl & Simon Okholm

Abstract 
We situate the well-trodden debate about defining health and disease within the project of a metaphysics of science and its aim to work with and contribute to science. We make use of Guay and Pradeu’s ‘metaphysical box’ to reframe this debate, showing what is at stake in recent attempts to move beyond it, revealing unforeseen points of agreement and disagreement among new and old positions, and producing new questions that may lead to progress. We then discuss the implications of the two-way benefits between medicine and philosophy when the latter is driven and constrained by medical science.
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Out of our skull, in our skin: the Microbiota-Gut-Brain axis and the Extended Cognition Thesis by F. Boem, G. Ferreti, S. Zipoli Caiani

 

 
Abstract
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 ‘Externally Extended Cognition Thesis.’ This notion has generated a lively debate. Here, we offer a novel notion of extended cognition, according to which cognition can be seen as being realized (and expanded) outside the brain, but still inside the body. This is what we call the ‘Internally Extended Cognition Thesis’. Not only our thesis but also our approach while defending it is innovative. The argument we offer is supported by recent empirical findings in the life sciences and biomedicine, which suggest that the gut microbiota’s activity has a functional role in regulating our cognitive processes and behaviors. In doing so, we embrace the holobiont-perspective, according to which it is possible to claim that what we call biological individuals are not autonomous entities with clear boundaries, but should rather be seen as networks of multiple interactions among species. Thus, by analyzing different sets of evidence in light of the holobiont-perspective, we argue that the gut microbiota could be seen as a component of our organism. On the basis of the philosophical interpretation of this evidence, however, we also suggest that there are no impediments standing the way of considering the gut microbiota also as a functional extension of our cognitive system. If so, this amounts to extending cognition out of ‘our skull’, though still confining it within ‘our body’: to ‘our gut’. This is an instance of the ‘Internally Extended Cognition Thesis,’ whose benefits for an original (biologically informed) theory of extended cognition are discussed.
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The visibility of philosophy of science in the sciences, 1980–2018 by Khelfaoui M, Gingras Y, Lemoine M, Pradeu T

 
Abstract
In this paper, we provide a macro level analysis of the visibility of philosophy of science in the sciences over the last four decades. Our quantitative analysis of publications and citations of philosophy of science papers, published in 17 main journals representing the discipline, contributes to the longstanding debate on the influence of philosophy of science on the sciences. It reveals the global structure of relationships that philosophy of science maintains with science, technology, engineering and mathematics (STEM) and social sciences and humanities (SSH) fields. Explored at the level of disciplines, journals and authors, this analysis of the relations between philosophy of science and a large and diversified array of disciplines allows us to answer several questions: what is the degree of openness of various disciplines to the specialized knowledge produced in philosophy of science? Which STEM and SSH fields and journals have privileged ties with philosophy of science? What are the characteristics, in terms of citation and publication patterns, of authors who get their philosophy of science papers cited outside their field? Complementing existing qualitative inquiries on the influence of specific authors, concepts or topics of philosophy of science, the bibliometric approach proposed in this paper offers a comprehensive portrait of the multiple relationships that links philosophy of science to the sciences.
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Diseases are Not Adaptations and Neither are Their Causes by Paul E. Griffiths & John Matthewson

 
In a recent article in this journal, Zachary Ardern criticizes our view that the most promising candidate for a naturalized criterion of disease is the “selected effects” account of biological function and dysfunction. Here we reply to Ardern’s criticisms and, more generally, clarify the relationship between adaptation and dysfunction in the evolution of health and disease.
 
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How to build an effective research network: lessons from two decades of the GARNet plant science community by Sabina Leonelli and al.

 
Successful collaborative research is dependent on excellent ideas and innovative experimental approaches, as well as the provision of appropriate support networks. Collaboration requires venues, infrastructures, training facilities, and, perhaps most importantly, a sustained commitment to work together as a community. These activities do not occur without significant effort, yet can be facilitated and overseen by the leadership of a research network that has a clearly defined role to help build resources for their community. Over the past 20 years, this is a role that the UKRI-BBSRC-funded GARNet network has played in the support of the UK curiosity-driven, discovery-led plant science research community. This article reviews the lessons learnt by GARNet in the hope that they can inform the practical implementation of current and future research networks.
 
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The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems by Sabina Leonelli and al.

 
The deployment of digital technology in Agriculture and Food Science accelerates the production of large quantities of multidisciplinary data. The Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture harnesses the international ontology expertise that can guide teams managing multidisciplinary agricultural information platforms to increase the data interoperability and reusability. The CoP develops and promotes ontologies to support quality data labeling across domains, e.g., Agronomy Ontology, Crop Ontology, Environment Ontology, Plant Ontology, and Socio-Economic Ontology.
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Data Science in Times of Pan(dem)ic by Sabina Leonelli

What are the priorities for data science in tackling COVID-19 and in which ways can big data analysis inform and support responses to the outbreak? It is imperative for data scientists to spend time and resources scoping, scrutinizing and questioning the possible scenarios of use of their work – particularly given the fast-paced knowledge production required by an emergency situation such as the coronavirus pandemic. In this paper I provide a scaffold for such considerations by identifying five ways in which the data science contributions to the pandemic response are imagined and projected into the future, and reflecting on how such imaginaries inform current allocations of investment and priorities within and beyond the scientific research landscape. The first two of these imaginaries, which consist of (1) population surveillance and (2) predictive modelling, have dominated the first wave of governmental and scientific responses with potentially problematic implications for both research and society. Placing more emphasis on the latter three imaginaries, which include (3) causal explanation, (4) evaluation of logistical decisions and (5) identification of social and environmental need, I argue, would provide a more balanced, sustainable and responsible avenue towards using data science to support human co-existence with coronavirus.
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Character identity mechanisms: a conceptual model for comparative-mechanistic biology by Günter P. Wagner and al.

 

 
There have been repeated attempts in the history of comparative biology to provide a mechanistic account of morphological homology. However, it is well-established that homologues can develop from diverse sets of developmental causes, appearing not to share any core causal architecture that underwrites character identity. We address this challenge with a new conceptual model of Character Identity Mechanisms (ChIMs). ChIMs are cohesive mechanisms with a recognizable causal profile that allows them to be traced through evolution as homologues despite having a diverse etiological organization. Our model hypothesizes that anatomical units at different levels of organization—cell types, tissues, and organs—have level-specific ChIMs with different conserved parts, activities, and organization. Relying on a methodology of conceptual engineering, we show how the ChIM concept advances our understanding of the developmental basis of morphological characters, while forging an important link between comparative and mechanistic biology.
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Multilayer intraclonal heterogeneity in chronic myelomonocytic leukemia by Lucie Laplane and al.

 

 
The functional diversity of cells that compose myeloid malignancies, i.e., the respective roles of genetic and epigenetic heterogeneity in this diversity, remains poorly understood. This question is addressed in chronic myelomonocytic leukemia, a myeloid neoplasm in which clinical diversity contrasts with limited genetic heterogeneity. To generate induced pluripotent stem cell clones, we reprogrammed CD34+ cells collected from a patient with a chronic myelomonocytic leukemia in which whole exome sequencing of peripheral blood monocyte DNA had identified 12 gene mutations, including a mutation in KDM6A and two heterozygous mutations in TET2 in the founding clone and a secondary KRAS(G12D) mutation. CD34+ cells from an age-matched healthy donor were also reprogrammed. We captured a part of the genetic heterogeneity observed in the patient, i.e. we analyzed five clones with two genetic backgrounds, without and with the KRAS(G12D) mutation. Hematopoietic differentiation of these clones recapitulated the main features of the patient’s disease, including overproduction of granulomonocytes and dysmegakaryopoiesis. These analyses also disclosed significant discrepancies in the behavior of hematopoietic cells derived from induced pluripotent stem cell clones with similar genetic background, correlating with limited epigenetic changes. These analyses suggest that, beyond the coding mutations, several levels of intraclonal heterogeneity may participate in the yet unexplained clinical heterogeneity of the disease.
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