Stem cells have a central place in biology. Through their ability to self-renew and differentiate, they maintain, repair and, in some cases, regenerate tissues. However, there is no consensus nowadays on what exactly is a stem cell. Experimental data accumulated in recent years have challenged the traditional view that stem cells are discrete and isolable entities and that differentiation is an irreversible process. They also revealed an unsuspected heterogeneity between different varieties of stem cells. This context of conceptual questioning is conducive to philosophical analysis, and several contributions from philosophers have already led to important clarifications, particularly on the properties of self-renewal and differentiation, or on conflicting conceptions of stem cells. But the work of stem cell philosophers constantly faces limitations due to lack of appropriate data. Based on this observation, our STEM project combines philosophy with phylogenetic and experimental approaches, which together will lead to a better understanding of stem cells. In an earlier analysis of stem cell diversity, we have showed that stemness could be four types of property, each having a different ontology. Depending on the tissue, it may be a categorical property (intrinsic), a dispositional property (intrinsic but whose expression depends on extrinsic stimuli), a relational property (extrinsic, induced by the microenvironment), or a systemic property (extrinsic, regulated at the level of the cell population). This analysis raised two issues that are the subject of STEM. (1) Stem cell unity: If stemness can be of different natures, does it mean that the stem cell category artificially regroups different cell types? In other words, are stem cells a natural kind? (2) Stability of stemness ontology: Are the four stemness ontologies mutually exclusive or porous? That is to say, is the nature of stemness stable for each stem cell variety or can it switch from being one type of property to being another in certain contexts such as regeneration or pathology? Both of these issues have important implications for biology and medicine as answers to these questions lead to different research programs and therapeutic strategies. To resolve the question of stem cell unity, we will use a phylogenetic approach to determine whether stem cells have a common evolutionary origin or whether our classification describes stem cell types with separate origins—in the latter case stem cells cannot belong to a natural kind. To study the stability of stemness, we will use experimental approaches to explore stemness in a regenerative context (with an animal model with high regenerative capacity) and in a pathological context (with a murine model of acute myeloid leukemia induced by a translocation that allows the acquisition of stemness by non-stem cells). We will examine implications of these data for stem cell biology and clinical applications. Experimental and phylogenetic analyses will also allow us to renew the work undertaken by other philosophers that faced limitations of available data, particularly the proposal to develop a definition of stem cells by homeostatic property cluster that holds great promise but failed to efficiently distinguish stem cells from non-stem cells. Finally, we will adopt a larger perspective on the methodology used in this project and analyze the benefits, risks and pitfalls of the integration of scientific approaches for philosophical purposes.

The evolution of scientific knowledge is directly related to the history of humanity. Document archives and bibliographic sources like the “Web Of Science” or PubMed contain a valuable source for the analysis and reconstruction of this evolution. The proposed project takes as starting point the contributions of D. Chavalarias and J.P. Cointet about the analysis of the dynamicity of evolutive corpora and the automatic construction of “phylomemetic” topic lattices (as an analogy with genealogic trees of natural species). Currently existing tools are limited to the processing of medium sized collections and a non interactive usage. The expected project outcome is situated at the crossroad between Computer science and Social sciences. Our goal is to develop new highly performant tools for building phylomemetic maps of science by exploiting recent technologies for parallelizing tasks and algorithms on complex and voluminous data. These tools are conceived and validated in collaboration with experts in philosophy and history of science over large scientific archives.

Quantum theory emerged over the past century as one of humanity’s most profound scientific achievements. Since its inception, it has generated extensive philosophical inquiry, as its conceptual structure challenges traditional views on the nature of scientific theories, the structure of scientific explanation, and the role of the observer. As the central achievement of the quantum revolution, quantum field theory (QFT) provides the theoretical foundation for the most empirically successful theories in contemporary particle physics while also driving key developments in condensed matter and statistical physics. Despite its extraordinary empirical success, QFT encapsulates the core conceptual challenges of quantum theory for philosophy. Because QFT calculations are notoriously complex, physicists employ various strategies, such as focusing on effective field theories (EFTs) or renormalisation techniques, to manage this complexity. This project centres on two main questions: (RQ1) What are the metaphysical implications of EFTs for inter-theoretic relationships, the nature of physical laws, and the possibility of emergent phenomena in physics? (RQ2) How should we interpret the epistemological status of indispensable mathematical idealisations, such as infinities and renormalisation, in QFT? The central objective of this project in the philosophy of science is to investigate the hierarchy of levels of explanation within fundamental physics. This requires examining how QFT achieves its predictive accuracy and analysing its conceptual foundations. The core research hypothesis is that the a-theorem provides a powerful new perspective on these questions. The a-theorem is a recent result in physics that, by focusing on renormalisation group (RG) flows, tracks how a physical theory evolves across energy scales. This hypothesis is pursued because the a-theorem has the potential to revolutionise our understanding of scale and emergence in QFT. The theorem reveals an irreversible loss of degrees of freedom along RG flows, suggesting a hierarchical, asymmetric structure in which, for instance, higher-energy descriptions contain more information than lower-energy ones. This project will be the first to explore the philosophical significance of these results, specifically how the a-theorem provides a rigorous framework for addressing foundational questions in the philosophy of physics and science. I will argue that the emerging picture strongly supports the idea that EFTs possess a genuine degree of explanatory independence, challenging traditional reductionist views. Additionally, I will argue that the a-theorem offers a concrete framework for understanding renormalisation, providing decisive elements for an anti-reductionist picture according to which physical laws may be scale-dependent. In the long term, this project aims to develop a framework for addressing longstanding debates in the philosophy of physics and science. In particular, it will connect QFT’s treatment of emergence, renormalisation, and scale hierarchy to discussions on realism, the status of scientific theories, and the role of mathematical structures in explanation. Through its emphasis on emergence, asymmetry, and hierarchical organisation, this project will contribute to a unifying framework with three key elements: (1) an asymptotic view of scientific realism, where explanations converge hierarchically toward truth; (2) a critique of mechanistic explanations in fundamental physics, defending the essential role of structural constraints; and (3) a pluralistic view of scientific explanation, where different levels retain autonomy while being structurally constrained. This project will deepen our understanding of QFT while offering a novel perspective on scientific knowledge.

What is the environment, and in particular the environment that can have an impact on our health? What is its nature? How do we conceptualise it? The environment, in the broadest sense of the term, is at the heart of some of society's most pressing challenges. It raises issues that can only be tackled by combining scientific research with the views of the general public. There is a growing awareness among the latter, not only of the impact that the environment, as we have transformed it, can have on our health, but also of the way in which our habits and experiences throughout our lives are changing us and may contribute to the development of certain diseases. The EnviroParCiPhil project raises the question of participatory research methodologies that could be used on a large scale to change the definition of the (spatio-temporal) boundaries of the environment as a determinant of our states of health and disease. The aim is to establish collaboration between scientists and citizens in order to co-develop a methodology that can be replicated on a large scale to gain a better understanding of 'health-environment' issues. The aim is to listen to the views and questions of members of civil society in order to broaden the scope of research in the biomedical sciences and the humanities and social sciences into the environmental determinants of disease, and thus to strengthen the relevance of this research from a purely epistemic point of view but also at the service of citizens directly concerned by "exposures" and the public health policies that can protect them from these exposures. The object of the co-construction is therefore to co-develop a method for amending the concept of environment in health within the framework of cohorts, and to enable cohort members to become more involved in developing future research questions and analysis methodologies that will concern other epidemiology projects. This methodology therefore has an iterative dimension, with the concepts of environments expressed also being studied in philosophy of science on subsequent cohorts. The aim of this pilot project is to set a precedent and encourage researchers to use, in health-environment studies, research methodologies that mobilise participation as a conceptually and pragmatically enriching tool in interdisciplinary research, for example with the co-design of intervention studies. At the end of the project, a colloquium will bring together researchers from the fields concerned to assess the results of the project and to study the feasibility of using the methodologies generated in future research.

This project investigates the interplay between informal mathematical theories and their formalization, and argues that this dynamism generates three different forms of understanding: 1. Different kinds of formalizations fix the boundaries and conceptual dependences between concepts in different ways, thus contributing to our understanding of the content of an informal mathematical theory. We argue that this form of understanding of an informal theory is achieved by recasting it as a formal theory, i.e. by transforming its expressive means. 2. Once a formal theory is available, it becomes an object of understanding. An essential contribution to this understanding is made by our recognition of the theory in question as a formalization of a particular corpus of informal mathematics. This form of understanding will be clarified by studying both singular intended models, and classes of models that reveal the underlying conceptual commonalities between objects in different areas of mathematics. 3. The third level concerns how the study of different formalizations of the same area of mathematics can lead to a transformation of the content of those areas, and a change in the geography of informal mathematics itself. In investigating these forms of mathematical understanding, the project will draw on philosophical and logical analyses of case studies from the history of mathematical practice, in order to construct a compelling new picture of the relationship of formalization to informal mathematical practice. One of the main consequences of this investigation will be to show that the process of acquiring mathematical understanding is far more complex than current philosophical views allow us to account for. While formalization is often thought to be negligible in terms of its impact on mathematical practice, we will defend the view that formalization is an epistemic tool, which not only enforces limits on the problems studied in the practice, but also produces new modes of reasoning that can augment the standard methods of proof in different areas of mathematics. Reflecting on the interplay between informal mathematical theories and their formalization means reflecting on mathematical practice and on what makes it rigorous, and how this dynamism generates different forms of understanding. We therefore also aim to investigate the connection between the three levels of understanding described above, and the notion of rigor in mathematics. The notion of formal rigor (in the proof theoretic sense) has been extensively investigated in philosophy and logic, though an account of the epistemic role of the process of formalization is currently missing. We argue that formal rigor is best understood as a dynamic abstraction from informally rigorous mathematical arguments. Such informally rigorous arguments will be studied by critically analyzing case studies from different subfields of mathematics, in order to identify patterns of rigorous reasoning.