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O objetivo principal de nosso trabalho é descrever e analisar criticamente o núcleo da teoria da gastrea de Ernst Haeckel. Ele gira em torno de duas noções principais: forma gastrular e metazoário. A teoria da gastrea é um conjunto de formulações que visa estabelecer uma definição de metazoário a partir da noção de forma gastrular. O argumento central da teoria da gastrea articula essas duas noções para organizar a partir de estudos de embriologia comparativa uma visão geral da história evolutiva do reino animal. / The main goal of our work is to describe and critically analyze the core of the gastrea theory of Ernst Haeckel. It centers around two main notions: gastrula form and metazoan. The gastrea theory is a set of formulations designed to establish a definition of metazoan from the notion of gastrula form. The central argument of the gastrea theory articulates these two notions to organize from studies of comparative embryology an overview of evolutionary history of the animal kingdom.

L’objectif de cette thèse est de fournir un cadre théorique pour l’analyse philosophique des pratiques classificatoires en sciences. La classification, définie comme étant un geste épistémique dont l’objectif est de fournir une description du monde par découpage et discrimination, et par mise en relation des catégories ainsi formées, est un point de rencontre naturel entre philosophie et sciences. La tradition des espèces naturelles, considérée en philosophie des sciences comme la principale approche disponible pour l’analyse des pratiques classificatoires, est toutefois lacunaire. Dans le cadre de cette thèse, je démontre les faiblesses de cette approche et le besoin de mobiliser d’autres ressources épistémologiques pour penser la classification. À cet effet, je m’inspire de travaux en philosophie de la mesure s’inscrivant dans un courant de pensée que j’appelle le cohérentisme historique. Ces approches mettent l’accent sur les pratiques inférentielles et sur la charge théorique des observations en plus d’insister sur le dynamisme scientifique et la multitude de facteurs qui l’influencent (principe de respect, impératif de progrès, développements théoriques, nouveaux outils [mathématiques ou matériels], nouvelles données, histoire du champ disciplinaire, structure sociale de la recherche, etc.). Une fois ce cadre d’analyse épistémologique présenté en détail, je le mobilise pour étudier un ensemble de pratiques classificatoires en sciences, soit les pratiques phylogénétiques contemporaines. La phylogénétique est la discipline biologique qui vise à retracer les liens généalogiques qui unissent les êtres vivants. Les gènes et organismes sont ainsi regroupés au sein d’unités taxonomiques qui sont par la suite mises en relation. Ce champ disciplinaire a longtemps été associé de façon intime et exclusive au modèle arborescent, lui-même associé à la théorie de l’évolution par voie de sélection naturelle : les liens phylogénétiques entre organismes sont généralement représentés sous la forme d’un arbre, soit l’Arbre du vivant. Or, les dernières décennies ont vu émerger, au sein de la discipline, un compétiteur : le modèle réticulé. En analysant les différences et similarités qui lient ces deux types de modèles (modèles arborescents et modèles réseaux), je démontre que la transition d’un modèle à l’autre n’influence que superficiellement la pratique puisque la majorité de ses déterminants demeure inchangée. En bref, cette thèse présente un cadre d’analyse philosophique pour appréhender les pratiques classificatoires en sciences. J’importe des principes et des outils issus de travaux de la philosophie de la mesure afin de développer une philosophie de la classification qui comble les lacunes de la tradition des espèces naturelles. En s’ancrant dans ce que j’appelle le cohérentisme historique, cette thèse contribue non seulement à la bonne compréhension des pratiques classificatoires d’un point de vue épistémologique, mais aussi à la bonne compréhension des pratiques phylogénétiques contemporaines et de l’importante transition qui éloigne cette discipline de son modèle classique, soit l’Arbre du vivant. / The main objective of this dissertation is to offer a philosophical framework for the analysis of scientific classificatory practices. Classification, here defined as an epistemic action that describes the world by breaking down phenomena into categories and by establishing relevant relationships between these categories, is a natural bridge between philosophy and science. The tradition of natural kinds, which is currently the main approach in philosophy of science for analysing classificatory practices, has important shortcomings when it comes to epistemologically analyzing scientific classification. In this dissertation, I highlight these weaknesses and the consequent need to develop a novel framework for tackling classificatory practices. To achieve this, I draw on an existing trend in philosophy of measurement, which I coined historical coherentism. This approach is centered on the analysis of inferential practices and stresses the importance of the theoretical charge of observations. It also focuses on the dynamic nature of scientific fields and on the variety of factors that determine scientific progress (principle of respect, imperative of progress, theoretical developments, mathematical and material innovations, new data, the history of a field of research, the social structure of the scientific community, etc.). After the detailed presentation and exploration of this epistemological framework, I use it to tackle a set of scientific classificatory practices, namely contemporary phylogenetic practices. Phylogenetics is the biological discipline that aims to reconstruct the genealogical relationships uniting living beings. Genes and organisms are grouped into operative taxonomic units, and these units are then connected within a system. Since its inception, phylogenetics has been intimately tied to tree-based models, with these tree-based models themselves tied to the theory of evolution by means of natural selection: the phylogenetic system connecting all living organisms takes the form of a tree, the Tree of Life. In the last few decades, however, an alternative type of models has gained more attention and support within the field: network-based models. Using historical coherentism, I analyze the differences and similarities between the two competing types of models (tree-based models and network-based models) and show that the transition from one to the other only superficially changes phylogenetic practices. Indeed, many factors that constrain these practices remain unchanged whether researchers use tree-based or network-based models. In short, this thesis presents a philosophical framework for the analysis of classificatory practices in sciences. I use various principles and tools imported from the philosophy of measurement to develop a philosophy of classification that covers the weaknesses of the tradition of natural kinds. By anchoring my work in historical coherentism, I contribute not only to our understanding of classificatory practices, from an epistemological perspective, but also to a better understanding of contemporary phylogenetic practices and of the significant transition that leads this discipline away from its classical model, the Tree of Life.

This thesis addresses key issues of scientific realism in the philosophy of biology and chemistry through investigation of an underexplored research domain: olfaction theory, or the science of smell. It also provides the first systematic overview of the development of olfactory practices and research into the molecular basis of odours across the 19th and 20th century. Historical and contemporary explanations and modelling techniques for understanding the material basis of odours are analysed with a specific focus on the entrenchment of technological process, research tradition and the definitions of materiality for understanding scientific advancement. The thesis seeks to make sense of the explanatory and problem solving strategies, different ways of reasoning and the construction of facts by drawing attention to the role and application of scientific representations in olfactory practices. Scientific representations such as models, classifications, maps, diagrams, lists etc. serve a variety of purposes that range from the stipulation of relevant properties and correlations of the research materials and the systematic formation of research questions, to the design of experiments that explore or test particular hypotheses. By examining a variety of modelling strategies in olfactory research, I elaborate on how I understand the relation between representations and the world and why this relation requires a pluralist perspective on scientific models, methods and practices. Through this work I will show how a plurality of representations does not pose a problem for realism about scientific entities and their theoretical contexts but, on the contrary, that this plurality serves as the most reliable grounding for a realistic interpretation of scientific representations of the world and the entities it contains. The thesis concludes that scientific judgement has to be understood through its disciplinary trajectory, and that scientific pluralism is a direct consequence of the historicity of scientific development.