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  1. Typology and Natural Kinds in Evo-Devo.Ingo Brigandt - 2021 - In Nuño De La Rosa Laura & Müller Gerd (eds.), Evolutionary Developmental Biology: A Reference Guide. Springer. pp. 483-493.
    The traditional practice of establishing morphological types and investigating morphological organization has found new support from evolutionary developmental biology (evo-devo), especially with respect to the notion of body plans. Despite recurring claims that typology is at odds with evolutionary thinking, evo-devo offers mechanistic explanations of the evolutionary origin, transformation, and evolvability of morphological organization. In parallel, philosophers have developed non-essentialist conceptions of natural kinds that permit kinds to exhibit variation and undergo change. This not only facilitates a construal of species (...)
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  • Explanation in Evo-Devo.Marie I. Kaiser - 2021 - In de la Rosa L. N. & Müller G. B. (eds.), Evolutionary Developmental Biology - A Reference Guide. Springer.
    Evo-devo is a multidisciplinary field that investigates the interplay between evolutionary and developmental processes and brings together different kinds of explanatory strategies. This chapter examines the structure of paradigmatic explanations in evo-devo (e.g., the explanation of the origin of an evolutionary novelty) and raises philosophical questions about explanation in evo-devo. Much research in evo-devo is concerned with studying the developmental mechanisms that constrain and facilitate phenotypic evolution, which suggests that a distinctive feature of evo-devo is that it constructs mechanistic explanations. (...)
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  • Coordination as Naturalistic Social Ontology: Constraints and Explanation.Valerii Shevchenko - 2023 - Philosophy of the Social Sciences 53 (2):103-121.
    In the paper, I propose a project of social coordination as naturalistic social ontology (CNSO) based on the rules-in-equilibria theory of social institutions (Guala and Hindriks 2015; Hindriks and Guala 2015). It takes coordination as the main ontological unit of the social, a mechanism homological across animals and humans, for both can handle coordination problems: in the forms of “animal conventions” and social institutions, respectively. On this account, institutions are correlated equilibria with normative force. However, if both humans and animals (...)
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  • What is social structural explanation? A causal account.Lauren N. Ross - 2023 - Noûs 1 (1):163-179.
    Social scientists appeal to various “structures” in their explanations including public policies, economic systems, and social hierarchies. Significant debate surrounds the explanatory relevance of these factors for various outcomes such as health, behavioral, and economic patterns. This paper provides a causal account of social structural explanation that is motivated by Haslanger (2016). This account suggests that social structure can be explanatory in virtue of operating as a causal constraint, which is a causal factor with unique characteristics. A novel causal framework (...)
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  • Multilevel Ensemble Explanations: A Case from Theoretical Biology.Luca Rivelli - 2019 - Perspectives on Science 27 (1):88-116.
    In this paper I will reconstruct and analyze a famous argument by Stuart Kauffman about complex systems and evolution, in order to highlight the use in theoretical biology of a kind of non-mechanistic and non-causal explanation which I propose to call, following Kauffman, ensemble explanation. The aim is to contribute to the ongoing philosophical debate about non-causal explanations in the special sciences, kinds of explanation apparently extraneous to the received causal-mechanistic view. Ensemble explanations resemble quite closely the explanations of the (...)
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  • What and How Do Cancer Systems Biologists Explain?Anya Plutynski & Marta Bertolaso - 2018 - Philosophy of Science 85 (5):942-954.
    In this article, we argue, first, that there are very different research projects that fall under the heading of “systems biology of cancer.” While they share some general features, they differ in their aims and theoretical commitments. Second, we argue that some explanations in systems biology of cancer are concerned with properties of signaling networks and how they may play an important causal role in patterns of vulnerability to cancer. Further, some systems biological explanations are compelling illustrations of how “top-down” (...)
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  • What could mathematics be for it to function in distinctively mathematical scientific explanations?Marc Lange - 2021 - Studies in History and Philosophy of Science Part A 87 (C):44-53.
    Several philosophers have suggested that some scientific explanations work not by virtue of describing aspects of the world’s causal history and relations, but rather by citing mathematical facts. This paper investigates what mathematical facts could be in order for them to figure in such “distinctively mathematical” scientific explanations. For “distinctively mathematical explanations” to be explanations by constraint, mathematical language cannot operate in science as representationalism or platonism describes. It can operate as Aristotelian realism describes. That is because Aristotelian realism enables (...)
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  • Unifying the Debates: Mathematical and Non-Causal Explanations.Daniel Kostić - 2019 - Perspectives on Science 27 (1):1-6.
    In the last couple of years a few seemingly independent debates on scientific explanation have emerged, with several key questions that take different forms in different areas. For example, the questions what makes an explanation distinctly mathematical and are there any non-causal explanations in sciences sometimes take a form of the question what makes mathematical models explanatory, especially whether highly idealized models in science can be explanatory and in virtue of what they are explanatory. These questions raise further issues about (...)
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  • Unifying the debates: mathematical and non-causal explanations.Daniel Kostić - 2019 - Perspectives on Science 27 (1):1-6.
    In the last couple of years a few seemingly independent debates on scientific explanation have emerged, with several key questions that take different forms in different areas. For example, the question what makes an explanation distinctly mathematical and are there any non-causal explanations in sciences (i.e. explanations that don’t cite causes in the explanans) sometimes take a form of the question what makes mathematical models explanatory, especially whether highly idealized models in science can be explanatory and in virtue of what (...)
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  • Minimal structure explanations, scientific understanding and explanatory depth.Daniel Kostić - 2018 - Perspectives on Science (1):48-67.
    In this paper, I outline a heuristic for thinking about the relation between explanation and understanding that can be used to capture various levels of “intimacy”, between them. I argue that the level of complexity in the structure of explanation is inversely proportional to the level of intimacy between explanation and understanding, i.e. the more complexity the less intimacy. I further argue that the level of complexity in the structure of explanation also affects the explanatory depth in a similar way (...)
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  • 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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  • The Multifaceted Legacy of the Human Genome Program for Evolutionary Biology: An Epistemological Perspective.Philippe Huneman - 2019 - Perspectives on Science 27 (1):117-152.
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  • Neutral Spaces and Topological Explanations in Evolutionary Biology: Lessons from Some Landscapes and Mappings.Philippe Huneman - 2018 - Philosophy of Science 85 (5):969-983.
    I consider recent uses of the notion of neutrality in evolutionary biology and ecology, questioning their relevance to the kind of explanation recently labeled ‘topological explanation’. Focusing on fitness landscapes and genotype-phenotype maps, I explore the explanatory uses of neutral subspaces, as modeled in two perspectives: hyperdimensional fitness landscapes and RNA sequence-structure maps. I argue that topological properties of such spaces account for features of evolutionary systems: respectively, capacity for adaptive evolution toward global optima and mutational robustness of genotypes. Thus (...)
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  • Reasons explanations (of actions) as structural explanations.Megan Fritts - 2021 - Synthese 199 (5-6):12683-12704.
    Non-causal accounts of action explanation have long been criticized for lacking a positive thesis, relying primarily on negative arguments to undercut the standard Causal Theory of Action The Stanford Encyclopedia of Philosophy, 2016). Additionally, it is commonly thought that non-causal accounts fail to provide an answer to Donald Davidson’s challenge for theories of reasons explanations of actions. According to Davidson’s challenge, a plausible non-causal account of reasons explanations must provide a way of connecting an agent’s reasons, not only to what (...)
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  • Descriptive understanding and prediction in COVID-19 modelling.Johannes Findl & Javier Suárez - 2021 - History and Philosophy of the Life Sciences 43 (4):1-31.
    COVID-19 has substantially affected our lives during 2020. Since its beginning, several epidemiological models have been developed to investigate the specific dynamics of the disease. Early COVID-19 epidemiological models were purely statistical, based on a curve-fitting approach, and did not include causal knowledge about the disease. Yet, these models had predictive capacity; thus they were used to ground important political decisions, in virtue of the understanding of the dynamics of the pandemic that they offered. This raises a philosophical question about (...)
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  • Taming vagueness: the philosophy of network science.Gábor Elek & Eszter Babarczy - 2022 - Synthese 200 (2):1-31.
    In the last 20 years network science has become an independent scientific field. We argue that by building network models network scientists are able to tame the vagueness of propositions about complex systems and networks, that is, to make these propositions precise. This makes it possible to study important vague properties such as modularity, near-decomposability, scale-freeness or being a small world. Using an epistemic model of network science, we systematically analyse the specific nature of network models and the logic behind (...)
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  • How do networks explain? A neo-hempelian approach to network explanations of the ecology of the microbiome.José Díez & Javier Suárez - 2023 - European Journal for Philosophy of Science 13 (3):1-26.
    Despite the importance of network analysis in biological practice, dominant models of scientific explanation do not account satisfactorily for how this family of explanations gain their explanatory power in every specific application. This insufficiency is particularly salient in the study of the ecology of the microbiome. Drawing on Coyte et al. (2015) study of the ecology of the microbiome, Deulofeu et al. (2021) argue that these explanations are neither mechanistic, nor purely mathematical, yet they are substantially empirical. Building on their (...)
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  • 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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  • Shades of Grey: Granularity, Pragmatics, and Non-Causal Explanation.Hugh Desmond - 2019 - Perspectives on Science 27 (1):68-87.
    Implicit contextual factors mean that the boundary between causal and noncausal explanation is not as neat as one might hope: as the phenomenon to be explained is given descriptions with varying degrees of granularity, the nature of the favored explanation alternates between causal and non-causal. While it is not surprising that different descriptions of the same phenomenon should favor different explanations, it is puzzling why re-describing the phenomenon should make any difference for the causal nature of the favored explanation. I (...)
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  • How to Philosophically Tackle Kinds without Talking About ‘Natural Kinds’.Ingo Brigandt - 2022 - Canadian Journal of Philosophy 52 (3):356-379.
    Recent rival attempts in the philosophy of science to put forward a general theory of the properties that all (and only) natural kinds across the sciences possess may have proven to be futile. Instead, I develop a general methodological framework for how to philosophically study kinds. Any kind has to be investigated and articulated together with the human aims that motivate referring to this kind, where different kinds in the same scientific domain can answer to different concrete aims. My core (...)
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  • Explanation of Molecular Processes without Tracking Mechanism Operation.Ingo Brigandt - 2018 - Philosophy of Science 85 (5):984-997.
    Philosophical discussions of systems biology have enriched the notion of mechanistic explanation by pointing to the role of mathematical modeling. However, such accounts still focus on explanation in terms of tracking a mechanism's operation across time (by means of mental or computational simulation). My contention is that there are explanations of molecular systems where the explanatory understanding does not consist in tracking a mechanism's operation and productive continuity. I make this case by a discussion of bifurcation analysis in dynamical systems, (...)
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  • Explainable Artificial Intelligence in Data Science.Joaquín Borrego-Díaz & Juan Galán-Páez - 2022 - Minds and Machines 32 (3):485-531.
    A widespread need to explain the behavior and outcomes of AI-based systems has emerged, due to their ubiquitous presence. Thus, providing renewed momentum to the relatively new research area of eXplainable AI (XAI). Nowadays, the importance of XAI lies in the fact that the increasing control transference to this kind of system for decision making -or, at least, its use for assisting executive stakeholders- already affects many sensitive realms (as in Politics, Social Sciences, or Law). The decision-making power handover to (...)
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  • New Mechanistic Philosophy and the Scientific Prospects of Code Biology.Majid Davoody Beni - 2019 - Biosemiotics 12 (2):197-211.
    Marcello Barbieri has presented code biology as an alternative to the Peircean approach to biosemiotics. Some critics questioned the viability of code biology on grounds that Barbieri’s conception of science is limited. It has been argued that code biology’s mechanistic tendency is the cause of the allegedly limited conception of science. In this paper, I evaluate the scientific viability of the code model from the perspective of scientific realism in the philosophy of science. To be more precise, I draw on (...)
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  • Natural Selection and the Nature of Statistical Explanations.Roger Deulofeu Batllori - forthcoming - Critica:27-52.
    There is a widespread philosophical interpretation of natural selection in evolutionary theory: natural selection, like mutation, migration, and drift are seen as forces that propel the evolution of populations. Natural selection is thus a population level causal process. This account has been challenged by the Statistics, claiming that natural selection is not a population level cause but rather a statistical feature of a population. This paper examines the nature of the aforementioned ontological debate and the nature of statistical explanations given (...)
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  • Mental machines.David L. Barack - 2019 - Biology and Philosophy 34 (6):63.
    Cognitive neuroscientists are turning to an increasingly rich array of neurodynamical systems to explain mental phenomena. In these explanations, cognitive capacities are decomposed into a set of functions, each of which is described mathematically, and then these descriptions are mapped on to corresponding mathematical descriptions of the dynamics of neural systems. In this paper, I outline a novel explanatory schema based on these explanations. I then argue that these explanations present a novel type of dynamicism for the philosophy of mind (...)
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  • Mental machines.David L. Barack - 2019 - Biology and Philosophy 34 (6):63.
    Cognitive neuroscientists are turning to an increasingly rich array of neurodynamical systems to explain mental phenomena. In these explanations, cognitive capacities are decomposed into a set of functions, each of which is described mathematically, and then these descriptions are mapped on to corresponding mathematical descriptions of the dynamics of neural systems. In this paper, I outline a novel explanatory schema based on these explanations. I then argue that these explanations present a novel type of dynamicism for the philosophy of mind (...)
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  • Mental kinematics: dynamics and mechanics of neurocognitive systems.David L. Barack - 2020 - Synthese 199 (1-2):1091-1123.
    Dynamical systems play a central role in explanations in cognitive neuroscience. The grounds for these explanations are hotly debated and generally fall under two approaches: non-mechanistic and mechanistic. In this paper, I first outline a neurodynamical explanatory schema that highlights the role of dynamical systems in cognitive phenomena. I next explore the mechanistic status of such neurodynamical explanations. I argue that these explanations satisfy only some of the constraints on mechanistic explanation and should be considered pseudomechanistic explanations. I defend this (...)
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  • Mental machines.David L. Barack - 2019 - Biology and Philosophy 34 (6):63.
    Cognitive neuroscientists are turning to an increasingly rich array of neurodynamical systems to explain mental phenomena. In these explanations, cognitive capacities are decomposed into a set of functions, each of which is described mathematically, and then these descriptions are mapped on to corresponding mathematical descriptions of the dynamics of neural systems. In this paper, I outline a novel explanatory schema based on these explanations. I then argue that these explanations present a novel type of dynamicism for the philosophy of mind (...)
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  • ¿Más es diferente, o es más de lo mismo? Introducción al debate contemporáneo sobre emergencia y reduccionismo.Aldo Filomeno, Carlos Romero & José Jerez - forthcoming - Revista de Humanidades de Valparaíso.
    Como introducción al monográfico sobre reduccionismo y emergencia brindamos aquí un contexto teórico al debate contemporáneo. Hablaremos primero del acercamiento naturalista en filosofía (§2), así como de dos de las características más importantes de la emergencia: autonomía y universalidad (§3). Finalmente, basándonos en la literatura contemporánea (principalmente en Patricia Palacios y Jessica Wilson, además de Mario Bunge y Alicia Juarrero) presentamos algunas de las definiciones y distinciones más importantes para entender mejor el debate sobre la emergencia (§4).
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  • Integrating Philosophy of Understanding with the Cognitive Sciences.Kareem Khalifa, Farhan Islam, J. P. Gamboa, Daniel Wilkenfeld & Daniel Kostić - 2022 - Frontiers in Systems Neuroscience 16.
    We provide two programmatic frameworks for integrating philosophical research on understanding with complementary work in computer science, psychology, and neuroscience. First, philosophical theories of understanding have consequences about how agents should reason if they are to understand that can then be evaluated empirically by their concordance with findings in scientific studies of reasoning. Second, these studies use a multitude of explanations, and a philosophical theory of understanding is well suited to integrating these explanations in illuminating ways.
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  • 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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