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)

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.

This is a review of Susanna Siegel's The Rationality of Perception.

In this chapter I introduce the thesis that perceptual appearances are cognitively penetrable and analyse cases made against phenomenal conservatism hinging on this thesis. In particular, I focus on objections coming from the externalist reliabilist camp and the internalist inferentialist camp. I conclude that cognitive penetrability doesn’t yield lethal or substantive difficulties for phenomenal conservatism.

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.

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)

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

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 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)

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)

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.

Is perception cognitively penetrable, and what are the epistemological consequences if it is? I address the latter of these two questions, partly by reference to recent work by Athanassios Raftopoulos and Susanna Seigel. Against the usual, circularity, readings of cognitive penetrability, I argue that cognitive penetration can be epistemically virtuous, when---and only when---it increases the reliability of perception.

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)

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.

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)

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.

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

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

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)

When we perceive an object, we perceive the object from a perspective. As a consequence of the perspectival nature of perception, when we perceive, say, a circular coin from different angles, there is a respect in which the coin looks circular throughout, but also a respect in which the coin's appearance changes. More generally, perception of shape and size properties has both a constant aspect—an aspect that remains stable across changes in perspective—and a perspectival aspect—an aspect that changes depending on (...) one's perspective on the object. How should we account for the perspectival aspect of spatial perception? We present a framework within which to discuss the perspectival aspect of perception and put forward three desiderata that any account of the perspectival aspect of perception should satisfy. We discuss views on which the perspectival aspect of perception is analyzed in terms of constitutively mind-dependent appearance properties as well as views on which the perspectival aspect of perception is analyzed in terms of representations of mind-independent perspectival properties. (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)

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 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)

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)

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)

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)

Tim Bayne and Susanna Siegel have recently offered interesting arguments in favor of the view that we can experience high-level properties like being a pine tree or being a stethoscope (Bayne 2009, Siegel 2006, 2011). We argue first that Bayne’s simpler argument fails. However, our main aim in this paper is to show that Siegel’s more sophisticated argument for her version of the high-level view can also be resisted if one adopts a view that distinguishes between perceptual experiences and seemings.

Commentary on Andy Clark's target article on predictive coding.

My contribution to the first round of a tetralog with Bill Brewer, Anil Gupta, and John McDowell. Each of us has written a response to the writings of the other three philosophers on the topic "Empirical Reason". My initial contribution focuses on what we know a priori about perception. In the second round, we will each respond to the each writer's first-round contributions.

Do we (sometimes) perceive apples as edible? One could argue that it is just a manner of speaking to say so: we do not really see an object as edible, we see it as having certain shape, size and color and we only infer on the basis of these properties that it is. I argue that we do indeed see objects as edible, and do not just believe that they are. My argument proceeds in two steps. First, I point out (...) that Susanna Siegel's influential argument in favor of the claim that we represent sortal properties perceptually does not work. Second, I argue that we can fix this argument if we replace the sortal property in question with the property of being edible, climbable or Q-able in general. (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 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)

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)

Entry for forthcoming handbook of skill and expertise. Discusses social perception, perceptual expertise, knowing what things look like, and a bit about about asethetics at the end.

Draft of a chapter on perception and bias including implicit bias.

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

Imaginative immersion refers to a phenomenon in which one loses oneself in make-believe. Susanna Schellenberg says that the best explanation of imaginative immersion involves a radical revision to cognitive architecture. Instead of there being an attitude of belief and a distinct attitude of imagination, there should only be one attitude that represents a continuum between belief and imagination. -/- We argue otherwise. Although imaginative immersion is a crucial data point for theorizing about the imagination, positing a continuum between belief and (...) imagination is neither necessary nor sufficient for explaining the phenomenon. In addition, arguing against Schellenberg’s account reveals important but underappreciated lessons for theorizing about the imagination and for interpreting boxological representations of the mind. (shrink)

This chapter critically assesses recent arguments that acquiring the ability to categorize an object as belonging to a certain high-level kind can cause the relevant kind property to be represented in visual phenomenal content. The first two arguments, developed respectively by Susanna Siegel (2010) and Tim Bayne (2009), employ an essentially phenomenological methodology. The third argument, developed by William Fish (2013), by contrast, is supported by an array of psychophysical and neuroscientific findings. I argue that while none of these arguments (...) ultimately proves successful, there is a substantial body of empirical evidence that information originating outside the visual system can nonetheless modulate the way an object’s low-level attributes visually appear. Visual phenomenal content, I show, is not only significantly influenced by crossmodal interactions between vision and other exteroceptive senses such as touch and audition, but also by interactions between vision and non-perceptual systems involved in motor planning and construction of the proprioceptive body-image. (shrink)