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  1. Causal Order and Kinds of Robustness.Arnon Levy - 2017 - In Snait Gissis, Ehud Lamm & Ayelet Shavit (eds.), Landscapes of Collectivity in the Life Sciences. Cambridge, Massachusetts: MIT Press. pp. 269-280.
    This paper derives from a broader project dealing with the notion of causal order. I use this term to signify two kinds of parts-whole dependence: Orderly systems have rich, decomposable, internal structure; specifically, parts play differential roles, and interactions are primarily local. Disorderly systems, in contrast, have a homogeneous internal structure, such that differences among parts and organizational features are less important. Orderliness, I suggest, marks one key difference between individuals and collectives. My focus here will be the connection between (...)
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  • Mechanisms, counterfactuals and laws.Stavros Ioannidis & Stathis Psillos - 2017 - In Stuart Glennan & Phyllis McKay Illari (eds.), The Routledge Handbook of Mechanisms and Mechanical Philosophy. Routledge. pp. 144-156.
    In this chapter we examine the relation between mechanisms and laws/counterfactuals by revisiting the main notions of mechanism found in the literature. We distinguish between two different conceptions of ‘mechanism’: mechanisms-of underlie or constitute a causal process; mechanisms-for are complex systems that function so as to produce a certain behavior. According to some mechanists, a mechanism fulfills both of these roles simultaneously. The main argument of the chapter is that there is an asymmetrical dependence between both kinds of mechanisms and (...)
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  • New Mechanistic Explanation and the Need for Explanatory Constraints.L. R. Franklin-Hall - 2016 - In Ken Aizawa & Carl Gillett (eds.), Scientific Composition and Metaphysical Ground. London: Palgrave-Macmillan. pp. 41-74.
    This paper critiques the new mechanistic explanatory program on grounds that, even when applied to the kinds of examples that it was originally designed to treat, it does not distinguish correct explanations from those that blunder. First, I offer a systematization of the explanatory account, one according to which explanations are mechanistic models that satisfy three desiderata: they must 1) represent causal relations, 2) describe the proper parts, and 3) depict the system at the right ‘level.’ Second, I argue that (...)
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  • Functional individuation, mechanistic implementation: the proper way of seeing the mechanistic view of concrete computation.Dimitri Coelho Mollo - 2017 - Synthese 195 (8):3477-3497.
    I examine a major objection to the mechanistic view of concrete computation, stemming from an apparent tension between the abstract nature of computational explanation and the tenets of the mechanistic framework: while computational explanation is medium-independent, the mechanistic framework insists on the importance of providing some degree of structural detail about the systems target of the explanation. I show that a common reply to the objection, i.e. that mechanistic explanation of computational systems involves only weak structural constraints, is not enough (...)
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  • Revisiting abstraction and idealization: how not to criticize mechanistic explanation in molecular biology.Martin Zach - 2022 - European Journal for Philosophy of Science 12 (1):1-20.
    Abstraction and idealization are the two notions that are most often discussed in the context of assumptions employed in the process of model building. These notions are also routinely used in philosophical debates such as that on the mechanistic account of explanation. Indeed, an objection to the mechanistic account has recently been formulated precisely on these grounds: mechanists cannot account for the common practice of idealizing difference-making factors in models in molecular biology. In this paper I revisit the debate and (...)
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  • Mechanisms without mechanistic explanation.Naftali Weinberger - 2017 - Synthese:1-18.
    Some recent accounts of constitutive relevance have identified mechanism components with entities that are causal intermediaries between the input and output of a mechanism. I argue that on such accounts there is no distinctive inter-level form of mechanistic explanation and that this highlights an absence in the literature of a compelling argument that there are such explanations. Nevertheless, the entities that these accounts call ‘components’ do play an explanatory role. Studying causal intermediaries linking variables Xand Y provides knowledge of the (...)
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  • Mechanisms without mechanistic explanation.Naftali Weinberger - 2019 - Synthese 196 (6):2323-2340.
    Some recent accounts of constitutive relevance have identified mechanism components with entities that are causal intermediaries between the input and output of a mechanism. I argue that on such accounts there is no distinctive inter-level form of mechanistic explanation and that this highlights an absence in the literature of a compelling argument that there are such explanations. Nevertheless, the entities that these accounts call ‘components’ do play an explanatory role. Studying causal intermediaries linking variables Xand Y provides knowledge of the (...)
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  • Mechanisms and generative material models.Sim-Hui Tee - 2019 - Synthese 198 (7):6139-6157.
    Mechanisms consist of component parts and processes organized in a specific way to produce changes that may give rise to one or more phenomena. I aim to examine the generative mechanism of generative material models in the production of new material models. A generative material model in biology is a living material model that is capable of generating new material models. I contend that generative mechanisms of a generative material model are not to be conflated with biological mechanisms: the former (...)
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  • Mechanistic Explanation of Biological Processes.Derek John Skillings - 2015 - Philosophy of Science 82 (5):1139-1151.
    Biological processes are often explained by identifying the underlying mechanisms that generate a phenomenon of interest. I characterize a basic account of mechanistic explanation and then present three challenges to this account, illustrated with examples from molecular biology. The basic mechanistic account is insufficient for explaining nonsequential and nonlinear dynamic processes, is insufficient for explaining the inherently stochastic nature of many biological mechanisms, and fails to give a proper framework for analyzing organization. I suggest that biological processes are best approached (...)
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  • Review of Physical Computation: A Mechanistic Account by Gualtiero Piccinini - Gualtiero Piccinini, Physical Computation: A Mechanistic Account. Oxford: Oxford University Press (2015), 313 pp., $65.00 (cloth). [REVIEW]Oron Shagrir - 2017 - Philosophy of Science 84 (3):604-612.
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  • Why there isn’t inter-level causation in mechanisms.Felipe Romero - 2015 - Synthese 192 (11):3731-3755.
    The experimental interventions that provide evidence of causal relations are notably similar to those that provide evidence of constitutive relevance relations. In the first two sections, I show that this similarity creates a tension: there is an inconsistent triad between Woodward’s popular interventionist theory of causation, Craver’s mutual manipulability account of constitutive relevance in mechanisms, and a variety of arguments for the incoherence of inter-level causation. I argue for an interpretation of the views in which the tension is merely apparent. (...)
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  • Information and explanation: an inconsistent triad and solution.Mark Povich - 2021 - European Journal for Philosophy of Science 11 (2):1-17.
    An important strand in philosophy of science takes scientific explanation to consist in the conveyance of some kind of information. Here I argue that this idea is also implicit in some core arguments of mechanists, some of whom are proponents of an ontic conception of explanation that might be thought inconsistent with it. However, informational accounts seem to conflict with some lay and scientific commonsense judgments and a central goal of the theory of explanation, because information is relative to the (...)
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  • A Philosophical Perspective on Evolutionary Systems Biology.Maureen A. O’Malley, Orkun S. Soyer & Mark L. Siegal - 2015 - Biological Theory 10 (1):6-17.
    Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context (...)
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  • On closing the gap between philosophical concepts and their usage in scientific practice: a lesson from the debate about natural selection as a mechanism.Lucas J. Matthews - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 55:21-28.
    In addition to theorizing about the role and value of mechanisms in scientific explanation or the causal structure of the world, there is a fundamental task of getting straight what a ‘mechanism’ is in the first place. Broadly, this paper is about the challenge of application: the challenge of aligning one's philosophical account of a scientific concept with the manner in which that concept is actually used in scientific practice. This paper considers a case study of the challenge of application (...)
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  • Embedded Mechanisms and Phylogenetics.Lucas J. Matthews - 2015 - Philosophy of Science 82 (5):1116-1126.
    A strong case has been made for the role and value of mechanistic explanation in neuroscience and molecular biology. A similar demonstration in other domains of scientific investigation, however, remains an important challenge of scope for the new mechanists. This article helps answer that challenge by demonstrating one valuable role mechanisms play in phylogenetics. Using the transition/transversion rate parameter as a case example, this article argues that models embedded with mechanisms produce stronger phylogenetic tree hypotheses, as measured by maximum likelihood (...)
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  • Ontic and Epistemic Differentiation: Mechanistic Problems for Microbiology and Biology.Flavia Marcacci, Michal Oleksowicz & Angela Conti - forthcoming - Foundations of Science:1-23.
    Species are considered the basic unit of biological classification and evolution. Hence, they are used as a benchmark in several fields, although the ontological status of such a category has always been a matter of debate. This paper aims to discuss the problem of the definition of species within the new mechanistic approach. Nevertheless, the boundary between entities, activities, and mechanisms remains difficult to establish and always requires an analysis of what is meant by explanation. As a case study, the (...)
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  • Relating traditional and academic ecological knowledge: mechanistic and holistic epistemologies across cultures.David Ludwig & Luana Poliseli - 2018 - Biology and Philosophy 33 (5-6):43.
    Current debates about the integration of traditional and academic ecological knowledge struggle with a dilemma of division and assimilation. On the one hand, the emphasis on differences between traditional and academic perspectives has been criticized as creating an artificial divide that brands TEK as “non-scientific” and contributes to its marginalization. On the other hand, there has been increased concern about inadequate assimilation of Indigenous and other traditional perspectives into scientific practices that disregards the holistic nature and values of TEK. The (...)
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  • Strategies of Explanatory Abstraction in Molecular Systems Biology.Nicholaos Jones - 2018 - Philosophy of Science 85 (5):955-968.
    I consider three explanatory strategies from recent systems biology that are driven by mathematics as much as mechanistic detail. Analysis of differential equations drives the first strategy; topological analysis of network motifs drives the second; mathematical theorems from control engineering drive the third. I also distinguish three abstraction types: aggregations, which simplify by condensing information; generalizations, which simplify by generalizing information; and structurations, which simplify by contextualizing information. Using a common explanandum as reference point—namely, the robust perfect adaptation of chemotaxis (...)
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  • Is synthetic biology mechanical biology?Sune Holm - 2015 - History and Philosophy of the Life Sciences 37 (4):413-429.
    A widespread and influential characterization of synthetic biology emphasizes that synthetic biology is the application of engineering principles to living systems. Furthermore, there is a strong tendency to express the engineering approach to organisms in terms of what seems to be an ontological claim: organisms are machines. In the paper I investigate the ontological and heuristic significance of the machine analogy in synthetic biology. I argue that the use of the machine analogy and the aim of producing rationally designed organisms (...)
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  • Bridging bioethics and biology.Sune Holm - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 55:133-136.
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  • What are ecological mechanisms? Suggestions for a fine-grained description of causal mechanisms in invasion ecology.Tina Heger - 2022 - Biology and Philosophy 37 (2):1-14.
    Invasion ecology addresses the spread of species outside of their native ranges. A central aim of this field is to find mechanistic explanations for why species are able to establish and spread in an area in which they did not evolve. Usually it remains unclear, however, what exactly is meant by ‘mechanistic explanation’ or ‘mechanism’. The paper argues that the field can benefit from the philosophical discussion of what a mechanism is. Based on conceptions of mechanisms as processes in concrete (...)
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  • The humanities as conceptual practices: The formation and development of high‐impact concepts in philosophy and beyond.Philipp Haueis & Jan Slaby - 2022 - Metaphilosophy 53 (4):385-403.
    This paper proposes an analysis of the discursive dynamics of high-impact concepts in the humanities. These are concepts whose formation and development have a lasting and wide-ranging effect on research and our understanding of discursive reality in general. The notion of a conceptual practice, based on a normative conception of practice, is introduced, and practices are identified, on this perspective, according to the way their respective performances are held mutually accountable. This normative conception of practices is then combined with recent (...)
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  • Putting History Back into Mechanisms.Justin Garson - 2023 - British Journal for the Philosophy of Science 74 (4):921-940.
    Mechanisms, in the prominent biological sense of the term, are historical entities. That is, whether or not something is a mechanism for something depends on its history. Put differently, while your spontaneously-generated molecule-for-molecule double has a heart, and its heart pumps blood around its body, its heart does not have a mechanism for pumping, since it does not have the right history. My argument for this claim is that mechanisms have proper functions; proper functions are historical entities; so, mechanisms are (...)
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  • What is Interpretability?Adrian Erasmus, Tyler D. P. Brunet & Eyal Fisher - 2021 - Philosophy and Technology 34:833–862.
    We argue that artificial networks are explainable and offer a novel theory of interpretability. Two sets of conceptual questions are prominent in theoretical engagements with artificial neural networks, especially in the context of medical artificial intelligence: Are networks explainable, and if so, what does it mean to explain the output of a network? And what does it mean for a network to be interpretable? We argue that accounts of “explanation” tailored specifically to neural networks have ineffectively reinvented the wheel. In (...)
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  • Mechanistic and topological explanations in medicine: the case of medical genetics and network medicine.Marie Darrason - 2018 - Synthese 195 (1):147-173.
    Medical explanations have often been thought on the model of biological ones and are frequently defined as mechanistic explanations of a biological dysfunction. In this paper, I argue that topological explanations, which have been described in ecology or in cognitive sciences, can also be found in medicine and I discuss the relationships between mechanistic and topological explanations in medicine, through the example of network medicine and medical genetics. Network medicine is a recent discipline that relies on the analysis of various (...)
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  • Newton on Islandworld: Ontic-Driven Explanations of Scientific Method.Adrian Currie & Kirsten Walsh - 2018 - Perspectives on Science 26 (1):119-156.
    . Philosophers and scientists often cite ontic factors when explaining the methods and success of scientific inquiry. That is, the adoption of a method or approach is explained in reference to the kind of system in which the scientist is interested: these are explanations of why scientists do what they do, that appeal to properties of their target systems. We present a framework for understanding such “Opticks to his Principia. Newton’s optical work is largely experiment-driven, while the Principia is primarily (...)
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  • Narratives, mechanisms and progress in historical science.Adrian Mitchell Currie - 2014 - Synthese 191 (6):1-21.
    Geologists, Paleontologists and other historical scientists are frequently concerned with narrative explanations targeting single cases. I show that two distinct explanatory strategies are employed in narratives, simple and complex. A simple narrative has minimal causal detail and is embedded in a regularity, whereas a complex narrative is more detailed and not embedded. The distinction is illustrated through two case studies: the ‘snowball earth’ explanation of Neoproterozoic glaciation and recent attempts to explain gigantism in Sauropods. This distinction is revelatory of historical (...)
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  • Real Patterns in Biological Explanation.Daniel C. Burnston - 2017 - Philosophy of Science 84 (5):879-891.
    In discussion of mechanisms, philosophers often debate about whether quantitative descriptions of generalizations or qualitative descriptions of operations are explanatorily fundamental. I argue that these debates have erred by conflating the explanatory roles of generalizations and patterns. Patterns are types of variations within or between quantities in a mechanism over time or across conditions. While these patterns must often be represented in addition to descriptions of operations in order to explain a phenomenon, they are not equivalent to generalizations because their (...)
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  • Molecular pathways and the contextual explanation of molecular functions.Giovanni Boniolo & Raffaella Campaner - 2018 - Biology and Philosophy 33 (3-4):24.
    Much of the recent philosophical debate on causation and causal explanation in the biological and biomedical sciences has focused on the notion of mechanism. Mechanisms, their nature and epistemic roles have been tackled by a range of so-called neo-mechanistic theories, and widely discussed. Without denying the merits of this approach, our paper aims to show how lately it has failed to give proper credit to processes, which are central to the field, especially of contemporary molecular biology. Processes can be summed (...)
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  • Teleonomy as a problem of self-causation.Nathalie Gontier - forthcoming - Biological Journal of the Linnean Society 139:388–414.
    A theoretical framework is provided to explore teleonomy as a problem of self-causation, distinct from upward, downward and reticulate causation. Causality theories in biology are often formulated within hierarchy theories, where causation is conceptualized as running up or down the rungs of a ladder-like hierarchy or, more recently, as moving between multiple hierarchies. Research on the genealogy of cosmologies demonstrates that in addition to hierarchy theories, causality theories also depend upon ideas of time. This paper explores the roots and impact (...)
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  • Cognition in Practice: Conceptual Development and Disagreement in Cognitive Science.Mikio Akagi - 2016 - Dissertation, University of Pittsburgh
    Cognitive science has been beset for thirty years by foundational disputes about the nature and extension of cognition—e.g. whether cognition is necessarily representational, whether cognitive processes extend outside the brain or body, and whether plants or microbes have them. Whereas previous philosophical work aimed to settle these disputes, I aim to understand what conception of cognition scientists could share given that they disagree so fundamentally. To this end, I develop a number of variations on traditional conceptual explication, and defend a (...)
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  • Reconciling New Mechanism and Psychological Explanation: A Pragmatic Approach.Michael De Vivo - unknown
    Recently, Gualtiero Piccinini and Carl Craver have argued that functional analyses in psychology lack explanatory autonomy from explanations in neuroscience. In this thesis I argue against this claim by motivating and defending a pragmatic-epistemic conception of autonomous psychological explanation. I argue that this conception of autonomy need not require that functional analyses be distinct in kind from neural-mechanistic explanations. I use the framework of Bas van Fraassen’s Pragmatic Theory of Explanation to show that explanations in psychology and neuroscience can be (...)
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  • Causal inquiry in the social sciences: the promise of process tracing.Rosa Runhardt - 2015 - Dissertation, London School of Economics
    In this thesis I investigate causal inquiry in the social sciences, drawing on examples from various disciplines and in particular from conflict studies. In a backlash against the pervasiveness of statistical methods, in the last decade certain social scientists have focused on finding the causal mechanisms behind observed correlations. To provide evidence for such mechanisms, researchers increasingly rely on ‘process tracing’, a method which attempts to give evidence for causal relations by specifying the chain of events connecting a putative cause (...)
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  • Did the bacterium really kill the colonel? Systemic view, inter-level causation, and levels of quasi-decompositionality in mechanistic explanations.Emilio Cáceres Vázquez & Cristian Saborido - 2018 - Theoria : An International Journal for Theory, History and Fundations of Science 33 (1):129-148.
    In this paper, we critically analyze the mechanicist approach to scientific explanation and propose to complement this view with a conception of level as interval of quasi-decompositionality. This conception allows us to metaphysically base the mechanicist proposals on characteristic systemic features. By means of concrete examples, we claim that this proposal is able to overcome some of the alleged limitations of predominant models of mechanistic explanation.
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