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Contents tagged “symmetries”

There are 14 contents with the tag “symmetries”:

  1. From physics to biology by extending criticality and symmetry breakings: An update

    From physics to biology by extending criticality and symmetry breakings: An update

    Acta Europeana Systemica


    We introduce our theoretical analysis in biology and show that symmetries play a radically different role in this discipline, by comparison with physics.

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    Abstract:

    Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not “just” processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), qualitative variability is at the core of these transitions.

    Keywords: Coherent structures, Critical transitions, downward causation, Hidden variables, Levels of organization, Symmetries, Systems biology

    Citation:

    Longo, Giuseppe, and Maël Montévil. 2020. “From Physics to Biology by Extending Criticality and Symmetry Breakings: An Update.” Acta Europeana Systemica 9 (1): 77–92. https://doi.org/10.14428/aes.v9i1.56043

  2. Measurement in biology is methodized by theory

    Measurement in biology is methodized by theory

    Biology & Philosophy


    We characterize measurement in biology from a theoretical perspective with a focus on historicity. We analyze experimental strategies and reproducibility.

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    Abstract:

    We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity.

    Keywords: Biological measurement, evolution, experiments, strains, symmetry, systematics

    Citation:
  3. Which first principles for mathematical modelling in biology?

    Which first principles for mathematical modelling in biology?

    Rendiconti di Matematica e delle sue Applicazioni


    Like theoretical physics, theoretical biology is not just mathematical modeling. Instead, it should strive to find suitable first principles to frame experiments and models.

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    Abstract:

    Like theoretical physics, theoretical biology is not just mathematical modeling. Instead, theoretical biology should strive to find suitable first principles to ground the understanding of biological phenomena and ultimately frame biological experiments and mathematical models. First principles in physics are expressed in terms of symmetries and the associated conservations, on the one side, and optimization on the other side. In biology, we argue instead that a strong notion of variation is fundamental. This notion encompasses new possibilities and the historicity of biological phenomena. By contrast, the relative regularity of some aspects of biological organisms, which we call constraints, should be regarded as the consequence of a mutual stabilization of the parts of organisms. We exemplify several aspects of this framework with the modeling of allometric relationships. Our change of perspective leads to reconsider the meaning of measurements and the structure of the space of description.

    Keywords: Allometry, first principles, Historicity, invariants, theoretical biology, Variability

    Citation:
  4. From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives

    From the Century of the Gene to that of the Organism: Introduction to New Theoretical Perspectives

    Life Sciences, Information Sciences


    Our group proposes three main principles for a theory of organisms, namely: the default state, the principle of variation and the principle of organization.

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    Abstract:

    Summary This chapter briefly presents and describes the three main principles that the group proposes for a theory of organisms, namely: the default state, proliferation with variation and motility, the principle of variation and the principle of organization. It is crucial to critique the philosophical and theoretical position on which the biological research feeding into the program is based and which has dominated biomedical research for the last 70 years. Physical theories are founded on stable mathematical structures, based onregularities and especially on theoretical symmetries. At the time of cell theory formulation and still today, cell theory plays a federating role between evolution biology and organism biology. Finally, analysis of the differences between the physics of inanimate and living matter leads to the proposal of three principles that provide aviable perspective for the construction of a necessary theory of organisms.

    Keywords: cell theory, evolution biology, mathematical structures, organism biology, philosophical position, physical theories, theoretical symmetries

    Citation:

    Montévil, Maël, Giuseppe Longo, and Ana M. Soto. 2018. “From the Century of the Gene to That of the Organism: Introduction to New Theoretical Perspectives.” In Life Sciences, Information Sciences, edited by T. Gaudin, D. Lacroix, M.‐C. Maurel, and J.‐C. Pomerol, 81–97. John Wiley & Sons, Ltd. https://doi.org/10.1002/9781119452713.ch9

  5. From Logic to Biology via Physics: a survey

    From Logic to Biology via Physics: a survey

    Logical Methods in Computer Science


    We summarize the theoretical ideas of our book, Perspectives on Organisms, where we discuss biological time, anti-entropy, randomness, incompleteness, etc.

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    This short text summarizes the work in biology proposed in our book, Perspectives on Organisms, where we analyse the unity proper to organisms by looking at it from different viewpoints. We discuss the theoretical roles of biological time, complexity, theoretical symmetries, singularities and critical transitions. We explicitly borrow from the conclusions in some key chapters and introduce them by a reflection on "incompleteness", also proposed in the book. We consider that incompleteness is a fundamental notion to understand the way in which we construct knowledge. Then we will introduce an approach to biological dynamics where randomness is central to the theoretical determination: randomness does not oppose biological stability but contributes to it by variability, adaptation, and diversity. Then, evolutionary and ontogenetic trajectories are continual changes of coherence structures involving symmetry changes within an ever-changing global stability.

    Keywords: Incompleteness, symmetries, randomness, critical transitions, biological evolution and ontogenesis

    Citation:

    Longo, Giuseppe, and Maël Montévil. 2017. “From Logic to Biology via Physics: A Survey.” Logical Methods in Computer Science 13 (November): Issue 4; 1860-5974. https://doi.org/10.23638/LMCS-13(4:21)2017

  6. Du siècle du gène à celui de l’organisme : introduction à de nouvelles perspectives théoriques

    Du siècle du gène à celui de l’organisme : introduction à de nouvelles perspectives théoriques

    Sciences de la vie, sciences de l’information


    Nous décrivons trois principes proposés pour une théorie des organismes : l'état par défaut des cellules et les principes de variation et d'organisation.

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    Abstract:

    Les organismes, qu’ils soient uni ou multi-cellulaires, sont des agents capables de créer leurs propres normes ; ils articulent continuellement leur capacité à créer de la nouveauté et de la stabilité, c’est-à-dire qu’ils combinent plasticité et robustesse. Ici, nous présentons et articulons brièvement les trois principes proposés récemment pour une théorie des organismes, à savoir : l’état par défaut, prolifération avec variation et motilité, le principe de variation et le principe d’organisation. Ces principes modifient profondément les observables biologiques et leur nature théorique par rapport aux cadres des théories physiques. Ce changement radical ouvre la possibilité d’ancrer la modélisation mathématique à des principes proprement biologiques.

    Citation:

    Montévil, Maël, G. Longo, and Ana M. Soto. 2017. “Du Siècle Du Gène à Celui de l’organisme : Introduction à de Nouvelles Perspectives Théoriques.” In Sciences de La Vie, Sciences de l’information, edited by T. Gaudin, D. Lacroix, M.-C. Maurel, and J.-C. Pomerol, 76–90. Paris: ISTE-Editions. https://www.istegroup.com/fr/produit/sciences-de-la-vie-sciences-de-linformation/

  7. 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 inertia. Then, quiescence requires an explanation.

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    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

    Citation:

    Soto, Ana M., G. Longo, Maël Montévil, and Carlos Sonnenschein. 2016. “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 122 (1): 16–23. https://doi.org/10.1016/j.pbiomolbio.2016.06.006

  8. 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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    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

  9. Perspectives on Organisms: Biological time, symmetries and singularities

    Perspectives on Organisms: Biological time, symmetries and singularities


    This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different...

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    Abstract:

    This authored monograph introduces a genuinely theoretical approach to biology. Starting point is the investigation of empirical biological scaling including their variability, which is found in the literature, e.g. allometric relationships, fractals, etc. The book then analyzes two different aspects of biological time: first, a supplementary temporal dimension to accommodate proper biological rhythms; secondly, the concepts of protension and retention as a means of local organization of time in living organisms. Moreover, the book investigates the role of symmetry in biology, in view of its ubiquitous importance in physics. In relation with the notion of extended critical transitions, the book proposes that organisms and their evolution can be characterized by continued symmetry changes, which accounts for the irreducibility of their historicity and variability. The authors also introduce the concept of anti-entropy as a measure for the potential of variability, being equally understood as alterations in symmetry. By this, the book provides a mathematical account of Gould’s analysis of phenotypic complexity with respect to biological evolution. The target audience primarily comprises researchers interested in new theoretical approaches to biology, from physical, biological or philosophical backgrounds, but the book may also be beneficial for graduate students who want to enter this field.

    Citation:

    Longo, G., and Maël Montévil. 2014. Perspectives on Organisms: Biological Time, Symmetries and Singularities. Lecture Notes in Morphogenesis. Heidelberg: Springer. https://doi.org/10.1007/978-3-642-35938-5

  10. Extended criticality, phase spaces and enablement in biology

    Extended criticality, phase spaces and enablement in biology

    Chaos, Solitons & Fractals


    Biological evolution requires a continual change of the pertinent phase space which is unpredictable. We discuss enablement and constraints.

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    Abstract:

    This paper analyzes, in terms of critical transitions, the phase spaces of biological dynamics. The phase space is the space where the scientific description and determination of a phenomenon is given. We argue that one major aspect of biological evolution is the continual change of the pertinent phase space and the unpredictability of these changes. This analysis will be based on the theoretical symmetries in biology and on their critical instability along evolution. Our hypothesis deeply modifies the tools and concepts used in physical theorizing, when adapted to biology. In particular, we argue that causality has to be understood differently, and we discuss two notions to do so: differential causality and enablement. In this context constraints play a key role: on one side, they restrict possibilities, on the other, they enable biological systems to integrate changing constraints in their organization, by correlated variations, in un-prestatable ways. This corresponds to the formation of new phenotypes and organisms.

    Keywords: Conservation properties, symmetries, biological causality, phase space, unpredictability, phylogenetic drift, enablement

    Citation:

    Longo, G., and Maël Montévil. 2013. “Extended Criticality, Phase Spaces and Enablement in Biology.” Chaos, Solitons & Fractals 55 (April): 64–79. https://doi.org/10.1016/j.chaos.2013.03.008

  11. No entailing laws, but enablement in the evolution of the biosphere

    No entailing laws, but enablement in the evolution of the biosphere

    Genetic and Evolutionary Computation Conference


    The evolution of life marks the end of a physics world view of law entailed dynamics. We discuss the notions of causation and of enablement.

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    Abstract:

    Biological evolution is a complex blend of ever changing structural stability, variability and emergence of new phe- notypes, niches, ecosystems. We wish to argue that the evo- lution of life marks the end of a physics world view of law entailed dynamics. Our considerations depend upon dis- cussing the variability of the very ”contexts of life”: the in- teractions between organisms, biological niches and ecosys- tems. These are ever changing, intrinsically indeterminate and even unprestatable: we do not know ahead of time the ”niches” which constitute the boundary conditions on selec- tion. More generally, by the mathematical unprestatability of the ”phase space” (space of possibilities), no laws of mo- tion can be formulated for evolution. We call this radical emergence, from life to life. The purpose of this paper is the integration of variation and diversity in a sound concep- tual frame and situate unpredictability at a novel theoretical level, that of the very phase space. Our argument will be carried on in close comparisons with physics and the mathematical constructions of phase spaces in that discipline. The role of (theoretical) symmetries as invariant preserving transformations will allow us to under- stand the nature of physical phase spaces and to stress the differences required for a sound biological theoretizing. In this frame, we discuss the novel notion of ”enablement”. Life lives in a web of enablement and radical emergence. This will restrict causal analyses to differential cases (a difference that causes a difference). Mutations or other causal differ- ences will allow us to stress that ”non conservation princi- ples” are at the core of evolution, in contrast to physical dynamics, largely based on conservation principles as sym- metries. Critical transitions, the main locus of symmetry changes in physics, will be discussed, and lead to ”extended criticality” as a conceptual frame for a better understanding of the living state of matter.

    Keywords: conservation properties, symmetries, biological causality

    Citation:

    Longo, G., Maël Montévil, and S. Kauffman. 2012. “No Entailing Laws, but Enablement in the Evolution of the Biosphere.” In Genetic and Evolutionary Computation Conference, GECCO’12. New York, NY, USA: GECCO’12; ACM. https://doi.org/10.1145/2330784.2330946

  12. The Inert vs. the Living State of Matter: Extended Criticality, Time Geometry, Anti-Entropy — an overview

    The Inert vs. the Living State of Matter: Extended Criticality, Time Geometry, Anti-Entropy — an overview

    Frontiers in Physiology


    The physical singularity of life phenomena is analyzed by a comparison with the theories of the inert and focus on criticality, time, and anti-entropy.

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    Abstract:

    The physical singularity of life phenomena is analyzed by means of comparison with the driving concepts of theories of the inert. We outline conceptual analogies, transferals of methodologies and theoretical instruments between physics and biology, in addition to indicating significant differences and sometimes logical dualities. In order to make biological phenomenalities intelligible, we introduce theoretical extensions to certain physical theories. In this synthetic paper, we summarize and propose a unified conceptual framework for the main conclusions drawn from work spanning a book and several articles, quoted throughout.

    Keywords: criticality, biological time, anti-entropy, theoretical biology, symmetry, allometry, incompleteness

    Citation:
  13. 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

    Citation:
  14. From physics to biology by extending criticality and symmetry breakings

    From physics to biology by extending criticality and symmetry breakings

    Progress in Biophysics and Molecular Biology


    Symmetries play a critical role in physics. By contrast, symmetry changes are ubiquitous for biological organisms, leading to deep theoretical consequences.

    Manuscript Citation Publisher Full text

    Abstract:

    Symmetries play a major role in physics, in particular since the work by E. Noether and H. Weyl in the first half of last century. Herein, we briefly review their role by recalling how symmetry changes allow to conceptually move from classical to relativistic and quantum physics. We then introduce our ongoing theoretical analysis in biology and show that symmetries play a radically different role in this discipline, when compared to those in current physics. By this comparison, we stress that symmetries must be understood in relation to conservation and stability properties, as represented in the theories. We posit that the dynamics of biological organisms, in their various levels of organization, are not just processes, but permanent (extended, in our terminology) critical transitions and, thus, symmetry changes. Within the limits of a relative structural stability (or interval of viability), variability is at the core of these transitions.

    Keywords: Symmetries, Systems biology, Critical transitions, Levels of organization, Hidden variables, Coherent structures, downward causation

    Citation:

    Longo, G., and Maël Montévil. 2011. “From Physics to Biology by Extending Criticality and Symmetry Breakings.” Progress in Biophysics and Molecular Biology 106 (2): 340–47. https://doi.org/10.1016/j.pbiomolbio.2011.03.005

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