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Genidentity and Biological Processes

In Daniel J. Nicholson & John Dupré (eds.), Everything Flows: Towards a Processual Philosophy of Biology. Oxford, United Kingdom: Oxford University Press (2018)

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  1. A process theory of enzyme catalytic power – the interplay of science and metaphysics.Ross L. Stein - 2006 - Foundations of Chemistry 8 (1):3-29.
    Enzymes are protein catalysts of extraordinary efficiency, capable of bringing about rate enhancements of their biochemical reactions that can approach factors of 1020. Theories of enzyme catalysis, which seek to explain the means by which enzymes effect catalytic transformation of the substrate molecules on which they work, have evolved over the past century from the “lock-and-key” model proposed by Emil Fischer in 1894 to models that explicitly rely on transition state theory to the most recent theories that strive to provide (...)
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  • Unto Others: The Evolution and Psychology of Unselfish Behavior.Elliott Sober & David Sloan Wilson - 1998 - Harvard University Press.
    The authors demonstrate that unselfish behavior is in fact an important feature of both biological and human nature. Their book provides a panoramic view of altruism throughout the animal kingdom--from self-sacrificing parasites to the human capacity for selflessness--even as it explains the evolutionary sense of such behavior.
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  • Unto Others: The Evolution and Psychology of Unselfish Behavior.Paul E. Griffiths - 2002 - Mind 111 (441):178-182.
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  • The nature of selection: evolutionary theory in philosophical focus.Elliott Sober - 1984 - Chicago: University of Chicago Press.
    The Nature of Selection is a straightforward, self-contained introduction to philosophical and biological problems in evolutionary theory. It presents a powerful analysis of the evolutionary concepts of natural selection, fitness, and adaptation and clarifies controversial issues concerning altruism, group selection, and the idea that organisms are survival machines built for the good of the genes that inhabit them. "Sober's is the answering philosophical voice, the voice of a first-rate philosopher and a knowledgeable student of contemporary evolutionary theory. His book merits (...)
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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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  • Evolution, population thinking, and essentialism.Elliott Sober - 1980 - Philosophy of Science 47 (3):350-383.
    Ernst Mayr has argued that Darwinian theory discredited essentialist modes of thought and replaced them with what he has called "population thinking". In this paper, I characterize essentialism as embodying a certain conception of how variation in nature is to be explained, and show how this conception was undermined by evolutionary theory. The Darwinian doctrine of evolutionary gradualism makes it impossible to say exactly where one species ends and another begins; such line-drawing problems are often taken to be the decisive (...)
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  • The Biology of the Spirit. [REVIEW]Y. H. Krikorian - 1956 - Journal of Philosophy 53 (16):502-506.
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  • Parts: a study in ontology.Peter M. Simons - 1987 - New York: Oxford University Press.
    Although the relationship of part to whole is one of the most fundamental there is, this is the first full-length study of this key concept. Showing that mereology, or the formal theory of part and whole, is essential to ontology, Simons surveys and critiques previous theories--especially the standard extensional view--and proposes a new account that encompasses both temporal and modal considerations. Simons's revised theory not only allows him to offer fresh solutions to long-standing problems, but also has far-reaching consequences for (...)
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  • How to Exist at a Time When You Have No Temporal Parts.Peter Simons - 2000 - The Monist 83 (3):419-436.
    Occurrents are entities that exist in time and, with few or no exceptions, extend over time as well, that is, they have parts corresponding to the different times at which they exist. This makes it very easy to say what makes it true that they exist at the times at which they do. Singular existential propositions, being contingent, positive and arguably atomic, stand in need of truth-makers, entities in virtue of whose existence they are true. The obvious candidate for what (...)
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  • Continuants and Occurrents.Peter Simons & Joseph Melia - 2000 - Aristotelian Society Supplementary Volume 74:59-92.
    Commonsense ontology contains both continuants and occurrents, but are continuants necessary? I argue that they are neither occurrents nor easily replaceable by them. The worst problem for continuants is the question in virtue of what a given continuant exists at a given time. For such truthmakers we must have recourse to occurrents, those vital to the continuant at that time. Continuants are, like abstract objects, invariants under equivalences over occurrents. But they are not abstract, and their being invariants enables us (...)
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  • Alfred North Whitehead’s Process and Reality.Peter Simons - 2015 - Topoi 34 (1):1-9.
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  • Abstraktion ohne abstrakte Gegenstande.Peter Simons - 2012 - Zeitschrift für Philosophische Forschung 66 (1):114-129.
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  • Four Dimensionalism: An Ontology of Persistence and Time.Theodore Sider - 2004 - Philosophy and Phenomenological Research 68 (3):642-647.
    Precis of my book by this title, for a symposium.
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  • Four Dimensionalism.Theodore Sider - 1997 - Philosophical Review 106 (2):197-231.
    Persistence through time is like extension through space. A road has spatial parts in the subregions of the region of space it occupies; likewise, an object that exists in time has temporal parts in the various subregions of the total region of time it occupies. This view — known variously as four dimensionalism, the doctrine of temporal parts, and the theory that objects “perdure” — is opposed to “three dimensionalism”, the doctrine that things “endure”, or are “wholly present”.1 I will (...)
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  • All the World’s a Stage.Theodore Sider - 1996 - Australasian Journal of Philosophy 74 (3):433 – 453.
    Some philosophers believe that everyday objects are 4-dimensional spacetime worms, that a person (for example) persists through time by having temporal parts, or stages, at each moment of her existence. None of these stages is identical to the person herself; rather, she is the aggregate of all her temporal parts.1 Others accept “three dimensionalism”, rejecting stages in favor of the notion that persons “endure”, or are “wholly present” throughout their lives.2 I aim to defend an apparently radical third view: not (...)
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  • Man on His Nature.Charles Sherrington - 1940 - Cambridge University Press.
    I NATURE AND TRADITION Quemcunque aegrum ingenio praestaittem curanJum invisebat , siquidem morbi vehementia pateretur, . . .familiarem cum eo sermonem aliquandiu conferebat, cum pbilosophis Pbilosopkica, cum Mathematicis Mathematica, ..
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  • Grammar and existence: A preface to ontology.Wilfrid Sellars - 1960 - Mind 69 (276):499-533.
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  • Foundations for a metaphysics of pure process: The Carus lectures of Wilfrid Sellars.Wilfrid Sellars - 1981 - The Monist 64 (1):3-90.
    1. The lever in question is, of course, that with which, provided that an appropriate fulcrum could be found, Archimedes could move the world. In the analogy I have in mind, the fulcrum is the given, by virtue of which the mind gets leverage on the world of knowledge.
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  • Ontological Scope and Linguistic Diversity: Are There Universal Categories?Johanna Seibt - 2015 - The Monist 98 (3):318-343.
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  • Non-countable [ndlviduals.Johanna Seibt - 1996 - Southwest Philosophy Review 12 (1):225-236.
    It is a common presupposition in ontology (metaphysics) that a so-called 'principle of individuation' amounts to a principle of counting. Against this presupposition I argue that the predicates 'x is the same individual as y' and 'x is one with y' are neither co-extensional nor co-intensional. Non-countable entities such as masses or stuffs (or the referents of nouns in classifier languages) also fulfill the requirements of individuality. I suggest that Leibniz' 'principle of the identity of indiscernibles' (PII) should be taken (...)
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  • Forms of emergent interaction in General Process Theory.Johanna Seibt - 2009 - Synthese 166 (3):479-512.
    General Process Theory (GPT) is a new (non-Whiteheadian) process ontology. According to GPT the domains of scientific inquiry and everyday practice consist of configurations of ‘goings-on’ or ‘dynamics’ that can be technically defined as concrete, dynamic, non-particular individuals called general processes. The paper offers a brief introduction to GPT in order to provide ontological foundations for research programs such as interactivism that centrally rely on the notions of ‘process,’ ‘interaction,’ and ‘emergence.’ I begin with an analysis of our common sense (...)
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  • Free process theory: Towards a typology of occurrings.Johanna Seibt - 2004 - Axiomathes 14 (1-3):23-55.
    The paper presents some essential heuristic and constructional elements of Free Process Theory (FPT), a non-Whiteheadian, monocategoreal framework. I begin with an analysis of our common sense concept of activities, which plays a crucial heuristic role in the development of the notion of a free process. I argue that an activity is not a type but a mode of occurrence, defined in terms of a network of inferences. The inferential space characterizing our concept of an activity entails that anything which (...)
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  • Constitution Theory and Metaphysical Neutrality.Johanna Seibt - 2000 - The Monist 83 (1):161-183.
    Carnap’s thought not only played a pivotal role for the development of formal semantics and modern philosophy of science, but also engendered the profound methodological reorientation that distinguishes analytical from traditional ontology. Historically and systematically, Carnap’s formal approach to category theory is the primary source of influence on the three research programs that have given analytical ontology its distinctive profile: the design of constructional systems, the investigation of the expressive power of first order theories, and the meta-linguistic reduction of abstract (...)
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  • Towards a more dynamic plant morphology.Rolf Sattler - 1990 - Acta Biotheoretica 38 (3-4):303-315.
    From the point of view of a dynamic morphology, form is not only the result of process(es) — it is process. This process may be analyzed in terms of two pairs of fundamental processes: growth and decay, differentiation and dedifferentiation. Each of these processes can be analyzed in terms of various modalities (parameters) and submodalities. This paper deals with those of growth (see Table 1). For the purpose of systematits and phylogenetic reconstruction the modalities and submodalities can be considered dynamic (...)
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  • Truth, Love and Immortality: An Introduction to McTaggart's Philosophy.David H. Sanford - 1982 - Philosophical Review 91 (3):445.
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  • Scientific Explanation and the Causal Structure of the World.Wesley C. Salmon - 1984 - Princeton University Press.
    The philosophical theory of scientific explanation proposed here involves a radically new treatment of causality that accords with the pervasively statistical character of contemporary science. Wesley C. Salmon describes three fundamental conceptions of scientific explanation--the epistemic, modal, and ontic. He argues that the prevailing view is untenable and that the modal conception is scientifically out-dated. Significantly revising aspects of his earlier work, he defends a causal/mechanical theory that is a version of the ontic conception. Professor Salmon's theory furnishes a robust (...)
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  • Scientific Explanation and the Causal Structure of the World. Wesley Salmon.James H. Fetzer - 1987 - Philosophy of Science 54 (4):597-610.
    If the decades of the forties through the sixties were dominated by discussion of Hempel's “covering law“ explication of explanation, that of the seventies was preoccupied with Salmon's “statistical relevance” conception, which emerged as the principal alternative to Hempel's enormously influential account. Readers of Wesley C. Salmon's Scientific Explanation and the Causal Structure of the World, therefore, ought to find it refreshing to discover that its author has not remained content with a facile defense of his previous investigations; on the (...)
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  • Biological Organization and Cross-Generation Functions.Cristian Saborido, Matteo Mossio & Alvaro Moreno - 2011 - British Journal for the Philosophy of Science 62 (3):583-606.
    The organizational account of biological functions interprets functions as contributions of a trait to the maintenance of the organization that, in turn, maintains the trait. As has been recently argued, however, the account seems unable to provide a unified grounding for both intra- and cross-generation functions, since the latter do not contribute to the maintenance of the same organization which produces them. To face this ‘ontological problem’, a splitting account has been proposed, according to which the two kinds of functions (...)
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  • From genotype to phenotype: buffering mechanisms and the storage of genetic information.Suzanne L. Rutherford - 2000 - Bioessays 22 (12):1095-1105.
    DNA sequence variation is abundant in wild populations. While molecular biologists use genetically homogeneous strains of model organisms to avoid this variation, evolutionary biologists embrace genetic variation as the material of evolution since heritable differences in fitness drive evolutionary change. Yet, the relationship between the phenotypic variation affecting fitness and the genotypic variation producing it is complex. Genetic buffering mechanisms modify this relationship by concealing the effects of genetic and environmental variation on phenotype. Genetic buffering allows the build-up and storage (...)
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  • Autonomy in evolution: from minimal to complex life.Kepa Ruiz-Mirazo & Alvaro Moreno - 2012 - Synthese 185 (1):21-52.
    Our aim in the present paper is to approach the nature of life from the perspective of autonomy, showing that this perspective can be helpful for overcoming the traditional Cartesian gap between the physical and cognitive domains. We first argue that, although the phenomenon of life manifests itself as highly complex and multidimensional, requiring various levels of description, individual organisms constitute the core of this multifarious phenomenology. Thereafter, our discussion focuses on the nature of the organization of individual living entities, (...)
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  • Bridging the gap between developmental systems theory and evolutionary developmental biology†.Jason Scott Robert, Brian K. Hall & Wendy M. Olson - 2001 - Bioessays 23 (10):954-962.
    Many scientists and philosophers of science are troubled by the relative isolation of developmental from evolutionary biology. Reconciling the science of development with the science of heredity preoccupied a minority of biologists for much of the twentieth century, but these efforts were not corporately successful. Mainly in the past fifteen years, however, these previously dispersed integrating programmes have been themselves synthesized and so reinvigorated. Two of these more recent synthesizing endeavours are evolutionary developmental biology and developmental systems theory. While the (...)
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  • A Breath of Fresh Air: Absence and the Structure of Olfactory Perception.Tom Roberts - 2016 - Pacific Philosophical Quarterly 97 (3):400-420.
    The question of whether we can perceive absences, in addition to ‘positives’, has received recent attention in the literature on the nature of vision and audition. The aim is to demonstrate that there can be objectless forms of perceptual consciousness; specifically, to show that such episodes can be distinguished from those in which there is merely no perception at all. The current article explores this question for the domain of olfaction, and argues that there can be experiences of the absence (...)
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  • The Direction of Time.Milic Capek - 1959 - Philosophy and Phenomenological Research 19 (3):402-405.
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  • VI.—Symposium: “Facts and Propositions.”.F. P. Ramsey & G. E. Moore - 1927 - Aristotelian Society Supplementary Volume 7 (1):153-206.
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  • Facts and Propositions.Frank P. Ramsey - 1927 - Aristotelian Society Supplementary Volume 7 (1):153-170.
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  • Designation and existence.Willard V. Quine - 1939 - Journal of Philosophy 36 (26):701-709.
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  • The self model and the conception of biological identity in immunology.Thomas Pradeu & Edgardo D. Carosella - 2006 - Biology and Philosophy 21 (2):235-252.
    The self/non-self model, first proposed by F.M. Burnet, has dominated immunology for 60 years now. According to this model, any foreign element will trigger an immune reaction in an organism, whereas endogenous elements will not, in normal circumstances, induce an immune reaction. In this paper we show that the self/non-self model is no longer an appropriate explanation of experimental data in immunology, and that this inadequacy may be rooted in an excessively strong metaphysical conception of biological identity. We suggest that (...)
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  • On the definition of a criterion of immunogenicity.Thomas Pradeu & Edgardo Carosella - 2006 - Proceedings of the National Academy of Sciences 103 (47):17858--17861.
    The main objective of immunology is to establish why and when an immune response occurs, that is, to determine a criterion of immunogenicity. According to the consensus view, the proper criterion of immunogenicity lies in the discrimination between self and nonself. Here we challenge this consensus by suggesting a simpler and more comprehensive criterion, the criterion of continuity. Moreover, we show that this criterion may be considered as an interpretation of the immune 'self'. We conclude that immunologists can continue to (...)
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  • Mutualistic viruses and the heteronomy of life.Thomas Pradeu - 2016 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 59:80-88.
    Though viruses have generally been characterized by their pathogenic and more generally harmful effects, many examples of mutualistic viruses exist. Here I explain how the idea of mutualistic viruses has been defended in recent virology, and I explore four important conceptual and practical consequences of this idea. I ask to what extent this research modifies the way scientists might search for new viruses, our notion of how the host immune system interacts with microbes, the development of new therapeutic approaches, and, (...)
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  • A Mixed Self: The Role of Symbiosis in Development.Thomas Pradeu - 2011 - Biological Theory 6 (1):80-88.
    Since the 1950s, the common view of development has been internalist: development is seen as the result of the unfolding of potentialities already present in the egg cell. In this article, I show that this view is incorrect because of the crucial influence of the environment on development. I focus on a fascinating example, that of the role played by symbioses in development, especially bacterial symbioses, a phenomenon found in virtually all organisms (plants, invertebrates, and vertebrates). I claim that we (...)
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  • From molecules to systems: the importance of looking both ways.Alexander Powell & John Dupré - 2009 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 40 (1):54-64.
    Although molecular biology has meant different things at different times, the term is often associated with a tendency to view cellular causation as conforming to simple linear schemas in which macro-scale effects are specified by micro-scale structures. The early achievements of molecular biologists were important for the formation of such an outlook, one to which the discovery of recombinant DNA techniques, and a number of other findings, gave new life even after the complexity of genotype–phenotype
    relations had become apparent. Against this (...)
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  • The conquest of vitalism or the eclipse of organicism? The 1930s Cambridge organizer project and the social network of mid-twentieth-century biology.Erik Peterson - 2014 - British Journal for the History of Science 47 (2):281-304.
    In the 1930s, two concepts excited the European biological community: the organizer phenomenon and organicism. This essay examines the history of and connection between these two phenomena in order to address the conventional ‘rise-and-fall’ narrative that historians have assigned to each. Scholars promoted the ‘rise-and-fall’ narrative in connection with a broader account of the devitalizing of biology through the twentieth century. I argue that while limited evidence exists for the ‘fall of the organizer concept’ by the 1950s, the organicism that (...)
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  • Explanation in two dimensions: Diagrams and biological explanation.Laura Perini - 2005 - Biology and Philosophy 20 (2-3):257-269.
    Molecular biologists and biochemists often use diagrams to present hypotheses. Analysis of diagrams shows that their content can be expressed with linguistic representations. Why do biologists use visual representations instead? One reason is simple comprehensibility: some diagrams present information which is readily understood from the diagram format, but which would not be comprehensible if the same information was expressed linguistically. But often diagrams are used even when concise, comprehensible linguistic alternatives are available. I explain this phenomenon by showing why diagrammatic (...)
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  • Sensational properties: Theses to accept and theses to reject.Christopher Peacocke - 2008 - Revue Internationale de Philosophie 62 (1):7-24.
    The subjective properties of an experience are those which specify what having the experience is like for its subject. The sensational properties of an experience are those of its subjective properties that it does not possess in virtue of features of the way the experience represents the world as being (its representational content). Perhaps no topic in the philosophy of mind has been more vigorously debated in the past quarter-century than whether there are any sensational properties, so conceived. The existence (...)
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  • A Contribution to the Theory of the Living Organism.James W. Papez & W. E. Agar - 1945 - Philosophical Review 54 (3):274.
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  • Causal democracy and causal contributions in developmental systems theory.Susan Oyama - 2000 - Philosophy of Science 67 (3):347.
    In reworking a variety of biological concepts, Developmental Systems Theory (DST) has made frequent use of parity of reasoning. We have done this to show, for instance, that factors that have similar sorts of impact on a developing organism tend nevertheless to be invested with quite different causal importance. We have made similar arguments about evolutionary processes. Together, these analyses have allowed DST not only to cut through some age-old muddles about the nature of development, but also to effect a (...)
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  • A sensorimotor account of vision and visual consciousness.J. Kevin O’Regan & Alva Noë - 2001 - Behavioral and Brain Sciences 24 (5):883-917.
    Many current neurophysiological, psychophysical, and psychological approaches to vision rest on the idea that when we see, the brain produces an internal representation of the world. The activation of this internal representation is assumed to give rise to the experience of seeing. The problem with this kind of approach is that it leaves unexplained how the existence of such a detailed internal representation might produce visual consciousness. An alternative proposal is made here. We propose that seeing is a way of (...)
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  • Size doesn’t matter: towards a more inclusive philosophy of biology. [REVIEW]Maureen A. O’Malley & John Dupré - 2007 - Biology and Philosophy 22 (2):155-191.
    Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...)
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  • Fundamental issues in systems biology.Maureen A. O'Malley & John Dupré - 2005 - Bioessays 27 (12):1270-1276.
    In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large‐scale molecular interactions; the other, which we shall refer to as ‘systems‐theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems (...)
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  • The Human Animal: Personal Identity Without Psychology.Eric Todd Olson - 1997 - New York, US: Oxford University Press.
    Most philosophers writing about personal identity in recent years claim that what it takes for us to persist through time is a matter of psychology. In this groundbreaking new book, Eric Olson argues that such approaches face daunting problems, and he defends in their place a radically non-psychological account of personal identity. He defines human beings as biological organisms, and claims that no psychological relation is either sufficient or necessary for an organism to persist. Olson rejects several famous thought-experiments dealing (...)
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