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)

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)

My replies to Errol Lord, Adam Pautz, and Peter Railton's commentaries on The Rationality of Perception (2017).

In this paper I argue that it's possible that the contents of some visual experiences are influenced by the subject's prior beliefs, hopes, suspicions, desires, fears or other mental states, and that this possibility places constraints on the theory of perceptual justification that 'dogmatism' or 'phenomenal conservativism' cannot respect.

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)

Recently, the thesis that experience is fundamentally a matter of representing the world as being a certain way has been questioned by austere relationalists. I defend this thesis by developing a view of perceptual content that avoids their objections. I will argue that on a relational understanding of perceptual content, the fundamental insights of austere relationalism do not compete with perceptual experience being representational. As it will show that most objections to the thesis that experience has content apply only to (...) accounts of perceptual content on which perceptual relations to the world play no explanatory role. With austere relationalists, I will argue that perceptual experience is fundamentally relational. But against austere relationalists, I will argue that it is fundamentally both relational and representational. (shrink)

I argue that any account of perceptual experience should satisfy the following two desiderata. First, it should account for the particularity of perceptual experience, that is, it should account for the mind-independent object of an experience making a difference to individuating the experience. Second, it should explain the possibility that perceptual relations to distinct environments could yield subjectively indistinguishable experiences. Relational views of perceptual experience can easily satisfy the first but not the second desideratum. Representational views can easily satisfy the (...) second but not the first desideratum. I argue that to satisfy both desiderata perceptual experience is best conceived of as fundamentally both relational and representational. I develop a view of perceptual experience that synthesizes the virtues of relationalism and representationalism, by arguing that perceptual content is constituted by potentially gappy de re modes of presentation. (shrink)

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

I am deeply indebted to Alex Byrne, Jonathan Cohen and Matthew McGrath for their careful, constructive, and penetrating comments on The Unity of Perception and I am grateful for the opportunity to clarify my view further.

Al-Taftāzānī introduces the Liar Paradox, in a commentary on al-Rāzī, in a short passage that is part of a polemic against the ethical rationalism of the Muʿtazila. In this essay, we consider his remarks and their place in the history of the Liar Paradox in Arabic Logic. In the passage, al-Taftāzānī introduces Liar Cycles into the tradition, gives the paradox a puzzling name—the fallacy of the “irrational root” —which became standard, and suggests a connection between the paradox and what it (...) tells us about truth and falsehood, and arguments for divine voluntarism and what they tell us about the nature of goodness and badness. On this last point, we also discuss a passage from al-Rāzī, which suggests similar connections. (shrink)

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

Perception grounds demonstrative reference, yields singular thoughts, and fixes the reference of singular terms. Moreover, perception provides us with knowledge of particulars in our environment and justifies singular thoughts about particulars. How does perception play these cognitive and epistemic roles in our lives? I address this question by exploring the fundamental nature of perceptual experience. I argue that perceptual states are constituted by particulars and discuss epistemic, ontological, psychologistic, and semantic approaches to account for perceptual particularity.

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)

I argue that perception is necessarily situation-dependent. The way an object is must not just be distinguished from the way it appears and the way it is represented, but also from the way it is presented given the situational features. First, I argue that the way an object is presented is best understood in terms of external, mind-independent, but situation-dependent properties of objects. Situation-dependent properties are exclusively sensitive to and ontologically dependent on the intrinsic properties of objects, such as their (...) shape, size, and color, and the situational features, such as the lighting conditions and the perceiver’s location in relation to the perceived object. Second, I argue that perceiving intrinsic properties is epistemically dependent on representing situation-dependent properties. Recognizing situation-dependent properties yields four advantages. It makes it possible to embrace the motivations that lead to phenomenalism and indirect realism by recognizing that objects are presented a certain way, while holding on to the intuition that subjects directly perceive objects. Second, it acknowledges that perceptions are not just individuated by the objects they are of, but by the ways those objects are presented given the situational features. Third, it allows for a way to accommodate the fact that there is a wide range of viewing conditions or situational features that can count as normal. Finally, it makes it possible to distinguish perception and thought about the same object with regard to what is represented. (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)

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

Perceptions guide our actions and provide us with evidence of the world around us. Illusions and hallucinations can mislead us: they may prompt as to act in ways that do not mesh with the world around us and they may lead us to form false beliefs about that world. The capacity view provides an account of evidence that does justice to these two facts. It shows in virtue of what illusions and hallucinations mislead us and prompt us to act. Moreover, (...) it shows in virtue of what we are in a better epistemic position when we perceive than when we hallucination. In this paper, I develop the capacity view, that is, the view that perceptual experience has epistemic force in virtue of the epistemic and metaphysical primacy of the perceptual capacities employed in perception. By grounding the epistemic force of experience in facts about the metaphysical structure of experience, the capacity view is not only an externalist view, but moreover a naturalistic view of the epistemology of perceptual experience. So it is an externalist and naturalistic alternative to reliabilism. I discuss the repercussions of this view for the justification of beliefs and the epistemic transparency of mental states, as well as, familiar problem cases. (shrink)

I develop a view of the common factor between subjectively indistinguishable perceptions and hallucinations that avoids analyzing experiences as involving awareness relations to abstract entities, sense-data, or any other peculiar entities. The main thesis is that hallucinating subjects employ concepts (or analogous nonconceptual structures), namely the very same concepts that in a subjectively indistinguishable perception are employed as a consequence of being related to external, mind-independent objects or property-instances. These concepts and nonconceptual structures are identified with modes of presentation types. (...) Since a hallucinating subject is not related to any such objects or property-instances, the concepts she employs remain empty. I argue that the phenomenology of hallucinations and perceptions can be identified with employing concepts and analogous nonconceptual structures. By doing so, I defend an ontologically minimalist view of the phenomenology of experience that (1) vindicates Aristotelianism about types and (2) amounts to a naturalized view of the phenomenology of experience. (shrink)

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.

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)

There are powerful reasons to think of perceptual content as determined at least in part by the environment of the perceiving subject. Externalist views such as this are often rejected on grounds that they do not give a good account of hallucinations. The chapter shows that this reason for rejecting content externalism is not well founded if we embrace a moderate externalism about content, that is, an externalist view on which content is only in part dependent on the experiencing subject“s (...) environment. The chapter starts by motivating content externalism. It then argues that hallucinations are best understood in terms of a deficiency of veridical perceptual experiences. The chapter discusses the consequences of this thesis by developing a view of hallucinations that is committed to externalism about content. (shrink)

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.

In this paper I offer a theory of what makes certain influences on visual experiences by prior mental states (including desires, beliefs, moods, and fears) reduce the justificatory force of those experiences. The main idea is that experiences, like beliefs, can have rationally assessable etiologies, and when those etiologies are irrational, the experiences are epistemically downgraded.

Can perceptual experiences be states of uncertainty? We might expect them to be, if the perceptual processes from which they're generated, as well as the behaviors they help produce, take account of probabilistic information. Yet it has long been presumed that perceptual experiences purport to tell us about our environment, without hedging or qualifying. Against this long-standing view, I argue that perceptual experiences may well occasionally be states of uncertainty, but that they are never probabilistically structured. I criticize a powerful (...) line of reasoning that we should expect perceptual experience to be probabilistic, given their interfaces with unconscious probabilistic information, with behavior responsive to it, and with credences. (shrink)

I offer an explanation of how subjects are able to perceive the intrinsic spatial properties of objects, given that subjects always perceive from a particular location. The argument proceeds in two steps. First, I argue that a conception of space is necessary to perceive the intrinsic spatial properties of objects. This conception of space is spelled out by showing that perceiving intrinsic properties requires perceiving objects as the kind of things that are perceivable from other locations. Second, I show that (...) having such a conception of space presupposes that a subject represent her location in relation to perceived objects. More precisely the thesis is that a subject represents her location as the location from which she both perceives objects and would act in relation to objects were she to act. So I argue that perception depends on the capacity to know what it would be to act in relation to objects. (shrink)

I argue that any account of imagination should satisfy the following three desiderata. First, imaginations induce actions only in conjunction with beliefs about the environment of the imagining subject. Second, there is a continuum between imaginations and beliefs. Recognizing this continuum is crucial to explain the phenomenon of imaginative immersion. Third, the mental states that relate to imaginations in the way that desires relate to beliefs are a special kind of desire, namely desires to make true in fiction. These desires (...) to make true in fiction do not differ from regular desires in kind, but only in content. I argue for these three desiderata in turn by critically discussing several recent accounts of imagination. (shrink)

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)

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

I argue that perceptual experience provides us with both phenomenal and factive evidence. To a first approximation, we can understand phenomenal evidence as determined by how our environment sensorily seems to us when we are experiencing. To a first approximation, we can understand factive evidence as necessarily determined by the environment to which we are perceptually related such that the evidence is guaranteed to be an accurate guide to the environment. I argue that the rational source of both phenomenal and (...) factive evidence lies in employing perceptual capacities that we have in virtue of being perceivers. In showing that both kinds of evidence have the same rational source, I provide a unified account of perceptual evidence and its rational source in perceptual experience. (shrink)

chapter on perception and bias including implicit bias.

This paper defends and develops the capacity view against insightful critiques from Matt McGrath, Adam Pautz, and Ram Neta. In response to Matt McGrath, I show why capacities are essential and cannot simply be replaced with representational content. I argue moreover, that the asymmetry between the employment of perceptual capacities in the good and the bad case is sufficient to account for the epistemic force of perceptual states yielded by the employment of such capacities. In response to Adam Pautz, I (...) show why a perceiver’s belief is better justified than the belief of someone who suffers a subjectively indistinguishable hallucination. I show, moreover, why the capacity view is compatible with standard Bayesian principles and how it accounts for degrees of justification. In response to Ram Neta, I discuss the relationship between evidence and rational confidence, as well as the notion of evidence in light of an externalism about perceptual content. (shrink)

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.

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)

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)

This paper makes the case that when wishful thinking ill-founds belief, the belief depends on the desire in ways can be recapitulated at the level of perceptual experience. The relevant kinds of desires include motivations, hopes, preferences, and goals. I distinguish between two modes of dependence of belief on desire in wishful thinking: selective or inquiry-related, and responsive or evidence-related. I offers a theory of basing on which beliefs are badly-based on desires, due to patterns of dependence that can found (...) in the relationship between experiences and desires as well. This conclusion brings us a large part of the way to the conclusion that like beliefs, experiences can be ill-founded by depending on a desire. (shrink)

The Unity of Perception: Content, Consciousness and Evidence By SchellenbergSusannaOxford University Press, 2018. 272 pp.

Inquiry is guided, in the minimal sense that it is not haphazard. It is also often thought to have as a natural stopping point ceasing to inquire, once inquiry into a question yields knowledge of an answer. On this picture, inquiry is both telic and guided. By contrast, mind-wandering is unguided and atelic, according to the most extensively developed philosophical theory of it. This paper articulates a puzzle that arises from this combination of claims: there seem to be plenty of (...) examples of inquiry progressing within mind-wandering, yet theories of inquiry and mind-wandering can make wandering inquiry seem impossible or incoherent. I offer several solutions to this puzzle and make the case that taken together, they illuminate a prevalent form of inquiry that the burgeoning literature on that topic overlooks: inquiry that progresses spontaneously. (shrink)

What is the metaphysical nature of perceptual experience? What evidence does experience provide us with? These questions are typically addressed in isolation. In order to make progress in answering both questions, perceptual experience needs to be studied in an integrated manner. I develop a unified account of the phenomenological and epistemological role of perceptual experience, by arguing that sensory states provide perceptual evidence due to their metaphysical structure. More specifically, I argue that sensory states are individuated by the perceptual capacities (...) employed and that there is an asymmetric dependence between their employment in perception and their employment in hallucination and illusion. Due to this asymmetric dependence, sensory states provide us with evidence. (shrink)

I give some reasons to think that perceptual experiences redound on the rational standing of the subject, and explore the consequences of this idea for the global structure of justification.

Written for newcomers to philosophy, especally experimental scientists and people in the literary humanities. I focus on the role of fiction and fictional examples in the philosophy of mind, and highlight three roles for invented situations: posing a loaded question (think of Frank Jackson’s Mary), illustrating a philosphical problem, and testing normative and modal hypotheses.

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)