According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Ideas 61.3 (2000) 453-471 [Access article in PDF] Liberty, Authority, and Trust in Burke's Idea of Empire Richard Bourke When Edmund Burke first embarked upon a parliamentary career, British political life was in the process of adapting to a series of critical reorientations in both the dynamics of party affiliation and the direction of imperial policy. During the period of the (...) Seven Years' War, a reconstituted militia became a focus for patriotic enthusiasm, uniting national sentiment against France and effectively eradicating the remnants of Jacobite rhetoric and aspiration. Traditional opposition between Tory and Whig became irrelevant, while Court and Country jointly came to the support of the Pitt-Newcastle ministry. However, in due course the Old Corps disintegrated as George III succeeded to the throne with the promise of an end to factional strife and the beginning of a patriotic alliance in government. But while competing ideologies and interests on the domestic political scene were undergoing comprehensive realignment, the pursuit of a blue-water policy in tandem with strategic continental campaigns brought Britain's struggle against France into North America, the Caribbean, and India. Trade continued to expand into Asia and West Africa, but the principles of commercial advantage were continually brought into open conflict with the exigencies of war. The division of power in Europe became embroiled in a substantial redivision of empire, and by 1763 British territorial expansion had reached its zenith.When Burke was appointed private secretary to the Marquis of Rockingham, with the national debt standing at an all time high and the demands of imperial defense unlikely to diminish, the politics of empire called for urgent attention from all sections of the political establishment. In particular the Rockinghamites, adopting a posture of aloofness from venality and petty interest, were obliged to advance policies for imperial government on the solid basis of political principle. 1 Coming into parliament as a member for Wendover in the wake of [End Page 453] Grenville's Stamp Act, at a time when the East India Company was assuming control of the revenue in Bengal, Burke set about formulating a doctrine of imperial sovereignty which would be serviceable to the party either in power or in opposition and which would be adequate to the complex reality of detached and extensive empire. The immediate reception of that inquiry, both in Britain and on the Continent, into the fraught world of post-Revolutionary political debate has had the long-term effect of distorting the order of emphasis in terms of which his career as a whole ought properly to be understood.The vigorous elaboration, in opposition to the Jacobin experiment in France, of the conditions under which moderate government could be exercised within the context of an absolute sovereignty was expressed in terms which had originally been invoked as part of a sustained attempt to reconcile civility with empire. As we shall see, that attempt involved a process of delicate coordination by means of which the interests of freedom would be brought into harmony with the demands of public power. In that sense the effort to make liberty and authority mutually responsible can be said to constitute the core ambition of Burke's political rhetoric. In this context responsibility defines the optimally beneficial relation between government and people on the one hand and national sovereignty and the extended empire on the other. This article outlines the practical and theoretical exploration of those relations within the frame of Burke's intervention in the world of eighteenth-century political discourse.Burke was of course well placed in 1765 to evolve a theory of imperial government that was at once ideologically compelling and politically viable. In his capacity as secretary to William Gerard Hamilton in the early 1760s he had already examined the corruption of legitimate empire as represented by the introduction of penal legislation into Ireland after 1694. The Tracts Relating to Popery Laws set out to convict the Irish Parliament in Dublin of flagrant misrule. A subordinate legislature within the empire is charged with having employed... (shrink)

This out-of-print collection in the area of the history, politics, ethics, and theory of privacy includes selections from Peter Gay, Alan Westin, Walter Benjamin, Catharine MacKinnon, Seyla Benhabib, Anita Allen, Ann Jennings, Charles Taylor, Richard Sennett, Mark Wicclair, Martha Nussbaum, and Robert Nozick.

Is there a political philosophy of conservatism? A history of the phenomenon written along sceptical lines casts doubt on the existence of a transhistorical doctrine, or even an enduring conservative outlook. The main typologies of conservatism uniformly trace its origins to opposition to the French Revolution. Accordingly, Edmund Burke is standardly singled out as the ‘father’ of this style of politics. Yet Burke was de facto an opposition Whig who devoted his career to assorted programmes of reform. In (...) restoring Burke to his original milieu, the argument presented here takes issue with 20th-century accounts of conservative ideology developed by such figures as Karl Mannheim, Klaus Epstein and Samuel Huntington. It argues that the idea of a conservative tradition is best seen as a belated construction, and that the notion of a univocal philosophy of conservatism is basically misconceived. (shrink)

Burke suggests that we should view society as a partnership between the past, the present, and the future. I defend this idea by outlining how we can understand the interests of the past and future people and the obligations that they have towards each other. I argue that we have forward-looking obligations to leave the world a decent place, and backward-looking obligations to respect the legacy of the past. The latter obligation requires an understanding of the role that traditions (...) and meta-traditions should (and should not) play in tying together societies—especially national societies—over time. (shrink)

This paper examines the role of ?situations? in John Dewey's philosophy of logic. To do this properly it is necessary to contrast Dewey's conception of experience and mentality with views characteristic of modern epistemology. The primary difference is that, rather than treat experience as peripheral and or external to mental functions (reason, etc.), we should treat experience as a field in and as a part of which thinking takes place. Experience in this broad sense subsumes theory and fact, hypothesis and (...) evidence, reason and observation, thought and perception. Logic in this view is a formal study of the generic features of all possible kinds of experience in this broad (thick, deep, wide, multifaceted) sense. The goal of this paper is to explain what Dewey thinks a situation is in the context of this view of experience, and to argue for the fundamental importance of that idea for logic and philosophy in general. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

A uniform construction for sequent calculi for finite-valued first-order logics with distribution quantifiers is exhibited. Completeness, cut-elimination and midsequent theorems are established. As an application, an analog of Herbrand’s theorem for the four-valued knowledge-representation logic of Belnap and Ginsberg is presented. It is indicated how this theorem can be used for reasoning about knowledge bases with incomplete and inconsistent information.

A general class of labeled sequent calculi is investigated, and necessary and sufficient conditions are given for when such a calculus is sound and complete for a finite -valued logic if the labels are interpreted as sets of truth values. Furthermore, it is shown that any finite -valued logic can be given an axiomatization by such a labeled calculus using arbitrary "systems of signs," i.e., of sets of truth values, as labels. The number of labels needed is logarithmic in the (...) number of truth values, and it is shown that this bound is tight. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The aim of this paper is to emphasize the fact that for all finitely-many-valued logics there is a completely systematic relation between sequent calculi and tableau systems. More importantly, we show that for both of these systems there are al- ways two dual proof sytems (not just only two ways to interpret the calculi). This phenomenon may easily escape one’s attention since in the classical (two-valued) case the two systems coincide. (In two-valued logic the assignment of a truth value and (...) the exclusion of the opposite truth value describe the same situation.). (shrink)

The proof theory of many-valued systems has not been investigated to an extent comparable to the work done on axiomatizatbility of many-valued logics. Proof theory requires appropriate formalisms, such as sequent calculus, natural deduction, and tableaux for classical (and intuitionistic) logic. One particular method for systematically obtaining calculi for all finite-valued logics was invented independently by several researchers, with slight variations in design and presentation. The main aim of this report is to develop the proof theory of finite-valued first order (...) logics in a general way, and to present some of the more important results in this area. In Systems covered are the resolution calculus, sequent calculus, tableaux, and natural deduction. This report is actually a template, from which all results can be specialized to particular logics. (shrink)

In The Boundary Stones of Thought, Rumfitt defends classical logic against challenges from intuitionistic mathematics and vagueness, using a semantics of pre-topologies on possibilities, and a topological semantics on predicates, respectively. These semantics are suggestive but the characterizations of negation face difficulties that may undermine their usefulness in Rumfitt’s project.

It is shown that Gqp↑, the quantified propositional Gödel logic based on the truth-value set V↑ = {1 - 1/n : n≥1}∪{1}, is decidable. This result is obtained by reduction to Büchi's theory S1S. An alternative proof based on elimination of quantifiers is also given, which yields both an axiomatization and a characterization of Gqp↑ as the intersection of all finite-valued quantified propositional Gödel logics.

The first-order temporal logics with □ and ○ of time structures isomorphic to ω (discrete linear time) and trees of ω-segments (linear time with branching gaps) and some of its fragments are compared: the first is not recursively axiomatizable. For the second, a cut-free complete sequent calculus is given, and from this, a resolution system is derived by the method of Maslov.

What we value, like, endorse, want, and prefer changes over the course of our lives. Richard Pettigrew presents a theory of rational decision making for agents who recognise that their values will change over time and whose decisions will affect those future times.

All first-order Gödel logics G_V with globalization operator based on truth value sets V C [0,1] where 0 and 1 lie in the perfect kernel of V are axiomatized by Ciabattoni’s hypersequent calculus HGIF.

It is shown that the infinite-valued first-order Gödel logic G° based on the set of truth values {1/k: k ε w {0}} U {0} is not r.e. The logic G° is the same as that obtained from the Kripke semantics for first-order intuitionistic logic with constant domains and where the order structure of the model is linear. From this, the unaxiomatizability of Kröger's temporal logic of programs (even of the fragment without the nexttime operator O) and of the authors' temporal (...) logic of linear discrete time with gaps follows. (shrink)

Priest has provided a simple tableau calculus for Chellas's conditional logic Ck. We provide rules which, when added to Priest's system, result in tableau calculi for Chellas's CK and Lewis's VC. Completeness of these tableaux, however, relies on the cut rule.

Textbook on Gödel’s incompleteness theorems and computability theory, based on the Open Logic Project. Covers recursive function theory, arithmetization of syntax, the first and second incompleteness theorem, models of arithmetic, second-order logic, and the lambda calculus.

Mobile phones are reportedly the most rapidly expanding e-reading device worldwide. However, the embodied, cognitive and affective implications of smartphone-supported fiction reading for leisure (m-reading) have yet to be investigated empirically. Revisiting the theoretical work of digitization scholar Anne Mangen, we argue that the digital reading experience is not only contingent on patterns of embodied reader–device interaction (Mangen, 2008 and later) but also embedded in the immediate environment and broader situational context. We call this the situation constraint. Its application to (...) Mangen’s general framework enables us to identify four novel research areas, wherein m-reading should be investigated with regard to its unique affordances. The areas are reader–device affectivity, situated embodiment, attention training and long-term immersion. (shrink)

This article offers a novel, conservative account of material constitution, one that incorporates sortal essentialism and features a theory of dominant sortals. It avoids coinciding objects, temporal parts, relativizations of identity, mereological essentialism, anti-essentialism, denials of the reality of the objects of our ordinary ontology, and other departures from the metaphysic implicit in ordinary ways of thinking. Defenses of the account against important objections are found in Burke 1997, 2003, and 2004, as well as in the often neglected six (...) paragraphs that conclude section V of this article. (shrink)

Effective altruism sounds so innocuous—who could possibly be opposed to doing good more effectively? Yet it has inspired significant backlash in recent years. This paper addresses some common misconceptions and argues that the core “beneficentric” ideas of effective altruism are both excellent and widely neglected. Reasonable people may disagree on details of implementation, but all should share the basic goals or values underlying effective altruism.

This paper draws on the 'Fitting Attitudes' analysis of value to argue that we should take the concept of fittingness (rather than value) as our normative primitive. I will argue that the fittingness framework enhances the clarity and expressive power of our normative theorising. Along the way, we will see how the fittingness framework illuminates our understanding of various moral theories, and why it casts doubt on the Global Consequentialist idea that acts and (say) eye colours are normatively on a (...) par. We will see why even consequentialists, in taking rightness to be in some sense determined by goodness, should not think that rightness is conceptually reducible to goodness. Finally, I will use the fittingness framework to explicate the distinction between consequentialist and deontological theories, with particular attention to the contentious case of Rule Consequentialism. (shrink)

This report from the WHO Consultative Group on Equity and Universal Health Coverage offers advice on how to make progress fairly towards universal health coverage.

In Mind and World, John McDowell argues against the view that perceptual representation is non-conceptual. The central worry is that this view cannot offer any reasonable account of how perception bears rationally upon belief. I argue that this worry, though sensible, can be met, if we are clear that perceptual representation is, though non-conceptual, still in some sense 'assertoric': Perception, like belief, represents things as being thus and so.

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

The effort of Fichte’s Foundations of the Entire Science of Knowledge is to ground the whole of the science in so called principles. This aim is a specific expression of the project of self-assurance of human being characterizing the important movement of modern metaphysics. The movement towards self-assurance even culminates here: it gets a form of showing human being as an entity founding itself and in totality with itself the whole of actuality. The foundation of science is therefore in this (...) Fichte’s work completely subordinated to the project of explicit self-constitution of human being based in practical-theoretical mastering of consciousness of its own ontological-ontical priority. (shrink)

There is too much that we do not know about COVID-19. The longer we take to find it out, the more lives will be lost. In this paper, we will defend a principle of risk parity: if it is permissible to expose some members of society (e.g. health workers or the economically vulnerable) to a certain level of ex ante risk in order to minimize overall harm from the virus, then it is permissible to expose fully informed volunteers to a (...) comparable level of risk in the context of promising research into the virus. We apply this principle to three examples of risky research: skipping animal trials for promising treatments, human challenge trials to speed up vaccine development, and low-dose controlled infection or “variolation.” We conclude that if volunteers, fully informed about the risks, are willing to help fight the pandemic by aiding promising research, there are strong moral reasons to gratefully accept their help. To refuse it would implicitly subject others to still graver risks. (shrink)

Utilitarianism is often rejected on the grounds that it fails to respect the separateness of persons, instead treating people as mere “receptacles of value”. I develop several different versions of this objection, and argue that, despite their prima facie plausibility, they are all mistaken. Although there are crude forms of utilitarianism that run afoul of these objections, I advance a new form of the view—‘token-pluralistic utilitarianism’—that does not.

The problem of closure for the traditional unstructured possible worlds model of attitudinal content is that it treats belief and other cognitive states as closed under entailment, despite apparent counterexamples showing that this is not a necessary property of such states. One solution to this problem, which has been proposed recently by several authors (Schaffer 2005; Yalcin 2018; Hoek forthcoming), is to restrict closure in an unstructured setting by treating propositional attitudes as question-sensitive. Here I argue that this line of (...) response is unsatisfying as it stands because the problem of closure is more general than is typically discussed. A version of the problem recurs for attitudes like wondering, entertaining, considering, and so on, which are directed at questions rather than propositions. For such questioning attitudes, the appeal to question-sensitivity is much less convincing as a solution to the problem of closure. (shrink)

This collection of writings on aesthetics includes selections from Theodor Adorno, Walter Benjamin, Mikhail Bakhtin, Sigmund Freud, Martin Heidegger, Amy Mullin, Friedrich Nietzsche, and Frederich Wilhelm Joseph von Schelling. This collection may still be available as a print-on-demand title at the Ryerson University bookstore.

This collection for a course in Social Thought and the Critique of Power includes selections from Sandra Bartkey, Wendy Brown, Judith Butler, Luc Boltanski, Eve Chiapello, Juergin Habermas, Margaret Kohn, Saskia Sassen, Margit Mayer, David Ciavatta, Michael Hardt, Antonio Negri, and Jeremy Waldron. Selections include material on the city, neoliberalism, computer-mediated life, precarity, cosmopolitanism, and gender. This packet may still be available as a print-on-demand title at the Ryerson University Bookstore.

This out-of-print collection in the area of European twentieth-century political philosophy includes selections from Adorno, Benjamin, Benhabib, Marcuse, Ciavatta, Comay, Honneth, and Fraser.

This collection in the area of continental philosophy of language, aesthetics, and semiotics includes articles and book selections from Derrida, Ricouer, McCumber, Oliver, Sheshradi-Krooks, Lacan, and Kristeva. This collection is available in the University of Guelph bookstore.

This out-of-print collection on animal rights, applied ethics, and continental philosophy includes readings by Martin Heidegger, Karin De Boer, Martha Nussbaum, David De Grazia, Giorgio Agamben, Peter Singer, Tom Regan, David Morris, Michael Thompson, Stephen Jay Gould, Sue Donaldson, Carolyn Merchant, and Jacques Derrida.

This out-of-print, two-volume, photocopy packet, in the area of "Surrealism and the Politics of the Particular" includes readings on language, meaning, and surrealism from Adorno, Benjamin, McCumber, Breton, Heidegger, Freud, Kristeva, Ricouer, and Bataille.

A textbook for modal and other intensional logics based on the Open Logic Project. It covers normal modal logics, relational semantics, axiomatic and tableaux proof systems, intuitionistic logic, and counterfactual conditionals.

An introductory textbook on metalogic. It covers naive set theory, first-order logic, sequent calculus and natural deduction, the completeness, compactness, and Löwenheim-Skolem theorems, Turing machines, and the undecidability of the halting problem and of first-order logic. The audience is undergraduate students with some background in formal logic.

According to certain normative theories in epistemology, rationality requires us to be logically omniscient. Yet this prescription clashes with our ordinary judgments of rationality. How should we resolve this tension? In this paper, I focus particularly on the logical omniscience requirement in Bayesian epistemology. Building on a key insight by Hacking :311–325, 1967), I develop a version of Bayesianism that permits logical ignorance. This includes: an account of the synchronic norms that govern a logically ignorant individual at any given time; (...) an account of how we reduce our logical ignorance by learning logical facts and how we should update our credences in response to such evidence; and an account of when logical ignorance is irrational and when it isn’t. At the end, I explain why the requirement of logical omniscience remains true of ideal agents with no computational, processing, or storage limitations. (shrink)

In this paper, we seek a reliabilist account of justified credence. Reliabilism about justified beliefs comes in two varieties: process reliabilism (Goldman, 1979, 2008) and indicator reliabilism (Alston, 1988, 2005). Existing accounts of reliabilism about justified credence comes in the same two varieties: Jeff Dunn (2015) proposes a version of process reliabilism, while Weng Hong Tang (2016) offers a version of indicator reliabilism. As we will see, both face the same objection. If they are right about what justification is, it (...) is mysterious why we care about justification, for neither of the accounts explains how justification is connected to anything of epistemic value. We will call this the Connection Problem. I begin by describing Dunn’s process reliabilism and Tang’s indicator reliabilism. I argue that, understood correctly, they are, in fact, extensionally equivalent. That is, Dunn and Tang reach the top of the same mountain, albeit by different routes. However, I argue that both face the Connection Problem. In response, I offer my own version of reliabilism, which is both process and indicator, and I argue that it solves that problem. Furthermore, I show that it is also extensionally equivalent to Dunn’s reliabilism and Tang’s. Thus, I reach the top of the same mountain as well. (shrink)

Satisficing Consequentialism is often rejected as hopeless. Perhaps its greatest problem is that it risks condoning the gratuitous prevention of goodness above the baseline of what qualifies as "good enough". I propose a radical new willpower-based version of the view that avoids this problem, and that better fits with the motivation of avoiding an excessively demanding conception of morality. I further demonstrate how, by drawing on the resources of an independent theory of blameworthiness, we may obtain a principled specification of (...) what counts as "good enough". (shrink)

This is the introduction to the inaugural issue of The Journal of Philosophy of Disability.

Some of the most important developments of symbolic logic took place in the 1920s. Foremost among them are the distinction between syntax and semantics and the formulation of questions of completeness and decidability of logical systems. David Hilbert and his students played a very important part in these developments. Their contributions can be traced to unpublished lecture notes and other manuscripts by Hilbert and Bernays dating to the period 1917-1923. The aim of this paper is to describe these results, focussing (...) primarily on propositional logic, and to put them in their historical context. It is argued that truth-value semantics, syntactic ("Post-") and semantic completeness, decidability, and other results were first obtained by Hilbert and Bernays in 1918, and that Bernays's role in their discovery and the subsequent development of mathematical logic is much greater than has so far been acknowledged. (shrink)