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  1. Reducing the Dauer Larva: Molecular Models of Biological Phenomena in Caenorhabditis Elegans Research.Arciszewski Michal - manuscript
    One important aspect of biological explanation is detailed causal modeling of particular phenomena in limited experimental background conditions. Recognising this allows a new avenue for intertheoretic reduction to be seen. Reductions in biology are possible, when one fully recognises that a sufficient condition for a reduction in biology is a molecular model of 1) only the demonstrated causal parameters of a biological model and 2) only within a replicable experimental background. These intertheoretic identifications –which are ubiquitous in biology and form (...)
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  2. Constitutive Relevance and Mutual Manipulability Revisited.Carl F. Craver, Stuart Glennan & Mark Povich - forthcoming - Synthese:1-22.
    An adequate understanding of the ubiquitous practice of mechanistic explanation requires an account of what Craver (2007) termed “constitutive relevance.” Entities or activities are constitutively relevant to a phenomenon when they are parts of the mechanism responsible for that phenomenon. Craver’s mutual manipulability (MM) account extended Woodward’s account of manipulationist counterfactuals to analyze how interlevel experiments establish constitutive relevance. Critics of MM (e.g., Baumgartner and Gebharter 2016 and Baumgartner and Casini 2017) argue that applying Woodward’s account to this philosophical problem (...)
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  3. The Quest for System-Theoretical Medicine in the COVID-19 Era.Felix Tretter, Olaf Wolkenhauer, Michael Meyer-Hermann, Johannes W. Dietrich, Sara Green, James Marcum & Wolfram Weckwerth - 2021 - Frontiers in Medicine 8:640974.
    Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits (...)
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  4. Glycemia Regulation: From Feedback Loops to Organizational Closure.Leonardo Bich, Matteo Mossio & Ana M. Soto - 2020 - Frontiers in Physiology 11.
    Endocrinologists apply the idea of feedback loops to explain how hormones regulate certain bodily functions such as glucose metabolism. In particular, feedback loops focus on the maintenance of the plasma concentrations of glucose within a narrow range. Here, we put forward a different, organicist perspective on the endocrine regulation of glycaemia, by relying on the pivotal concept of closure of constraints. From this perspective, biological systems are understood as organized ones, which means that they are constituted of a set of (...)
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  5. A Theory of Evolution as a Process of Unfolding.Agustin Ostachuk - 2020 - Cosmos and History: The Journal of Natural and Social Philosophy 16 (1):347-379.
    In this work I propose a theory of evolution as a process of unfolding. This theory is based on four logically concatenated principles. The principle of evolutionary order establishes that the more complex cannot be generated from the simpler. The principle of origin establishes that there must be a maximum complexity that originates the others by logical deduction. Finally, the principle of unfolding and the principle of actualization guarantee the development of the evolutionary process from the simplest to the most (...)
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  6. The Unfolding of a New Vision of Life, Cosmos and Evolution.Agustin Ostachuk - 2020 - Ludus Vitalis 28 (53):81-83.
    Has science already answered the fundamental questions about the concepts of Life, Cosmos and Evolution? Has science not relegated these fundamental questions by following up on more immediate, “useful” and practical endeavors that ultimately ensure that the wheel of capitalism keeps spinning in its frantic search for material and economic progress? There is something terribly wrong with the current theory of evolution, understood as the Darwinian theory with its successive versions and extensions. The concept of natural selection, the cornerstone of (...)
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  7. Holobiont Evolution: Mathematical Model with Vertical Vs. Horizontal Microbiome Transmission.Joan Roughgarden - 2020 - Philosophy, Theory, and Practice in Biology 12 (2).
    A holobiont is a composite organism consisting of a host together with its microbiome, such as a coral with its zooxanthellae. To explain the often intimate integration between hosts and their microbiomes, some investigators contend that selection operates on holobionts as a unit and view the microbiome’s genes as extending the host’s nuclear genome to jointly comprise a hologenome. Because vertical transmission of microbiomes is uncommon, other investigators contend that holobiont selection cannot be effective because a holobiont’s microbiome is an (...)
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  8. Integrative Pluralism for Biological Function.Beckett Sterner & Samuel Cusimano - 2019 - Biology and Philosophy 34 (6):1-21.
    We introduce a new type of pluralism about biological function that, in contrast to existing, demonstrates a practical integration among the term’s different meanings. In particular, we show how to generalize Sandra Mitchell’s notion of integrative pluralism to circumstances where multiple epistemic tools of the same type are jointly necessary to solve scientific problems. We argue that the multiple definitions of biological function operate jointly in this way based on how biologists explain the evolution of protein function. To clarify how (...)
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  9. Merleau-Ponty’s Implicit Critique of the New Mechanists.Benjamin Sheredos - 2018 - Synthese (Suppl 9):1-25.
    I argue (1) that what (ontic) New Mechanistic philosophers of science call mechanisms would be material Gestalten, and (2) that Merleau-Ponty’s engagement with Gestalt theory can help us frame a standing challenge against ontic conceptions of mechanisms. In short, until the (ontic) New Mechanist can provide us with a plausible account of the organization of mechanisms as an objective feature of mind-independent ontic structures in the world which we might discover – and no ontic Mechanist has done so – it (...)
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  10. An Abductive Theory of Constitution.Michael Baumgartner & Lorenzo Casini - 2017 - Philosophy of Science 84 (2):214-233.
    The first part of this paper finds Craver’s (2007) mutual manipulability theory (MM) of constitution inadequate, as it definitionally ties constitution to the feasibility of idealized experiments, which, however, are unrealizable in principle. As an alternative, the second part develops an abductive theory of constitution (NDC), which exploits the fact that phenomena and their constituents are unbreakably coupled via common causes. The best explanation for this common-cause coupling is the existence of an additional dependence relation, viz. constitution. Apart from adequately (...)
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  11. Explanatory Pluralism: An Unrewarding Prediction Error for Free Energy Theorists.Matteo Colombo & Cory Wright - 2017 - Brain and Cognition 112:3–12.
    Courtesy of its free energy formulation, the hierarchical predictive processing theory of the brain (PTB) is often claimed to be a grand unifying theory. To test this claim, we examine a central case: activity of mesocorticolimbic dopaminergic (DA) systems. After reviewing the three most prominent hypotheses of DA activity—the anhedonia, incentive salience, and reward prediction error hypotheses—we conclude that the evidence currently vindicates explanatory pluralism. This vindication implies that the grand unifying claims of advocates of PTB are unwarranted. More generally, (...)
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  12. Reengineering Metaphysics: Modularity, Parthood, and Evolvability in Metabolic Engineering.Catherine Kendig & Todd T. Eckdahl - 2017 - Philosophy, Theory, and Practice in Biology 9 (8).
    The premise of biological modularity is an ontological claim that appears to come out of practice. We understand that the biological world is modular because we can manipulate different parts of organisms in ways that would only work if there were discrete parts that were interchangeable. This is the foundation of the BioBrick assembly method widely used in synthetic biology. It is one of a number of methods that allows practitioners to construct and reconstruct biological pathways and devices using DNA (...)
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  13. Making Sense of Interlevel Causation in Mechanisms From a Metaphysical Perspective.Beate Krickel - 2017 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 48 (3):453-468.
    According to the new mechanistic approach, an acting entity is at a lower mechanistic level than another acting entity if and only if the former is a component in the mechanism for the latter. Craver and Bechtel :547–563, 2007. doi:10.1007/s10539-006-9028-8) argue that a consequence of this view is that there cannot be causal interactions between acting entities at different mechanistic levels. Their main reason seems to be what I will call the Metaphysical Argument: things at different levels of a mechanism (...)
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  14. Reduction in the Biomedical Sciences.Holly Andersen - 2016 - In Miriam Solomon, Jeremy Simon & Harold Kincaid (eds.), Routledge Companion to Philosophy of Medicine. Routledge.
    This chapter discusses several kinds of reduction that are often found in the biomedical sciences, in contrast to reduction in fields such as physics. This includes reduction as a methodological assumption for how to investigate phenomena like complex diseases, and reduction as a conceptual tool for relating distinct models of the same phenomenon. The case of Parkinson’s disease illustrates a wide variety of ways in which reductionism is an important tool in medicine.
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  15. Levels of Organization: A Deflationary Account.Markus Eronen - 2015 - Biology and Philosophy 30 (1):39-58.
    The idea of levels of organization plays a central role in the philosophy of the life sciences. In this article, I first examine the explanatory goals that have motivated accounts of levels of organization. I then show that the most state-of-the-art and scientifically plausible account of levels of organization, the account of levels of mechanism proposed by Bechtel and Craver, is fundamentally problematic. Finally, I argue that the explanatory goals can be reached by adopting a deflationary approach, where levels of (...)
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  16. Why It Is Time To Move Beyond Nagelian Reduction.Marie I. Kaiser - 2012 - In D. Dieks, W. J. Gonzalez, S. Hartmann, M. Stöltzner & M. Weber (eds.), Probabilities, Laws, and Structures. The Philosophy of Science in a European Perspective. Heidelberg, GER: Springer. pp. 255-272.
    In this paper I argue that it is finally time to move beyond the Nagelian framework and to break new ground in thinking about epistemic reduction in biology. I will do so, not by simply repeating all the old objections that have been raised against Ernest Nagel’s classical model of theory reduction. Rather, I grant that a proponent of Nagel’s approach can handle several of these problems but that, nevertheless, Nagel’s general way of thinking about epistemic reduction in terms of (...)
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  17. Mechanism Schemas and the Relationship Between Biological Theories.Tudor M. Baetu - 2011 - In Phyllis McKay Illari Federica Russo (ed.), Causality in the Sciences. Oxford University Press.
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  18. From Physics to Biology by Extending Criticality and Symmetry Breakings.Giuseppe Longo & Maël Montévil - 2011 - Progress in Biophysics and Molecular Biology 106:340 - 347.
    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 (...)
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  19. A Realism-Based Approach to the Evolution of Biomedical Ontologies.Barry Smith - 2006 - In Proceedings of the Annual AMIA Symposium. Washington, DC: American Medical Informatics Association. pp. 121-125.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
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  20. Antagonistic Redundancy -- A Theory of Error-Correcting Information Transfer in Organisms.Johannes W. Dietrich & Bernhard O. Boehm - 2004 - In Robert Trappl (ed.), Cybernetics and Systems 2004. Wien, Österreich: pp. 225-30.
    Living organisms are exposed to numerous influencing factors. This holds also true for their infrastructures that are processing and transducing information like endocrine networks or nerval channels. Therefore, the ability to compensate for noise is crucial for survival. An efficient mechanism to neutralise disturbances is instantiated in form of parallel complementary communication channels exerting antagonistic effects at their common receivers. Different signal processing types share the ability to suppress noise, to widen the system’s regulation capacity, and to provide for variable (...)
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  21. Why and How to Naturalize Semiotic Concepts for Biosemiotics.Tommi Vehkavaara - 2002 - Sign Systems Studies 30 (1):293-312.
    Any attempt to develop biosemiotics either towards a new biological ground theory or towards a metaphysics of living nature necessitates some kind of naturalization of its semiotic concepts. Instead of standard physicalistic naturalism, a certain kind of semiotic naturalism is pursued here. The naturalized concepts are defined as referring only to the objects of our external experience. When the semiotic concepts are applied to natural phenomena in biosemiotics, there is a risk of falling into anthropomorphic errors if the semiotic concepts (...)
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  22. Die Architektur der Synthese. Entstehung und Philosophie der modernen Evolutionstheorie.Marcel Weber - 1996 - Dissertation, University of Konstanz
    This Ph.D. thesis provides a pilosophical account of the structure of the evolutionary synthesis of the 1930s and 40s. The first, more historical part analyses how classical genetics came to be integrated into evolutionary thinking, highlighting in particular the importance of chromosomal mapping of Drosophila strains collected in the wild by Dobzansky, but also the work of Goldschmidt, Sumners, Timofeeff-Ressovsky and others. The second, more philosophical part attempts to answer the question wherein the unity of the synthesis consisted. I argue (...)
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  23. Zwischen milieu intérieur und medical decision making – Aspekte einer medizinischen Kybernetik.Johannes W. Dietrich - manuscript
    Seit wenigen Jahren erfreuen sich in den Lebenswissenschaften mehrere Theorien eines immer weitergehenden Einflusses, die unter Etikettierungen wie Systembiologie, Netzwerktheorie oder Signalomics nur scheinbar unabhängige Herangehensweisen an komplexe Zusammenhänge darstellen. Navigation ist der übergreifende Gedanke, der so unterschiedliche Gebiete wie Regelungstheorie, Entscheidungstheorie und Systemwissenschaft verbindet. Navigation als Lage- und Kursbestimmung nebst den zugehörigen Signalverarbeitungsprozessen und Steuerkommandos ist die Grundlage dessen, was lebende Organismen von der blo§en Ansammlung materieller Ingredienzien unterscheidet – von der molekularen Ebene bis zum Sozialverhalten. Denn stets stellen (...)
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