The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (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)

1. Of what use is the concept of causation? Bertrand Russell [1912-13] argued that it is not useful: it is “a relic of a bygone age, surviving, like the monarchy, only because it is erroneously supposed to do no harm.” His argument for this was that the kind of physical theories that we have come to regard as fundamental leave no place for the notion of causation: not only does the word ‘cause’ not appear in the advanced sciences, but the (...) laws that these sciences state are incompatible with causation as we normally understand it. But Nancy Cartwright has argued [1979] that abandoning the concept of causation would cripple science; her conclusion was based not on fundamental physics, but on more ordinary science such as the search for the causes of cancer. She argues that Russell was right that the fundamental theories of modern physics say nothing, even implicitly, about causation, and concludes on this basis that such theories are incomplete. It is with this cluster of issues that I will begin my discussion. (shrink)

A. Belden Fields invites people to think more deeply about human rights in this book in an attempt to overcome many of the traditional arguments in the human rights literature. He argues that human rights should be reconceptualized in a holistic way to combine philosophical, historical, and empirical-practical dimensions. Human rights are viewed not as a set of universal abstractions but rather as a set of past and ongoing social practices rooted in the claims and struggles of peoples against what (...) they consider to be political, economic, or social domination. By aptly showing how a people’s fight for recognition is often closely tied to rights claims, Fields argues that these connections to identity can help bridge the gulf between universalistic and cultural relativistic arguments in the human rights debate. (shrink)

This chapter considers the ways in which whiteness as a skin color and ideology becomes a dominant level that sets the background against which all things, people and relations appear. Drawing on Merleau-Ponty's phenomenology, it takes up a series of films by Bruce Nauman and Marlon Riggs to consider ways in which this level is phenomenally challenged providing insights into the embodiment of racialization.

Postmodernism’s unifying theme of the absent center raises an important question for metaphysics done in the Catholic tradition. Is novelty a “totally other” that utterly eludes human knowing? In posing this question, postmodernism spurs this tradition on to consider afresh how it integrates novelty and contingency. The following study concludes that no adequate account of this integration is possible without a rich concept of the singular. Rahner’s and Balthasar’s metaphysics of the singular shows that contingency, far from being an impasse (...) to a deeper penetration into reality, is the heart of creative process in both human and non-human events. Rahner’s doctrine of substance and Balthasar’s doctrine of analogy deconstruct the relativism in postmodernism’s view of the singular, even as they develop a more extensive view of the singular for which some strains of postmodernism seem instinctively to be groping. (shrink)

Science Without Numbers caused a stir in 1980, with its bold nominalist approach to the philosophy of mathematics and science. It has been unavailable for twenty years and is now reissued in a revised edition with a substantial new preface presenting the author's current views and responses to the issues raised in subsequent debate.

Life education, also known as life and death education, is an important subject in Taiwan with institutions offering degree programs and courses that focus on quality learning and implementation of life education. What is interesting from the perspective of Taiwanese Education is that the teaching of life education also incorporates a number of Eastern-derived and conceptualized tenets, for example, Buddhist teaching and the importance of spiritual wisdom. This premise contends then that life education in Taiwan, in general, is concerned with (...) the promotion, fulfillment, and cherishing of quality life experiences (e.g., personal contentment, happiness). One example of life education, which resonates with other spiritual beliefs and religious faiths (e.g., Hinduism), is related to spiritual cultivation and the enlightenment of life wisdom. Our own teaching of the subject, likewise, places emphasis on the goal of teaching students to seek meaningful understanding of and appreciation for three major, interrelated components of life education: life wisdom, life practice, and life care. Life education is a beneficial subject as its theoretical understanding may help individuals cope with pathologies and negative life experiences. One negative life experience, in this case, is the ultimate fate of humankind: death. Approaching death and/or the onset of grief is something that we all have to experience. How does one approach death? It is not easy feat and, of course, grief for a loved one is personal and some of us struggle with this. We contend that spiritual cultivation and enlightenment, arising from life education, may assist us with the coping of death (e.g., the possibility of transcendence beyond the realm of life). Forming the premise of the present article, we propose that a person’s ‘spiritual and enlightened self’, reflecting the convergence of three major aspects of life education (i.e., Philosophical reflection, Enrichment of personal well-being, and Spiritual cultivation), would result in the initiation and creation of a number of virtues and positive characteristics – for example: having a positive outlook in life, showing compassion, forgiveness, etc. These virtues and quality characteristics, from our philosophical reasoning, are equivalent to those qualities that positive psychology advocates for. (shrink)

Is logic normative for belief? A standard approach to answering this question has been to investigate bridge principles relating claims of logical consequence to norms for belief. Although the question is naturally an epistemic one, bridge principles have typically been investigated in isolation from epistemic debates over the correct norms for belief. In this paper we tackle the question of whether logic is normative for belief by proposing a Kripkean model theory accounting for the interaction between logical, doxastic, epistemic and (...) deontic notions and using this model theory to show which bridge principles are implied by epistemic norms that we have independent reason to accept, for example, the knowledge norm and the truth norm. We propose a preliminary theory of the interaction between logical, doxastic, epistemic and deontic notions that has among its commitments bridge principles expressing how logic is normative for belief. We also show how our framework suggests that logic is exceptionally normative. (shrink)

A selective background -- Broadly classical approaches -- Paracompleteness -- More on paracomplete solutions -- Paraconsistent dialetheism.

"Disillusioned with life as a literary publicist in London, as well as with her hotshot, unevolved TV presenter boyfriend, Rosie Richardson chucks the glitz and escapes to run a refugee camp in the African desert. When famine strikes and a massive refugee influx threatens to overwhelm the camp... Richardson returns to London to organize a star-studded and risky emergency appeal."--Front jacket.

Presenting a selection of thirteen essays on various topics at the foundations of philosophy--one previously unpublished and eight accompanied by substantial new postscripts--this book offers outstanding insight on truth, meaning, and propositional attitudes; semantic indeterminacy and other kinds of "factual defectiveness;" and issues concerning objectivity, especially in mathematics and in epistemology. It will reward the attention of any philosopher interested in language, epistemology, or mathematics.

The paper tries to spell out a connection between deductive logic and rationality, against Harman's arguments that there is no such connection, and also against the thought that any such connection would preclude rational change in logic. One might not need to connect logic to rationality if one could view logic as the science of what preserves truth by a certain kind of necessity (or by necessity plus logical form); but the paper points out a serious obstacle to any such (...) view. (shrink)

What are people who disagree about logic disagreeing about? The paper argues that (in a wide range of cases) they are primarily disagreeing about how to regulate their degrees of belief. An analogy is drawn between beliefs about validity and beliefs about chance: both sorts of belief serve primarily to regulate degrees of belief about other matters, but in both cases the concepts have a kind of objectivity nonetheless.

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

The paper outlines a view of normativity that combines elements of relativism and expressivism, and applies it to normative concepts in epistemology. The result is a kind of epistemological anti-realism, which denies that epistemic norms can be (in any straightforward sense) correct or incorrect; it does allow some to be better than others, but takes this to be goal-relative and is skeptical of the existence of best norms. It discusses the circularity that arises from the fact that we need to (...) use epistemic norms to gather the facts with which to evaluate epistemic norms; relatedly, it discusses how epistemic norms can rationally evolve. It concludes with some discussion of the impact of this view on "ground level" epistemology. (shrink)

It is a commonly-held belief that ignorance excuses. But what of moral ignorance? Is a person blameless who acts from “false” moral principles? In this paper I shall try to show that such a person is blameworthy. I shall produce an argument that connects the acceptance of moral principles with character, character with moral responsibility, and moral responsibility with the justifiability of blame.

Nonclassical theories of truth that take truth to be transparent have some obvious advantages over any classical theory of truth. But several authors have recently argued that there’s also a big disadvantage of nonclassical theories as compared to their “external” classical counterparts: proof-theoretic strength. While conceding the relevance of this, the paper argues that there is a natural way to beef up extant internal theories so as to remove their proof-theoretic disadvantage. It is suggested that the resulting internal theories are (...) preferable to their external counterparts. (shrink)

There are quite a few theses about logic that are in one way or another pluralist: they hold (i) that there is no uniquely correct logic, and (ii) that because of this, some or all debates about logic are illusory, or need to be somehow reconceived as not straightforwardly factual. Pluralist theses differ markedly over the reasons offered for there being no uniquely correct logic. Some such theses are more interesting than others, because they more radically affect how we are (...) initially inclined to understand debates about logic. Can one find a pluralist thesis that is high on the interest scale, and also true? (shrink)

The Enkratic Principle enjoys something of a protected status as a requirement of rationality. I argue that this status is undeserved, at least in the epistemic domain. Compliance with the principle should not be thought of as a requirement of epistemic rationality, but rather as defeasible indication of epistemic blamelessness. To show this, I present the Puzzle of Inconsistent Requirements, and argue that the best way to solve it is to distinguish two kinds of epistemic evaluation – requirement evaluations and (...) appraisal evaluations. This allows us to solve the puzzle while accommodating traditional motivations for thinking of the Enkratic Principle as a requirement of rationality. (shrink)

Can we make mistakes about what rationality requires? A natural answer is that we can, since it is a platitude that rational belief does not require truth; it is possible for a belief to be rational and mistaken, and this holds for any subject matter at all. However, the platitude causes trouble when applied to rationality itself. The possibility of rational mistakes about what rationality requires generates a puzzle. When combined with two further plausible claims – the enkratic principle, and (...) the claim that rational requirements apply universally – we get the result that rationality generates inconsistent requirements. One popular and attractive solution to the puzzle denies that it is possible to make rational mistakes about what rationality requires. I show why (contra Titelbaum (2015b), and Littlejohn (2015)) this solution is doomed to fail. (shrink)

Bayesian decision theory can be viewed as the core of psychological theory for idealized agents. To get a complete psychological theory for such agents, you have to supplement it with input and output laws. On a Bayesian theory that employs strict conditionalization, the input laws are easy to give. On a Bayesian theory that employs Jeffrey conditionalization, there appears to be a considerable problem with giving the input laws. However, Jeffrey conditionalization can be reformulated so that the problem disappears, and (...) in fact the reformulated version is more natural and easier to work with on independent grounds. (shrink)

Any theory of truth must find a way around Curry’s paradox, and there are well-known ways to do so. This paper concerns an apparently analogous paradox, about validity rather than truth, which JC Beall and Julien Murzi call the v-Curry. They argue that there are reasons to want a common solution to it and the standard Curry paradox, and that this rules out the solutions to the latter offered by most “naive truth theorists.” To this end they recommend a radical (...) solution to both paradoxes, involving a substructural logic, in particular, one without structural contraction. In this paper I argue that substructuralism is unnecessary. Diagnosing the “v-Curry” is complicated because of a multiplicity of readings of the principles it relies on. But these principles are not analogous to the principles of naive truth, and taken together, there is no reading of them that should have much appeal to anyone who has absorbed the morals of both the ordinary Curry paradox and the second incompleteness theorem. (shrink)

Are there questions for which 'there is no determinate fact of the matter' as to which answer is correct? Most of us think so, but there are serious difficulties in maintaining the view, and in explaining the idea of determinateness in a satisfactory manner. The paper argues that to overcome the difficulties, we need to reject the law of excluded middle; and it investigates the sense of 'rejection' that is involved. The paper also explores the logic that is required if (...) we reject excluded middle, with special emphasis on the conditional. There is also discussion of higher order indeterminacy (in several different senses) and of penumbral connections; and there is a suggested definition of determinateness in terms of the conditional and a discussion of the extent to which the notion of determinateness is objective. And there are suggestions about a unified treatment of vagueness and the semantic paradoxes. (shrink)

This book offers a detailed study of the political philosophies of Thomas Hobbes and Benedict de Spinoza, focussing on their concept of power as potentia, concrete power, rather than power as potestas, authorised power. The focus on power as potentia generates a new conception of popular power. Radical democrats–whether drawing on Hobbes's 'sleeping sovereign' or on Spinoza's 'multitude'–understand popular power as something that transcends ordinary institutional politics, as for instance popular plebsites or mass movements. However, the book argues that these (...) understandings reflect a residual scholasticism which Hobbes and Spinoza ultimately repudiate. Instead, on the book's revisionist conception, a political phenomenon should be said to express popular power when it is both popular (it eliminates oligarchy and encompasses the whole polity), and also powerful (it robustly determines political and social outcomes). Two possible institutional forms that this popular power might take are distinguished: Hobbesian repressive egalitarianism, or Spinozist civic strengthening. But despite divergent institutional proposals, the book argues that both Hobbes and Spinoza share the conviction that there is nothing spontaneously egalitarian or good about human collective existence. From this point of view, the book accuses radical democrats of pernicious romanticism; the slow, meticulous work of organizational design and maintenance is the true centre of popular power. Three minute video summary available via HPBin3. Extended discussion on The Political Theory Review podcast. First chapter open access available via Oxford Scholarship Online. Videos of book talks at National University of Singapore (Centre for Legal Theory) and Universidad de Buenos Aires (Instituto de Investigaciones Gino Germani) available via YouTube. (See links below.). (shrink)

This paper extends Kripke’s theory of truth to a language with a variably strict conditional operator, of the kind that Stalnaker and others have used to represent ordinary indicative conditionals of English. It then shows how to combine this with a different and independently motivated conditional operator, to get a substantial logic of restricted quantification within naive truth theory.

This paper is concerned with the debate between substantival and relational theories of space-time, and discusses two difficulties that beset the relationalist: a difficulty posed by field theories, and another difficulty called the problem of quantities. A main purpose of the paper is to argue that possibility can not always be used as a surrogate of ontology, and that in particular that there is no hope of using possibility to solve the problem of quantities.

The term ‘social capital’ is a way of defining the intangible resources of community, shared values and trust upon which we draw in daily life. It has achieved considerable international currency across the social sciences through the very different work of Pierre Bourdieu in France and James Coleman and Robert Putnam in the United States, and has been widely taken up within politics and sociology as an explanation for the decline in social cohesion and community values in western societies. It (...) has also been adopted by policy makers, particularly in international governmental bodies such as the World Bank. (shrink)