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)

What is the role of conscious experience in the epistemology of perceptual knowledge: how should we characterise what is going on in seeing that o is F in order to illuminate the contribution of seeing o to their status as cases of knowing that o is F? My proposal is that seeing o involves conscious acquaintance with o itself, the concrete worldly source of the truth that o is F, in a way that may make it evident to the subject (...) that o is an instance of ‘x is F’ as she understands this, and hence evident that o is F. Seeing that o is F is thus a way of its being evident that o is F and is therefore a way of knowing that o is F. (shrink)

Humean supervenience is the doctrine that there are no necessary connections in the world. David Lewis identifies one big bad bug to the programme of providing Humean analyses for apparently non-Humean features of the world. The bug is chance. We put the bug under the microscope, and conclude that chance is no special problem for the Humean.

The question I am interested in is this. What exactly is the role of conscious experience in the acquisition of knowledge on the basis of perception? The problem here, as I see it, is to solve simultaneously for the nature of this experience, and its role in acquiring and sustaining the relevant beliefs, in such a way as to vindicate what I regard as an undeniable datum, that perception is a basic source of knowledge about the mind-independent world, in a (...) sense of ‘basic’ which is also to be elucidated. I shall sketch the way in which I think that this should be done. In section I, I argue that perceptual experiences must provide reasons for empirical beliefs. In section II, I explain how they do so. My thesis is that a correct account of the sense in which perceptual experiences are experiences of mind-independent things is itself an account of the way in which they provide peculiarly basic reasons for beliefs about the world around the perceiver. (shrink)

Bill Brewer presents an original view of the role of conscious experience in the acquisition of empirical knowledge. He argues that perceptual experiences must provide reasons for empirical beliefs if there are to be any determinate beliefs at all about particular objects in the world. This fresh approach to epistemology turns away from the search for necessary and sufficient conditions for knowledge and works instead from a theory of understanding in a particular area.

David Lewis’s ‘Humean Supervenience’ (henceforth ‘HS’) combines realism about laws, chances, and dispositions with a sparse ontology according to which everything supervenes on the overall spatiotemporal distribution of non-dispositional properties (Lewis 1986a, Philosophical papers: Volume II, pp. ix–xvii, New York: Oxford Univesity Press, 1994, Mind 103:473–490). HS faces a serious problem—a “big bad bug” (Lewis 1986a, p. xiv): it contradicts the Principal Principle, a seemingly obvious norm of rational credence. Two authors have tried to rescue Lewis’s ontology from the ‘big (...) bad bug’ (henceforth ‘the Bug’) by rejecting realism about laws, chances, and dispositions (Halpin 1994, Aust J Phil 72:317–338, 1998, Phil Sci 65:349–360; Ward 2005, Phil Sci 71:241–261). I will argue that this strategy cannot possibly work: it is the ontology, not the realist thesis, that lies at the root of the problem. (shrink)

Early modern empiricists thought that the nature of perceptual experience is given by citing the object presented to the mind in that experience. Hallucination and illusion suggest that this requires untenable mind-dependent objects. Current orthodoxy replaces the appeal to direct objects with the claim that perceptual experience is characterized instead by its representational content. This paper argues that the move to content is problematic, and reclaims the early modern empiricist insight as perfectly consistent, even in cases of illusion, with the (...) realist contention that these direct objects of perception are the persisting mind-independent physical objects we all know and love. (shrink)

In this paper I discuss a number of different relationships between two kinds of obligation: those which have individuals as their subject, and those which have groups of individuals as their subject. I use the name collective obligations to refer to obligations of the second sort. I argue that there are collective obligations, in this sense; that such obligations can give rise to and explain obligations which fall on individuals; that because of these facts collective obligations are not simply reducible (...) to individual obligations; and that collective obligations supervene on individual obligations, without being reducible to them. The sort of supervenience I have in mind here is what is sometimes called ‘global supervenience’. In other words, there cannot be two worlds which differ in respect of the collective obligations which exist in them without also differing in respect of the individual obligations which exist in them. (shrink)

A taped conversational interview with Daniel Dennett and Bill Uzgalis covers a wide range of topics arising from Dennett’s thoughts about computing and human beings. The background of Dennett’s work is explored as are his views about mind-brain identity theory, artificial intelligence, functionalism, human exceptionalism, animal culture, language, pain, freedom and determinism, and quality of life.

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Physical objects are such things as stones, tables, trees, people and other animals: the persisting macroscopic constituents of the world we live in. therefore expresses a commonsense commitment to physical realism: the persisting macroscopic constituents of the world we live in exist, and are as they are, quite independently of anyone.

It is close to current orthodoxy that perceptual experience is to be characterized, at least in part, by its representational content, roughly, by the way it represents things as being in the world around the perceiver. Call this basic idea the content view.

Bill Cosby’s immorality has raised intriguing aesthetic and ethical issues. Do the crimes that he has been convicted of lessen the aesthetic value of his stand-up and, even if we can enjoy it, should we? This article first discusses the intimate relationship between the comedian and audience. The art form itself is structurally intimate, and at the same time the comedian claims to express an authentic self on stage. After drawing an analogy between the question of the moral character (...) of comedians and the aesthetic value of their stand-up and the debate over the ethical criticism of art, this article argues that it is reasonable to find a comedian’s performance less funny, because stand-up’s artistic success relies on this intimacy. It contrasts the comedy of Bill Cosby with that of Louis C.K. C.K.’s moral flaws are much more present in his comedy, and it is therefore more difficult to find him funny. Last, it is ethically permissible to enjoy their comedy, if no harm to others results, both because it does not corrupt the audience’s character and because amusement is valuable. (shrink)

There’s a long history of discussion of probability in philosophy, but objective chance separated itself off and came into its own as a topic with the advent of a physical theory - quantum mechanics - in which chances play a central, and apparently ineliminable, role. In 1980 David Lewis wrote a paper pointing out that a very broad class of accounts of the nature of chance apparently lead to a contradiction when combined with a principle that expresses the role of (...) chance in guiding belief. There is still no settled agreement on the proper response to the Lewis problem. At the time he wrote the article, Lewis despaired of a solution, but, although he never achieved one that satisfied him completely, by 1994, due to work primarily by Thau and Hall, he had come to think the problem could be disarmed if we fudged a little on the meaning of ‘chance’. I’ll say more about this below. What I’m going to suggest, however, is that the qualification is unnecessary. The problem depends on an assumption that should be rejected, viz., that using information about chance to guide credence requires one to conditionalize on the theory of chance that one is using. I’m going to propose a general recipe for using information about chance to guide belief that does not require conditionalization on a theory of chance at any stage. Lewis’ problem doesn’t arise in this setting. (shrink)

We perceive a world of mind-independent macroscopic material objects such as stones, tables, trees, and animals. Our experience is the joint upshot of the way these things are and our route through them, along with the various relevant circumstances of perception; and it depends on the normal operation of our perceptual systems. How should we characterise our perceptual experience so as to respect its basis and explain its role in grounding empirical thought and knowledge? I offered an answer to this (...) question in Perception and its objects. Here I aim to clarify some of my central arguments and to develop and defend the position further in the light of subsequent critical discussion. (shrink)

Many authors hold that collectives, as well as individuals can be the subjects of obligations. Typically these authors have focussed on the obligations of highly structured groups, and of small, informal groups. One might wonder, however, whether there could also be collective obligations which fall on everyone – what I shall call ' global collective obligations '. One reason for thinking that this is not possible has to do with considerations about agency : it seems as though an entity can (...) only be the subject of obligations if it is an agent. In this paper, I try to show that the argument from agency is not a good reason for being sceptical about the existence of global collective obligations : it derives whatever plausibility it has from the idea that claims about obligation need to be addressable to some agent. My suggestion is that we should accept this principle about the addressability of obligations, but deny that the addressee of an obligation need be the subject of that obligation. The collective obligations of unstructured collections of individuals, including global collective obligations, meet the addressability requirement insofar as they require something of the individuals who make up the collective. (shrink)

I take it for granted that sense experiential states provide reasons for empirical beliefs; indeed this claim forms the first premise of my central argument for (CC). 1 The subsequent stages of the argument are intended to establish that a person has such a reason for believing something about the way things are in the world around him only if he is in some mental state or other with a conceptual content: a conceptual state. Thus, given that sense experiential states (...) do provide reasons for empirical beliefs, they must have conceptual content. (shrink)

Several philosophers think there are important analogies between emotions and perceptual states. Furthermore, considerations about the rational assessibility of emotions have led philosophers—in some cases, the very same philosophers—to think that the content of emotions must be propositional content. If one finds it plausible that perceptual states have propositional contents, then there is no obvious tension between these views. However, this view of perception has recently been attacked by philosophers who hold that the content of perception is object-like. I shall (...) argue for a view about the content of emotions and perceptual states which will enable us to hold both that emotional content is analogous to perceptual content and that both emotions and perceptual states can have propositional contents. This will involve arguing for a pluralist view of perceptual content, on which perceptual states can have both contents which are proposition-like and contents which are object-like. I shall also address two significant objections to the claim that emotions can have proposition-like contents. Meeting one of these objections will involve taking on a further commitment: the pluralist account of perceptual content will have to be one on which the contents of perception can be non-conceptual. (shrink)

From time to time we explain what people do by referring to their habits. We explain somebody’s putting the kettle on in the morning as done through “force of habit”. We explain somebody’s missing a turning by saying that she carried straight on “out of habit”. And we explain somebody’s biting her nails as a manifestation of “a bad habit”. These are all examples of what will be referred to here as habit explanations. Roughly speaking, they explain by referring to (...) a pattern of a particular kind of behaviour which is regularly performed in characteristic circumstances, and has become automatic for that agent due to this repetition. (shrink)

According to Wringe 2006 we have good reasons for accepting the existence of Global Collective Obligations - in other words, collective obligations which fall on the world’s population as a whole. One such reason is that the existence of such obligations provides a plausible solution a problem which is sometimes thought to arise if we think that individuals have a right to have their basic needs satisfied. However, obligations of this sort would be of little interest – either theoretical or (...) practical – if they did not give rise, either directly or indirectly, to any kinds of reasons for individuals to behave in certain ways. -/- In this paper, I shall argue that in many situations, forward-looking global obligations give rise to an obligation on individuals to work towards bringing into existence and support an institutional system which will enable their obligations to be met. My argument for this conclusion involves two steps. In the first step, I address a general question about how collective obligations can give rise to individual obligations without being reducible to them, and which obligations they give rise to. Here I give a Kant-inspired argument, based on the principles that ‘ought implies can’ and that the content of the moral law is given by reflecting on how agents should legislate in a kingdom of ends, which is designed to show that collective obligations can give rise to individual obligations. In the second step I apply this principle to the case of global forward-looking obligations. (shrink)

The question how to account for illusion has had a prominent role in shaping theories of perception throughout the history of philosophy. Prevailing philosophical wisdom today has it that phenomena of illusion force us to choose between the following two options. First, reject altogether the early modern empiricist idea that the core subjective character of perceptual experience is to be given simply by citing the object presented in that experience. Instead we must characterize perceptual experience entirely in terms of its (...) representational content. Second, retain the early modern idea that the core subjective character of experience is simply constituted by the identity of its direct objects, but admit that these must be mind-dependent entities, distinct from the mind-independent physical objects we all know and love. I argue here that the early modern empiricists had an indispensable insight. The idea that the core subjective character of perceptual experience is to be given simply by citing the object presented in that experience is more fundamental than any appeal to perceptual content, and can account for illusion, and indeed hallucination, without resorting to the problematic postulation of any such mind-dependent objects. (shrink)

According to Kant, it is impermissible to treat humanity as a mere means. If we accept Kant's equation of humanity with rational agency, and are literalists about ascriptions of agency to collectives it appears to follow that we may not treat collectives as mere means. On most standard accounts of what it is to treat something as a means this conclusion seems highly implausible. I conclude that we are faced with a range of options. One would be to rethink the (...) equation of humanity with rationality. Another would be to abandon the prohibition on treating as a means. The last would be to abandon literalist construals of attribution of agency to collectives. (shrink)

In this paper, I discuss a distinctively non-paradigmatic instance of punishment: the punishment of non-citizens. I shall argue that the punishment of non-citizens presents considerable difficulties for one currently popular account of criminal punishment: Antony Duff’s communicative expressive theory of punishment. Duff presents his theory explicitly as an account of the punishment of citizens - and as I shall argue, this is not merely an incidental feature of his account. However, it is plausible that a general account of the criminal (...) law of the kind of idealized state that Duff focusses on will need to say something about how that law deals with non-citizens. In particular, I claim, it will need to provide a justification for punishing them. Because Duff's account says nothing about the punishment of non-citizens, it cannot do so. Furthermore, although Duff's more recent suggestion that non-citizens should be thought of as being guests in the state on whose territory they are present may provide for an account of their criminalization, it cannot easily be extended into an account that provides a justification for their punishment. (shrink)

Many philosophers hold that punishment has an expressive dimension. Advocates of expressive theories have different views about what makes punishment expressive, what kinds of mental states and what kinds of claims are, or legitimately can be expressed in punishment, and to what kind of audience or recipients, if any, punishment might express whatever it expresses. I shall argue that in order to assess the plausibility of an expressivist approach to justifying punishment we need to pay careful attention to whether the (...) things which punishment is supposed to express are aimed at an audience. For the ability of any version of expressivism to withstand two important challenges, which I call the harsh treatment challenge’ and the ‘publicity challenge’ respectively. will depend on the way it answers them. The first of these challenges has received considerable discussion in the literature on expressive theories of punishment; the second considerably less. This is unfortunate. For careful consideration of the publicity challenge should lead us to favor a version of the expressive theory which has been under-discussed: the view on which punishment has an intended audience, and on which the audience is society at large, rather than—as on the most popular version of that view—the criminal. Furthermore, this view turns out to be better equipped to meet the harsh treatment challenge, and to be so precisely because of the way in which it meets the publicity challenge. (shrink)

I will talk here about three problems that have bothered me for a number of years, during which time I have experimented with a variety of solutions and encouraged others to work on them. I have raised each of them separately both in full and in passing in various contexts, but thought it would be worthwhile on this occasion to bring them to your attention side by side. In this talk I will explain the problems, together with some things that (...) have been tried in the past and some new ideas for their solution. (shrink)

In this paper, I argue that a well-known objection to subsistence rights developed by Onora O'Neill - namely, that such rights would generate obligations without an obligation-bearer, can be answered if we take such rights to impose an obligation on the world's population, taken collectively.

The authors argue that corporate philanthropy is far too important as a social instrument for good to depend on ethical egoism for its support. They claim that rule utilitarianism provides a more compelling, though not exclusive, moral foundation. The authors cite empirical and legal evidence as additional support for their claim.

In The Varieties of Reference (1982), Gareth Evans claims that considerations having to do with certain basic ways we have of gaining knowledge of our own physical states and properties provide "the most powerful antidote to a Cartesian conception of the self" (220). In this chapter, I start with a discussion and evaluation of Evans' own argument, which is, I think, in the end unconvincing. Then I raise the possibility of a more direct application of similar considerations in defence of (...) common sense anti-Cartesianism. Progress in this direction depends upon a far more psychologically informed understanding of normal and abnormal bodily awareness than is generally found in philosophical discussions of these issues. In the context of my attempt at some such understanding, I go on to assess the potential of this more direct line of argument. (shrink)

It has recently been suggested that the fact that punishment involves an intention to cause suffering undermines expressive justifications of punishment. I argue that while punishment must involve harsh treatment, harsh treatment need not involve an intention to cause suffering. Expressivists should adopt this conception of harsh treatment.

Nathan Hanna has recently argued against a position I defend in a 2013 paper in this journal and in my 2016 book on punishment, namely that we can punish someone without intending to harm them. In this discussion note I explain why two alleged counterexamples to my view put forward by Hanna are not in fact counterexamples to any view I hold, produce an example which shows that, if we accept a number of Hanna’s own assumptions, punishment does not require (...) an intention to harm, and discuss whether a definition and counter-example approach is the best way to proceed in the philosophy of punishment. I conclude with a brief exegetical discussion of H.L.A Hart’s Prolegomenon to the Principles of Punishment. (shrink)

The surge of interest in Jean-Francois Lyotard's writings has pushed him into the centre of debate on the postmodern.

Traditional ecocentric ethics relies on an ecology that emphasizes the stability and integrity of ecosystems. Numerous ecologists now focus on natural systems that are less clearly characterized by these properties. We use the elimination and restoration of wolves in Yellowstone to illustrate troubles for traditional ecocentric ethics caused by ecological models emphasizing instability in natural systems. We identify several other problems for a stability-integrity based ecocentrism as well. We show how an ecocentric ethic can avoid these difficulties by emphasizing the (...) value of the wildness of natural systems and we defend wildness value from a rising tide of criticisms. (shrink)

With increasing appreciation that the Y2K problem may turn out to have unpredictable and potentially far-reaching effects, we are faced with what in some ways resembles the looming global ecological crisis, only this time what is at stake are not vital ecosystem services but rather the vital structures of our highly complex socially constructed reality—and this time we have a date-certain deadline for the onset of the crisis. Regardless of what actually happens when the calendar turns from 1999 to 2000, (...) this period of waiting for the millennium bug can be a productive one if it induces some of us to contemplate what things we actually depend upon to sustain our lives and, utilizing John Searle's analysis, in what ways we might reconstruct our social reality if faced with the opportunity—and why we haven't begun to do so sooner. (shrink)

With increasing appreciation that the Y2K problem may turn out to have unpredictable and potentially far-reaching effects, we are faced with what in some ways resembles the looming global ecological crisis, only this time what is at stake are not vital ecosystem services but rather the vital structures of our highly complex socially constructed reality—and this time we have a date-certain deadline for the onset of the crisis. Regardless of what actually happens when the calendar turns from 1999 to 2000, (...) this period of waiting for the millennium bug can be a productive one if it induces some of us to contemplate what things we actually depend upon to sustain our lives and, utilizing John Searle's analysis, in what ways we might reconstruct our social reality if faced with the opportunity—and why we haven't begun to do so sooner. (shrink)

Virtuous actions seem to be both habitual and rational. But if we combine an intuitive understanding of habituality with the currently predominant paradigm of rational action, these two features of virtuous actions are hard to reconcile. Intuitively, acting habitually is acting as one has before in similar contexts, and automatically, that is, without thinking about it. Meanwhile, contemporary philosophers tend to assume the truth of what I call the reasons theory of rational action, which states that all rational actions are (...) actions for reasons. Whilst interpretations of this phrase are disputed, I argue that neither of the two leading views – which I call reasons internalism and reasons externalism – makes room for habitual actions to count as actions for reasons; by the reasons theory, they cannot be rational either. I suggest one way of effecting the reconciliation which, whilst it allows us to keep the reasons theory, requires us to conceive of reasons as even more radically external than current externalists believe them to be. (shrink)

Realism concerning a given domain of things is the view that the things in that domain exist, and are as they are, quite independently of anyone.

Psychiatry is unique in medicine in being on the border between science and the humanities. Science provides insight into the 'causes' of a problem, enabling us to formulate an 'explanation', while the humanities provide insight into its 'meanings' and helps with our 'understanding'. The new interdisciplinary field of 'philosophy of psychiatry' has developed to explore the range of issues relevant to this border country. The Oxford Textbook of Philosophy and Psychiatry is a unique textbook which provides a detailed introduction to (...) the field, a framework for study and skill development, and an overview of current research. It focuses on case studies in 5 key topic areas. Each case study is supported by selected readings from both philosophy and mental health, thinking skills exercises, self-test questions, key learning points and detailed guides to further reading. (shrink)

Virtues are habits of character that advance excellence in all of ones endeavors. In the Aristotelian formulation, training in the virtuesis driven by a sense of the “good,” that is, by a widely shared agreement on the components of a good society and on the roles (and appropriate virtues or excellencies) of the “social animals” that energize that society. In the modern era, however, a strong sense of community has been much diminished. Freedom from the restraints of the Church and (...) other social institutions and an emphasis on individual autonomy has fostered a different ethical perspective, a perspective in which the market enters importantly into one’s conception of the good. Does the market generate virtues which in turn sustain it? What guides the development of virtue in market economies that are entering the “information superhighway,” and a new millennium as well? (shrink)

It is sometimes thought that the normative justification for responding to large-scale violations of human rights via the judicial appararatus of trial and punishment is undermined by the desirability of reconciliation between conflicting parties as part of the process of conflict resolution. I take there to be philosophical, as well as practical and psychological issues involved here: on some conceptions of punishment and reconciliation, the attitudes that they involve conflict with one another on rational grounds. But I shall argue that (...) there is a conception of political reconciliation available which does not involve forgiveness and this forms of reconciliation may be the best we can hope for in many conflicts. Reconciliation is nevertheless likely to require the expression of what Darrell Moellendorf has called 'political regret' and the denunciatory role aspect of punishment makes it particularly well-suited to this role. (shrink)