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  1. Non-equilibrium thermodynamics and the free energy principle in biology.Matteo Colombo & Patricia Palacios - 2021 - Biology and Philosophy 36 (5):1-26.
    According to the free energy principle, life is an “inevitable and emergent property of any random dynamical system at non-equilibrium steady state that possesses a Markov blanket” :20130475, 2013). Formulating a principle for the life sciences in terms of concepts from statistical physics, such as random dynamical system, non-equilibrium steady state and ergodicity, places substantial constraints on the theoretical and empirical study of biological systems. Thus far, however, the physics foundations of the free energy principle have received hardly any attention. (...)
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  • Possibility Spaces and the Notion of Novelty: From Music to Biology.Maël Montévil - 2019 - Synthese 196 (11):4555-4581.
    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 (...)
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  • Revisiting D.W. Smithers’s “Cancer: An Attack on Cytologism”.Ana M. Soto & Carlos Sonnenschein - 2020 - Biological Theory 15 (4):180-187.
    David Waldron Smithers was, among other things, a physician and a pioneer of cancer radiotherapy and a well-respected figure in British medicine and public health. From the 1940s until his retirement from medical practice in 1973, he was the director of the Radiotherapy Department at the Royal Marsden Hospital and London University Chair of Radiotherapy at the Institute of Cancer Research. Using massive amounts of clinical observations, which he interpreted from an organicist viewpoint, and his impressive synthetic thinking, he proposed (...)
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  • Conceptual Challenges in the Theoretical Foundations of Systems Biology.Marta Bertolaso & Emanuele Ratti - 2018 - In Mariano Bizzarri (ed.), Systems Biology. New York: Springer, Humana Press. pp. 1-13.
    In the last decade, Systems Biology has emerged as a conceptual and explanatory alternative to reductionist-based approaches in molecular biology. However, the foundations of this new discipline need to be fleshed out more carefully. In this paper, we claim that a relational ontology is a necessary tool to ground both the conceptual and explanatory aspects of Systems Biology. A relational ontology holds that relations are prior—both conceptually and explanatory—to entities, and that in the biological realm entities are defined primarily by (...)
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  • Peircean Semiotic Indeterminacy and Its Relevance for Biosemiotics.Robert Lane - 2014 - In Vinicius Romanini (ed.), Peirce and Biosemiotics.
    This chapter presents a detailed explanation of Peirce’s early and late views on semiotic indeterminacy and then considers how those views might be applied within biosemiotics. Peirce distinguished two different forms of semiotic indeterminacy: generality and vagueness. He defined each in terms of the “right” that indeterminate signs extend, either to their interpreters in the case of generality or to their utterers in the case of vagueness, to further determine their meaning. On Peirce’s view, no sign is absolutely determinate, i.e., (...)
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  • Symmetry Breaking and the Emergence of Path-Dependence.Hugh Desmond - 2017 - Synthese (10):4101-4131.
    Path-dependence offers a promising way of understanding the role historicity plays in explanation, namely, how the past states of a process can matter in the explanation of a given outcome. The two main existing accounts of path-dependence have sought to present it either in terms of dynamic landscapes or branching trees. However, the notions of landscape and tree both have serious limitations and have been criticized. The framework of causal networks is both more fundamental and more general that that of (...)
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  • Randomness Increases Order in Biological Evolution.Giuseppe Longo & Maël Montévil - 2012 - In M. Dinneen, B. Khoussainov & A. Nies (eds.), Computation, Physics and Beyond. Berlin Heidelberg: pp. 289-308.
    n this text, we revisit part of the analysis of anti-entropy in Bailly and Longo (2009} and develop further theoretical reflections. In particular, we analyze how randomness, an essential component of biological variability, is associated to the growth of biological organization, both in ontogenesis and in evolution. This approach, in particular, focuses on the role of global entropy production and provides a tool for a mathematical understanding of some fundamental observations by Gould on the increasing phenotypic complexity along evolution. Lastly, (...)
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  • The Inert Vs. The Living State of Matter: Extended Criticality, Time Geometry, Anti-Entropy - An Overview.Giuseppe Longo & Maël Montévil - 2012 - Frontiers in Physiology 3:39.
    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 (...)
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  • Integral Biomathics Reloaded: 2015.Plamen L. Simeonov & Ron Cottam - forthcoming - Journal Progress in Biophysics and Molecular Biology 119 (2).
    An updated survey of the research scope in Integral Biomathics.
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  • Symmetries and Symmetry-Breakings: The Fabric of Physical Interactions and the Flow of Time. [REVIEW]Giuseppe Longo - 2011 - Foundations of Science 16 (4):331-333.
    This short note develops some ideas along the lines of the stimulating paper by Heylighen (Found Sci 15 4(3):345–356, 2010a ). It summarizes a theme in several writings with Francis Bailly, downloadable from this author’s web page. The “geometrization” of time and causality is the common ground of the analysis hinted here and in Heylighen’s paper. Heylighen adds a logical notion, consistency, in order to understand a possible origin of the selective process that may have originated this organization of natural (...)
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