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  1. The Conscious Mind: In Search of a Fundamental Theory.David J. Chalmers - 1996 - Oxford University Press.
    The book is an extended study of the problem of consciousness. After setting up the problem, I argue that reductive explanation of consciousness is impossible , and that if one takes consciousness seriously, one has to go beyond a strict materialist framework. In the second half of the book, I move toward a positive theory of consciousness with fundamental laws linking the physical and the experiential in a systematic way. Finally, I use the ideas and arguments developed earlier to defend (...)
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  • Criteria for Holobionts from Community Genetics.Elisabeth A. Lloyd & Michael J. Wade - 2019 - Biological Theory 14 (3):151-170.
    We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, between (...)
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  • Metaphysical Emergence: Weak and Strong.Jessica Wilson - 2015 - In Tomasz Bigaj & Christian Wuthrich (eds.), Metaphysics in Contemporary Physics. Poznan Studies in the Philosophy of the Sciences and the Humanities. pp. 251-306.
    Motivated by the seeming structure of the sciences, metaphysical emergence combines broadly synchronic dependence coupled with some degree of ontological and causal autonomy. Reflecting the diverse, frequently incompatible interpretations of the notions of dependence and autonomy, however, accounts of emergence diverge into a bewildering variety. Here I argue that much of this apparent diversity is superficial. I first argue, by attention to the problem of higher-level causation, that two and only two strategies for addressing this problem accommodate the genuine emergence (...)
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  • The Ontology of Organisms: Mechanistic Modules or Patterned Processes?Christopher Austin - 2016 - Biology and Philosophy 31 (5):639-662.
    Though the realm of biology has long been under the philosophical rule of the mechanistic magisterium, recent years have seen a surprisingly steady rise in the usurping prowess of process ontology. According to its proponents, theoretical advances in the contemporary science of evo-devo have afforded that ontology a particularly powerful claim to the throne: in that increasingly empirically confirmed discipline, emergently autonomous, higher-order entities are the reigning explanantia. If we are to accept the election of evo-devo as our best conceptualisation (...)
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  • Rethinking Individuality: The Dialectics of the Holobiont.Scott F. Gilbert & Alfred I. Tauber - 2016 - Biology and Philosophy 31 (6):839-853.
    Given immunity’s general role in the organism’s economy—both in terms of its internal environment as well as mediating its external relations—immune theory has expanded its traditional formulation of preserving individual autonomy to one that includes accounting for nutritional processes and symbiotic relationships that require immune tolerance. When such a full ecological alignment is adopted, the immune system becomes the mediator of both defensive and assimilative environmental intercourse, where a balance of immune rejection and tolerance governs the complex interactions of the (...)
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  • Functions: Consensus Without Unity.Peter Godfrey-Smith - 1993 - Pacific Philosophical Quarterly 74 (3):196-208.
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  • Emergence: Logical, Functional and Dynamical. [REVIEW]Sandra D. Mitchell - 2012 - Synthese 185 (2):171-186.
    Philosophical accounts of emergence have been explicated in terms of logical relationships between statements (derivation) or static properties (function and realization). Jaegwon Kim is a modern proponent. A property is emergent if it is not explainable by (or reducible to) the properties of lower level components. This approach, I will argue, is unable to make sense of the kinds of emergence that are widespread in scientific explanations of complex systems. The standard philosophical notion of emergence posits the wrong dichotomies, confuses (...)
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  • Emergence: Core Ideas and Issues.Jaegwon Kim - 2006 - Synthese 151 (3):547-559.
    This paper explores the fundamental ideas that have motivated the idea of emergence and the movement of emergentism. The concept of reduction, which lies at the heart of the emergence idea is explicated, and it is shown how the thesis that emergent properties are irreducible gives a unified account of emergence. The paper goes on to discuss two fundamental unresolved issues for emergentism. The first is that of giving a “positive” characterization of emergence; the second is to give a coherent (...)
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  • Emergence, Closure and Inter-Level Causation in Biological Systems.Matteo Mossio, Leonardo Bich & Alvaro Moreno - 2013 - Erkenntnis 78 (2):153-178.
    In this paper, we advocate the idea that an adequate explanation of biological systems requires appealing to organizational closure as an emergent causal regime. We first develop a theoretical justification of emergence in terms of relatedness, by arguing that configurations, because of the relatedness among their constituents, possess ontologically irreducible properties, providing them with distinctive causal powers. We then focus on those emergent causal powers exerted as constraints, and we claim that biological systems crucially differ from other natural systems in (...)
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  • Everything Flows: Towards a Processual Philosophy of Biology.Daniel J. Nicholson & John Dupré (eds.) - 2018 - Oxford University Press.
    This collection of essays explores the metaphysical thesis that the living world is not made up of substantial particles or things, as has often been assumed, but is rather constituted by processes. The biological domain is organised as an interdependent hierarchy of processes, which are stabilised and actively maintained at different timescales. Even entities that intuitively appear to be paradigms of things, such as organisms, are actually better understood as processes. Unlike previous attempts to articulate processual views of biology, which (...)
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  • Biological Individuality: Integrating Scientific, Philosophical, and Historical Perspectives.Scott Lidgard & Lynn K. Nyhart (eds.) - 2017 - Chicago: University of Chicago Press.
    Introduction: working together on individuality / Lynn K. Nyhart and Scott Lidgard -- The work of biological individuality: concepts and contexts / Scott Lidgard and Lynn K. Nyhart -- Cells, colonies, and clones: individuality in the volvocine algae / Matthew D. Herron -- Individuality and the control of life cycles / Beckett Sterner -- Discovering the ties that bind: cell-cell communication and the development of cell sociology / Andrew S. Reynolds -- Alternation of generations and individuality, 1851 / Lynn K. (...)
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  • Individuals Across The Sciences.Thomas Pradeu & Alexandre Guay (eds.) - 2016 - New York, État de New York, États-Unis: Oxford University Press.
    What are individuals? How can they be identified? These are crucial questions for philosophers and scientists alike. Criteria of individuality seem to differ markedly between metaphysics and the empirical sciences - and this might well explain why no work has hitherto attempted to relate the contributions of metaphysics, physics and biology on this question. This timely volume brings together various strands of research into 'individuality', examining how different sciences handle the issue, and reflecting on how this scientific work relates to (...)
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  • Processes of Life: Essays in the Philosophy of Biology.John Dupré - 2011 - Oxford University Press UK.
    John Dupré explores recent revolutionary developments in biology and considers their relevance for our understanding of human nature and human society. Epigenetics and related areas of molecular biology have eroded the exceptional status of the gene and presented the genome as fully interactive with the rest of the cell. Developmental systems theory provides a space for a vision of evolution that takes full account of the fundamental importance of developmental processes. Dupré shows the importance of microbiology for a proper understanding (...)
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  • A Survey of Metaphysics.E. J. Lowe - 2002 - Oxford University Press.
    A systematic overview of modern metaphysics, A Survey of Metaphysics covers all of the most important topics in the field. It adopts the fairly traditional conception of metaphysics as a subject that deals with the deepest questions that can be raised concerning the fundamental structure of reality as a whole. The book is divided into six main sections that address the following themes: identity and change, necessity and essence, causation, agency and events, space and time, and universals and particulars. It (...)
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  • The Hologenome Concept of Evolution: A Philosophical and Biological Study.Javier Suárez - 2019 - Dissertation, University of Exeter
    The hologenome concept of evolution is a hypothesis about the evolution of animals and plants. It asserts that the evolution of animals and plants was partially triggered by their interactions with their symbiotic microbiomes. In that vein, the hologenome concept posits that the holobiont (animal host + symbionts of the microbiome) is a unit of selection. -/- The hologenome concept has been severely criticized on the basis that selection on holobionts would only be possible if there were a tight transgenerational (...)
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  • Multispecies individuals.Pierrick Bourrat & Paul E. Griffiths - 2018 - History and Philosophy of the Life Sciences 40 (2):33.
    We assess the arguments for recognising functionally integrated multispecies consortia as genuine biological individuals, including cases of so-called ‘holobionts’. We provide two examples in which the same core biochemical processes that sustain life are distributed across a consortium of individuals of different species. Although the same chemistry features in both examples, proponents of the holobiont as unit of evolution would recognize one of the two cases as a multispecies individual whilst they would consider the other as a compelling case of (...)
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  • 3D/4D Controversy: A Strom in a Teacup'.E. J. Lowe & Storrs McCall - 2006 - Noûs 40 (3):570-578.
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  • The 3d/4d Controversy: A Storm in a Teacup.Storrs McCall & E. J. Lowe - 2006 - Noûs 40 (3):570–578.
  • Understanding Colonial Traits Using Symbiosis Research and Ecosystem Ecology.Frédéric Bouchard - 2009 - Biological Theory 4 (3):240-246.
    E. O. Wilson (1974: 54) describes the problem that social organisms pose: “On what bases do we distinguish the extremely modified members of an invertebrate colony from the organs of a metazoan animal?” This framing of the issue has inspired many to look more closely at how groups of organisms form and behave as emergent individuals. The possible existence of “superorganisms” test our best intuitions about what can count and act as genuine biological individuals and how we should study them. (...)
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  • The Problem of Biological Individuality.Ellen Clarke - 2010 - Biological Theory 5 (4):312-325.
    Darwin’s classic ‘Origin of Species’ (Darwin 1859) described forces of selection acting upon individuals, but there remains a great deal of controversy about what exactly the status and definition of a biological individual is. Recently some authors have argued that the individual is dispensable – that an inability to pin it down is not problematic because little rests on it anyway. The aim of this paper is to show that there is a real problem of biological individuality, and an urgent (...)
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  • Holobionts as Units of Selection and a Model of Their Population Dynamics and Evolution.Joan Roughgarden, Scott F. Gilbert, Eugene Rosenberg, Ilana Zilber-Rosenberg & Elisabeth A. Lloyd - 2018 - Biological Theory 13 (1):44-65.
    Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont (...)
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  • How Research on Microbiomes is Changing Biology: A Discussion on the Concept of the Organism.Adrian Stencel & Agnieszka M. Proszewska - 2018 - Foundations of Science 23 (4):603-620.
    Multicellular organisms contain numerous symbiotic microorganisms, collectively called microbiomes. Recently, microbiomic research has shown that these microorganisms are responsible for the proper functioning of many of the systems of multicellular organisms. This has inclined some scholars to argue that it is about time to reconceptualise the organism and to develop a concept that would place the greatest emphasis on the vital role of microorganisms in the life of plants and animals. We believe that, unfortunately, there is a problem with this (...)
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  • The Many Faces of Biological Individuality.Thomas Pradeu - 2016 - Biology and Philosophy 31 (6):761-773.
    Biological individuality is a major topic of discussion in biology and philosophy of biology. Recently, several objections have been raised against traditional accounts of biological individuality, including the objections of monism, theory-centrism, ahistoricity, disciplinary isolationism, and the multiplication of conceptual uncertainties. In this introduction, I will examine the current philosophical landscape about biological individuality, and show how the contributions gathered in this special issue address these five objections. Overall, the aim of this issue is to offer a more diverse, unifying, (...)
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  • Microorganisms as Scaffolds of Host Individuality: An Eco-Immunity Account of the Holobiont.Lynn Chiu & Gérard Eberl - 2016 - Biology and Philosophy 31 (6):819-837.
    There is currently a great debate about whether the holobiont, i.e. a multicellular host and its residential microorganisms, constitutes a biological individual. We propose that resident microorganisms have a general and important role in the individuality of the host organism, not the holobiont. Drawing upon the Equilibrium Model of Immunity, we argue that microorganisms are scaffolds of immune capacities and processes that determine the constituency and persistence of the host organism. A scaffolding perspective accommodates the contingency and heterogeneity of resident (...)
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  • Evo-Devo: A Science of Dispositions.Christopher Austin - 2017 - European Journal for Philosophy of Science 7 (2):373-389.
    Evolutionary developmental biology represents a paradigm shift in the understanding of the ontogenesis and evolutionary progression of the denizens of the natural world. Given the empirical successes of the evo-devo framework, and its now widespread acceptance, a timely and important task for the philosophy of biology is to critically discern the ontological commitments of that framework and assess whether and to what extent our current metaphysical models are able to accommodate them. In this paper, I argue that one particular model (...)
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  • It’s the Song, Not the Singer: An Exploration of Holobiosis and Evolutionary Theory.W. Ford Doolittle & Austin Booth - 2017 - Biology and Philosophy 32 (1):5-24.
    That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...)
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  • Emergence and Its Place in Nature: A Case Study of Biochemical Networks.F. C. Boogerd, F. J. Bruggeman, Robert C. Richardson, Achim Stephan & H. Westerhoff - 2005 - Synthese 145 (1):131 - 164.
    We will show that there is a strong form of emergence in cell biology. Beginning with C.D. Broad's classic discussion of emergence, we distinguish two conditions sufficient for emergence. Emergence in biology must be compatible with the thought that all explanations of systemic properties are mechanistic explanations and with their sufficiency. Explanations of systemic properties are always in terms of the properties of the parts within the system. Nonetheless, systemic properties can still be emergent. If the properties of the components (...)
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  • Symbiosis, Selection, and Individuality.Austin Booth - 2014 - Biology and Philosophy 29 (5):657-673.
    A recent development in biology has been the growing acceptance that holobionts, entities comprised of symbiotic microbes and their host organisms, are widespread in nature. There is agreement that holobionts are evolved outcomes, but disagreement on how to characterize the operation of natural selection on them. The aim of this paper is to articulate the contours of the disagreement. I explain how two distinct foundational accounts of the process of natural selection give rise to competing views about evolutionary individuality.
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  • Ecosystem Evolution is About Variation and Persistence, Not Populations and Reproduction.Frédéric Bouchard - 2014 - Biological Theory 9 (4):382-391.
    Building upon a non-standard understanding of evolutionary process focusing on variation and persistence, I will argue that communities and ecosystems can evolve by natural selection as emergent individuals. Evolutionary biology has relied ever increasingly on the modeling of population dynamics. Most have taken for granted that we all agree on what is a population. Recent work has reexamined this perceived consensus. I will argue that there are good reasons to restrict the term “population” to collections of monophyletically related replicators and (...)
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  • Biological Autonomy: A Philosophical and Theoretical Enquiry.Alvaro Moreno & Matteo Mossio - 2015 - Springer.
    Since Darwin, Biology has been framed on the idea of evolution by natural selection, which has profoundly influenced the scientific and philosophical comprehension of biological phenomena and of our place in Nature. This book argues that contemporary biology should progress towards and revolve around an even more fundamental idea, that of autonomy. Biological autonomy describes living organisms as organised systems, which are able to self-produce and self-maintain as integrated entities, to establish their own goals and norms, and to promote the (...)
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  • The Limits of the Self: Immunology and Biological Identity.Thomas Pradeu - 2012 - Oxford University Press.
    The Limits of the Self, will be essential reading for anyone interested in the definition of biological individuality and the understanding of the immune system.
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  • Metaphysics and Science.Stephen Mumford & Matthew Tugby (eds.) - 2013 - Oxford University Press.
    Metaphysics and Science brings together important new work within an emerging philosophical discipline: the metaphysics of science. In the opening chapter, a definition of the metaphysics of science is offered, one which explains why the topics of laws, causation, natural kinds, and emergence are at the discipline's heart. The book is then divided into four sections, which group together papers from leading academics on each of those four topics. Among the questions discussed are: How are laws and measurement methods related? (...)
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  • 3. A Rebuttal on Functions.Christopher Boorse - 2002 - In Andre Ariew, Robert C. Cummins & Mark Perlman (eds.), Functions: New Essays in the Philosophy of Psychology and Biology. Oxford University Press. pp. 63.
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  • Philosophy of Biology.Elliott Sober - 1993 - Westview Press.
    Perhaps because of it implications for our understanding of human nature, recent philosophy of biology has seen what might be the most dramatic work in the philosophies of the ”special” sciences. This drama has centered on evolutionary theory, and in the second edition of this textbook, Elliott Sober introduces the reader to the most important issues of these developments. With a rare combination of technical sophistication and clarity of expression, Sober engages both the higher level of theory and the direct (...)
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  • Issues in Theoretical Diversity: Persistence, Composition, and Time.Kristie Miller - 2006 - Springer.
    Our world is full of composite objects that persist through time: dogs, persons, chairs and rocks. But in virtue of what do a bunch of little objects get to compose some bigger object, and how does that bigger object persist through time? This book aims to answer these questions, but it does so by looking at accounts of composition and persistence through a new methodological lens. It asks the question: what does it take for two theories to be genuinely different, (...)
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  • The Triple Helix: Gene, Organism, and Environment.Richard C. Lewontin - 2000 - Harvard University Press.
    One of our most brilliant evolutionary biologists, Richard Lewontin has also been a leading critic of those--scientists and non-scientists alike--who would misuse the science to which he has contributed so much. In The Triple Helix, Lewontin the scientist and Lewontin the critic come together to provide a concise, accessible account of what his work has taught him about biology and about its relevance to human affairs. In the process, he exposes some of the common and troubling misconceptions that misdirect and (...)
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  • Causal Powers, Forces, and Superdupervenience.Jessica M. Wilson - 2002 - Grazer Philosophische Studien 63 (1):53-77.
    Horgan (1993) proposed that "superdupervenience" - supervenience preserving physicalistic acceptability - is a matter of robust explanation. I argued against him (1999) that (as nearly all physicalist and emergentist accounts reflect) superdupervenience is a matter of Condition on Causal Powers (CCP): every causal power bestowed by the supervenient property is identical with a causal power bestowed by its base property. Here I show that CCP is, as it stands, unsatisfactory,for on the usual understandings of causal power bestowal, it is trivially (...)
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  • The Metaphysics of Emergence.Timothy O'Connor - 2005 - Noûs 39 (4):658-678.
    The objective probability of every physical event is fixed by prior physical events and laws alone. (This thesis is sometimes expressed in terms of explanation: In tracing the causal history of any physical event, one need not advert to any non-physical events or laws. To the extent that there is any explanation available for a physical event, there is a complete explanation available couched entirely in physical vocabulary. We prefer the probability formulation, as it should be acceptable to any physicalist, (...)
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  • Philosophy of Biology.Elliott Sober & Pénel Jean-Dominique - 1995 - Revue Philosophique de la France Et de l'Etranger 185 (3):382-383.
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  • Reply to Alexander Rosenberg's Review of The Nature of Selection.Elliott Sober - 1986 - Behaviorism 14 (1):77-88.
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  • The stability of traits conception of the hologenome: An evolutionary account of holobiont individuality.Javier Suárez - 2020 - History and Philosophy of the Life Sciences 42 (1):1-27.
    Bourrat and Griffiths :33, 2018) have recently argued that most of the evidence presented by holobiont defenders to support the thesis that holobionts are evolutionary individuals is not to the point and is not even adequate to discriminate multispecies evolutionary individuals from other multispecies assemblages that would not be considered evolutionary individuals by most holobiont defenders. They further argue that an adequate criterion to distinguish the two categories is fitness alignment, presenting the notion of fitness boundedness as a criterion that (...)
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  • What is an Organism? An Immunological Answer.Thomas Pradeu - 2010 - History and Philosophy of the Life Sciences 32 (2-3):247-267.
    The question “What is an organism?”, formerly considered as essential in biology, has now been increasingly replaced by a larger question, “What is a biological individual?”. On the grounds that i) individuation is theory-dependent, and ii) physiology does not offer a theory, biologists and philosophers of biology have claimed that it is the theory of evolution by natural selection which tells us what counts as a biological individual. Here I show that one physiological field, immunology, offers a theory, which makes (...)
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  • Making Sense of Emergence.Jaegwon Kim - 1999 - Philosophical Studies 95 (1-2):3-36.
  • Functions.Larry Wright - 1973 - Philosophical Review 82 (2):139-168.
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  • Functions.John Bigelow & Robert Pargetter - 1987 - Journal of Philosophy 84 (4):181-196.
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  • A Modern History Theory of Functions.Peter Godfrey-Smith - 1994 - Noûs 28 (3):344-362.
    Biological functions are dispositions or effects a trait has which explain the recent maintenance of the trait under natural selection. This is the "modern history" approach to functions. The approach is historical because to ascribe a function is to make a claim about the past, but the relevant past is the recent past; modern history rather than ancient.
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  • In Defense of Proper Functions.Ruth Garrett Millikan - 1989 - Philosophy of Science 56 (June):288-302.
    I defend the historical definition of "function" originally given in my Language, Thought and Other Biological Categories (1984a). The definition was not offered in the spirit of conceptual analysis but is more akin to a theoretical definition of "function". A major theme is that nonhistorical analyses of "function" fail to deal adequately with items that are not capable of performing their functions.
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  • An Organizational Account of Biological Functions.Matteo Mossio, Cristian Saborido & Alvaro Moreno - 2009 - British Journal for the Philosophy of Science 60 (4):813-841.
    In this paper, we develop an organizational account that defines biological functions as causal relations subject to closure in living systems, interpreted as the most typical example of organizationally closed and differentiated self-maintaining systems. We argue that this account adequately grounds the teleological and normative dimensions of functions in the current organization of a system, insofar as it provides an explanation for the existence of the function bearer and, at the same time, identifies in a non-arbitrary way the norms that (...)
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  • Fitness and Function.D. M. Walsh - 1996 - British Journal for the Philosophy of Science 47 (4):553-574.
    According to historical theories of biological function, a trait's function is determined by natural selection in the past. I argue that, in addition to historical functions, ahistorical functions ought to be recognized. I propose a theory of biological function which accommodates both. The function of a trait is the way it contributes to fitness and fitness can only be determined relative to a selective regime. Therefore, the function of a trait can only be specified relative to a selective regime. Apart (...)
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  • No General Structure.C. Kenneth Waters - unknown
    This chapter introduces a distinctive approach for scientific metaphysics. Instead of drawing metaphysical conclusions by interpreting the most basic theories of science, this approach draws metaphysical conclusions by analyzing how multifaceted practices of science work. Broadening attention opens the door to drawing metaphysical conclusions from a wide range of sciences. This chapter analyzes conceptual practice in genetics to argue that the reality investigated by biologists lacks an overall structure. It expands this conclusion to motivate the no general structure thesis, which (...)
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