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Contents tagged “closure”

There are 10 contents with the tag “closure”:

  1. The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions

    The Identity of Organisms in Scientific Practice: Integrating Historical and Relational Conceptions

    Frontiers in Physiology


    We address the identity of biological organisms in scientific practices by combining historical and relational, organizational conceptions.

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    Abstract:

    We address the identity of biological organisms at play in experimental and modeling practices. We first examine the central tenets of two general conceptions, and we assess their respective strengths and weaknesses. The historical conception, on the one hand, characterizes organisms’ identity by looking at their past, and specifically at their genealogical connection with a common ancestor. The relational conception, on the other hand, interprets organisms’ identity by referring to a set of distinctive relations between their parts, and between the organism and its environment. While the historical and relational conceptions are understood as opposed and conflicting, we submit that they are also fundamentally complementary. Accordingly, we put forward a hybrid conception, in which historical and relational (and more specifically, organizational) aspects of organisms’ identity sustain and justify each other. Moreover, we argue that organisms’ identity is not only hybrid but also bounded, insofar as the compliance with specific identity criteria tends to vanish as time passes, especially across generations. We spell out the core conceptual framework of this conception, and we outline an original formal representation. We contend that the hybrid and bounded conception of organisms’ identity suits the epistemological needs of biological practices, particularly with regards to the generalization and reproducibility of experimental results, and the integration of mathematical models with experiments.

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  2. Possibility spaces and the notion of novelty: from music to biology

    Possibility spaces and the notion of novelty: from music to biology

    Synthese


    What is a biological novelty? Is it possible to coin a sound concept of new possibility? What articulation between the concepts of novelty and function?

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    We provide a new perspective on the relation between the space of description of an object and the appearance of novelties. One of the aims of this perspective is to facilitate the interaction between mathematics and historical sciences. The definition of novelties is paradoxical: if one can define in advance the possibles, then they are not genuinely new. By analyzing the situation in set theory, we show that defining generic (i.e., shared) and specific (i.e., individual) properties of elements of a set are radically different notions. As a result, generic and specific definitions of possibilities cannot be conflated. We argue that genuinely stating possibilities requires that their meaning has to be made explicit. For example, in physics, properties playing theoretical roles are generic; then, generic reasoning is sufficient to define possibilities. By contrast, in music, we argue that specific properties matter, and generic definitions become insufficient. Then, the notion of new possibilities becomes relevant and irreducible. In biology, among other examples, the generic definition of the space of DNA sequences is insufficient to state phenotypic possibilities even if we assume complete genetic determinism. The generic properties of this space are relevant for sequencing or DNA duplication, but they are inadequate to understand phenotypes. We develop a strong concept of biological novelties which justifies the notion of new possibilities and is more robust than the notion of changing description spaces. These biological novelties are not generic outcomes from an initial situation. They are specific and this specificity is associated with biological functions, that is to say, with a specific causal structure. Thus, we think that in contrast with physics, the concept of new possibilities is necessary for biology.

    Keywords: Novelty, Possibility space, Biological functions, Organization, Emergence

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  3. Entretien sur l’entropie, le vivant et la technique : Première partie

    Entretien sur l’entropie, le vivant et la technique : Première partie

    Links series


    Entretien entre B. Stiegler et M. Montévil sur l'entropie et l'anti-entropie dans l'étude du vivant et des techniques et pour les enjeux de l'Anthropocène.

  4. Philosophical Accounts of Biological Functions

    Philosophical Accounts of Biological Functions

    Science & Education


    Review of "A critical overview of biological functions" by Justin Garson (2016). I focus on the etiological and the organizational accounts of functions.

  5. From the century of the genome to the century of the organism: New theoretical approaches

    From the century of the genome to the century of the organism: New theoretical approaches

    Progress in Biophysics and Molecular Biology, Special issue


    This focused issue of Progress in Biophysics and Molecular Biology is entitled "From the century of the genome to the century of the organism: New theoretical approaches." It was developed during Ana M. Soto’s tenure as Blaise Pascal Chair of Biology 2013-15 at the Ecole Normale Supérieure (ENS,...

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    Abstract:

    This focused issue of Progress in Biophysics and Molecular Biology is entitled "From the century of the genome to the century of the organism: New theoretical approaches." It was developed during Ana M. Soto’s tenure as Blaise Pascal Chair of Biology 2013-15 at the Ecole Normale Supérieure (ENS, Paris, France). Giuseppe Longo was the Pascal Chair host at the ENS. This ongoing theoretical was also used as the content of a 10 session course attended by graduate students and post-graduates, which took place at the National Museum of Natural History and at the ENS. The attendants of course encouraged the guest editors to make this material easily available, hence the origin of PBMB issue.

    Citation:

    Soto, Ana M., G. Longo, Denis Noble, Nicole Perret, Maël Montévil, Carlos Sonnenschein, Matteo Mossio, Arnaud Pocheville, Paul-Antoine Miquel, and Su-Young Hwang. 2016. “From the Century of the Genome to the Century of the Organism: New Theoretical Approaches.” Progress in Biophysics and Molecular Biology, Special Issue 122 (1): 1–82. https://www.sciencedirect.com/journal/progress-in-biophysics-and-molecular-biology/vol/122/issue/1

  6. 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 cell and the principle of organization.

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    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

  7. 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.

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    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

  8. 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.

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    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

  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 distinguished from processes at a given time scale.

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    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

  10. Temps biologique et transitions critiques étendues - Vers une objectivation de l’état vivant de la matière

    Temps biologique et transitions critiques étendues - Vers une objectivation de l’état vivant de la matière


    Cette thèse se place dans le contexte d’une démarche théorique en biologie, s’inspirant, sans toutefois s’y réduire, des méthodes d’objectivation utilisées en physique. Pour cela, nous rapportons les possibles symétries et invariants biologiques sous forme de “lois d’échelles” empiriques (allométrie...

    Citation Publisher Details

    Abstract:

    Cette thèse se place dans le contexte d’une démarche théorique en biologie, s’inspirant, sans toutefois s’y réduire, des méthodes d’objectivation utilisées en physique. Pour cela, nous rapportons les possibles symétries et invariants biologiques sous forme de “lois d’échelles” empiriques (allométrie et fractales en particulier), ainsi que la variabilité associée. Nous abordons ensuite plusieurs aspects du temps biologique. Nous considérons une dimension temporelle supplémentaire, correspondant à l’autonomie de certains rythmes biologiques. Nous développons aussi une approche de la protension, comme principe d’organisation locale de la temporalité biologique.
    La notion de symétrie ayant un statut fondationel pour les théories physiques, nous interrogeons ensuite leur rôles en biologie. Partant de la notion de criticité étendue, nous proposons que la dynamique du vivant soit régie par une omniprésence des changements de symétries, constituant dès lors une historicité irréductible et conférant un statut théorique particulier à l’object et à la mesure en biologie. Nous appréhendons aussi la notion d’anti-entropie comme mesure d’un potentiel de variabilité.
    Nous nous intéressons ensuite à la question des niveaux d’organisation, par deux voies complémentaires. Nous l’abordons dans un premier temps par la notion de clôture organisationnelle. Ensuite nous la considérons comme associée à des singularités fortes, telles que dans les situations critiques. Enfin, nous esquissons un schème opératoriel de l’unité de l’organisme, qui combine un grand nombre des aspects préalablement exposés.

    Keywords: criticité, symmétries, historicité, variabilité, temps biologique, organisme, mesure, renormalisation

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