A critical examination of the charge of self-refutation, particularly as leveled by orthodoxy-defending philosophers against those maintaining epistemologically unorthodox, especially relativistic or skeptical, views. Beginning with an analysis of its classic illustration in Plato’s *Theaetetus* as leveled against Protagoras’s “Man is the measure ...,” I consider various aspects of the charge, including logical, rhetorical, pedagogic, affective, and cognitive.

Richard Rorty's rejection of prevailing interior-mirror understandings of the presumed relationship between “minds” and “nature,” along with his promotion of nonrepresentational accounts of knowledge, truth, and science, participates in a rich tradition of jointly pragmatist and constructivist views that spans the twentieth century. This contribution to the symposium “Whatever Happened to Richard Rorty?” considers Rorty's complex and ambivalent relation to that tradition, particularly to the work of his American pragmatist predecessors, William James and John Dewey, and to subsequent pragmatist-constructivist antirepresentationalism (...) in contemporary science and technology studies (STS) and “4E” (embodied, embedded, extended, enactive) cognitive theory. A final section on Nicholas Gaskill's contribution to the symposium questions his sense of Rorty's rhetorical recklessness and suggests that his worries over relativism, in Rorty's texts and more generally, are misplaced. (shrink)

The objective of this research programme is to contribute to the establishment of the emerging science of Formal Ontology in Information Systems via a collaborative project involving researchers from a range of disciplines including philosophy, logic, computer science, linguistics, and the medical sciences. The re­searchers will work together on the construction of a unified formal ontology, which means: a general framework for the construction of ontological theories in specific domains. The framework will be constructed using the axiomatic-deductive method of modern (...) formal ontology. It will be tested via a series of applications relating to on-going work in Leipzig on medical taxonomies and data dictionaries in the context of clinical trials. This will lead to the production of a domain-specific ontology which is designed to serve as a basis for applications in the medical field. (shrink)

Advocates of literary Darwinism, cognitive cultural studies, neuroaesthetics, digital humanities, and other such hybrid fields now seek explicitly to make the aims and methods of one or another humanities discipline approximate more closely the aims and methods of science, and at their most visionary, they urge as well the overall integration of the humanities and natural sciences. This essay indicates some major considerations—historical, conceptual, and pragmatic—that may be useful for assessing these efforts and predicting their future. Arguments promoting integration often (...) involve dubious teleological models of intellectual history and betray limited understandings of the distinctive epistemic orientations and cultural functions of the humanities vis-à-vis the sciences. Recurrent institutional difficulties encountered by scholars and/or scientists in hybrid fields reflect steep prestige differentials between the humanities and sciences, along with significant differences of training, experience, style, and temperament. Meanwhile, both the sciences and humanities are being shaken up by technological and related intellectual developments. Though worrisome, the new disciplinary configurations are thus likely to play out in surprising and, not inconceivably, positive ways. (shrink)

Contemporary issues involving knowledge and science examined from a constructivist-pragmatist perspective often labeled "relativism." Individual chapters include a review of the difference between constructivist-pragmatist epistemology and "social constructivism;" an examination of recent writings by Bruno Latour; a critique of computational methods in literary studies; a skeptical look at current efforts to "integrate" the humanities and the natural sciences; and reflections on the social dynamics of belief in relation to denials of climate change and to hopes expressed by environmentalists.

I reply here to an article by philosopher Paul Boghossian in which my article "Cutting-Edge Equivocation: Conceptual Moves and Rhetorical Strategies in Contemporary Anti-Epistemology" (Smith, *SAQ* 2002) provides him with an occasion for a supposed exposure and refutation of the alleged illogic of the "unpalatable relativism" of what Boghossian, at some distance from his topic, (mis)understands as the "constructivism" of contemporary sociology of science.

In this response to comments on my article, “The Chimera of Relativism,” in the same issue of *Common Knowledge* , by cognitive neuroscientist Andreas Roepstorff, classicist G. E. R. Lloyd, and anthropologist Martin Holbraad, I illustrate and reinforce Lloyd's cautions regarding the hazards of intercultural—here, Chinese-Western—comparisons in studies of culture and cognition. Examination of a foundational study in East-West cultural/cognitive differences cited by Roepstorff indicates extensive conceptual and methodological problems in that tradition of research. Although Holbraad champions a more radical (...) relativism than that offered in my work, the moves he urges have either been present in my work from the beginning or are both dubiously radical and otherwise undesirable. (shrink)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

The Emergence of Relativism offers a range of perspectives on how “the problem of relativism” was framed in German intellectual discourses over the course of the long nineteenth century. The review suggests that the volume is at odds with itself in various ways and, both wittingly and unwittingly, illuminates some problems of philosophy, both across the period examined and in our own.

An examination of conceptually and rhetorically equivocating positions among academic philosophers and other theorists who are sympathetic to constructivist epistemological developments but unwilling to relinquish key aspects of traditional understandings of truth and knowledge and/or anxious to avoid charges of relativism. A major problem with the resulting hybrid formulations is that, seeking, as they often claim, to “steer a course between Scylla and Charybdis” and being composed of essentially incompatible elements, they can do little theoretical work. While the personal-intellectual and (...) professional-institutional pressures leading to such dubious navigations are substantial, so also, it is argued, are their intellectual costs. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion is (...) Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)

Despite the importance of human blood to clinical practice and research, hematology and blood transfusion data remain scattered throughout a range of disparate sources. This lack of systematization concerning the use and definition of terms poses problems for physicians and biomedical professionals. We are introducing here the Blood Ontology, an ongoing initiative designed to serve as a controlled vocabulary for use in organizing information about blood. The paper describes the scope of the Blood Ontology, its stage of development and some (...) of its anticipated uses. (shrink)

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

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

An analysis of Cardinal Joseph Ratzinger's statements regarding relativism in his 2005 homily to the conclave meeting to elect the new pope in the context of the charge of "relativism" in 20th-century philosophy. Parts of this essay are adapted from Barbara Herrnstein Smith,"Pre-Post-Modern Relativism," in *Scandalous Knowledge: Science, Truth and the Human* (Edinburgh: Edinburgh University Press, 2005; Durham, NC: Duke University Press, 2006), 18 – 45.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (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)

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. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

The essay considers two sets of interrelated difficulties that follow from our kinship to animals: those that arise chronically from our individual psychologically complex and often ambivalent relations to animals, and those that reflect the intellectually and ideologically criss-crossed connections among the various discourses currently concerned with those relations, including the movement for animal rights, ecological ethics, posthumanist theory, and such fields as primatology and evolutionary psychology. I begin with some general observations on classification and then turn to the increasingly (...) complex play of claims and counter-claims regarding the so-called species barrier. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy and Literature 25.2 (2001) 215-232 [Access article in PDF] Eighteenth-Century Print Culture and the "Truth" of Fictional Narrative Lisa Zunshine As a session entitled "Truth" at a recent Modern Language Association of America annual convention has demonstrated, the obsession with the epistemologies of truth is alive and well. Our "familiar ways of thinking and talking about truth," as one of the speakers, Barbara Herrnstein Smith, observed, (...) remain "theoretically elusive, discursively slippery, and hard or perhaps impossible to articulate clearly in relation to other current concepts and ideas" 1 --an irresistible invitation to further thinking and talking on the subject. My essay enters this conversation by attempting to contemplate truth not as a stable attribute but as a ongoing attribution, that is, not as an inherent property but rather as a dynamic process predicated upon functional idiosyncrasies of our evolved cognitive architecture. The broad question posed here is this: What if our never-ending quest for truth is itself cognitively constructed and the various forms that this quest takes manifest the (not necessarily harmonious) interaction between our evolved cognitive capacities and the ever-changing specifics of our cultural environment?Consider just one of the forms of such an interaction, namely, our age-long preoccupation with the "truth" of literary narrative. In many respects, this preoccupation is counterproductive: the most "fantastic" story contains a number of contingently useful "truths" about the world, whereas the most "factual" narrative manipulates facts by virtue of being a narrative or a subjective arrangementof information. Still, we persevere in wanting to put the label "fiction" or "nonfiction" onto any story that comes our way. As I will argue, the bookstore's organization of its sections satisfies this species of "cognitive" craving as well as [End Page 215] reinforces it, making it seem culturally inevitable. Viewed from this perspective, our culture appears to be a multifaceted feedback mechanism engaged in the process of satisfying, reinforcing, struggling with, and manipulating our cognitive predispositions.The cultural manipulation of our cognitive predispositions is the topic of the present essay, which discusses several examples of such manipulation that respond to our desire to assign a certain "truth-value" to a given narrative, i.e., to attach a label to it announcing its "factuality" or "fictionality." "Truth-value" is a loaded term, resisting definition, and liable to lead me into trouble. Imperfect as it is, however, I need it in order to shuffle between two scholarly discourses that do not (yet) have much vocabulary in common: literary criticism and cognitive science. The reason for turning to cognitive science in my discussion of literary narrative is that cognitive anthropologists and psychologists frequently engage the same problems that we do when we ask, What is "Fiction"? How is it different from "History"? How do we decide whether what we are reading is "true?" The key difference between the two approaches is, however, that whereas the literary critic focuses on specific texts produced and read in specific cultural circumstances, the cognitive anthropologist pays attention to the cross-cultural insistence with which people wish to and often claim to distinguish "truth" from "fiction" and inquires into the possible evolutionary history of the cognitive architecture implicated in our never-ending quest for "truth." The latter perspective can thus be useful for literary studies because, by suggesting that our evolved cognitive architecture often "encourages" us to construe the world as a negotiation of "truths" and "nontruths," this perspective begins to account--at least on some level--for the fact that people may approach a complex cultural artifact, such as a novel, with a "truth"/"non-truth" binary in mind that is ultimately not very productive. 2 Evolutionary psychologists and anthropologists frequently point to disjunctions between the tasks that our brain evolved to solve and the tasks that we have to deal with in the modern environment; our vexed insistence on determining the truth-value of the 500-page printed narrative--not an object one would come across in the Pleistocene--can be seen as yet another instance of such a disjunction.Thus, I suggest that, on the... (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.

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)

Recreational Drugs European Network (ReDNet) project aims to use the Psychonaut Web Mapping Project database (Psychonaut Web Mapping Group, 2009) containing novel psychoactive compounds usually not mentioned in the scientific literature and thus unknown to clinicians as a unique source of information. The database will be used to develop an integrated ICT prevention approach targeted at vulnerable individuals and focused on novel synthetic and herbal compounds and combinations. Particular care will be taken in keeping the health professionals working directly with (...) young people showing problematic behaviors regularly updated in terms of novel compounds and combinations as well. A user-friendly project website will be developed aimed primarily at delivering the information/prevention approaches, but will also be a way of communicating with project partners and relevant stakeholders (e.g. thematic forum facilities, instant messages, blogs, video chat, wikiblog, newsletters distributed via mailing list). The website will support various ICT prevention tools, including an SMS alert service. Different areas and sections will be aimed specifically at the different target groups. -/- . (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)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (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)

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)

According to ecological psychology, animals perceive not just the qualities of things in their environment, but their affordances: in James Gibson’s words, ’what things furnish, for good or ill’. I propose a metaphysics for affordances that fits into a contemporary anti-Humean metaphysics of powers or potentialities. The goal is to connect two debates, one in the philosophy of perception and one in metaphysics, that stand to gain much from each other.

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)

Dispositionalism about modality is the view that metaphysical modality is a matter of the dispositions possessed by actual objects. In a recent paper, David Yates has raised an important worry about the formal adequacy of dispositionalism. This paper responds to Yates’s worry by developing a reply that Yates discusses briefly but dismisses as ad hoc: an appeal to a ’plenitude of powers’ including such powers as the necessarily always manifested power for 2+2\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} (...) \begin{document}$$2+2$$\end{document} to be 4. I argue that the reply is not ad hoc at all, by defending the metaphysics of dispositions that should underly it. I then argue, first, that a proper understanding of dispositions’ degrees provides us with an argument for such necessarily always manifested dispositions; second, that all the natural attempts to block that argument can be resisted without being ad hoc; and third, that pragmatic considerations explain our intuitive resistance to the ascription of necessarily always manifested dispositions. Dispositionalism can be formally adequate after all. (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.

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 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)

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)

(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)

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

This is a revised version of the introductory essay in C. Eschenbach, C. Habel and B. Smith (eds.), Topological Foundations of Cognitive Science, Hamburg: Graduiertenkolleg Kognitionswissenschaft, 1994, the text of a talk delivered at the First International Summer Institute in Cognitive Science in Buffalo in July 1994.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

The paper uses the tools of mereotopology (the theory of parts, wholes and boundaries) to work out the implications of certain analogies between the 'ecological psychology' of J. J Gibson and the phenomenology of Edmund Husserl. It presents an ontological theory of spatial boundaries and of spatially extended entities. By reference to examples from the geographical sphere it is shown that both boundaries and extended entities fall into two broad categories: those which exist independently of our cognitive acts (for example, (...) the planet Earth, its exterior surface); and those which exist only in virtue of such acts (for example: the equator, the North Sea). The visual field, too, can be conceived as an example of an extended entity that is dependent in the sense at issue. The paper suggests extending this analogy by postulating entities which would stand to true judgments as the visual field stands to acts of visual perception. The judgment field is defined more precisely as that complex extended entity which comprehends all entities which are relevant to the truth of a given (true) judgment. The work of cognitive linguists such as Talmy and Langacker, when properly interpreted, can be shown to yield a detailed account of the structures of the judgment fields corresponding to sentences of different sorts. A new sort of correspondence-theoretic definition of truth for sentences of natural language can then be formulated on this basis. (shrink)

In her ‘On the apparent paradox of ideal theory’, Laura Valentini combines three supposedly plausible premises to derive the paradoxical result that ideal theory is both unable to, and indispensable for, guiding action. Her strategy is to undermine one of the three premises by arguing that there are good and bad kinds of ideal theory, and only the bad kinds are vulnerable to the strongest version of their opponents’ attack. By undermining one of the three premises she releases ideal theorists (...) from the paradox, which is as follows. (1) Any sound theory of justice is action-guiding. (2) Any sound theory of justice is ideal. (3) Any ideal theory fails to be action-guiding. Here I shall respond to Valentini in two ways. First, I shall show that both (1) and (2) are false. The falsity of either is sufficient to release ideal theorists from the paradox. Second, I shall show that Valentini’s response to (3) can be extended, because her bad kinds of ideal theory do not necessarily fail to guide action. The cumulative effect of my arguments further strengthens Valentini’s support of ideal theory. I will deal with premises (1) and (2) in Sections I and II, and (3) in Section III. (shrink)

According to essentialism, metaphysical modality is founded in the essences of things, where the essence of a thing is roughly akin to its real definition. According to potentialism (also known as dispositionalism), metaphysical modality is founded in the potentialities of things, where a potentiality is roughly the generalized notion of a disposition. Essentialism and potentialism have much in common, but little has been written about their relation to each other. The aim of this paper is to understand better the relations (...) between essence and potentiality, on the one hand, and between essentialism and potentialism, on the other. It is argued, first, that essence and potentiality are not duals but interestingly linked by a weaker relation dubbed ‘semi-duality’; second, that given this weaker relation, essentialism and potentialism are not natural allies but rather natural competitors; and third, that the semi-duality of essence and potentiality allows the potentialist to respond to an important explanatory challenge by using essentialist resources without thereby committing to essentialism. (shrink)

Modal dispositionalism is the view that possibilities are a matter of the dispositions of individual objects: it is possible that p if and only if something has a disposition for p to be the case. We raise a problem for modal dispositionalism: nothing within the theory rules out that there could be necessary, perfect masks, which make the manifestation of a disposition impossible. Unless such necessary perfect masks are ruled out, modal dispositionalism runs the risk of failing to provide a (...) sufficient condition for possibility, and indeed of engendering contradictions. But to rule them out, modal dispositionalism would have to revise a crucial tenet of the view, its localism. (shrink)

In a recent paper, Björn Lundgren and H. Orri Stefánsson (forthcoming) present three objections to normic de minimis expected utility theory (NDEUT) – a decision theoretic framework defended in Smith (2024). In this paper, I respond to these objections and outline some possible ways in which NDEUT might be modified or further developed. Like any de minimis framework, NDEUT employs a risk threshold to sort possibilities into those that must be considered when making a decision, and those that can (...) be legitimately ignored – the so-called ‘de minimis risks’. While this threshold would usually take the form of a probability value, in NDEUT the de minimis risks are identified instead on the basis of their abnormality. In the first section I will set up some of the formalism used in NDEUT and consider Lundgren and Stefánsson’s first objection – which is essentially formal in nature. In the second section I will delve further into the interpretation of NDEUT and consider the second and third objections, which turn on particular examples. (shrink)

My aim in this paper is to sketch, with a broad brush and in bare outlines, an approach to modal epistemology that is characterized by three distinctive features. First, the approach is agency-based: it locates the roots of our modal thought and knowledge in our experience of our own agency. Second, the approach is ambitious in that it takes the experience of certain modal properties in agency to be the sole distinctive feature of specifically modal thought and knowledge; everything that (...) we know about modality beyond the experience of agency is a matter of applying standard methods of inquiry such as deduction, induction and abductive methods for choosing between theories. Third, the account holds that modal thought and knowledge is, first and foremost, about modal properties that are sufficiently like those encountered in agency. (shrink)

In this paper I investigate central temporal and spatial notions in the second part of Plato’s Parmenides and argue that also these notions, and not only the metaphysical ones usually discussed in the literature, can be understood as a response to positions and problems put on the table by Parmenides and Zeno. Of the spatial notions examined in the dialogue, I look at the problems raised for possessing location and shape, while with respect to temporal notions, I focus on the (...) discussion of ‘being in time’ and exaiphnês (the latter notion will be shown to be also an important influence for Aristotle’s Physics). In displaying a paradoxical character and taking up crucial notions from Parmenides, the second part of the Parmenides seems to display some resemblance to Zeno’s paradoxes. I will show, however, that in contrast to Zeno, the second part of Plato’s Parmenides also demonstrates Parmenides’ One to be problematic on its own terms. Furthermore, the dialogue presents not only important problems that these spatial and temporal notions seem to lead us into, but also establishes some positive features necessary to think of time and space. In this way, Plato’s Parmenides can be seen as contributing to the development of temporal and spatial conceptualisations in ancient Greek thought. (shrink)