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  1. Metabolism Instead of Machine: Towards an Ontology of Hybrids.Julia Rijssenbeek, Vincent Blok & Zoë Robaey - 2022 - Philosophy and Technology 35 (3):1-23.
    The emerging field of synthetic biology aims to engineer novel biological entities. The envisioned future bio-based economy builds largely on “cell factories”: organisms that have been metabolically engineered to sustainably produce substances for human ends. In this paper, we argue that synthetic biology’s goal of creating efficient production vessels for industrial applications implies a set of ontological assumptions according to which living organisms are machines. Traditionally, a machine is understood as a technological, isolated and controllable production unit consisting of parts. (...)
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  • Natural Selection According to Darwin: Cause or Effect?Ben Bradley - 2022 - History and Philosophy of the Life Sciences 44 (2):1-26.
    In the 1940s, the ‘modern synthesis’ of Darwinism and genetics cast genetic mutation and recombination as the source of variability from which environmental events naturally select the fittest, such ‘natural selection’ constituting the cause of evolution. Recent biology increasingly challenges this view by casting genes as followers and awarding the leading role in the genesis of adaptations to the agency and plasticity of developing phenotypes—making natural selection a consequence of other causal processes. Both views of natural selection claim to capture (...)
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  • Can There be a Process Without Time? Processualism Within Timeless Physics.Emilia Margoni - 2022 - Foundations of Physics 52 (2):1-19.
    Process ontology is making deep inroads into the hard sciences. For it offers a workable understanding of dynamic phenomena which sits well with inquiries that problematize the traditional conception of self-standing, definite, independent objects as the basic stuff of the universe. Process-based approaches are claimed by their advocates to yield better ontological descriptions of various domains of physical reality in which dynamical, indefinite activities are prior to definite “things” or “states of things”. However, if applied to physics, a main problem (...)
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  • Process epistemology in the COVID-19 era: rethinking the research process to avoid dangerous forms of reification.John Dupré & Sabina Leonelli - 2022 - European Journal for Philosophy of Science 12 (1):1-22.
    Whether we live in a world of autonomous things, or a world of interconnected processes in constant flux, is an ancient philosophical debate. Modern biology provides decisive reasons for embracing the latter view. How does one understand the practices and outputs of science in such a dynamic, ever-changing world - and particularly in an emergency situation such as the COVID-19 pandemic, where scientific knowledge has been regarded as bedrock for decisive social interventions? We argue that key to answering this question (...)
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  • Mistake-Making: A Theoretical Framework for Generating Research Questions in Biology, with Illustrative Application to Blood Clotting.Jonathan Hill, David Oderberg, Jon Gibbins & Ingo Bojak - unknown
    It is a matter of contention whether or not a general explanatory framework for the biological sciences would be of scientific value, or whether it is even achievable. In this paper we suggest that both are the case, and we outline proposals for a framework capable of generating new scientific questions. Starting with one clear characteristic of biological systems – that they all have the potential to make mistakes - we aim to describe the nature of this potential and the (...)
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  • One or two? A Process View of pregnancy.Anne Sophie Meincke - 2022 - Philosophical Studies 179 (5):1495-1521.
    How many individuals are present where we see a pregnant individual? Within a substance ontological framework, there are exactly two possible answers to this question. The standard answer—two individuals—is typically championed by scholars endorsing the predominant Containment View of pregnancy, according to which the foetus resides in the gestating organism like in a container. The alternative answer—one individual—has recently found support in the Parthood View, according to which the foetus is a part of the gestating organism. Here I propose a (...)
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  • The logic of explanation in molecular biology: historical-processual and logical-procedural aspects.Giovanni Boniolo & Raffaella Campaner - 2022 - European Journal for Philosophy of Science 12 (1):1-24.
    This work addresses biological explanations and aims to provide a philosophical account which brings together logical-procedural and historical-processual aspects when considering molecular pathways. It is argued that, having molecular features as explananda, a particular non-classical logical language – Zsyntax – can be used to formally represent, in terms of logical theorems, types of molecular processes, and to grasp how we get from one molecular interaction to another, hence explaining why a given outcome occurs. Expressing types of molecular biology processes in (...)
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  • Philosophy of Developmental Biology.Marcel Weber - 2022 - Cambridge: Cambridge University Press.
    The history of developmental biology is interwoven with debates as to whether mechanistic explanations of development are possible or whether alternative explanatory principles or even vital forces need to be assumed. In particular, the demonstrated ability of embryonic cells to tune their developmental fate precisely to their relative position and the overall size of the embryo was once thought to be inexplicable in mechanistic terms. Taking a causal perspective, this Element examines to what extent and how developmental biology, having turned (...)
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  • 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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  • More Plant Biology in Philosophy Education.Özlem Yilmaz - 2021 - Dublin, Ireland: Graphikon Teo.
    This is an article in Thomas J.J. McCloughlin (Ed.) The Nature of Science in Biology: A Resource for Educators. Graphikon Teo, Dublin. -/- Abstract: Philosophers usually tend to think of animals when they think about life, plants often only appear in their works as on the margins, in the background; they are rarely in the centre. However, plant life involves unique processes, including remarkable modes of interaction between plants and their environments. Needless to say, plants are vital parts of ecosystems. (...)
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  • Semiosis is Cognitive Niche Construction.Pedro Atã & João Queiroz - 2019 - Semiotica 2019 (228):3-16.
    Journal Name: Semiotica Issue: Ahead of print.
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  • Uexküll and Whitehead on Meaning, Process and Life.Arthur Araújo - 2020 - Sign Systems Studies 48 (2-4):415-449.
    The paper approximates Jakob von Uexküll’s theory of meaning and the process-thought in Alfred Whitehead’s philosophy. As the main idea, the paper points at the compatibility of meaning and process according to the perspectives of Uexküll and Whitehead. It suggests that Uexküll’s common meaning rule can describe the processes of novelty in the world as does Whitehead’s principle of creativity. It is also suggested that Uexküll and Whitehead abandon a substantialist view of the organism – the organism means much more (...)
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  • Biosemiotics and Applied Evolutionary Epistemology: A Comparison.Nathalie Gontier & M. Facoetti - 2021 - In In: Pagni E., Theisen Simanke R. (eds) Biosemiotics and Evolution. Interdisciplinary Evolution Research, vol 6. Springer, Cham. Cham: pp. 175-199.
    Both biosemiotics and evolutionary epistemology are concerned with how knowledge evolves. (Applied) Evolutionary Epistemology thereby focuses on identifying the units, levels, and mechanisms or processes that underlie the evolutionary development of knowing and knowledge, while biosemiotics places emphasis on the study of how signs underlie the development of meaning. We compare the two schools of thought and analyze how in delineating their research program, biosemiotics runs into several problems that are overcome by evolutionary epistemologists. For one, by emphasizing signs, biosemiotics (...)
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  • New Developments in Enactive Social Cognition.Alan Walter Jurgens - 2020 - Dissertation, University of Wollongong
    The long standing and still highly influential mindreading framework claims that social cog- nition is best understood as an ability to predict and explain others’ behavior in terms of their mental states. This ability is explained by appealing to mental representations and inferential reasoning via rule-based knowledge. However, recent enactive work on social cognition questions most, if not all, of the main assumptions on which mindreading is founded. Enac- tivism’s emphasis on the structural coupling of the brain-body-world constitutes the foundation (...)
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  • Code Biology and the Problem of Emergence.Arran Gare - 2021 - Biosystems 208.
    It should now be recognized that codes are central to life and to understanding its more complex forms, including human culture. Recognizing the ‘conventional’ nature of codes provides solid grounds for rejecting efforts to reduce life to biochemistry and justifies according a place to semantics in life. The question I want to consider is whether this is enough. Focussing on Eigen’s paradox of how a complex code could originate, I will argue that along with Barbieri’s efforts to account for the (...)
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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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  • How Should We Select Conceptual Content for Biology High School Curricula?Ítalo Nascimento de Carvalho, Charbel N. El-Hani & Nei Nunes-Neto - 2020 - Science & Education 29 (3):513-547.
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  • Token Physicalism and Functional Individuation.James DiFrisco - 2018 - European Journal for Philosophy of Science 8 (3):309-329.
    Token physicalism is often viewed as a modest and unproblematic physicalist commitment, as contrasted with type physicalism. This paper argues that the prevalence of functional individuation in biology creates serious problems for token physicalism, because the latter requires that biological entities can be individuated physically and without reference to biological functioning. After characterizing the main philosophical roles for token physicalism, I describe the distinctive uses of functional individuation in models of biological processes. I then introduce some requirements on token identity (...)
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  • On Radical Solutions in the Philosophy of Biology: What Does “Individuals Thinking” Actually Solve?Thomas A. C. Reydon - 2019 - Synthese 198 (4):3389-3411.
    The philosophy of biology is witnessing an increasing enthusiasm for what can be called “individuals thinking”. Individuals thinking is a perspective on the metaphysics of biological entities according to which conceiving of them as individuals rather than kinds enables us to expose ongoing metaphysical debates as focusing on the wrong question, and to achieve better accounts of the metaphysics of biological entities. In this paper, I examine two cases of individuals thinking, the claim that species are individuals and the claim (...)
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  • For a Creative Ontology of the Future. An Ode to Love.Jamie Brassett - 2021 - In Jamie Brassett & John O’Reilly (eds.), A Creative Philosophy of Anticipation.
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  • Schwerpunkt: Technische und organische Form – ein altes neues Problem?Marco Tamborini & Mathias Gutmann - 2020 - Deutsche Zeitschrift für Philosophie 68 (5):705-711.
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  • The Process of microRNAs Discovery.Paweł Kawalec - 2020 - Philosophical Problems in Science 68:219-242.
    The widespread particularist account of the onset of molecular biology that identifies it with the discovery of the DNA structure in 1953 has been recently contested. The paper contributes to this debate by focusing on a more recent discovery of small noncoding RNAs. First, it outlines a particularist account of the microRNAs discovery and the origins of the particularist predilection of the modern scientometric studies of science dynamics. Next, it discusses its limitations and proposes an alternative, modified processualist account of (...)
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  • What is a Hologenomic Adaptation? Emergent Individuality and Inter-Identity in Multispecies Systems.Javier Suárez & Vanessa Triviño - 2020 - Frontiers in Psychology 187 (11).
    Contemporary biological research has suggested that some host–microbiome multispecies systems (referred to as “holobionts”) can in certain circumstances evolve as unique biological individual, thus being a unit of selection in evolution. If this is so, then it is arguably the case that some biological adaptations have evolved at the level of the multispecies system, what we call hologenomic adaptations. However, no research has yet been devoted to investigating their nature, or how these adaptations can be distinguished from adaptations at the (...)
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  • Organisms, activity, and being: on the substance of process ontology.Christopher J. Austin - 2020 - European Journal for Philosophy of Science 10 (2):1-21.
    According to contemporary ‘process ontology’, organisms are best conceptualised as spatio-temporally extended entities whose mereological composition is fundamentally contingent and whose essence consists in changeability. In contrast to the Aristotelian precepts of classical ‘substance ontology’, from the four-dimensional perspective of this framework, the identity of an organism is grounded not in certain collections of privileged properties, or features which it could not fail to possess, but in the succession of diachronic relations by which it persists, or ‘perdures’ as one entity (...)
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  • Scientific Knowledge in the Age of Computation: Explicated, Computable and Manageable?Sophia Efstathiou, Rune Nydal, Astrid Laegreid & Martin Kuiper - 2019 - Theoria. An International Journal for Theory, History and Foundations of Science 34 (2):213.
    We have two theses about scientific knowledge in the age of computation. Our general claim is that scientific Knowledge Management practices emerge as second-order practices whose aim is to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data. Our specific thesis is that knowledge management practices are transforming biological research in at least three ways. We argue that scientific Knowledge Management a. operates with founded concepts of biological knowledge as explicated and computable, b. enables new outputs and (...)
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  • Psa 2018.Philsci-Archive -Preprint Volume- - unknown
    These preprints were automatically compiled into a PDF from the collection of papers deposited in PhilSci-Archive in conjunction with the PSA 2018.
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  • Individuating Genes as Types or Individuals: Philosophical Implications on Individuality, Kinds, and Gene Concepts.Ruey-Lin Chen - unknown
    “What is a gene?” is an important philosophical question that has been asked over and over. This paper approaches this question by understanding it as the individuation problem of genes, because it implies the problem of identifying genes and identifying a gene presupposes individuating the gene. I argue that there are at least two levels of the individuation of genes. The transgenic technique can individuate “a gene” as an individual while the technique of gene mapping in classical genetics can only (...)
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  • Scientific Knowledge in the Age of Computation.Sophia Efstathiou, Rune Nydal, Astrid LÆgreid & Martin Kuiper - 2019 - Theoria: Revista de Teoría, Historia y Fundamentos de la Ciencia 34 (2):213-236.
    With increasing publication and data production, scientific knowledge presents not simply an achievement but also a challenge. Scientific publications and data are increasingly treated as resources that need to be digitally ‘managed.’ This gives rise to scientific Knowledge Management : second-order scientific work aiming to systematically collect, take care of and mobilise first-hand disciplinary knowledge and data in order to provide new first-order scientific knowledge. We follow the work of Leonelli, Efstathiou and Hislop in our analysis of the use of (...)
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  • Autopoiesis, Biological Autonomy and the Process View of Life.Anne Sophie Meincke - 2018 - European Journal for Philosophy of Science 9 (1):5.
    In recent years, an increasing number of theoretical biologists and philosophers of biology have been opposing reductionist research agendas by appealing to the concept of biological autonomy which draws on the older concept of autopoiesis. In my paper, I investigate some of the ontological implications of this approach. The emphasis on autonomy and autopoiesis, together with the associated idea of organisational closure, might evoke the impression that organisms are to be categorised ontologically as substances: ontologically independent, well-individuated, discrete particulars. However, (...)
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  • Typology and Natural Kinds in Evo-Devo.Ingo Brigandt - 2021 - In Laura Nuño De La Rosa & Gerd Müller (eds.), Evolutionary Developmental Biology: A Reference Guide. Cham: 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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  • New Powers for Dispositionalism.Giacomo Giannini - 2020 - Synthese (ST: New Foundations for Disposit):1-30.
    Establishing Dispositionalism as a viable theory of modality requires the successful fulfilment of two tasks: showing that all modal truths can be derived from truths about actual powers, and offering a suitable metaphysics of powers. These two tasks are intertwined: difficulties in one can affect the chances of success in the other. In this paper, I generalise an objection to Dispositionalism by Jessica Leech and argue that the theory in its present form is ill-suited to account for de re truths (...)
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  • When the Part Mirrors the Whole: Interactions Beyond “Simple Location”.Alex Gomez-Marin & Juan Arnau - 2021 - Frontiers in Psychology 11.
    Reductionism relies on expectations that it is possible to make sense of the whole by studying its parts, whereas emergentism considers that program to be unattainable, partly due to the existence of emergent properties. The emergentist holistic stance is particularly relevant in biology and cognitive neuroscience, where interactions amongst system components and environment are key. Here we consider Alfred North Whitehead's philosophy as providing important insights to metaphysics of science in general, and to the reductionism vs. emergentism debate in particular. (...)
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  • Zoocentrism in the weeds? Cultivating plant models for cognitive yield.Adam Linson & Paco Calvo - 2020 - Biology and Philosophy 35 (5):1-27.
    It remains at best controversial to claim, non-figuratively, that plants are cognitive agents. At the same time, it is taken as trivially true that many animals are cognitive agents, arguably through an implicit or explicit appeal to natural science. Yet, any given definition of cognition implicates at least some further processes, such as perception, action, memory, and learning, which must be observed either behaviorally, psychologically, neuronally, or otherwise physiologically. Crucially, however, for such observations to be intelligible, they must be counted (...)
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  • Natural, Un-Natural and Detached Mimicry.John Pickering - 2019 - Biosemiotics 12 (1):115-130.
    Natural mimicry is ubiquitous. Plants mimic animals, animals mimic plants, animals mimic each other and animals may even mimic counterfactual states that deceive or distract other animals. Almost all natural mimicry is based on iconicity which hence anchors it in real world resemblances. The vast majority of natural mimicry is done unconsciously but when humans mimic, they know what they are doing. As Merlin Donald suggest, mimicry may in fact have played a crucial role in the emergence of the human (...)
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  • Defining the Environment in Organism–Environment Systems.Amanda Corris - 2020 - Frontiers in Psychology 11:1285.
    Enactivism and ecological psychology converge on the relevance of the environment in understanding perception and action. On both views, perceiving organisms are not merely passive receivers of environmental stimuli, but rather form a dynamic relationship with their environments in such a way that shapes how they interact with the world. In this paper, I suggest that while enactivism and ecological psychology enjoy a shared specification of the environment as the cognitive domain, on both accounts, the structure of the environment, itself, (...)
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  • Technische Form und Konstruktion.Marco Tamborini - 2020 - Deutsche Zeitschrift für Philosophie 68 (5):712-733.
    In this paper, I delineate the first pages of a philosophical genealogy which outlines the cornerstones of a philosophy of bio-technical forms. In so doing, the essay contributes to the philosophical understanding of some key scientific concepts. In particular, it analyses the philosophical and historical preconditions, the epistemic assumptions, as well as the ontological commitments of the concept of form as used in digital design and in bionics. In the first section, I investigate Ernst Kapp’s philosophy of technical forms. In (...)
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  • Infinity, Technology, Degeneracy: A Note on Werkhoven’s Dispositional Theory of Health.Shane N. Glackin - forthcoming - British Journal for the Philosophy of Science:axz033.
    Werkhoven’s ‘A Dispositional Theory of Health’ is an important and original contribution to debates about the disease concept, which persuasively demonstrates that dispositions must play some role in a full account of what it is to be healthy or ill. Unfortunately, as a theory, it cannot as it stands be correct.I first demonstrate what appears to be a significant, and possibly fatal, flaw; the proliferation of dispositions which Werkhoven’s theory requires makes impossible, at least in the absence of significant further (...)
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  • Process Philosophy.Johanna Seibt - 2013 - Stanford Encyclopedia of Philosophy.
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  • Philosophy of Immunology.Bartlomiej Swiatczak & Alfred I. Tauber - 2020 - Stanford Encyclopedia of Philosophy 2020.
    Philosophy of immunology is a subfield of philosophy of biology dealing with ontological and epistemological issues related to the studies of the immune system. While speculative investigations and abstract analyses have always been part of immune theorizing, until recently philosophers have largely ignored immunology. Yet the implications for understanding the philosophical basis of organismal functions framed by immunity offer new perspectives on fundamental questions of biology and medicine. Developed in the context of history of medicine, theoretical biology, and medical anthropology, (...)
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  • Biological Individuals.Robert A. Wilson & Matthew J. Barker - 2019 - Stanford Encyclopedia of Philosophy 1 (1).
    The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...)
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  • Life.Bruce Weber - 2008 - Stanford Encyclopedia of Philosophy.
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  • Process Philosophy.Nicholas Rescher - 2008 - Stanford Encyclopedia of Philosophy.
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