The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

An objection to shifty epistemologies such as subject-sensitive invariantism is that it predicts that agents are susceptible to guaranteed losses. Bob Beddor (Analysis, 81, 193–198, 2021) argues that these guaranteed losses are not a symptom of irrationality, on the grounds that forgetful agents are susceptible to guaranteed losses without being irrational. I agree that forgetful agents are susceptible to guaranteed losses without being irrational– but when we investigate why, the analogy with shifty epistemology breaks down. I argue that agents with (...) shifty epistemologies are susceptible to guaranteed losses in a way which is a symptom of irrationality. Along the way I make a suggestion about what it takes for an agent to be coherent over time. I close by offering a taxonomy of shifty epistemologies. (shrink)

What if your peers tell you that you should disregard your perceptions? Worse, what if your peers tell you to disregard the testimony of your peers? How should we respond if we get evidence that seems to undermine our epistemic rules? Several philosophers have argued that some epistemic rules are indefeasible. I will argue that all epistemic rules are defeasible. The result is a kind of epistemic particularism, according to which there are no simple rules connecting descriptive and normative facts. (...) I will argue that this type of particularism is more plausible in epistemology than in ethics. The result is an unwieldy and possibly infinitely long epistemic rule — an Uber-rule. I will argue that the Uber-rule applies to all agents, but is still defeasible — one may get misleading evidence against it and rationally lower one’s credence in it. (shrink)

If an agent believes that the probability of E being true is 1/2, should she accept a bet on E at even odds or better? Yes, but only given certain conditions. This paper is about what those conditions are. In particular, we think that there is a condition that has been overlooked so far in the literature. We discovered it in response to a paper by Hitchcock (2004) in which he argues for the 1/3 answer to the Sleeping Beauty problem. (...) Hitchcock argues that this credence follows from calculating her fair betting odds, plus the assumption that Sleeping Beauty’s credences should track her fair betting odds. We will show that this last assumption is false. Sleeping Beauty’s credences should not follow her fair betting odds due to a peculiar feature of her epistemic situation. (shrink)

Many who take a dismissive attitude towards metaphysics trace their view back to Carnap’s ‘Empiricism, Semantics and Ontology’. But the reason Carnap takes a dismissive attitude to metaphysics is a matter of controversy. I will argue that no reason is given in ‘Empiricism, Semantics and Ontology’, and this is because his reason for rejecting metaphysical debates was given in ‘Pseudo-Problems in Philosophy’. The argument there assumes verificationism, but I will argue that his argument survives the rejection of verificationism. The root (...) of his argument is the claim that metaphysical statements cannot be justified; the point is epistemic, not semantic. I will argue that this remains a powerful challenge to metaphysics that has yet to be adequately answered. (shrink)

Many epistemological problems can be solved by the objective Bayesian view that there are rationality constraints on priors, that is, inductive probabilities. But attempts to work out these constraints have run into such serious problems that many have rejected objective Bayesianism altogether. I argue that the epistemologist should borrow the metaphysician’s concept of naturalness and assign higher priors to more natural hypotheses.

Should philosophers prefer simpler theories? Huemer (Philos Q 59:216–236, 2009) argues that the reasons to prefer simpler theories in science do not apply in philosophy. I will argue that Huemer is mistaken—the arguments he marshals for preferring simpler theories in science can also be applied in philosophy. Like Huemer, I will focus on the philosophy of mind and the nominalism/Platonism debate. But I want to engage with the broader issue of whether simplicity is relevant to philosophy.

What does logic tells us how about we ought to reason? If P entails Q, and I believe P, should I believe Q? I will argue that we should embed the issue in an independently motivated contextualist semantics for ‘ought’, with parameters for a standard and set of propositions. With the contextualist machinery in hand, we can defend a strong principle expressing how agents ought to reason while accommodating conflicting intuitions. I then show how our judgments about blame and guidance (...) can be handled by this machinery. (shrink)

How should our beliefs change over time? Much has been written about how our beliefs should change in the light of new evidence. But that is not the question I’m asking. Sometimes our beliefs change without new evidence. I previously believed it was Sunday. I now believe it’s Monday. In this paper I discuss the implications of such beliefs for philosophy of language. I will argue that we need to allow for ‘dynamic’ beliefs, that we need new norms of belief (...) change to model how they function, and that this gives Perry’s (1977) two tier account the advantage over Lewis’s (1979) theory -/- . (shrink)

How do temporal and eternal beliefs interact? I argue that acquiring a temporal belief should have no effect on eternal beliefs for an important range of cases. Thus, I oppose the popular view that new norms of belief change must be introduced for cases where the only change is the passing of time. I defend this position from the purported counter-examples of the Prisoner and Sleeping Beauty. I distinguish two importantly different ways in which temporal beliefs can be acquired and (...) draw some general conclusions about their impact on eternal beliefs. (shrink)

An attractive picture of the world is that some features are metaphysically fundamental and others are derivative, with the derivative features grounded in the fundamental features. But how do we have justified beliefs about which features are fundamental? What is the epistemology of fundamentality? I sketch a response in this paper. The guiding idea is that the same properties cause the same experiences. I argue that a probabilistic connection between epistemic fundamentality and metaphysical fundamentality is sufficient for justified beliefs about (...) the metaphysically fundamental. (shrink)

Sometimes we learn what the world is like, and sometimes we learn where in the world we are. Are there any interesting differences between the two kinds of cases? The main aim of this article is to argue that learning where we are in the world brings into view the same kind of observation selection effects that operate when sampling from a population. I will first explain what observation selection effects are ( Section 1 ) and how they are relevant (...) to learning where we are in the world ( Section 2 ). I will show how measurements in the Many Worlds Interpretation of quantum mechanics can be understood as learning where you are in the world via some observation selection effect ( Section 3 ). I will apply a similar argument to the Sleeping Beauty Problem ( Section 4 ) and explain what I take the significance of the analogy to be ( Section 5 ). Finally, I will defend the Restricted Principle of Indifference on which some of my arguments depend ( Section 6 ). (shrink)

Self-locating beliefs cause a problem for conditionalization. Miriam Schoenfield offers a solution: that on learning E, agents should update on the fact that they learned E. However, Schoenfield is not explicit about whether the fact that they learned E is self-locating. I will argue that if the fact that they learned E is self-locating then the original problem has not been addressed, and if the fact that they learned E is not self-locating then the theory generates implausible verdicts which Schoenfield (...) explicitly rejects. (shrink)

There is a widely shared belief that the higher-level sciences can provide better explanations than lower-level sciences. But there is little agreement about exactly why this is so. It is often suggested that higher-level explanations are better because they omit details. I will argue instead that the preference for higher-level explanations is just a special case of our general preference for informative, logically strong, beliefs. I argue that our preference for informative beliefs entirely accounts for why higher-level explanations are sometimes (...) better—and sometimes worse—than lower-level explanations. The result is a step in the direction of the unity of science hypothesis. 1Introduction2Background: Is Omitting Details an Explanatory Virtue? 2.1Anti-reductionist arguments2.2Reductionist argument2.3Logical strength3Bases, Links and Logical Strength4Functionalism and Fodor’s Argument5Two Generalizations6Should the Base Really Be Maximally Strong?7Anti-reductionist Arguments Regarding the Base8Should the Antecedent of the Link Really Be Maximally Weak? (shrink)

The fine-tuning argument can be used to support the Many Universe hypothesis. The Inverse Gambler’s Fallacy objection seeks to undercut the support for the Many Universe hypothesis. The objection is that although the evidence that there is life somewhere confirms Many Universes, the specific evidence that there is life in this universe does not. I will argue that the Inverse Gambler’s Fallacy is not committed by the fine-tuning argument. The key issue is the procedure by which the universe with life (...) is selected for observation. Once we take account of the procedure, we find that the support for the Many Universe hypothesis remains. (shrink)

There is a divide in epistemology between those who think that, for any hypothesis and set of total evidence, there is a unique rational credence in that hypothesis, and those who think that there can be many rational credences. Schultheis offers a novel and potentially devastating objection to Permissivism, on the grounds that Permissivism permits dominated credences. I will argue that Permissivists can plausibly block Schultheis' argument. The issue turns on getting clear about whether we should be certain whether our (...) credences are rational. (shrink)

This article defends the Doomsday Argument, the Halfer Position in Sleeping Beauty, the Fine-Tuning Argument, and the applicability of Bayesian confirmation theory to the Everett interpretation of quantum mechanics. It will argue that all four problems have the same structure, and it gives a unified treatment that uses simple models of the cases and no controversial assumptions about confirmation or self-locating evidence. The article will argue that the troublesome feature of all these cases is not self-location but selection effects.

An important line of response to scepticism appeals to the best explanation. But anti-sceptics have not engaged much with work on explanation in the philosophy of science. I plan to investigate whether plausible assumptions about best explanations really do favour anti-scepticism. I will argue that there are ways of constructing sceptical hypotheses in which the assumptions do favour anti-scepticism, but the size of the support for anti-scepticism is small.

The main argument given for relevant alternatives theories of knowledge has been that they answer scepticism about the external world. I will argue that relevant alternatives also solve two other problems that have been much discussed in recent years, a) the bootstrapping problem and b) the apparent conflict between semantic externalism and armchair self-knowledge. Furthermore, I will argue that scepticism and Mooreanism can be embedded within the relevant alternatives framework.

A discussion of a number of ways that information can be present in a computer program without being explicitly represented.

Cian Dorr (2002) gives an argument for the 1/3 position in Sleeping Beauty. I argue this is based on a mistake about Sleeping Beauty's epistemic position.

The independence problems for functionalism stem from the worry that if functional properties are defined in terms of their causes and effects then such functional properties seem to be too intimately connected to these purported causes and effects. I distinguish three different ways the independence problems can be filled out – in terms of necessary connections, analytic connections and vacuous explanations. I argue that none of these present serious problems. Instead, they bring out some important and over-looked features of functionalism.

What sort of logic do we get if we adopt a supervaluational semantics for vagueness? As it turns out, the answer depends crucially on how the standard notion of validity as truth preservation is recasted. There are several ways of doing that within a supervaluational framework, the main alternative being between “global” construals (e.g., an argument is valid iff it preserves truth-under-all-precisifications) and “local” construals (an argument is valid iff, under all precisifications, it preserves truth). The former alternative is by (...) far more popular, but I argue in favor of the latter, for (i) it does not suffer from a number of serious objections, and (ii) it makes it possible to restore global validity as a defined notion. (shrink)

We can see mereology as a theory of parthood and topology as a theory of wholeness. How can these be combined to obtain a unified theory of parts and wholes? This paper examines various non-equivalent ways of pursuing this task, with specific reference to its relevance to spatio-temporal reasoning. In particular, three main strategies are compared: (i) mereology and topology as two independent (though mutually related) chapters; (ii) mereology as a general theory subsuming topology; (iii) topology as a general theory (...) subsuming mereology. Some more speculative strategies and directions for further research are also considered. (shrink)

I focus on three mereological principles: the Extensionality of Parthood (EP), the Uniqueness of Composition (UC), and the Extensionality of Composition (EC). These principles are not equivalent. Nonetheless, they are closely related (and often equated) as they all reflect the basic nominalistic dictum, No difference without a difference maker. And each one of them—individually or collectively—has been challenged on philosophical grounds. In the first part I argue that such challenges do not quite threaten EP insofar as they are either self-defeating (...) or unsupported. In the second part I argue that they hardly undermine the tenability of EC and UC as well. (shrink)

We discuss at some length evidence from the cognitive science suggesting that the representations of objects based on spatiotemporal information and featural information retrieved bottomup from a visual scene precede representations of objects that include conceptual information. We argue that a distinction can be drawn between representations with conceptual and nonconceptual content. The distinction is based on perceptual mechanisms that retrieve information in conceptually unmediated ways. The representational contents of the states induced by these mechanisms that are available to a (...) type of awareness called phenomenal awareness constitute the phenomenal content of experience. The phenomenal content of perception contains the existence of objects as separate things that persist in time and time, spatiotemporal information, and information regarding relative spatial relations, motion, surface properties, shape, size, orientation, color, and their functional properties. (shrink)

Sober and Elgin defend the claim that there are a priori causal laws in biology. Lange and Rosenberg take issue with this on Humean grounds, among others. I will argue that Sober and Elgin don’t go far enough – there are a priori causal laws in many sciences. Furthermore, I will argue that this thesis is compatible with a Humean metaphysics and an empiricist epistemology.

There are conflicting intuitions concerning the status of a boundary separating two adjacent entities (or two parts of the same entity). The boundary cannot belong to both things, for adjacency excludes overlap; and it cannot belong to neither, for nothing lies between two adjacent things. Yet how can the dilemma be avoided without assigning the boundary to one thing or the other at random? Some philosophers regard this as a reductio of the very notion of a boundary, which should accordingly (...) be treated a mere façon de parler. In this paper I resist this temptation and examine some ways of taking the puzzle at face value within a realist perspective—treating boundaries as ontologically on a par with (albeit parasitic upon) extended parts. (shrink)

It is widely believed that deflationary truth has no explanatory power. I will argue that it does. Specifically, I will consider some objections to deflationary truth having explanatory power, and argue that they fail. The position which will emerge is that the deflationary concept of truth is analogous to the concept of an average. Scientists take averages to be explanatory, and I will argue that the concept of deflationary truth is explanatory in the same way. I then argue that this (...) deflationary _concept_ of truth motivates a theory of the _property_ of truth which is metaphysically disunified, but that this is no obstacle to explanation. This leads to a way of understanding the deflationary/substantive distinction in terms of grounding. (shrink)

We give an analysis of the Monty Hall problem purely in terms of confirmation, without making any lottery assumptions about priors. Along the way, we show the Monty Hall problem is structurally identical to the Doomsday Argument.

Some have argued that the vagueness exhibited by geographic names and descriptions such as ‘Albuquerque’, ‘the Outback’, or ‘Mount Everest’ is ultimately ontological: these terms are vague because they refer to vague objects, objects with fuzzy boundaries. I take the opposite stand and hold the view that geographic vagueness is exclusively semantic, or conceptual at large. There is no such thing as a vague mountain. Rather, there are many things where we conceive a mountain to be, each with its precise (...) boundary, and when we say ‘Everest’ we are just being vague as to which thing we are referring to. This paper defends this view against some plausible objections. (shrink)

In her 2004 book Carol Gould addresses the fundamental issue of democratizing globalization, that is to say of finding ways to open transnational institutions and communities to democratic participation by those widely affected by their decisions. The book develops a framework for expanding participation in crossborder decisions, arguing for a broader understanding of human rights and introducing a new role for the ideas of care and solidarity at a distance. Reinterpreting the idea of universality to accommodate a multiplicity of cultural (...) perspectives, the author takes up a number of applied issues, including the persistence of racism, cultural rights, women's human rights, the democratic management of firms, the use of the Internet to enhance political participation, and the importance of empathy and genuine democracy in understanding terrorism and responding to it. Accessibly written with a minimum of technical jargon this is a major contribution to political philosophy. (shrink)

In Bradley, I offered an analysis of Sleeping Beauty and the Everettian interpretation of quantum mechanics. I argued that one can avoid a kind of easy confirmation of EQM by paying attention to observation selection effects, that halfers are right about Sleeping Beauty, and that thirders cannot avoid easy confirmation for the truth of EQM. Wilson agrees with my analysis of observation selection effects in EQM, but goes on to, first, defend Elga’s thirder argument on Sleeping Beauty and, second, argue (...) that the analogy I draw between Sleeping Beauty and EQM fails. I will argue that neither point succeeds. 1 Introduction2 Background3 Wilson’s Argument for ⅓ in Sleeping Beauty4 Reply: Explaining Away the Crazy5 Wilson's Argument for the Breakdown of the Analogy6 Reply: The Irrelevance of Chance7 Conclusion. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

This book aims to develop certain aspects of Gottlob Frege’s theory of meaning, especially those relevant to intensional logic. It offers a new interpretation of the nature of senses, and attempts to devise a logical calculus for the theory of sense and reference that captures as closely as possible the views of the historical Frege. (The approach is contrasted with the less historically-minded Logic of Sense and Denotation of Alonzo Church.) Comparisons of Frege’s theory with those of Russell and others (...) are given. It is in the end shown that developing Frege’s theory in these ways reveals serious problems hitherto largely unnoticed, including those possibly rendering a Fregean intensional logic inconsistent even if his naïve class theory is excluded. (shrink)

In previous work I have argued that talk about negative events should not be taken at face value: typically, what we are inclined to think of as a negative event (John’s failure to go jogging) is just an ordinary, positive event (his going to the movie instead); it is a positive event under a negative description. Here I consider more closely the difficulties that arise in those cases where no positive event seems available to do the job, as with putative (...) cases of causation by omission. In particular, I elaborate on Helen Beebee’s idea that not all causal explanations are reports of causation. When we mention John’s failure to turn off the gas as an explanans of why there was an explosion, we do not say what caused the explosion. We do not mention any of the relevant causes. We just remark that one sort of event that was supposed to occur, and whose occurrence would have prevented the explosion, did not in fact occur. (shrink)

That parthood is a transitive relation is among the most basic principles of classical mereology. Alas, it is also very controversial. In a recent paper, Ingvar Johansson has put forward a novel diagnosis of the problem, along with a corresponding solution. The diagnosis is on the right track, I argue, but the solution is misleading. And once the pieces are properly put together, we end up with a reinforcement of the standard defense of transitivity on behalf of classical mereology.

Are there any bona fide boundaries, i.e., boundaries that carve at the joints? Or is any boundary —hence any object—the result of a fiat articulation reflecting our cognitive biases and our so-cial practices and conventions? Does the choice between these two options amount to a choice between realism and wholesome relativism?

Leuridan (2011) questions whether mechanisms can really replace laws at the heart of our thinking about science. In doing so, he enters a long-standing discussion about the relationship between the mech-anistic structures evident in the theories of contemporary biology and the laws of nature privileged especially in traditional empiricist traditions of the philosophy of science (see e.g. Wimsatt 1974; Bechtel and Abrahamsen 2005; Bogen 2005; Darden 2006; Glennan 1996; MDC 2000; Schaffner 1993; Tabery 2003; Weber 2005). In our view, Leuridan (...) misconstrues this discussion. His weak positive claim that mechanistic sciences appeal to generalizations is true but uninteresting. His stronger claim, that all causal claims require laws, is unsupported by his arguments. Though we proceed by criticizing Leuridan’s arguments, our greater purpose is to embellish his arguments in order to show how thinking about mechanisms enriches and transforms old philosophical debates about laws in biology and provides new insights into how generalizations afford prediction, explanation and control. (shrink)

Cognitive penetration of perception is the idea that what we see is influenced by such states as beliefs, expectations, and so on. A perceptual belief that results from cognitive penetration may be less justified than a nonpenetrated one. Inferentialism is a kind of internalist view that tries to account for this by claiming that some experiences are epistemically evaluable, on the basis of why the perceiver has that experience, and the familiar canons of good inference provide the appropriate standards by (...) which experiences are evaluated. I examine recent defenses of inferentialism by Susanna Siegel, Peter Markie, and Matthew McGrath and argue that the prospects for inferentialism are dim. (shrink)

I argue that Universalism (the thesis that mereological composition is unrestricted) entails Extensionalism (the thesis that sameness of composition is sufficient for identity) as long as the parthood relation is transitive and satisfies the Weak Supplementation principle (to the effect that whenever a thing has a proper part, it has another part disjoint from the first).

In this paper I argue that whether or not a computer can be built that passes the Turing test is a central question in the philosophy of mind. Then I show that the possibility of building such a computer depends on open questions in the philosophy of computer science: the physical Church-Turing thesis and the extended Church-Turing thesis. I use the link between the issues identified in philosophy of mind and philosophy of computer science to respond to a prominent argument (...) against the possibility of building a machine that passes the Turing test. Finally, I respond to objections against the proposed link between questions in the philosophy of mind and philosophy of computer science. (shrink)

Cognitive agents, whether human or computer, that engage in natural-language discourse and that have beliefs about the beliefs of other cognitive agents must be able to represent objects the way they believe them to be and the way they believe others believe them to be. They must be able to represent other cognitive agents both as objects of beliefs and as agents of beliefs. They must be able to represent their own beliefs, and they must be able to represent beliefs (...) as objects of beliefs. These requirements raise questions about the number of tokens of the belief representation language needed to represent believers and propositions in their normal roles and in their roles as objects of beliefs. In this paper, we explicate the relations among nodes, mental tokens, concepts, actual objects, concepts in the belief spaces of an agent and the agent's model of other agents, concepts of other cognitive agents, and propositions. We extend, deepen, and clarify our theory of intensional knowledge representation for natural-language processing, as presented in previous papers and in light of objections raised by others. The essential claim is that tokens in a knowledge-representation system represent only intensions and not extensions. We are pursuing this investigation by building CASSIE, a computer model of a cognitive agent and, to the extent she works, a cognitive agent herself. CASSIE's mind is implemented in the SNePS knowledge-representation and reasoning system. (shrink)

A lot of work in metaphysics relies on linguistic analysis and intuitions. Do we want to know what sort of things there are or could be? Then let’s see what sort of things there must be in order for what we truthfully say to be true. Do we want to see whether x is distinct from y? Then let’s see whether there is any statement that is true of x but not of y. And so on. In this paper I (...) argue that this way of proceeding is full of traps and is bound to be pretty useless unless we already have a good idea of what sort of things there are, and of how we are going to count them. (shrink)

Peter Simons has argued that the expression ‘the universe’ is not a genuine singular term: it can name neither a single, completely encompassing individual, nor a collection of individuals. (It is, rather, a semantically plural term standing equally for every existing object.) I offer reasons for resisting Simons’s arguments on both scores.

Colin Howson (1995 ) offers a counter-example to the rule of conditionalization. I will argue that the counter-example doesn't hit its target. The problem is that Howson mis-describes the total evidence the agent has. In particular, Howson overlooks how the restriction that the agent learn 'E and nothing else' interacts with the de se evidence 'I have learnt E'.