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)

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)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

In part one I present a positive argument for the claim that philosophical argument can rationally overturn common sense. It is widely agreed that science can overturn common sense. But every scientific argument, I argue, relies on philosophical assumptions. If the scientific argument succeeds, then its philosophical assumptions must be more worthy of belief than the common sense proposition under attack. But this means there could be a philosophical argument against common sense, each of whose premises is just as worthy (...) of belief as the scientist’s philosophical assumptions. If so, then the purely philosophical argument will also succeed. In part two I consider three motivations, each of which comprises a distinct philosophical methodology, for the opposing view: (1) the Moorean idea that common sense enjoys greater plausibility than philosophy; (2) case judgments should trump general principles; (3) reflective equilibrium and conservatism. I argue that all three motivations fail. (shrink)

Many have thought that it is impossible to rationally persuade an external world skeptic that we have knowledge of the external world. This paper aims to show how this could be done. I argue, while appealing only to premises that a skeptic could accept, that it is not rational to believe external world skepticism, because doing so commits one to more extreme forms of skepticism in a way that is self-undermining. In particular, the external world skeptic is ultimately committed to (...) believing a proposition P while believing that she shouldn’t believe P, an irrational combination of beliefs. Suspending judgment on skepticism is also problematic, for similar reasons; and, I argue, rational dilemmas are not possible; so, we should believe that skepticism is false. (shrink)

Ce texte a déjà paru dans la Revue philosophique de Louvain, 108, 2010, p. 527-548. Mon sujet sera le motif du « rythme » d'après des textes de Philippe Lacoue-Labarthe. Bien sûr, j'aurais aimé parler du rythme de Philippe Lacoue-Labarthe, du dictamen de sa phrase. Rythme admirable, oui, mais sujet pour moi intraitable dans le cadre d'un essai philosophique. Le rythme de la phrase de Lacoue-Labarthe se fait au creux d'autres rythmes et s'amplifie en chambre d'échos des voix qu'il met (...) en scène, - Philosophie – Nouvel article. (shrink)

This is a much shorter version of our entry on the Epistemology of Perception, which will be published in the Oxford Handbook for the Philosophy of Perception in 2013. The longer version has far more references in it, whereas this version is pared down to the essentials.

Schellenberg sheds light on the recent debate between Dreyfus and McDowell about the role and nature of concepts in perceptual experience, by considering the following trilemma: (C1) Non-rational animals and humans can be in mental states with the same kind of content when they are perceptually related to the very same environment. (C2) Non-rational animals do not possess concepts. (C3) Content is constituted by modes of presentations and is, thus, conceptually structured. She discusses reasons for accepting and rejecting each of (...) the three claims. By developing a substantive notion of modes of presentation as constituting nonconceptual content, she argues that the trilemma is best resolved by giving up (C3). In doing so, she discusses the nature of mental content and its relation to bodily skills and conceptual capacities as well as the notion of conceptual and nonconceptual content. (shrink)

This is a compilations of short talks presented at a workshop held at Harvard in April 14 on the life of analytic philosophy today in Spanish. Authors include Susanna Siegel, Diana Acosta and Patricia Marechal, Diana Perez, Laura Pérez, and Josefa Toribio.

This paper argues for a sufficient evidence condition on knowledge and I argue that there is no belief condition on knowledge.

Despite their importance in the history of philosophy and in particular in the work of Aristotle and Kant, mental capacities have been neglected in recent philosophical work. By contrast, the notion of a capacity is deeply entrenched in psychology and the brain sciences. Driven by the idea that a cognitive system has the capacity it does in virtue of its internal components and their organization, it is standard to appeal to capacities in cognitive psychology. The main benefit of invoking capacities (...) in an account of the mind is that it allows for an elegant counterfactual analysis of mental states: it allows us to analyze mental states on three distinct yet interrelated levels. A first level of analysis pertains to the function of mental capacities. A second level of analysis pertains to the mental capacities employed, irrespective of the context in which they are employed. A third level of analysis pertains to the mental capacities employed, taking into account the context in which they are employed. This paper develops an account of perceptual capacities. This account involves an analysis of their function, their individuation and possession conditions, the relation between perceptual capacities and their employment, as well as their informational and neural base conditions. (shrink)

Despite their importance in the history of philosophy and in particular in the work of Aristotle and Kant, mental capacities have been neglected in recent philosophical work. By contrast, the notion of a capacity is deeply entrenched in psychology and the brain sciences. Driven by the idea that a cognitive system has the capacity it does in virtue of its internal components and their organization, it is standard to appeal to capacities in cognitive psychology. The main benefit of invoking capacities (...) in an account of the mind is that it allows for an elegant counterfactual analysis of mental states: it allows us to analyze mental states on three distinct yet interrelated levels. A first level of analysis pertains to the function of mental capacities. A second level of analysis pertains to the mental capacities employed, irrespective of the context in which they are employed. A third level of analysis pertains to the mental capacities employed, taking into account the context in which they are employed. This paper develops an account of perceptual capacities. This account involves an analysis of their function, their individuation and possession conditions, the relation between perceptual capacities and their employment, as well as their informational and neural base conditions. (shrink)

This paper develops and defends the capacity view, that is, the view that the ability to perceive the perspective-independent or intrinsic properties of objects depends on the perceiver’s capacity to act. More specifically, I argue that self-location and spatial know-how are jointly necessary to perceive the intrinsic spatial properties of objects. Representing one’s location allows one to abstract from one’s particular vantage point to perceive the perspective-independent properties of objects. Spatial know-how allows one to perceive objects as the kind of (...) things that are perceivable from points of view other than one’s own and thus to perceive them as three-dimensional space occupiers. (shrink)

I argue that a Sellarsian approach to experience allows one to take seriously the thought that there is something given to us in perception without denying that we can only be conscious of conceptually structured content. I argue against the traditional empiricist reading of Sellars, according to which sensations are understood as epistemically graspable prior to concrete propositional representations, by showing that it is unclear on such a view why sensations are not just the given as Sellars so famously criticizes (...) it. I suggest an alternative transcendental reading, according to which there are two sides to the subject matter of perceptual judgments: The matter given in perception, and its form. I present an account of sensations and intuitions on which it is unproblematic to see sensations as what is given in perception: They are not intelligible independently of their role as the matter of intuitions, the content of which is accessible to us only in the context of a judgment. (shrink)

A summary of The Rationality of Perception, and my replies to symposium papers on it by Andy Clark and Christopher Peacocke.

Sometimes different partitions of the same space each seem to divide that space into propositions that call for equal epistemic treatment. Famously, equal treatment in the form of equal point-valued credence leads to incoherence. Some have argued that equal treatment in the form of equal interval-valued credence solves the puzzle. This paper shows that, once we rule out intervals with extreme endpoints, this proposal also leads to incoherence.

Philosophy and Phenomenological Research, Volume 104, Issue 2, Page 434-453, March 2022.

This paper defends a principle I call Equal Treatment, according to which the rationality of a belief is determined in precisely the same way as the rationality of any other state. For example, if wearing a raincoat is rational just in case doing so maximizes expected value, then believing some proposition P is rational just in case doing so maximizes expected value. This contrasts with the popular view that the rationality of belief is determined by evidential support. It also contrasts (...) with the common idea that in the case of belief, there are two different incommensurable senses of rationality, one of which is distinctively epistemic. I present considerations that favor Equal Treatment over these two alternatives, reply to objections, and criticize some arguments for Evidentialism. I also show how Equal Treatment opens the door to a distinctive kind of response to skepticism. (shrink)

There is a trade-off between specificity and accuracy in existing models of belief. Descriptions of agents in the tripartite model, which recognizes only three doxastic attitudes—belief, disbelief, and suspension of judgment—are typically accurate, but not sufficiently specific. The orthodox Bayesian model, which requires real-valued credences, is perfectly specific, but often inaccurate: we often lack precise credences. I argue, first, that a popular attempt to fix the Bayesian model by using sets of functions is also inaccurate, since it requires us to (...) have interval-valued credences with perfectly precise endpoints. We can see this problem as analogous to the problem of higher order vagueness. Ultimately, I argue, the only way to avoid these problems is to endorse Insurmountable Unclassifiability. This principle has some surprising and radical consequences. For example, it entails that the trade-off between accuracy and specificity is in-principle unavoidable: sometimes it is simply impossible to characterize an agent’s doxastic state in a way that is both fully accurate and maximally specific. What we can do, however, is improve on both the tripartite and existing Bayesian models. I construct a new model of belief—the minimal model—that allows us to characterize agents with much greater specificity than the tripartite model, and yet which remains, unlike existing Bayesian models, perfectly accurate. (shrink)

This paper proposes that the question “What should I believe?” is to be answered in the same way as the question “What should I do?,” a view I call Equal Treatment. After clarifying the relevant sense of “should,” I point out advantages that Equal Treatment has over both simple and subtle evidentialist alternatives, including versions that distinguish what one should believe from what one should get oneself to believe. I then discuss views on which there is a distinctively epistemic sense (...) of should. Next I reply to an objection which alleges that non-evidential considerations cannot serve as reasons for which one believes. I then situate Equal Treatment in a broader theoretical framework, discussing connections to rationality, justification, knowledge, and theoretical vs. practical reasoning. Finally, I show how Equal Treatment has important implications for a wide variety of issues, including the status of religious belief, philosophical skepticism, racial profiling and gender stereotyping, and certain issues in psychology, such as depressive realism and positive illusions. (shrink)

Some prominent evidentialists argue that practical considerations cannot be normative reasons for belief because they can’t be motivating reasons for belief. Existing pragmatist responses turn out to depend on the assumption that it’s possible to believe in the absence of evidence. The evidentialist may deny this, at which point the debate ends in an impasse. I propose a new strategy for the pragmatist. This involves conceding that belief in the absence of evidence is impossible. We then argue that evidence can (...) play a role in bringing about belief without being a motivating reason for belief, thereby leaving room for practical considerations to serve as motivating reasons. I present two ways in which this can happen. First, agents can use evidence as a mere means by which to believe, with practical considerations serving as motivating reasons for belief, just as we use tools (e.g. a brake pedal) as mere means by which to do something (e.g. slow down) which we are motivated to do for practical reasons. Second, evidence can make it possible for one to choose whether or not to believe – a choice one can then make for practical reasons. These arguments push the debate between the evidentialist and the pragmatist into new territory. It is no longer enough for an evidentialist to insist that belief is impossible without evidence. Even if this is right, the outcome of the debate remains unsettled. It will hang on the ability of the evidentialist to respond to the new pragmatist strategy presented here. (shrink)

Evidentialists and Pragmatists about reasons for belief have long been in dialectical stalemate. However, recent times have seen a new wave of Evidentialists who claim to provide arguments for their view which should be persuasive even to someone initially inclined toward Pragmatism. This paper reveals a central flaw in this New Evidentialist project: their arguments rely on overly demanding necessary conditions for a consideration to count as a genuine reason. In particular, their conditions rule out the possibility of pragmatic reasons (...) for action. Since the existence of genuine pragmatic reasons for action is common ground between the Evidentialist and the Pragmatist, this problem for the New Evidentialist arguments is fatal. The upshot is that the deadlock between these two positions is restored: neither side can claim to be in possession of an argument that could convince the other. As it happens, I myself favor Pragmatism about reasons for belief, and although I don't claim to be able to convince a committed Evidentialist, I do make a prima facie case for Pragmatism by describing particular scenarios in which it seems to be true. I then go on to develop my own preferred version of the view: Robust Pragmatism, according to which a consideration never constitutes a reason for believing a proposition purely in virtue of being evidence for it. (shrink)

A number of Bayesians claim that, if one has no evidence relevant to a proposition P, then one's credence in P should be spread over the interval [0, 1]. Against this, I argue: first, that it is inconsistent with plausible claims about comparative levels of confidence; second, that it precludes inductive learning in certain cases. Two motivations for the view are considered and rejected. A discussion of alternatives leads to the conjecture that there is an in-principle limitation on formal representations (...) of belief: they cannot be both fully accurate and maximally specific. (shrink)

The canonical Bayesian solution to the ravens paradox faces a problem: it entails that black non-ravens disconfirm the hypothesis that all ravens are black. I provide a new solution that avoids this problem. On my solution, black ravens confirm that all ravens are black, while non-black non-ravens and black non-ravens are neutral. My approach is grounded in certain relations of epistemic dependence, which, in turn, are grounded in the fact that the kind raven is more natural than the kind black. (...) The solution applies to any generalization “All F’s are G” in which F is more natural than G. (shrink)

Philosophers have predominantly regarded morality and aesthetics judgments as fundamentally different. However, whether this claim is empirically founded has remained unclear. In a novel task, we measured brain activity of participants judging the aesthetic beauty of artwork or the moral goodness of actions depicted. To control for the content of judgments, participants assessed the age of the artworks and the speed of depicted actions. Univariate analyses revealed whole-brain corrected, content-controlled common activation for aesthetics and morality judgments in frontopolar, dorsomedial and (...) ventrolateral prefrontal cortex. Temporoparietal cortex showed activation specific for morality judgments, occipital cortex for aesthetics judgments. Multivariate analyses revealed both common and distinct whole-brain corrected representations for morality and aesthetics judgments in temporoparietal and prefrontal regions. Overall, neural commonalities are more pronounced than predominant philosophical views would predict. They are compatible with minority accounts that stress commonalities between aesthetics and morality judgments, such as sentimentalism and a valuation framework. (shrink)

We describe the earliest occurrences of the Liar Paradox in the Arabic tradition. e early Mutakallimūn claim the Liar Sentence is both true and false; they also associate the Liar with problems concerning plural subjects, which is somewhat puzzling. Abharī (1200-1265) ascribes an unsatisfiable truth condition to the Liar Sentence—as he puts it, its being true is the conjunction of its being true and false—and so concludes that the sentence is not true. Tūsī (1201-1274) argues that self-referential sentences, like the (...) Liar, are not truth-apt, and defends this claim by appealing to a correspondence theory of truth. Translations of the texts are provided as an appendix. (shrink)

Includes a summary of my book *The Rationality of Perception* (Oxford, 2017) and replies to commentaries on it by Endre Begby, Harmen Ghijsen, and Katia Samoilova. These commentaries and my summary and replies will be published soon in Analysis Reviews. Begby focuses on my analysis of the epistemic features of the interface between individual minds and their cultural milieu (discussed in chapter 10 of *The Rationality of Perception*), Ghijsen focuses on the notion of inference and reliabilism (chapters 5 and 6), (...) and Samoilova focuses on the relationship between epistemic charge (chapter 3) and shifts in the amount of justification needed for knowledge. (shrink)

This paper defends an analysis of the epistemic contours of the interface between individuals and their cultural milieu.

An overview of the epistemology of perception, covering the nature of justification, immediate justification, the relationship between the metaphysics of perceptual experience and its rational role, the rational role of attention, and cognitive penetrability. The published version will contain a smaller bibliography, due to space constraints in the volume.

I discuss the roles of journalism in aspirational democracies, and argue that they generate set of pressures on attention that apply to people by virtue of the type of society they live in. These pressures, I argue, generate a problem of democratic attention: for journalism to play its roles in democracy, the attentional demands must be met, but there are numerous obstacles to meeting them. I propose a principle of salience to guide the selection and framing of news stories that (...) I argue may help address the puzzle: the public-as-protagonist principle. -/- . (shrink)

This handout contains my replies to comments on the Rationality of Perception by Jennifer Nagel, Adam Pautz, and Peter Railton from a symposium at the 2018 Eastern APA in Savannah.

Siegel and Byrne debate whether perceptual experiences present rich properties or exclusively thin properties.

Preface to The Rationality of Perception.

Entry in Routledge handbook of skill and expertise. Discusses social perception, perceptual expertise, knowing what things look like, and a bit about about aesthetics at the end.

chapter on perception and bias including implicit bias.

I argue that inference can tolerate forms of self-ignorance and that these cases of inference undermine canonical models of inference on which inferrers have to appreciate (or purport to appreciate) the support provided by the premises for the conclusion. I propose an alternative model of inference that belongs to a family of rational responses in which the subject cannot pinpoint exactly what she is responding to or why, where this kind of self-ignorance does nothing to undermine the intelligence of the (...) response. (shrink)

I argue that in Sheridan Hough's book Kierkegaard's Dancing Tax Collector, the distinctive and novelistic literary form is not a playful, whimsical, or otherwise contingent feature, but a structure that's needed to convey the account of Kierkegaardian faith as practical in nature.

I distinguish between two kinds of selection effects on experience: selection of objects or features for experience, and anti-selection of experiences for cognitive uptake. I discuss the idea that both kinds of selection effects can lead to a form of confirmation bias at the level of perception, and argue that when this happens, selection effects can influence the rational role of experience.

This paper defends the Content View: the thesis that all visual experiences have contents.