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  1. A framework for philosophical biology.Sepehr Ehsani - manuscript
    Advances in biology, at least over the past two centuries, have mostly relied on theories that were subsequently revised, expanded or eventually refuted using experimental and other means. The field of theoretical biology used to primarily provide a basis, similar to theoretical physics in the physical sciences, to rationally examine the frameworks within which biological experiments were carried out and to shed light on overlooked gaps in understanding. Today, however, theoretical biology has generally become synonymous with computational and mathematical biology. (...)
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  2. Eye-contact and complex dynamic systems: an hypothesis on autism's direct cause and a clinical study addressing prevention.Maxson J. McDowell - manuscript
    (This version was submitted to Behavioral and Brain Science. A revised version was published by Biological Theory) Estimates of autism’s incidence increased 5-10 fold in ten years, an increase which cannot be genetic. Though many mutations are associated with autism, no mutation seems directly to cause autism. We need to find the direct cause. Complexity science provides a new paradigm - confirmed in biology by extensive hard data. Both the body and the personality are complex dynamic systems which spontaneously self-organize (...)
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  3. THE ROLE OF TIME IN THE CONSTRUCTION OF BIO-MATERIALS: A NOVEL INSIGHT.Varanasi Ramabrahmam - manuscript
    Various understandings and definitions of time will be reviewed. The nature and structure of time will be reviewed and the concepts of time and passage of time will be refreshed. The fundamental role played by energy and four natural forces in the actions, reactions and interactions concerning matter, anti-matter, energy in space and time will be critically analyzed. The reality how time is constructed during the construction of materials will be presented and discussed. The classical and quantum ideas in this (...)
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  4. Causal Specificity, Biological Possibility and Non-parity about Genetic Causes.Marcel Weber - manuscript
    Several authors have used the notion of causal specificity in order to defend non-parity about genetic causes (Waters 2007, Woodward 2010, Weber 2017, forthcoming). Non-parity in this context is the idea that DNA and some other biomolecules that are often described as information-bearers by biologists play a unique role in life processes, an idea that has been challenged by Developmental Systems Theory (e.g., Oyama 2000). Indeed, it has proven to be quite difficult to state clearly what the alleged special role (...)
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  5. Causal Control: A Rationale for Causal Selection.Lauren N. Ross - 2015
    Causal selection has to do with the distinction we make between background conditions and “the” true cause or causes of some outcome of interest. A longstanding consensus in philosophy views causal selection as lacking any objective rationale and as guided, instead, by arbitrary, pragmatic, and non-scientific considerations. I argue against this position in the context of causal selection for disease traits. In this domain, causes are selected on the basis of the type of causal control they exhibit over a disease (...)
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  6. On the Epistemic Roles of the Individualized Niche Concept in Ecology, Behavioral and Evolutionary Biology.Marie I. Kaiser & Katie H. Morrow - forthcoming - Philosophy of Science.
    We characterize four fruitful and underappreciated epistemic roles played by the concept of an individualized niche in contemporary biology, utilizing results of a qualitative empirical study conducted within an interdisciplinary biological research center. We argue that the individualized niche concept (1) shapes the research agenda of the center, (2) facilitates explaining core phenomena related to inter-individual differences, (3) helps with managing individual-level causal complexity, and (4) promotes integrating local knowledge from ecology, evolutionary biology, behavioral biology and other biological fields. We (...)
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  7. (1 other version)Mechanistic Explanations and Teleological Functions.Andrew Rubner - forthcoming - The British Journal for the Philosophy of Science.
    This paper defines and defends a notion of teleological function which is fit to figure in explanations concerning how organic systems, and the items which compose them, are able to perform certain activities, such as surviving and reproducing or pumping blood. According to this notion, a teleological function of an item (such as the heart) is a typical way in which items of that type contribute to some containing system's ability to do some activity. An account of what it is (...)
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  8. Causal Selection versus Causal Parity in Biology: Relevant Counterfactuals and Biologically Normal Interventions.Marcel Weber - forthcoming - In Waters C. Kenneth & Woodward James (eds.), Philosophical Perspectives on Causal Reasoning in Biology. Minnesota Studies in Philosophy of Science. Vol. XXI. University of Minnesota Press.
    Causal selection is the task of picking out, from a field of known causally relevant factors, some factors as elements of an explanation. The Causal Parity Thesis in the philosophy of biology challenges the usual ways of making such selections among different causes operating in a developing organism. The main target of this thesis is usually gene centrism, the doctrine that genes play some special role in ontogeny, which is often described in terms of information-bearing or programming. This paper is (...)
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  9. Situating homeostasis in organisms: maintaining organization through time.William Bechtel & Leonardo Bich - 2024 - Journal of Physiology (x):1-18.
    Since it was inspired by Bernard and developed and named by Cannon, the conceptof homeostasis has been invoked by many as the central theoretical framework for physiology. Ithas also been the target of numerous criticisms that have elicited the introduction of a plethoraof alternative concepts. We argue that many of the criticisms actually target the more restrictiveaccount of homeostasis advanced by the cyberneticists. What was crucial to Bernard and Cannonwas a focus on the maintenance of the organism as the goal (...)
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  10. The evolution of reproductive characters: an organismal-relational approach.David Cortés-García, Arantza Etxeberria & Laura Nuño de la Rosa - 2024 - Biology and Philosophy 39 (26):1-23.
    This paper delves into the character concept as applied to reproduction. Our argument is that the prevailing functional-adaptationist perspective falls short in explaining the evolution of reproductive traits, and we propose an alternative organismal-relational approach that incorporates the developmental and interactive aspects of reproduction. To begin, we define the functional individuation of reproductive traits as evolutionary strategies aimed at enhancing fitness, and we demonstrate how this perspective influences the classification of reproductive characters and modes, the comprehension of shared traits as (...)
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  11. The Ontic-Epistemic Debates of Explanation Revisited: The Three-Dimensional Approach.Jinyeong Gim - 2024 - Philosophical Problems in Science (Zagadnienia Filozoficzne W Nauce) 74:99-169.
    After Wesley Salmon’s causal-mechanical stance on explanation in the 1980s, the ontic-epistemic debate of scientific explanations appeared to be resolved in the philosophy of science. However, since the twenty-first century, this debate has been rekindled among philosophers who focus on mechanistic explanations. Nevertheless, its issues have evolved, necessitating scrutiny of the new trends in this debate and a comparison with the original controversy between Carl Hempel and Salmon. The primary objective of this paper is to elucidate three categorical dimensions in (...)
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  12. The Explanatory Role of Umwelt in Evolutionary Theory: Introducing von Baer's Reflections on Teleological Development.Tiago Rama - 2024 - Biosemiotics 1:1-26.
    Abstract: This paper argues that a central explanatory role for the concept of Umwelt in theoretical biology is to be found in developmental biology, in particular in the effort to understand development as a goal-directed and adaptive process that is controlled by the organism itself. I will reach this conclusion in two (interrelated) ways. The first is purely theoretical and relates to the current scenario in the philosophy of biology. Challenging neo-Darwinism requires a new understanding of the various components involved (...)
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  13. Is a Cognitive Revolution in Theoretical Biology Underway?Tiago Rama - 2024 - Foundations of Science 1:1-22.
    The foundations of biology have been a topic of debate for the past few decades. The traditional perspective of the Modern Synthesis, which portrays organisms as passive entities with limited role in evolutionary theory, is giving way to a new paradigm where organisms are recognized as active agents, actively shaping their own phenotypic traits for adaptive purposes. Within this context, this article raises the question of whether contemporary biological theory is undergoing a cognitive revolution. This inquiry can be approached in (...)
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  14. Explanation, teleology, and analogy in natural history and comparative anatomy around 1800: Kant and Cuvier.Hein van den Berg - 2024 - Studies in History and Philosophy of Science Part A 105 (C):109-119.
    This paper investigates conceptions of explanation, teleology, and analogy in the works of Immanuel Kant (1724-1804) and Georges Cuvier (1769-1832). Richards (2000, 2002) and Zammito (2006, 2012, 2018) have argued that Kant’s philosophy provided an obstacle for the project of establishing biology as a proper science around 1800. By contrast, Russell (1916), Outram (1986), and Huneman (2006, 2008) have argued, similar to suggestions from Lenoir (1989), that Kant’s philosophy influenced the influential naturalist Georges Cuvier. In this article, I wish to (...)
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  15. Divergent Processing of Cell Stress Signals as the Basis of Cancer Progression: Licensing NFκB on Chromatin.Spiros A. Vlahopoulos - 2024 - IJMS 25 (16):8621.
    Inflammation is activated by diverse triggers that induce the expression of cytokines and adhesion molecules, which permit a succession of molecules and cells to deliver stimuli and functions that help the immune system clear the primary cause of tissue damage, whether this is an infection, a tumor, or a trauma. During inflammation, short-term changes in the expression and secretion of strong mediators of inflammation occur, while long-term changes occur to specific groups of cells. Long-term changes include cellular transdifferentiation for some (...)
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  16. (1 other version)Hyperthermia-Induced Vasoconstriction: A Physiological Counter Mechanism.Rowena Kong - 2023 - Journal of Psychiatry and Psychology Research 6 (S2):4.
    The paradoxical phenomena of hyperthermia-induced vasoconstriction, hyperthermia- induced hypothermia, and hyperthermia induced arterial vasoconstriction have been observed in animal heatstroke clinical case studies. We attempt to explain the basic mechanism behind such findings in terms of the principle of body heat conservation and natural countermeasure against heat exposure through reduction in the extent of vascular surface area exposed. One study which examined the outcome of heating a rabbit carotid artery produced graded vasoconstriction which is proportional to temperature increase. These interesting (...)
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  17. Decoupling Topological Explanations from Mechanisms.Daniel Kostic & Kareem Khalifa - 2023 - Philosophy of Science 90 (2):245 - 268.
    We provide three innovations to recent debates about whether topological or “network” explanations are a species of mechanistic explanation. First, we more precisely characterize the requirement that all topological explanations are mechanistic explanations and show scientific practice to belie such a requirement. Second, we provide an account that unifies mechanistic and non-mechanistic topological explanations, thereby enriching both the mechanist and autonomist programs by highlighting when and where topological explanations are mechanistic. Third, we defend this view against some powerful mechanist objections. (...)
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  18. Populations of Neurons and Rocks? Against a Generalization of the Selected Effects Theory of Functions.Jakob Roloff - 2023 - Kriterion – Journal of Philosophy 37 (2-4):69-87.
    Millikan’s (1984. Language, Thought, and Other Biological Categories: New Foundations for Realism. MIT Press) selected effects theory of functions states that functions are effects for which the ancestors of a trait were selected for. As the function is an effect a thing’s ancestors produced, only things that are reproductions in some sense can have functions. Against this reproduction requirement, Garson (2019. What Biological Functions Are and Why They Matter. Cambridge University Press) argues that not only processes of differential reproduction but (...)
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  19. What’s at stake in the debate over naturalizing teleology? An overlooked metatheoretical debate.Carl Sachs & Auguste Nahas - 2023 - Synthese 201 (4):1-22.
    Recent accounts of teleological naturalism hold that organisms are intrinsically goaldirected entities. We argue that supporters and critics of this view have ignored the ways in which it is used to address quite different problems. One problem is about biology and concerns whether an organism-centered account of teleological ascriptions would improve our descriptions and explanations of biological phenomena. This is different from the philosophical problem of how naturalized teleology would affect our conception of nature, and of ourselves as natural beings. (...)
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  20. An account of conserved functions and how biologists use them to integrate cell and evolutionary biology.Jeremy G. Wideman, Steve Elliott & Beckett Sterner - 2023 - Biology and Philosophy 38 (5):1-23.
    We characterize a type of functional explanation that addresses why a homologous trait originating deep in the evolutionary history of a group remains widespread and largely unchanged across the group’s lineages. We argue that biologists regularly provide this type of explanation when they attribute conserved functions to phenotypic and genetic traits. The concept of conserved function applies broadly to many biological domains, and we illustrate its importance using examples of molecular sequence alignments at the intersection of evolution and cell biology. (...)
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  21. Organization needs organization: Understanding integrated control in living organisms.Leonardo Bich & William Bechtel - 2022 - Studies in History and Philosophy of Science Part A 93:96-106.
    Organization figures centrally in the understanding of biological systems advanced by both new mechanists and proponents of the autonomy framework. The new mechanists focus on how components of mechanisms are organized to produce a phenomenon and emphasize productive continuity between these components. The autonomy framework focuses on how the components of a biological system are organized in such a way that they contribute to the maintenance of the organisms that produce them. In this paper we analyze and compare these two (...)
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  22. Control Mechanisms: Explaining the Integration and Versatility of Biological Organisms.Leonardo Bich & William Bechtel - 2022 - Adaptive Behavior.
    Living organisms act as integrated wholes to maintain themselves. Individual actions can each be explained by characterizing the mechanisms that perform the activity. But these alone do not explain how various activities are coordinated and performed versatilely. We argue that this depends on a specific type of mechanism, a control mechanism. We develop an account of control by examining several extensively studied control mechanisms operative in the bacterium E. coli. On our analysis, what distinguishes a control mechanism from other mechanisms (...)
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  23. Topological Explanations: An Opinionated Appraisal.Daniel Kostić - 2022 - In Insa Lawler, Kareem Khalifa & Elay Shech (eds.), Scientific Understanding and Representation: Modeling in the Physical Sciences. New York, NY: Routledge. pp. 96-115.
    This chapter provides a systematic overview of topological explanations in the philosophy of science literature. It does so by presenting an account of topological explanation that I (Kostić and Khalifa 2021; Kostić 2020a; 2020b; 2018) have developed in other publications and then comparing this account to other accounts of topological explanation. Finally, this appraisal is opinionated because it highlights some problems in alternative accounts of topological explanations, and also it outlines responses to some of the main criticisms raised by the (...)
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  24. Free energy: a user’s guide.Stephen Francis Mann, Ross Pain & Michael D. Kirchhoff - 2022 - Biology and Philosophy 37 (4):1-35.
    Over the last fifteen years, an ambitious explanatory framework has been proposed to unify explanations across biology and cognitive science. Active inference, whose most famous tenet is the free energy principle, has inspired excitement and confusion in equal measure. Here, we lay the ground for proper critical analysis of active inference, in three ways. First, we give simplified versions of its core mathematical models. Second, we outline the historical development of active inference and its relationship to other theoretical approaches. Third, (...)
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  25. (1 other version)Vitalism and Cognition in a Conscious Universe.Marco Masi - 2022 - Communicative and Integrative Biology 1 (15):121-136.
    According to the current scientific paradigm, what we call ‘life’, ‘mind’, and ‘consciousness’ are considered epiphenomenal occurrences, or emergent properties or functions of matter and energy. Science does not associate these with an inherent and distinct existence beyond a materialistic/energetic conception. ‘Life’ is a word pointing at cellular and multicellular processes forming organisms capable of specific functions and skills. ‘Mind’ is a cognitive ability emerging from a matrix of complex interactions of neuronal processes, while ‘consciousness’ is an even more elusive (...)
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  26. Immunoglobulins and Antibodies: Conceptual Projections All the Way Down.Bartlomiej Swiatczak - 2022 - Constructivist Foundations 18 (1):85-86.
    Central to vaccination-induced responses, antibodies are suggested by Vaz to operate as observer-dependent entities that owe their status to categorization schemes of immunologists. Inspired by color research by Maturana, he argues that antibodies should be distinguished from immunoglobulins, which unlike the former can be considered as constituents of structural dynamics of an organism, products of millions of years of evolution. However, a deeper understanding of the historical roots of the concept of immunoglobulin and associated “languaging” and naming processes reveals that (...)
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  27. Understanding life through metaphors. [REVIEW]Bartlomiej Swiatczak - 2022 - Metascience 2022:1-3.
    There is a deep-seated neopositivist view which regards the language of science as a neutral medium of communication, radically different from indirect symbolic forms of discourse characteristic of arts and humanities. But naturalists, like poets and social scientists, also draw on the dominant images in their culture to organize their thoughts and simplify complex concepts. By conceptualizing one thing in terms of another, metaphors in science not only aid mutual communication between researchers but also structure their understanding of experience and (...)
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  28. Coherent Causal Control: A New Distinction within Causation.Marcel Weber - 2022 - European Journal for Philosophy of Science 12 (4):69.
    The recent literature on causality has seen the introduction of several distinctions within causality, which are thought to be important for understanding the widespread scientific practice of focusing causal explanations on a subset of the factors that are causally relevant for a phenomenon. Concepts used to draw such distinctions include, among others, stability, specificity, proportionality, or actual-difference making. In this contribution, I propose a new distinction that picks out an explanatorily salient class of causes in biological systems. Some select causes (...)
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  29. Continuing After Species: An Afterword.Robert A. Wilson - 2022 - In John S. Wilkins, Igor Pavlinov & Frank Zachos (eds.), Species Problems and Beyond: Contemporary Issues in Philosophy and Practice. Boca Raton: CRC Press. pp. 343-353.
    This afterword to Species and Beyond provides some reflections on species, with special attention to what I think the most significant developments have been in the thinking of biologists and philosophers working on species over the past 25 years, as well as some bad jokes.
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  30. An externalist teleology.Gunnar Babcock & Daniel W. McShea - 2021 - Synthese 199 (3-4):8755-8780.
    Teleology has a complicated history in the biological sciences. Some have argued that Darwin’s theory has allowed biology to purge itself of teleological explanations. Others have been content to retain teleology and to treat it as metaphorical, or have sought to replace it with less problematic notions like teleonomy. And still others have tried to naturalize it in a way that distances it from the vitalism of the nineteenth century, focusing on the role that function plays in teleological explanation. No (...)
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  31. Autonomous Systems and the Place of Biology Among Sciences. Perspectives for an Epistemology of Complex Systems.Leonardo Bich - 2021 - In Gianfranco Minati (ed.), Multiplicity and Interdisciplinarity. Essays in Honor of Eliano Pessa. Springer. pp. 41-57.
    This paper discusses the epistemic status of biology from the standpoint of the systemic approach to living systems based on the notion of biological autonomy. This approach aims to provide an understanding of the distinctive character of biological systems and this paper analyses its theoretical and epistemological dimensions. The paper argues that, considered from this perspective, biological systems are examples of emergent phenomena, that the biological domain exhibits special features with respect to other domains, and that biology as a discipline (...)
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  32. Mechanism, autonomy and biological explanation.Leonardo Bich & William Bechtel - 2021 - Biology and Philosophy 36 (6):1-27.
    The new mechanists and the autonomy approach both aim to account for how biological phenomena are explained. One identifies appeals to how components of a mechanism are organized so that their activities produce a phenomenon. The other directs attention towards the whole organism and focuses on how it achieves self-maintenance. This paper discusses challenges each confronts and how each could benefit from collaboration with the other: the new mechanistic framework can gain by taking into account what happens outside individual mechanisms, (...)
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  33. To Marvel at the Manifold Connections: Philosophy, Biology, and Laudato Si’.Louis Caruana - 2021 - Gregorianum 102 (3):617-631.
    One of the aims of the encyclical "Laudato Si’" is to help us “marvel at the manifold connections existing among creatures”, to show how we are also involved, and to motivate us thereby to care for our common home. Are there new dimensions of beauty available to us today because of recent advances in biology? In this paper I seek to answer this question by first recalling the basic criteria for beauty, as expressed by Aristotle and Aquinas, and then evaluating (...)
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  34. First principles in the life sciences: the free-energy principle, organicism, and mechanism.Matteo Colombo & Cory Wright - 2021 - Synthese 198 (14):3463–3488.
    The free-energy principle states that all systems that minimize their free energy resist a tendency to physical disintegration. Originally proposed to account for perception, learning, and action, the free-energy principle has been applied to the evolution, development, morphology, anatomy and function of the brain, and has been called a postulate, an unfalsifiable principle, a natural law, and an imperative. While it might afford a theoretical foundation for understanding the relationship between environment, life, and mind, its epistemic status is unclear. Also (...)
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  35. The meaning of "cause" in genetics.Kate E. Lynch - 2021 - Combining Human Genetics and Causal Inference to Understand Human Disease and Development. Cold Spring Harbor Perspectives in Medicine.
    Causation has multiple distinct meanings in genetics. One reason for this is meaning slippage between two concepts of the gene: Mendelian and molecular. Another reason is that a variety of genetic methods address different kinds of causal relationships. Some genetic studies address causes of traits in individuals, which can only be assessed when single genes follow predictable inheritance patterns that reliably cause a trait. A second sense concerns the causes of trait differences within a population. Whereas some single genes can (...)
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  36. A New Role for Mathematics in Empirical Sciences.Atoosa Kasirzadeh - 2021 - Philosophy of Science 88 (4):686-706.
    Mathematics is often taken to play one of two roles in the empirical sciences: either it represents empirical phenomena or it explains these phenomena by imposing constraints on them. This article identifies a third and distinct role that has not been fully appreciated in the literature on applicability of mathematics and may be pervasive in scientific practice. I call this the “bridging” role of mathematics, according to which mathematics acts as a connecting scheme in our explanatory reasoning about why and (...)
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  37. Lewontin (1972).Rasmus Grønfeldt Winther - 2021 - In Ludovica Lorusso & Rasmus Grønfeldt Winther (eds.), Remapping Race in a Global Context. Routledge. pp. 9-47.
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  38. 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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  39. (1 other version)From Life-Like to Mind-Like Explanation: Natural Agency and the Cognitive Sciences.Alex Djedovic - 2020 - Dissertation, University of Toronto, St. George Campus
    This dissertation argues that cognition is a kind of natural agency. Natural agency is the capacity that certain systems have to act in accordance with their own norms. Natural agents are systems that bias their repertoires in response to affordances in the pursuit of their goals. Cognition is a special mode of this general phenomenon. Cognitive systems are agents that have the additional capacity to actively take their worlds to be certain ways, regardless of whether the world is really that (...)
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  40. Analytic philosophy for biomedical research: the imperative of applying yesterday's timeless messages to today's impasses.Sepehr Ehsani - 2020 - In Patrick Glauner & Philipp Plugmann (eds.), Innovative Technologies for Market Leadership: Investing in the Future. Springer. pp. 167-200.
    The mantra that "the best way to predict the future is to invent it" (attributed to the computer scientist Alan Kay) exemplifies some of the expectations from the technical and innovative sides of biomedical research at present. However, for technical advancements to make real impacts both on patient health and genuine scientific understanding, quite a number of lingering challenges facing the entire spectrum from protein biology all the way to randomized controlled trials should start to be overcome. The proposal in (...)
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  41. General Theory of Topological Explanations and Explanatory Asymmetry.Daniel Kostic - 2020 - Philosophical Transactions of the Royal Society B: Biological Sciences 375 (1796):1-8.
    In this paper, I present a general theory of topological explanations, and illustrate its fruitfulness by showing how it accounts for explanatory asymmetry. My argument is developed in three steps. In the first step, I show what it is for some topological property A to explain some physical or dynamical property B. Based on that, I derive three key criteria of successful topological explanations: a criterion concerning the facticity of topological explanations, i.e. what makes it true of a particular system; (...)
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  42. Dynamical causes.Russell Meyer - 2020 - Biology and Philosophy 35 (5):1-21.
    Mechanistic explanations are often said to explain because they reveal the causal structure of the world. Conversely, dynamical models supposedly lack explanatory power because they do not describe causal structure. The only way for dynamical models to produce causal explanations is via the 3M criterion: the model must be mapped onto a mechanism. This framing of the situation has become the received view around the viability of dynamical explanation. In this paper, I argue against this position and show that dynamical (...)
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  43. Natural goodness without natural history.Parisa Moosavi - 2020 - Philosophy and Phenomenological Research:78-100.
    Neo‐Aristotelian ethical naturalism purports to show that moral evaluation of human action and character is an evaluation of natural goodness—a kind of evaluation that applies to living things in virtue of their nature and based on their form of life. The standard neo‐Aristotelian view defines natural goodness by way of generic statements describing the natural history, or the ‘characteristic’ life, of a species. In this paper, I argue that this conception of natural goodness commits the neo‐Aristotelian view to a problematic (...)
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  44. On Being the Right Size, Revisited: The Problem with Engineering Metaphors in Molecular Biology.Daniel J. Nicholson - 2020 - In Sune Holm & Maria Serban (eds.), Philosophical Perspectives on the Engineering Approach in Biology: Living Machines? New York: Routledge. pp. 40-68.
    In 1926, Haldane published an essay titled 'On Being the Right Size' in which he argued that the structure, function, and behavior of an organism are strongly conditioned by the physical forces that exert the greatest impact at the scale at which it exists. This chapter puts Haldane’s insight to work in the context of contemporary cell and molecular biology. Owing to their minuscule size, cells and molecules are subject to very different forces than macroscopic organisms. In a sense, macroscopic (...)
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  45. Mechanist idealisation in systems biology.Dingmar van Eck & Cory Wright - 2020 - Synthese 199 (1-2):1555-1575.
    This paper adds to the philosophical literature on mechanistic explanation by elaborating two related explanatory functions of idealisation in mechanistic models. The first function involves explaining the presence of structural/organizational features of mechanisms by reference to their role as difference-makers for performance requirements. The second involves tracking counterfactual dependency relations between features of mechanisms and features of mechanistic explanandum phenomena. To make these functions salient, we relate our discussion to an exemplar from systems biological research on the mechanism for countering (...)
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  46. The use and limitations of null-model-based hypothesis testing.Mingjun Zhang - 2020 - Biology and Philosophy 35 (2):1-22.
    In this article I give a critical evaluation of the use and limitations of null-model-based hypothesis testing as a research strategy in the biological sciences. According to this strategy, the null model based on a randomization procedure provides an appropriate null hypothesis stating that the existence of a pattern is the result of random processes or can be expected by chance alone, and proponents of other hypotheses should first try to reject this null hypothesis in order to demonstrate their own (...)
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  47. Explaining the behaviour of random ecological networks: the stability of the microbiome as a case of integrative pluralism.Roger Deulofeu, Javier Suárez & Alberto Pérez-Cervera - 2019 - Synthese 198 (3):2003-2025.
    Explaining the behaviour of ecosystems is one of the key challenges for the biological sciences. Since 2000, new-mechanicism has been the main model to account for the nature of scientific explanation in biology. The universality of the new-mechanist view in biology has been however put into question due to the existence of explanations that account for some biological phenomena in terms of their mathematical properties (mathematical explanations). Supporters of mathematical explanation have argued that the explanation of the behaviour of ecosystems (...)
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  48. Organic Selection and Social Heredity: The Original Baldwin Effect Revisited.Nam Le - 2019 - Artificial Life Conference Proceedings 2019 (31):515-522.
    The so-called “Baldwin Effect” has been studied for years in the fields of Artificial Life, Cognitive Science, and Evolutionary Theory across disciplines. This idea is often conflated with genetic assimilation, and has raised controversy in trans-disciplinary scientific discourse due to the many interpretations it has. This paper revisits the “Baldwin Effect” in Baldwin’s original spirit from a joint historical, theoretical and experimental approach. Social Heredity – the inheritance of cultural knowledge via non-genetic means in Baldwin’s term – is also taken (...)
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  49. 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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  50. What Constitutes an Explanation in Biology?Angela Potochnik - 2019 - In Kostas Kampourakis & Tobias Uller (eds.), Philosophy of Science for Biologists. New York, NY: Cambridge University Press.
    One of biology's fundamental aims is to generate understanding of the living world around—and within—us. In this chapter, I aim to provide a relatively nonpartisan discussion of the nature of explanation in biology, grounded in widely shared philosophical views about scientific explanation. But this discussion also reflects what I think is important for philosophers and biologists alike to appreciate about successful scientific explanations, so some points will be controversial, at least among philosophers. I make three main points: (1) causal relationships (...)
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