Truth by convention, once thought to be the foundation of a uniquely promising approach to explaining our access to the truth in nonempirical domains, is nowadays widely considered an absurdity. Its fall from grace has been due largely to the influence of an argument that can be sketched as follows: our linguistic conventions have the power to make it the case that a sentence expresses a particular proposition, but they can’t by themselves generate truth; whether a given proposition is true—and (...) so whether the sentence that expresses it is true—is a matter of what the world is like, which means it isn’t a matter of convention alone. The consensus is that this argument is decisive against truth by convention. Strikingly, though, it has rarely been formulated with much precision. Here I provide a new rendering of the argument, one that reveals its structure and makes transparent just what assumptions it requires, and then I assess conventionalists’ prospects for resisting each of those assumptions. I conclude that the consensus is mistaken: contrary to what is almost universally thought, there remains a promising way forward for the conventionalist project. Along the way, I clarify conventionalists’ commitments by thinking about what truth by convention would need to be like in order for conventionalism to do the epistemological work it’s intended to do. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

One recent topic of debate in Bayesian epistemology has been the question of whether imprecise credences can be rational. I argue that one account of imprecise credences, the orthodox treatment as defended by James M. Joyce, is untenable. Despite Joyce’s claims to the contrary, a puzzle introduced by Roger White shows that the orthodox account, when paired with Bas C. van Fraassen’s Reflection Principle, can lead to inconsistent beliefs. Proponents of imprecise credences, then, must either provide a compelling reason to (...) reject Reflection or admit that the rational credences in White’s case are precise. (shrink)

A Benacerraf–Field challenge is an argument intended to show that common realist theories of a given domain are untenable: such theories make it impossible to explain how we’ve arrived at the truth in that domain, and insofar as a theory makes our reliability in a domain inexplicable, we must either reject that theory or give up the relevant beliefs. But there’s no consensus about what would count here as a satisfactory explanation of our reliability. It’s sometimes suggested that giving such (...) an explanation would involve showing that our beliefs meet some modal condition, but realists have claimed that this sort of modal interpretation of the challenge deprives it of any force: since the facts in question are metaphysically necessary and so obtain in all possible worlds, it’s trivially easy, even given realism, to show that our beliefs have the relevant modal features. Here I show that this claim is mistaken—what motivates a modal interpretation of the challenge in the first place also motivates an understanding of the relevant features in terms of epistemic possibilities rather than metaphysical possibilities, and there are indeed epistemically possible worlds where the facts in question don’t obtain. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Recent work by Brian Skyrms offers a very general way to think about how information flows and evolves in biological networks — from the way monkeys in a troop communicate, to the way cells in a body coordinate their actions. A central feature of his account is a way to formally measure the quantity of information contained in the signals in these networks. In this paper, we argue there is a tension between how Skyrms talks of signalling networks and his (...) formal measure of information. Although Skyrms refers to both how information flows through networks and that signals carry information, we show that his formal measure only captures the latter. We then suggest that to capture the notion of flow in signalling networks, we need to treat them as causal networks. This provides the formal tools to define a measure that does capture flow, and we do so by drawing on recent work defining causal specificity. Finally, we suggest that this new measure is crucial if we wish to explain how evolution creates information. For signals to play a role in explaining their own origins and stability, they can’t just carry information about acts: they must be difference-makers for acts. (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)

The thesis that agents should calibrate their beliefs in the face of higher-order evidence—i.e., should adjust their first-order beliefs in response to evidence suggesting that the reasoning underlying those beliefs is faulty—is sometimes thought to be in tension with Bayesian approaches to belief update: in order to obey Bayesian norms, it’s claimed, agents must remain steadfast in the face of higher-order evidence. But I argue that this claim is incorrect. In particular, I motivate a minimal constraint on a reasonable treatment (...) of the evolution of self-locating beliefs over time and show that calibrationism is compatible with any generalized Bayesian approach that respects this constraint. I then use this result to argue that remaining steadfast isn’t the response to higher-order evidence that maximizes expected accuracy. (shrink)

The purpose of this project is to argue that we possess a minimal self. It will demonstrate that minimal selfhood arrives early in our development and continues to remain and influence us throughout our entire life. There are two areas of research which shape my understanding of the minimal self: phenomenology and enactivism. Phenomenology emphasizes the sense of givenness, ownership, or mineness that accompanies all of our experiences. Enactivism says there is a sensorimotor coupling that occurs between us and the (...) environment in a way which modulates the dynamic patterns of our self development; the laying down of these basic patterns helps make us who we are and gives rise to the phenomenological, experiential mineness. Drawing on these two core ideas, I will be arguing for a Phenomenological-Enactive Minimal Self. I will be emphasizing the role of the body and the role of affects as the most important components relevant to understanding minimal selfhood. Put more concretely, the set of conditions which constitute the PEMS view are: The minimal self is the experiential subject; the minimal sense of self is present whenever there is awareness. It is the subjectivity of experience, the sense of mineness, or givenness which our experiences contain. The phenomenological part of the PEMS view turns on the idea of a bodily and dynamic integration of sensorimotor coupling and affective experience. It is, ontologically speaking, the lived body in enactive engagement with the environment. It is this embodied subject which anchors and forms the foundation for the later ‘narrative’ self, which emerges from it and which is continually influenced by it. It is the subject enactively engaged with others, dependent on sensorimotor processes and affects. We have an identity, but it emerges from relational and dynamic processes. (shrink)

Which rules should guide our reasoning? Human reasoners often use reasoning shortcuts, called heuristics, which function well in some contexts but lack the universality of reasoning rules like deductive implication or inference to the best explanation. Does it follow that human reasoning is hopelessly irrational? I argue: no. Heuristic reasoning often represents human reasoners reaching a local rational maximum, reasoning more accurately than if they try to implement more “ideal” rules of reasoning. I argue this is a genuine rational achievement. (...) Our ideal rational advisors would advise us to reason with heuristic rules, not more complicated ideal rules. I argue we do not need a radical new account of epistemic norms to make sense of the success of heuristic reasoning. (shrink)

Hilary Greaves and David Wallace argue that conditionalization maximizes expected accuracy and so is a rational requirement, but their argument presupposes a particular picture of the bridge between rationality and accuracy: the Best-Plan-to-Follow picture. And theorists such as Miriam Schoenfield and Robert Steel argue that it's possible to motivate an alternative picture—the Best-Plan-to-Make picture—that does not vindicate conditionalization. I show that these theorists are mistaken: it turns out that, if an update procedure maximizes expected accuracy on the Best-Plan-to-Follow picture, it's (...) guaranteed to maximize expected accuracy on the Best-Plan-to-Make picture as well, in which case moving from the former to the latter can't help us avoid the conclusion that conditionalization is a rational requirement. If there's a problem with Greaves and Wallace’s argument, it must lie elsewhere. (shrink)

Sensitivity has sometimes been thought to be a highly epistemologically significant property, serving as a proxy for a kind of responsiveness to the facts that ensure that the truth of our beliefs isn’t just a lucky coincidence. But it's an imperfect proxy: there are various well-known cases in which sensitivity-based anti-luck conditions return the wrong verdicts. And as a result of these failures, contemporary theorists often dismiss such conditions out of hand. I show here, though, that a sensitivity-based understanding of (...) epistemic luck can be developed that respects what was attractive about sensitivity-based approaches in the first place but that's immune to these failures. (shrink)

The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its (...) external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The notion of a genetic program has been widely criticized by both biologists and philosophers. But the debate has revolved around a narrow conception of what programs are and how they work, and many criticisms are linked to this same conception. To remedy this, I outline a modern and more apt idea of a program that possesses many of the features critics thought missing from programs. Moving away from over-simplistic conceptions of programs opens the way to a more fruitful interplay (...) of ideas between the complexity of biology and our most complex engineering discipline. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

I identify an undertheorized problem with decisions we make with the aid of algorithms: the problem of inauthenticity. When we make decisions with the aid of algorithms, we can make ones that go against our commitments and values in a normatively important way. In this paper, I present a framework for algorithm-aided decision-making that can lead to inauthenticity. I then construct a taxonomy of the features of the decision environment that make such outcomes likely, and I discuss three possible solutions (...) to the problem. (shrink)

I argue that Quinean naturalists’ holism-based arguments against analyticity and apriority are more difficult to resist than is generally supposed, for two reasons. First, although opponents of naturalism sometimes dismiss these arguments on the grounds that the holistic premises on which they depend are unacceptably radical, it turns out that the sort of holism required by these arguments is actually quite minimal. And second, although it’s true, as Grice and Strawson pointed out long ago, that these arguments can succeed only (...) if there isn’t any principled criterion for meaning change, such a criterion turns out to be hard to come by. David Chalmers has recently argued that such a criterion must exist, since the norms governing belief revision are subject to obvious exceptions that can be explained only by appeal to meaning change. But this, I argue, is incorrect: if choices about how to use language are themselves rationally assessable, then there are no such exceptions to be explained. To show that this is so, I formulate a new kind of coherence norm that may be useful for reasoning formally about the relationship between meaning and evidence. (shrink)

Robin McKenna’s excellent Non-Ideal Epistemology is, among other things, a testament to restraint. McKenna does not want to unnecessarily inflame tensions between ideal and non-ideal theorists in epistemology. Often ideal and non-ideal projects are aimed at different target domains and not in tension with one another (though not always; e.g. McKenna 2023, ch. 6, especially pp. 112-21). In this commentary, I will have much less tact. I sketch a route by which the non-ideal epistemologist might become more belligerent towards their (...) ideal counterparts. I do this by focusing on an area that McKenna mostly sets aside: non-ideal individual epistemology. (shrink)

Some sensory experiences are pleasant, some unpleasant. This is a truism. But understanding what makes these experiences pleasant and unpleasant is not an easy job. Various difficulties and puzzles arise as soon as we start theorizing. There are various philosophical theories on offer that seem to give different accounts for the positive or negative affective valences of sensory experiences. In this paper, we will look at the current state of art in the philosophy of mind, present the main contenders, critically (...) compare and contrast them. In particular, we want to examine how they handle the reason-giving power of affective states. We will look into two representationalist proposals (Evaluativism and Imperativism) and a functionalist proposal, and argue that, contrary to their own advertisements, the representationalist proposals don’t have good accounts of why and how sensory affect can motivate, rationalize, and justify subsequent behavior and intentional mental activity. We will show that our own functionalist proposal does a much better job in this regard, and that when the representationalist proposals are modified to do a better job, they fare better not because of their representationalist credentials but due to their functionalist ones. (shrink)

We argue that the concept of practical wisdom is particularly useful for organizing, understanding, and improving human-machine interactions. We consider the relationship between philosophical analysis of wisdom and psychological research into the development of wisdom. We adopt a practical orientation that suggests a conceptual engineering approach is needed, where philosophical work involves refinement of the concept in response to contributions by engineers and behavioral scientists. The former are tasked with encoding as much wise design as possible into machines themselves, as (...) well as providing sandboxes or workspaces to help various stakeholders build practical wisdom in systems that are sufficiently realistic to aid transferring skills learned to real-world use. The latter are needed for the design of exercises and methods of evaluation within these workspaces, as well as ways of empirically assessing the transfer of wisdom from workspace to world. Systematic interaction between these three disciplines (and others) is the best approach to engineering wisdom for the machine age. (shrink)

In domains as disparate as playing Go and predicting the structure of proteins, artificial intelligence (AI) technologies have begun to perform at levels beyond which any humans can achieve. Does this fact represent something lamentable? Does superhuman AI performance somehow undermine the value of human achievements in these areas? Go grandmaster Lee Sedol suggested as much when he announced his retirement from professional Go, blaming the advances of Go-playing programs like AlphaGo for sapping his will to play the game at (...) a high level. In this paper, I attempt to make sense of Sedol’s lament. I consider a number of ways that the existence of superhuman-performing AI technologies could undermine the value of human achievements. I argue there is very little in the nature of the technology itself that warrants such despair. (Compare: does the existence of a fighter jet undermine the value of being the fastest human sprinter?) But I also argue there are several more localized domains where these technologies threaten to displace human beings from being able to achieve valuable things at all. This is a particular worry for those in unequal societies, I argue, given the difficulty of many achievements and the corresponding amount of resources needed to achieve great things. (shrink)

Representationalism is the view that the phenomenal character of experiences is identical to their representational content of a certain sort. This view requires a strong transparency condition on phenomenally conscious experiences. We argue that affective qualities such as experienced pleasantness or unpleasantness are counter-examples to the transparency thesis and thus to the sort of representationalism that implies it.

Implicit attitudes are mental states posited by psychologists to explain behaviors including implicit racial and gender bias. In this paper I investigate the belief view of the implicit attitudes, on which implicit attitudes are a kind of implicit belief. In particular, I focus on why implicit attitudes, if they are beliefs, are often resistant to updating in light of new evidence. I argue that extant versions of the belief view do not give a satisfactory account of this phenomenon. This is (...) because proponents of the belief view have focused on overly narrow explanations of recalcitrance in terms of belief storage. Expanding the focus of the belief view to the kinds of irrational and arational transitions between beliefs and other mental states provides compelling (if preliminary) explanations of recalcitrance. (shrink)

On a widespread naturalist view, the meanings of mathematical terms are determined, and can only be determined, by the way we use mathematical language—in particular, by the basic mathematical principles we’re disposed to accept. But it’s mysterious how this can be so, since, as is well known, minimally strong first-order theories are non-categorical and so are compatible with countless non-isomorphic interpretations. As for second-order theories: though they typically enjoy categoricity results—for instance, Dedekind’s categoricity theorem for second-order and Zermelo’s quasi-categoricity theorem (...) for second-order —these results require full second-order logic. So appealing to these results seems only to push the problem back, since the principles of second-order logic are themselves non-categorical: those principles are compatible with restricted interpretations of the second-order quantifiers on which Dedekind’s and Zermelo’s results are no longer available. In this paper, we provide a naturalist-friendly, non-revisionary solution to an analogous but seemingly more basic problem—Carnap’s Categoricity Problem for propositional and first-order logic—and show that our solution generalizes, giving us full second-order logic and thereby securing the categoricity or quasi-categoricity of second-order mathematical theories. Briefly, the first-order quantifiers have their intended interpretation, we claim, because we’re disposed to follow the quantifier rules in an open-ended way. As we show, given this open-endedness, the interpretation of the quantifiers must be permutation-invariant and so, by a theorem recently proved by Bonnay and Westerståhl, must be the standard interpretation. Analogously for the second-order case: we prove, by generalizing Bonnay and Westerståhl’s theorem, that the permutation invariance of the interpretation of the second-order quantifiers, guaranteed once again by the open-endedness of our inferential dispositions, suffices to yield full second-order logic. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

The discipline of applied ethics already has a certain familiarity in the Anglo-Saxon world, above all through the work of Peter Singer. Applied ethics uses the tools of moral philosophy to resolve practical problems of the sort which arise, for example, in the running of hospitals. In the University at Buffalo (New York) there was organized on April 24-25 1998 the world's first conference on a new, sister discipline, the discipline of applied ontology. Applied ontologists seek to apply ontological tools (...) to solving practical problems of the sort which arise in various extra-philosophical domains, including law and government administration. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

One common attitude toward abstract objects is a kind of platonism: a view on which those objects are mind-independent and causally inert. But there's an epistemological problem here: given any naturalistically respectable understanding of how our minds work, we can't be in any sort of contact with mind-independent, causally inert objects. So platonists, in order to avoid skepticism, tend to endorse epistemological theories on which knowledge is easy, in the sense that it requires no such contact—appeals to Boghossian’s notion of (...) epistemic analyticity are particularly common here, as are appeals to some broadly pragmatic account of the good standing of basic beliefs. I argue, though, that these appeals are hopeless: an argument adapted from the Benacerraf–Field challenge shows that, even if some such theory can deliver the verdict that our beliefs about abstract objects have some prima facie good standing, this good standing will inevitably be defeated. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The present essay seeks, by way of the Austrian example, to make a contribution to what might be called the philosophy of the supranational state. More specifically, we shall attempt to use certain ideas on the philosophy of Gestalten as a basis for understanding some aspects of that political and cultural phenomenon which was variously called the Austrian Empire, the Habsburg Empire, the Danube Monarchy or Kakanien.

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

We offer a sceptical examination of a thesis recently advanced in a monograph published by Princeton University Press, entitled Greek Buddha: Pyrrho’s Encounter with Early Buddhism in Central Asia. In this dense and probing work, Christopher I. Beckwith, a professor of Central Eurasian studies at Indiana University, Bloomington, argues that Pyrrho of Elis adopted a form of early Buddhism during his years in Bactria and Gandhāra, and that early Pyrrhonism must be understood as a sect of early Buddhism. In making (...) his case Beckwith claims that virtually all scholars of Greek, Indian, and Chinese philosophy have been operating under flawed assumptions and with flawed methodologies, and so have failed to notice obvious and undeniable correspondences between the philosophical views of the Buddha and of Pyrrho. In this study we take Beckwith’s proposal and challenge seriously, and we examine his textual basis and techniques of translation, his methods of examining passages, his construal of problems and his reconstruction of arguments. We find that his presuppositions are contentious and doubtful, his own methods are extremely flawed, and that he draws unreasonable conclusions. Although the result of our study is almost entirely negative, we think it illustrates some important general points about the methodology of comparative philosophy. (shrink)

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

In his book The Sensory Order, Hayek anticipates many of the central ideas behind what we now call the connectionist paradigm, and develops on this basis a theory of the workings of the human mind that extends the thinking of Hume and Mach. He shows that the idea of neural networks is can be applied not only in psychology and neurology but also in the sphere of economics. For the mind, from the perspective of The Sensory Order, is a dynamic, (...) relational affair that is in many respects analogous to a market process. The mind, as Hayek puts it, is a 'continuous stream of impulses, the significance of each and every contribution of which is determined by the place in the pattern of channels through which they flow' , so that the flow of representative neural impulses can be compared 'to a stock of capital being nourished by inputs and giving a continuous stream of outputs'. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...) pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

One of the most intriguing claims in Sven Rosenkranz’s Justification as Ignorance is that Timothy Williamson’s celebrated anti-luminosity argument can be resisted when it comes to the condition ~K~KP—the condition that one is in no position to know that one is in no position to know P. In this paper, I critically assess this claim.

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)