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Contents tagged “constraints”

There are 9 contents with the tag “constraints”:

  1. Il faut qu’il y ait en informatique théorique un symbole tel qu’il empêche de calculer

    Prendre Soin de l’informatique et Des Générations


    Pour progresser sur la question du rapport entre l’informatique et le calculable, je propose de réinterpréter l’objet de l’informatique théorique puis de faire un détour par la biologie théorique où la question d’un symbole qui empêche de calculer se pose. Enfin, je reviens vers l’informatique en...

    Abstract

    Pour progresser sur la question du rapport entre l’informatique et le calculable, je propose de réinterpréter l’objet de l’informatique théorique puis de faire un détour par la biologie théorique où la question d’un symbole qui empêche de calculer se pose. Enfin, je reviens vers l’informatique en transférant de manière critique certains concepts issus de mes travaux en biologie théorique.

    Citation
    Montévil, Maël. n.d. “Il Faut Qu’il y Ait En Informatique Théorique Un Symbole Tel Qu’il Empêche de Calculer.” In Prendre Soin de l’informatique et Des Générations, edited by Anne Alombert, Victor Chaix, and Maël Montévil. Fip
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  2. Le sens des formes en biologie

    Le sens des formes en biologie

    Biomorphisme. Approches sensibles et conceptuelles des formes du vivant


    Dans l’interface entre biologie et mathématiques, les formes et les processus de morphogenèse sont souvent étudiées pour eux-mêmes. Nous pensons que cette manière de procéder est insuffisante pour capturer le sens biologique de ces formes. La biologie comporte des spécificités qui se manifestent...

    Abstract

    Dans l’interface entre biologie et mathématiques, les formes et les processus de morphogenèse sont souvent étudiées pour eux-mêmes. Nous pensons que cette manière de procéder est insuffisante pour capturer le sens biologique de ces formes. La biologie comporte des spécificités qui se manifestent tant sur le plan philosophique que sur celui des principes théoriques : en particulier, tout processus biologique tel qu’un processus de morphogenèse ou une régulation physiologique (i) s’inscrit dans l’évolution et dans une histoire naturelle et (ii) s’intègre dans un organisme dont il dépend et auquel il participe. Nous aborderons alors le sens des formes biologiques à l’aune de ces principes, tant au niveau de la théorie qu’au niveau de la compréhension de l’accès expérimental aux objets biologiques.

    Citation
    Montévil, Maël. 2021. “Le Sens Des Formes En Biologie.” In Biomorphisme. Approches Sensibles et Conceptuelles Des Formes Du Vivant, edited by David Romand, Julien Bernard, Sylvie Pic, and Jean Arnaud. NAIMA. https://www.naimaunlimited.com/biblio/biomorphisme-approches-sensibles-et-conceptuelles-des-formes-du-vivant/
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  3. Historicity at the heart of biology

    Historicity at the heart of biology

    Theory in Biosciences


    Most mathematical modeling in biology rely on the epistemology of physics. By contrast, we argue that historicity comes first in biology.

    Abstract

    Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration where equations no longer play a central role. We argue that all observations depend on objects defined by their historical origin instead of their relations as in physics. Therefore, we propose that biological variations and historicity come first, and regularities are constraints with limited validity in biology. Their proper theoretical and empirical use requires specific rationales.

    Keywords: Historicity, Organization, Epistemology, Mathematical modeling, Constraints

  4. Theoretical approach of ductal morphogenesis

    Theoretical approach of ductal morphogenesis

    Journal of Theoretical and Applied Vascular Research


    We propose a theoretical framework to model the behavior of cells in tissues and develop an application in the case of duct morphogenesis in mammary glands.

    Abstract

    We developed 3D culture methods that reproduce in vitro mammary gland ductal morphogenesis. We are proposing a conceptual framework to understand morphogenetic events based on epistemologically sound biological principles instead of the common practice of using only physical principles. 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 on 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 to reductive ones involving only molecules in general and genes in particular.

    Keywords: Morphogenesis, extracellular matrix, theoretical principles, default state of cells, modelization.

    Citation
    Montevil, M., Carlos Sonnenschein, and Ana M. Soto. 2016. “Theoretical Approach of Ductal Morphogenesis.” Journal of Theoretical and Applied Vascular Research 1 (1): 45–49. https://doi.org/10.24019/jtavr.7
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  5. Modeling mammary organogenesis from biological first principles: Cells and their physical constraints

    Modeling mammary organogenesis from biological first principles: Cells and their physical constraints

    Progress in Biophysics and Molecular Biology


    We developed a mathematical model of mammary gland based on proper biological principles: the default state of cells and the principle of organization.

    Abstract

    Abstract In multicellular organisms, relations among parts and between parts and the whole are contextual and interdependent. These organisms and their cells are ontogenetically linked: an organism starts as a cell that divides producing non-identical cells, which organize in tri-dimensional patterns. These association patterns and cells types change as tissues and organs are formed. This contextuality and circularity makes it difficult to establish detailed cause and effect relationships. Here we propose an approach to overcome these intrinsic difficulties by combining the use of two models; 1) an experimental one that employs 3D culture technology to obtain the structures of the mammary gland, namely, ducts and acini, and 2) a mathematical model based on biological principles. The typical approach for mathematical modeling in biology is to apply mathematical tools and concepts developed originally in physics or computer sciences. Instead, we propose to construct a mathematical model based on proper biological principles. Specifically, we use principles identified as fundamental for the elaboration of a theory of organisms, namely i) the default state of cell proliferation with variation and motility and ii) the principle of organization by closure of constraints. This model has a biological component, the cells, and a physical component, a matrix which contains collagen fibers. Cells display agency and move and proliferate unless constrained; they exert mechanical forces that i) act on collagen fibers and ii) on other cells. As fibers organize, they constrain the cells on their ability to move and to proliferate. The model exhibits a circularity that can be interpreted in terms of closure of constraints. Implementing the mathematical model shows that constraints to the default state are sufficient to explain ductal and acinar formation, and points to a target of future research, namely, to inhibitors of cell proliferation and motility generated by the epithelial cells. The success of this model suggests a step-wise approach whereby additional constraints imposed by the tissue and the organism could be examined in silico and rigorously tested by in vitro and in vivo experiments, in accordance with the organicist perspective we embrace.

    Keywords: Ductal morphogenesis, Mathematical models, Organicism, Organizational closure, Acinar morphogenesis, Mammary gland morphogenesis

    Citation
    Montévil, Maël, L. Speroni, Carlos Sonnenschein, and Ana M. Soto. 2016. “Modeling Mammary Organogenesis from Biological First Principles: Cells and Their Physical Constraints.” Progress in Biophysics and Molecular Biology 122 (1): 58–69. https://doi.org/10.1016/j.pbiomolbio.2016.08.004
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  6. Theoretical principles for biology: Organization

    Theoretical principles for biology: Organization

    Progress in Biophysics and Molecular Biology


    In the search of a theory of biological organisms, we propose to adopt organization as a theoretical principle and define it as closure of constraints.

    Abstract

    Abstract In the search of a theory of biological organisms, we propose to adopt organization as a theoretical principle. Organization constitutes an overarching hypothesis that frames the intelligibility of biological objects, by characterizing their relevant aspects. After a succinct historical survey on the understanding of organization in the organicist tradition, we offer a specific characterization in terms of closure of constraints. We then discuss some implications of the adoption of organization as a principle and, in particular, we focus on how it fosters an original approach to biological stability, as well as and its interplay with variation.

    Keywords: Theoretical principle, Organization, Constraints, Closure, Stability, Organicism

    Citation
    Mossio, Matteo, Maël Montévil, and G. Longo. 2016. “Theoretical Principles for Biology: Organization.” Progress in Biophysics and Molecular Biology 122 (1): 24–35. https://doi.org/10.1016/j.pbiomolbio.2016.07.005
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  7. Toward a theory of organisms: Three founding principles in search of a useful integration

    Toward a theory of organisms: Three founding principles in search of a useful integration

    Progress in Biophysics and Molecular Biology


    We articulate three principles for a theory of organisms proposed, namely: the default state the principle of variation and the principle of organization.

    Abstract

    Abstract Organisms, be they uni- or multi-cellular, are agents capable of creating their own norms; they are continuously harmonizing their ability to create novelty and stability, that is, they combine plasticity with robustness. Here we articulate the three principles for a theory of organisms, namely: the default state of proliferation with variation and motility, the principle of variation and the principle of organization. These principles profoundly change both biological observables and their determination with respect to the theoretical framework of physical theories. This radical change opens up the possibility of anchoring mathematical modeling in biologically proper principles.

    Keywords: Default state, Biological organization, Organizational closure, Variation, Individuation

    Citation
    Soto, Ana M., G. Longo, P.-A. Miquel, M. Montevil, Matteo Mossio, N. Perret, A. Pocheville, and Carlos Sonnenschein. 2016. “Toward a Theory of Organisms: Three Founding Principles in Search of a Useful Integration.” Progress in Biophysics and Molecular Biology 122 (1): 77–82. https://doi.org/10.1016/j.pbiomolbio.2016.07.006
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  8. The biological default state of cell proliferation with variation and motility, a fundamental principle for a theory of organisms

    The biological default state of cell proliferation with variation and motility, a fundamental principle for a theory of organisms

    Progress in Biophysics and Molecular Biology


    We propose a biological default state of proliferation with variation and motility by analogy with physics inertia. Then, quiescence requires an explanation.

    Abstract

    Abstract The principle of inertia is central to the modern scientific revolution. By postulating this principle Galileo at once identified a pertinent physical observable (momentum) and a conservation law (momentum conservation). He then could scientifically analyze what modifies inertial movement: gravitation and friction. Inertia, the default state in mechanics, represented a major theoretical commitment: there is no need to explain uniform rectilinear motion, rather, there is a need to explain departures from it. By analogy, we propose a biological default state of proliferation with variation and motility. From this theoretical commitment, what requires explanation is proliferative quiescence, lack of variation, lack of movement. That proliferation is the default state is axiomatic for biologists studying unicellular organisms. Moreover, it is implied in Darwin’s “descent with modification”. Although a “default state” is a theoretical construct and a limit case that does not need to be instantiated, conditions that closely resemble unrestrained cell proliferation are readily obtained experimentally. We will illustrate theoretical and experimental consequences of applying and of ignoring this principle.

    Keywords: Default state, Theory, Organicism, Emergence, Mathematical symmetries, Biological organization

  9. Biological organisation as closure of constraints

    Biological organisation as closure of constraints

    Journal of Theoretical Biology


    We characterize biological organization as a closure of constraints, where constraints are defined at a given time scale and are interdependent.

    Abstract

    We propose a conceptual and formal characterisation of biological organisation as a closure of constraints. We first establish a distinction between two causal regimes at work in biological systems: processes, which refer to the whole set of changes occurring in non-equilibrium open thermodynamic conditions; and constraints, those entities which, while acting upon the processes, exhibit some form of conservation (symmetry) at the relevant time scales. We then argue that, in biological systems, constraints realise closure, i.e. mutual dependence such that they both depend on and contribute to maintaining each other. With this characterisation in hand, we discuss how organisational closure can provide an operational tool for marking the boundaries between interacting biological systems. We conclude by focusing on the original conception of the relationship between stability and variation which emerges from this framework.

    Keywords: Biological organisation, Closure, Constraints, Symmetries, Time scales

    Citation
    Montévil, Maël, and Matteo Mossio. 2015. “Biological Organisation as Closure of Constraints.” Journal of Theoretical Biology 372 (May): 179–91. https://doi.org/10.1016/j.jtbi.2015.02.029
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