In this presentation we will discuss three theoretical principles for biology: the principle of organization, the principle of variation and the default state of cells. We will propose possible applications to understand hormone action.
Journal of biosciences
Lacking an operational theory to understand life cycles hinders progress in biology. We discuss elements towards such a theory, such as inertia and thermodynamics.
Lacking an operational theory to explain the organization and behaviour of matter in unicellular and multicellular organisms hinders progress in biology. Such a theory should address life cycles from ontogenesis to death. This theory would complement the theory of evolution that addresses phylogenesis, and would posit theoretical extensions to accepted physical principles and default states in order to grasp the living state of matter and define proper biological observables. Thus, we favour adopting the default state implicit in Darwin’s theory, namely, cell proliferation with variation plus motility, and a framing principle, namely, life phenomena manifest themselves as non-identical iterations of morphogenetic processes. From this perspective, organisms become a consequence of the inherent variability generated by proliferation, motility and self-organization. Morphogenesis would then be the result of the default state plus physical constraints, like gravity, and those present in living organisms, like muscular tension.
Keywords: Animals, Biological Evolution, Biophysics/methods, Cell Division, Mice, Models, Morphogenesis, Thermodynamics
We argue that a theory of biological systems should rely on organization and variation as theoretical principles. As such, these principles are fundamental for the biological domain: biological systems are organized natural systems that undergo (functional) variation. In this paper, we provide a specific characterization of each principle, by emphasizing their mutual relations: organization provides the relevant kind of complexity for functional variation to occur; in turn, variation enables the maintenance of organization over time, notably at the evolutionary scale. We will illustrate this discussion with examples from plant morphogenesis.
We developed 3D culture methods that reproduce mammary gland ductal morphogenesis in in vitro conditions. We are proposing a conceptual framework to understand morphogenetic events based on epistemological sound biological principles instead of the common practice of using purely biophysical approaches. More specifically, our theoretical framework is based on the principle that the default state of cells is proliferation with variation and motility. We emphasize the role played by the agency of cells embedded in a gel and the circularity that is relevant for the intended process, whereby cells act upon other cells and matrix elements, and are subject to the agentivity of neighboring cells. This circularity strongly differs from classical linear causality. Finally, our approach opens up the study of causal determination to multilevel explanations rather than reductive ones involving only molecules in general and genes in particular.
We argue that a theory of biological systems should rely on organization and variation as fundamental theoretical principles. Biological systems are organized natural systems that undergo functional variation. In this presentation we will provide a specific characterization of each principle while emphasizing their mutual relations. Organization provides the relevant kind of complexity for functional variation occur; and, in turn, variation enables the maintenance of organization over time, notably at the evolutionary scale.
La relation entre biodiversité, variabilité, adaptabilité et résilience des systèmes vivants, soumis aux perturbations imprédictibles caractéristiques des systèmes complexes, quelles que soient leurs échelles, doit être questionnée, même en l’absence de mécanismes causalistes identifiables. La rencontre interdisciplinaires entre biologistes, immunologistes, écologues, philosophes, mathématiciens, physiciens, informaticiens permettra l’étude des concepts de diversité et de variabilité dans le vivant adaptatif et de leurs rôles dans la résilience des systèmes vivants multi-échelles et organisés. Le système immunitaire adaptatif en cognition de l’environnement moléculaire des êtres vivants a co-évolué pour permettre la tolérance ou destruction de tissus et du microbiote et présente une biodiversité cellulaire et moléculaire exceptionnelle. Ces systèmes représentent des modèles d’étude de l’organisation et variation de systèmes dynamiques multi-échelles tout comme les écosystèmes macroscopiques. Il s’agira donc à travers les échelles des systèmes étudiés d’établir les modalités de synergie entre biodiversité et résilience ou robustesse.
Le vivant critique et chaotique
Ce texte présente un modèle pour le temps biologique ainsi que des idées plus générales sur l’articulation entre mathématiques et objets biologiques.
Ce texte présente un modèle pour le temps biologique ainsi qu’un certain nombre d’idées plus générales sur l’articulation entre mathématiques et objets biologiques, fondées sur des propositions théoriques. Nous décrivons d’abord un modèle géométrisant le temps des mammifères, basé en partie sur la notion d’allométrie. Ce modèle permet de mettre en évidence la structure de la variabilité des rythmes biologiques et de discriminer cas sains et cas pathologiques. Nous utilisons cet exemple pour illustrer les principes permettant la mathématisation. Nous discutons comment s’articulent mathématiques et définition théorique des objets physiques. Nous mettons en particulier l’accent sur le rôle que jouent les symétries théoriques pour justifier ces définitions, tant au niveau de la constitution d’un espace de description que de l’obtention d’équations déterminant la trajectoire suivie par un objet. Nous abordons aussi les transitions de phases comme situations paradigmatiques où les symétries d’un système changent. Ceci nous amène à proposer que les objets biologiques (organismes, cellules) sont caractérisés par une instabilité de leurs symétries théoriques. Les objets prennent alors un sens différent de celui qu’ils ont en physique : ils font preuve de variabilité et sont fondamentalement historiques. Ceci n’empêche pas la présence d’éléments de stabilité chez le vivant, mais les symétries biologiques prennent un sens différent des symétries fondamentales de la physique.
Biophysical approaches to biological phenomena have provided fruitful insights, yet they generally suffer from the direct transposition of physical paradigms and methods in biology, without the deep justifications that exist in physics (as for the conservation of energy for example). In this context, we feel that it is extremely fruitful to propose theoretical principles that are genuinely biological, and frame the discussion and the mathematical analysis of biological processes. In this talk, we will discuss a framing principle for biology: biological processes can be interpreted as the never-identical iteration of morphogenetic processes. The iteration mentioned in this principle takes place both at the level of tissues and organs, where it can lead to fractal-like structures, for example, and at the level of organisms (including cells), where it leads to the flow of generations, which phylogeny aims to reconstruct. The non-identical character of these iterations correspond to a specific form of variation: it is not just quantitative changes that we aim to characterize but changes in the mathematical regularities that enable to study the corresponding processes. We will discuss how the concept of never identical iteration of a morphogenetic process enables to better understand both ontogenetic and phylogenetic processes, and illustrate this with the morphology of mammary gland epithelium. Note for example that phylogenetic analyses are based on the notion that individuals that are afar in the genealogy have different relevant characters. Last we will briefly discuss the epistemological consequences of this proposal as for the nature of the articulation between mathematics and biological phenomena.
We propose a theoretical and formal way to account for the various levels of organization that biological systems may realize. Our key assumption is that levels of organization are to be understood as specific networks of interdependences among the functional constituents. More precisely, we will rely on the notion of organizational closure, which refers to the mutual construction and stabilization of constituents playing the role of constraints within the system. A level of biological organization, we will argue, is a level of closure of constraints. With this characterization in hand, we will first discuss those situations in which different levels of organization can be distinguished, and hierarchically articulated, by relying on sharp discontinuities. In particular, this is the case of cells within multicellular organisms. We will then focus on those more complex cases in which the description of a level of organization requires appealing to the notion of “tendency to closure”, which aims to deal with the qualitative notion of level of organization by quantitative means. In particular, the tendency to closure involves a quantitative measure of functional interdependences at the relevant spatial scale at which constraints operate. We conclude with a preliminary discussion of the spatiotemporal conditions (in particular: the dependence on large space scale and small time scale) that enable the coherence of organisms realizing high levels of organization (e.g. mammals).
In this presentation, we will contrast the articulation between mathematics and phenomena that is performed in physical theorizing with the situation in biology.short, physical theorizing is grounded on stable mathematical structures, defined by theoretical symmetries and corresponding conservation principles. By contrast, itfair to postulate that biological organizations exhibit changes of such structures over time. This will enable us to define a strong notion of variability, which differs from quantitative variations. Variability will then play the role of a fundamental principle for biology. We will also discuss the consequences of these ideas on the form that a general theory of biological organization may have.
