A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topological Spaces, Christopher Habel ** Mass Reference and the Geometry of Solids, Almerindo (...) E. Ojeda ** Defining a 'Doughnut' Made Difficult, N .M. Gotts ** A Theory of Spatial Regions with Indeterminate Boundaries, A.G. Cohn and N.M. Gotts ** Mereotopological Construction of Time from Events, Fabio Pianesi and Achille C. Varzi ** Computational Mereology: A Study of Part-of Relations for Multi-media Indexing, Wlodek Zadrozny and Michelle Kim. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

I examine some recent claims put forward by L. A. Paul, Barry Dainton and Simon Prosser, to the effect that perceptual experiences of movement and change involve an (apparent) experience of ‘passage’, in the sense at issue in debates about the metaphysics of time. Paul, Dainton and Prosser all argue that this supposed feature of perceptual experience – call it a phenomenology of passage – is illusory, thereby defending the view that there is no such a thing as passage, (...) conceived of as a feature of mind-independent reality. I suggest that in fact there is no such phenomenology of passage in the first place. There is, however, a specific structural aspect of the phenomenology of perceptual experiences of movement and change that can explain how one might mistakenly come to the belief that such experiences do involve a phenomenology of passage. (shrink)

This volume brings together a range of influential essays by distinguished philosophers and political theorists on the issue of global justice. Global justice concerns the search for ethical norms that should govern interactions between people, states, corporations and other agents acting in the global arena, as well as the design of social institutions that link them together. The volume includes articles that engage with major theoretical questions such as the applicability of the ideals of social and economic equality to the (...) global sphere, the degree of justified partiality to compatriots, and the nature and extent of the responsibilities of the affluent to address global poverty and other hardships abroad. It also features articles that bring the theoretical insights of global justice thinkers to bear on matters of practical concern to contemporary societies, such policies associated with immigration, international trade, and climate change. -/- Contents: Introduction; Part I Standards of Global Justice: (i) Assistance-Based Responsibilities to the Global Poor: Famine, affluence and mortality, Peter Singer; We don't owe them a thing! A tough-minded but soft-hearted view of aid to the faraway needy, Jan Narveson; Does distance matter morally to the duty to rescue? Frances Myrna Kamm. (ii) Contribution-Based Responsibilities to the Global Poor: 'Assisting' the global poor, Thomas Pogge; Should we stop thinking about poverty in terms of helping the poor?, Alan Patten; Poverty and the moral significance of contribution, Gerhard Øverland. (iii)Cosmopolitans, Global Egalitarians, and its Critics: The one and the many faces of cosmopolitanism, Catherine Lu; Cosmopolitan justice and equalizing opportunities, Simon Caney; The problem of global justice, Thomas Nagel; Against global egalitarianism, David Miller; Egalitarian challenges to global egalitarianism: a critique, Christian Barry and Laura Valentini. Part II Pressing Global Socioeconomic Issues: (i) Governing the Flow of People: Immigration and freedom of association, Christopher Wellman; Democratic theory and border coercion: no right to unilaterally control your own borders, Arash Abizadeh; Justice in migration: a closed borders utopia?, Lea Ypi. (ii) Climate Change: Global environment and international inequality, Henry Shue; Valuing policies in response to climate change: some ethical issues, John Broome; Saved by disaster? Abrupt climate change, political inertia, and the possibility of an intergenerational arms race, Stephen M. Gardiner; Polycentric systems for coping with collective action and global environmental change, Elinor Ostrom. (iii) International Trade: Responsibility and global labor justice, Iris Marion Young; Property rights and the resource curse, Leif Wenar; Fairness in trade I: obligations arising from trading and the pauper-labor argument, Mathias Risse; Name index. -/- See: www.ashgate.com/default.aspx?page=637&calctitle=1&pageSubject=483&sort=pubdate&forthcoming=1&title_i d=9958&edition_id=13385. (shrink)

Creativity pervades human life. It is the mark of individuality, the vehicle of self-expression, and the engine of progress in every human endeavor. It also raises a wealth of neglected and yet evocative philosophical questions: What is the role of consciousness in the creative process? How does the audience for a work for art influence its creation? How can creativity emerge through childhood pretending? Do great works of literature give us insight into human nature? Can a computer program really be (...) creative? How do we define creativity in the first place? Is it a virtue? What is the difference between creativity in science and art? Can creativity be taught? The new essays that comprise The Philosophy of Creativity take up these and other key questions and, in doing so, illustrate the value of interdisciplinary exchange. Written by leading philosophers and psychologists involved in studying creativity, the essays integrate philosophical insights with empirical research. CONTENTS I. Introduction Introducing The Philosophy of Creativity Elliot Samuel Paul and Scott Barry Kaufman II. The Concept of Creativity 1. An Experiential Account of Creativity Bence Nanay III. Aesthetics & Philosophy of Art 2. Creativity and Insight Gregory Currie 3. The Creative Audience: Some Ways in which Readers, Viewers and/or Listeners Use their Imaginations to Engage Fictional Artworks Noël Carroll 4. The Products of Musical Creativity Christopher Peacocke IV. Ethics & Value Theory 5. Performing Oneself Owen Flanagan 6. Creativity as a Virtue of Character Matthew Kieran V. Philosophy of Mind & Cognitive Science 7. Creativity and Not So Dumb Luck Simon Blackburn 8. The Role of Imagination in Creativity Dustin Stokes 9. Creativity, Consciousness, and Free Will: Evidence from Psychology Experiments Roy F. Baumeister, Brandon J. Schmeichel, and C. Nathan DeWall 10. The Origins of Creativity Elizabeth Picciuto and Peter Carruthers 11. Creativity and Artificial Intelligence: a Contradiction in Terms? Margaret Boden VI. Philosophy of Science 12. Hierarchies of Creative Domains: Disciplinary Constraints on Blind-Variation and Selective-Retention Dean Keith Simonton VII. Philosophy of Education (& Education of Philosophy) 13. Educating for Creativity Berys Gaut 14. Philosophical Heuristics Alan Hájek. (shrink)

Conditionalization is a widely endorsed rule for updating one’s beliefs. But a sea of complaints have been raised about it, including worries regarding how the rule handles error correction, changing desiderata of theory choice, evidence loss, self-locating beliefs, learning about new theories, and confirmation. In light of such worries, a number of authors have suggested replacing Conditionalization with a different rule — one that appeals to what I’ll call “ur-priors”. But different authors have understood the rule in different ways, and (...) these different understandings solve different problems. In this paper, I aim to map out the terrain regarding these issues. I survey the different problems that might motivate the adoption of such a rule, flesh out the different understandings of the rule that have been proposed, and assess their pros and cons. I conclude by suggesting that one particular batch of proposals, proposals that appeal to what I’ll call “loaded evidential standards”, are especially promising. (shrink)

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 (...) of the biological realm with metaphysical rigour, must we depose our mechanistic ontology for failing to properly “carve at the joints” of organisms? In this paper, I challenge the legitimacy of that claim: not only can the theoretical benefits offered by a process ontology be had without it, they cannot be sufficiently grounded without the metaphysical underpinning of the very mechanisms which processes purport to replace. The biological realm, I argue, remains one best understood as under the governance of mechanistic principles. (shrink)

The advent of contemporary evolutionary theory ushered in the eventual decline of Aristotelian Essentialism (Æ) – for it is widely assumed that essence does not, and cannot have any proper place in the age of evolution. This paper argues that this assumption is a mistake: if Æ can be suitably evolved, it need not face extinction. In it, I claim that if that theory’s fundamental ontology consists of dispositional properties, and if its characteristic metaphysical machinery is interpreted within the framework (...) of contemporary evolutionary developmental biology, an evolved essentialism is available. The reformulated theory of Æ offered in this paper not only fails to fall prey to the typical collection of criticisms, but is also independently both theoretically and empirically plausible. The paper contends that, properly understood, essence belongs in the age of evolution. (shrink)

Selection against embryos that are predisposed to develop disabilities is one of the less controversial uses of embryo selection technologies. Many bio-conservatives argue that while the use of ESTs to select for non-disease-related traits, such as height and eye-colour, should be banned, their use to avoid disease and disability should be permitted. Nevertheless, there remains significant opposition, particularly from the disability rights movement, to the use of ESTs to select against disability. In this article we examine whether and why the (...) state could be justified in restricting the use of ESTs to select against disability. We first outline the challenge posed by proponents of ‘liberal eugenics’. Liberal eugenicists challenge those who defend restrictions on the use of ESTs to show why the use of these technologies would create a harm of the type and magnitude required to justify coercive measures. We argue that this challenge could be met by adverting to the risk of harms to future persons that would result from a loss of certain forms of cognitive diversity. We suggest that this risk establishes a pro tanto case for restricting selection against some disabilities, including dyslexia and Asperger's syndrome. (shrink)

In his paper, Jakob Hohwy outlines a theory of the brain as an organ for prediction-error minimization, which he claims has the potential to profoundly alter our understanding of mind and cognition. One manner in which our understanding of the mind is altered, according to PEM, stems from the neurocentric conception of the mind that falls out of the framework, which portrays the mind as “inferentially-secluded” from its environment. This in turn leads Hohwy to reject certain theses of embodied cognition. (...) Focusing on this aspect of Hohwy’s argument, we first outline the key components of the PEM framework such as the “evidentiary boundary,” before looking at why this leads Hohwy to reject certain theses of embodied cognition. We will argue that although Hohwy may be correct to reject specific theses of embodied cognition, others are in fact implied by the PEM framework and may contribute to its development. We present the metaphor of the “body as a laboratory” in order to highlight wha... (shrink)

The Salivaomics Knowledge Base (SKB) is designed to serve as a computational infrastructure that can permit global exploration and utilization of data and information relevant to salivaomics. SKB is created by aligning (1) the saliva biomarker discovery and validation resources at UCLA with (2) the ontology resources developed by the OBO (Open Biomedical Ontologies) Foundry, including a new Saliva Ontology (SALO). We define the Saliva Ontology (SALO; http://www.skb.ucla.edu/SALO/) as a consensus-based controlled vocabulary of terms and relations dedicated to the salivaomics (...) domain and to saliva-related diagnostics following the principles of the OBO (Open Biomedical Ontologies) Foundry. The Saliva Ontology is an ongoing exploratory initiative. The ontology will be used to facilitate salivaomics data retrieval and integration across multiple fields of research together with data analysis and data mining. The ontology will be tested through its ability to serve the annotation ('tagging') of a representative corpus of salivaomics research literature that is to be incorporated into the SKB. Background Saliva (oral fluid) is an emerging biofluid for non-invasive diagnostics used in the detection of human diseases. The need to advance saliva research is strongly emphasized by the National Institute of Dental and Craniofacial Research (NIDCR), and is included in the NIDCR's 2004- 2009 expert panel long-term research agenda [1]. The ability to monitor health status, disease onset, progression, recurrence and treatment outcome through noninvasive means is highly important to advancing health care management. Saliva is a perfect medium to be explored for personalized individual medicine including diagnostics, offering a non-invasive, easy to obtain means for detecting and monitoring diseases. Saliva testing potentially allows the patient to collect their own saliva samples at home, yielding convenience for the patient and savings in health costs, and facilitating multiple sampling. Specimen collection is less objectionable to patients and easier in children and elderly individuals. Due to these advantages. (shrink)

Some of the most interesting recent work in formal epistemology has focused on developing accuracy-based approaches to justifying Bayesian norms. These approaches are interesting not only because they offer new ways to justify these norms, but because they potentially offer a way to justify all of these norms by appeal to a single, attractive epistemic goal: having accurate beliefs. Recently, Easwaran & Fitelson (2012) have raised worries regarding whether such “all-accuracy” or “purely alethic” approaches can accommodate and justify evidential Bayesian (...) norms. In response, proponents of purely alethic approaches, such as Pettigrew (2013b) and Joyce (2016), have argued that scoring rule arguments provide us with compatible and purely alethic justifications for the traditional Bayesian norms, including evidential norms. In this paper I raise several challenges to this claim. First, I argue that many of the justifications these scoring rule arguments provide are not compatible. Second, I raise worries for the claim that these scoring rule arguments provide purely alethic justifications. Third, I turn to assess the more general question of whether purely alethic justifications for evidential norms are even possible, and argue that, without making some contentious assumptions, they are not. Fourth, I raise some further worries for the possibility of providing purely alethic justifications for content-sensitive evidential norms, like the Principal Principle. (shrink)

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 (...) is a natural fit: an ontology of dispositional properties coherently and adequately captures the crucial casual-cum-explanatory role that the fundamental elements of evo-devo play within that framework. (shrink)

Very broadly, an argument from collections is an argument that purports to show that our beliefs about sets imply — in some sense — the existence of God. Plantinga (2007) first sketched such an argument in “Two Dozen” and filled it out somewhat in his 2011 monograph Where the Conflict Really Lies: Religion, Science, and Naturalism. In this paper I reconstruct what strikes me as the most plausible version of Plantinga’s argument. While it is a good argument in at least (...) a fairly weak sense, it doesn’t initially appear to have any explanatory advantages over a non-theistic understanding of sets — what I call set theoretic realism. However, I go on to argue that the theist can avoid an important dilemma faced by the realist and, hence, that Plantinga’s argument from collections has explanatory advantages that realism does not have. (shrink)

Dispositional properties are often referred to as ‘causal powers’, but what does dispositional causation amount to? Any viable theory must account for two fundamental aspects of the metaphysics of causation – the causal complexity and context sensitivity of causal interactions. The theory of mutual manifestations attempts to do so by locating the complexity and context sensitivity within the nature of dispositions themselves. But is this theory an acceptable first step towards a viable theory of dispositional causation? This paper argues that (...) the reconceptualization that the theory entails comes at too high a price, and is an unnecessary step in the wrong direction: these two central aspects concerning the metaphysics of causation can and should be accounted for in a dispositional account of causation without it. (shrink)

Some explanations in social science, psychology and biology belong to a higher level than other explanations. And higher explanations possess the virtue of abstracting away from the details of lower explanations, many philosophers argue. As a result, these higher explanations are irreplaceable. And this suggests that there are genuine higher laws or patterns involving social, psychological and biological states. I show that this ‘abstractness argument’ is really an argument schema, not a single argument. This is because the argument uses the (...) ‘is lower than’ relation, and this relation admits of different readings. I then suggest four rigorous definitions of the ‘is lower than’ relation, and show that the abstractness argument’s prospects are much brighter for some of these definitions than for others. To show this, I evaluate the so-called ‘disjunctive threat’ to the abstractness argument. (shrink)

This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual measures results (...) in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity. (shrink)

At the heart of the Bayesianism is a rule, Conditionalization, which tells us how to update our beliefs. Typical formulations of this rule are underspecified. This paper considers how, exactly, this rule should be formulated. It focuses on three issues: when a subject’s evidence is received, whether the rule prescribes sequential or interval updates, and whether the rule is narrow or wide scope. After examining these issues, it argues that there are two distinct and equally viable versions of Conditionalization to (...) choose from. And which version we choose has interesting ramifications, bearing on issues such as whether Conditionalization can handle continuous evidence, and whether Jeffrey Conditionalization is really a generalization of Conditionalization. (shrink)

I distinguish several doctrines that economic methodologists have found attractive, all of which have a positivist flavour. One of these is the doctrine that preference assignments in economics are just shorthand descriptions of agents' choice behaviour. Although most of these doctrines are problematic, the latter doctrine about preference assignments is a respectable one, I argue. It doesn't entail any of the problematic doctrines, and indeed it is warranted independently of them.

The ‘traditional’ interpretation of the Receptacle in Plato’s Timaeus maintains that its parts act as substrata to ordinary particulars such as dogs and tables: particulars are form-matter compounds to which Forms supply properties and the Receptacle supplies a substratum, as well as a space in which these compounds come to be. I argue, against this view, that parts of the Receptacle cannot act as substrata for those particulars. I also argue, making use of contemporary discussions of supersubstantivalism, against a substratum (...) interpretation that separates substratum and space in the Timaeus. (shrink)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

This paper explores the level of obligation called for by Milton Friedman’s classic essay “The Social Responsibility of Business is to Increase Profits.” Several scholars have argued that Friedman asserts that businesses have no or minimal social duties beyond compliance with the law. This paper argues that this reading of Friedman does not give adequate weight to some claims that he makes and to their logical extensions. Throughout his article, Friedman emphasizes the values of freedom, respect for law, and duty. (...) The principle that a business professional should not infringe upon the liberty of other members of society can be used by business ethicists to ground a vigorous line of ethical analysis. Any practice, which has a negative externality that requires another party to take a significant loss without consent or compensation, can be seen as unethical. With Friedman’s framework, we can see how ethics can be seen as arising from the nature of business practice itself. Business involves an ethics in which we consider, work with, and respect strangers who are outside of traditional in-groups. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This chapter surveys hybrid theories of well-being. It also discusses some criticisms, and suggests some new directions that philosophical discussion of hybrid theories might take.

The Realist that investigates questions of ontology by appeal to the quantificational structure of language assumes that the semantics for the privileged language of ontology is externalist. I argue that such a language cannot be (some variant of) a natural language, as some Realists propose. The flexibility exhibited by natural language expressions noted by Chomsky and others cannot obviously be characterized by the rigid models available to the externalist. If natural languages are hostile to externalist treatments, then the meanings of (...) natural language expressions serve as poor guides for ontological investigation, insofar as their meanings will fail to determine the referents of their constituents. This undermines the Realist’s use of natural languages to settle disputes in metaphysics. (shrink)

What would the Merleau-Ponty of Phenomenology of Perception have thought of the use of his phenomenology in the cognitive sciences? This question raises the issue of Merleau-Ponty’s conception of the relationship between the sciences and philosophy, and of what he took the philosophical significance of his phenomenology to be. In this article I suggest an answer to this question through a discussion of certain claims made in connection to the “post-cognitivist” approach to cognitive science by Hubert Dreyfus, Shaun Gallagher and (...) Francisco Varela, Evan Thompson and Eleanor Rosch. I suggest that these claims are indicative of an appropriation of Merleau-Ponty’s thought that he would have welcomed as innovative science. Despite this, I argue that he would have viewed this use of his work as potentially occluding the full philosophical significance that he believed his phenomenological investigations to contain. (shrink)

Artificial intelligence (AI) research enjoyed an initial period of enthusiasm in the 1970s and 80s. But this enthusiasm was tempered by a long interlude of frustration when genuinely useful AI applications failed to be forthcoming. Today, we are experiencing once again a period of enthusiasm, fired above all by the successes of the technology of deep neural networks or deep machine learning. In this paper we draw attention to what we take to be serious problems underlying current views of artificial (...) intelligence encouraged by these successes, especially in the domain of language processing. We then show an alternative approach to language-centric AI, in which we identify a role for philosophy. (shrink)

Some explanations are relatively abstract: they abstract away from the idiosyncratic or messy details of the case in hand. The received wisdom in philosophy is that this is a virtue for any explanation to possess. I argue that the apparent consensus on this point is illusory. When philosophers make this claim, they differ on which of four alternative varieties of abstractness they have in mind. What’s more, for each variety of abstractness there are several alternative reasons to think that the (...) variety of abstractness in question is a virtue. I identify the most promising reasons, and dismiss some others. The paper concludes by relating this discussion to the idea that explanations in biology, psychology and social science cannot be replaced by relatively micro explanations without loss of understanding. (shrink)

The paper offers an interpretation of a disputed portion of Plato’s Theaetetus that is often called the Secret Doctrine. It is presented as a process ontology that takes two types of processes, swift and slow motions, as fundamental building blocks for ordinary material objects. Slow motions are powers which, when realized, generate swift motions, which, in turn, are subjectively bundled to compose sensible objects and perceivers. Although the reading of the Secret Doctrine offered here—a new version of the “Causal Theory (...) interpretation”—is not without problems, these problems are acknowledged in Plato’s text, confirming that this interpretation is correct. (shrink)

Once we have distinguished between beauty and aesthetic value, we are faced with the question of whether beauty is a thing of value in itself. A number of theorists have suggested that the answer might be no. They have thought that the pursuit of beauty is just the indulgence of one particular taste: a taste that has, for contingent historical reasons, been privileged. This paper attempts to resist a line of thought that leads to that conclusion. It does so by (...) arguing that there really are objective facts about beauty. To do this, the paper draws distinctions between objectivity and subjectivity, and between realism and anti-realism. It argues that, regarding attributions of beauty, we should be realists and objectivists. This is shown to be compatible with taking the semantic content of such attributions to vary between contexts. This form of context sensitivity is able to account of those features of beauty-attributions that have been taken as evidence for its subjectivity. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

The paper argues that Motion and Rest are “greatest kinds” and not just convenient examples, since they are all-pervading. Thus Motion and Rest can be jointly predicated of a single subject and can be predicated of each other, just as Sameness and Otherness can. While Sameness and Otherness are opposites, a single subject may be the same in one respect, namely, the same as itself, and other in another respect, namely, other than other things. Thus they can be predicated of (...) a single subject, and they can be predicated of each other, as well, since Sameness is other than other things and Otherness is the same as itself. The same explanation applies to Motion and Rest, as the paper demonstrates: a given subject may be in motion in one respect while being at rest in another respect. This distinction is made in the Sophist itself, right in the passage concerning the greatest kinds. Thus Motion and Rest should be considered greatest kinds on par with Being, Sameness, and Otherness, and each of these kinds pervades all other kinds. (shrink)

We best understand Rule Consequentialism as a theory of pattern-based reasons, since it claims that we have reasons to perform some action because of the goodness of the pattern consisting of widespread performance of the same type of action in the same type of circumstances. Plausible forms of Rule Consequentialism are also pluralist, in the sense that, alongside pattern-based reasons, they recognise ordinary act-based reasons, based on the goodness of individual actions. However, Rule Consequentialist theories are distinguished from other pluralist (...) theories of pattern-based reasons by implausible claims about the relative importance of act-based and pattern-based reasons in different cases. Rule Consequentialists should give up these claims. They should either embrace some other pluralist pattern-based view, or reject pattern-based reasons altogether. Note, though, that these arguments apply only to compliance-based, rather than acceptance-based, versions of Rule Consequentialism. This suggests that these two kinds of theory are more different from each other than we might previously have realised. (shrink)

In their 2013 study of traumatic flashback formation, Bourne, Mackay and Holmes raise the question of whether the propensity of a traumatic experience to produce flashbacks is determined by the emotions that are felt at the time of that experience. They suggest that it is not, but the grounds on which they make this suggestion are flawed. Further research is required. That research will need to overcome a significant methodological difficulty — one which is hard to avoid when fMRI data (...) and introspective reports are combined in a single causal inference. (shrink)

A meaningful life, we shall argue, is a life upon which a certain sort of valuable pattern has been imposed by the person in question - a pattern which involves in serious ways the person having an effect upon the world. Meaningfulness is thus a special kind of value which a human life can bear. Two interrelated difficulties face ths proposal. One concerns responsiblity: how are we to account for the fact that a life that satisfies the above criteria can (...) have more meaning than a life with the same positive outcomes but which lacks responsiblity on the part of the agent? The other turns on these outcomes themselves: how can the meaningfulness engendered by actions you perform now be affected by what those actions go on to produce in the future, perhaps even after your death? We provide a response to both of these difficulties. (shrink)

This dissertation argues that we have no good reason to accept any one theory of properties as correct. To show this, I present three possible bases for theory-choice in the properties debate: coherence, explanatory adequacy, and explanatory value. Then I argue that none of these bases resolve the underdetermination of our choice between theories of properties. First, I argue considerations about coherence cannot resolve the underdetermination, because no traditional theory of properties is obviously incoherent. Second, I argue considerations of explanatory (...) adequacy cannot resolve the underdetermination, because every traditional theory of properties lacks the theoretical resources to adequately explain resemblance, causal powers, and predication. However, these inadequacies are easily remedied with theoretical modifications. But this results in an overabundance of modified, but adequate, theories of properties. Third, I argue explanatory virtues cannot resolve the underdetermination, because we have no reason to think explanatory virtues make theories of properties more likely to be true. I reject the common argument that explanatory virtues are truth-conducive in theories of properties because they are truth-conducive in scientific theories. Since none of the three bases for theory choice can resolve the underdetermination, I conclude that we have no good reason to accept any one theory of properties as correct. Finally, I consider the possibility of choosing one theory over the others on pragmatic grounds. But I argue that pragmatic grounds cannot resolve the underdetermination either. Instead, I suggest we accept the view I call 'instrumental pluralism,' which allows practitioners to use whatever theory of properties they find useful. Adviser: Jennifer McKitrick. (shrink)

This is a review article on Franz Brentano’s Descriptive Psychology published in 1982. We provide a detailed exposition of Brentano’s work on this topic, focusing on the unity of consciousness, the modes of connection and the types of part, including separable parts, distinctive parts, logical parts and what Brentano calls modificational quasi-parts. We also deal with Brentano’s account of the objects of sensation and the experience of time.

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

Although the fact that Merleau-Ponty has a dialectical approach in Phenomenology of Perception has been discussed in recent Anglophone readings, there has not been an explicit clarification as to how his varying usages of the term hang together. Given his repeated references to Hegel and to dialectics, coupled with the fact that dialectics are not part of the Husserlian phenomenology or Heideggerean existentialism from which Merleau-Ponty draws so much, the question of just what he does with the idea of dialectics (...) presents itself. In this paper I argue that, in Phenomenology of Perception, Merleau- Ponty saw Hegel as providing a model for the conception of rationality and meaning that must underpin the existentialist response to the problems bequeathed him by Husserlian phenomenology: namely, the problems of embodiment, perception and the constitution of the world. In connection with this, I suggest an interpretation of Merleau-Ponty’s “existential dialectics” that focuses on his three principal uses of the term: 1) a “dialectic of objective thought,” 2) a set of existential-dialectical categories intended to capture the ontological structure of the “body-subject” as “being-in-the-world,” and 3) a dialectic at the cultural level concerning others and history. (shrink)