Smith’s Descartes Dictionary is geared specifically for undergraduate students and contains an Introduction, a Terms and Names section and a Bibliography. It is a good resource for students coming to Descartes’ writings for the first time and has the potential of being an even better pedagogical and study aid once its wrinkles are smoothened out, maybe in a second edition.

The Austrian philosopher Christian von Ehrenfels published his essay "On 'Gestalt Qualities'" in 1890. The essay initiated a current of thought which enjoyed a powerful position in the philosophy and psychology of the first half of this century and has more recently enjoyed a minor resurgence of interest in the area of cognitive science, above all in criticisms of the so-called 'strong programme' in artificial intelligence. The theory of Gestalt is of course associated most specifically with psychologists of the Berlin (...) school such as Max Wertheimer, Wolfgang Kohler and Kurt Koffka. We shall see in what follows, however, that an adequate philosophical understanding of the Gestalt idea and of Ehrenfels' achievement will require a close examination not merely of the work of the Berlin school but also of a much wider tradition in Austrian and German philosophy in general. (shrink)

In 1890 Christian von Ehrenfels published his classic paper "Über 'Gestaltqualitäten'", the first systematic investigation of the philosophy and psychology of Gestalt. Ehrenfels thereby issued an important challenge to the psychological atomism that was still predominant in his day. His paper not only exerted a powerful influence on the philosophy of the Meinong school, it also marked the beginning of the Gestalt tradition in psychology, later associated with the work of Wertheimer, Köhler and Koffka in Berlin. Includes papers by C. (...) Von Ehrenfels, Kurt Grelling and Paul Oppenheim and contributions by K. Mulligan, P.M. Simons and Barry Smith. (shrink)

One reason for the renewed interest in Austrian philosophy, and especially in the work of Brentano and his followers, turns on the fact that analytic philosophers have become once again interested in the traditional problems of metaphysics. It was Brentano, Husserl, and the philosophers and psychologists whom they influenced, who drew attention to the thorny problem of intentionality, the problem of giving an account of the relation between acts and objects or, more generally, between the psychological environments of cognitive subjects (...) and the different sorts of external (physical, geographical, social) environments which they inhabit. The present essay addresses this environmental version of the problem of intentionality. It draws not only on the work of Husserl and Scheler but also on the Gestalt psychological writings of Kurt Koffka and Kurt Lewin. It considers the influential subjective idealist theory of animal environments put forward by J. von Uexküll and contrasts this with a realist theory of organism-environment interaction based on the work of the ecological psychologists J. J. Gibson and Roger Barker. This realist theory is then exploited as a basis for an ontology of social objects of a range of different sorts. (This is the English original of the French translation.). (shrink)

The paper introduces the concepts at the heart of point-set-topology and of mereotopology (topology founded in the non-atomistic theory of parts and wholes) in an informal and intuitive fashion. It will then seek to demonstrate how mereotopological ideas can be of particular utility in cognitive science applications. The prehistory of such applications (in the work of Husserl, the Gestaltists, of Kurt Lewin and of J. J. Gibson) will be sketched, together with an indication of the field of possibilities in (...) linguistics, perceptual psychology, cate¬gorization and geographic information systems. Topological structures will be shown to play a central role in studies of naive physics not least in virtue of the fact that even well-attested departures from true physics on the part of common sense leave the topology and vectorial orientation of the underlying physical phenomena invariant: our common sense would thus seem to have a veridical grasp of the topology and broad general orientation of physical phenomena, both static and dynamic, even where it illegitimately modifies the relevant shape and metric properties. The implications of this and related insights for the methodology of psychology will be explored. (shrink)

The term ‘Gestalt’ was introduced into psychology by the Austrian philosopher Christian von Ehrenfels in an essay entitled “On ‘Gestalt-Qualities’” published in 1890. ‘Gestalt,’ in colloquial German, means roughly: ‘shape’ or ‘structure’ or ‘configuration’, and Ehrenfels demonstrates in his essay that there are certain inherently structural features of experience which need to be acknowledged in addition to simple tones, colours and other mental ‘atoms’ or ‘elements’. His essay thus initiated a reaction against the then still dominant atomism in psychology, a (...) reaction which culminated in the work on ‘cerebral intregation’ of the so-called Berlin school of Gestalt psychology. Max Wertheimer, one of the leading members of this school, was a student of Ehrenfels in Prague. Ehrenfels himself belonged to an impressive list of original thinkers – a list which includes also Edmund Husserl, Alexius Meinong and Carl Stumpf, the founder of the Berlin school – who were students of Franz Brentano. Each of these thinkers attempted to elaborate, both ontologically and psychologically, the doctrine of intentionality put forward by Brentano. The work of Ehrenfels and of the later Gestaltists, too, may be seen as a contribution to the understanding of this mental directedness, and in particular to the understanding of the directedness of perceptual experience. (shrink)

This book presents Robert S. Hartman’s formal theory of value and critically examines many other twentieth century value theorists in its light, including A.J. Ayer, Kurt Baier, Brand Blanshard, Paul Edwards, Albert Einstein, William K. Frankena, R.M. Hare, Nicolai Hartmann, Martin Heidegger, G.E. Moore, P.H. Nowell-Smith, Jose Ortega y Gasset, Charles Stevenson, Paul W. Taylor, Stephen E. Toulmin, and J.O. Urmson.

Population obesity and associated morbidities pose significant public health and economic burdens in the United Kingdom, United States, and globally. As a response, public health initiatives often seek to change individuals’ unhealthy behavior, with the dual aims of improving their health and conserving health care resources. One such initiative—taxes on sugar‐sweetened beverages (SSB)—has sparked considerable ethical debate. Prominent in the debate are arguments seeking to demonstrate the supposed impermissibility of SSB taxes and similar policies on the grounds that they interfere (...) with individuals’ freedom and autonomy. Commentators have often assumed that a policy intended to restrict or change private individuals’ consumption behavior will necessarily curtail freedom and, as a corollary, will undermine individuals’ autonomy with respect to their consumption choices. Yet this assumption involves a conceptual mistake. To address the misunderstanding, it’s necessary to attend to the differences between negative liberty, freedom of options, and autonomy. Ultimately, concerns about negative liberty, freedom, and autonomy do not provide strong grounds for opposing SSB taxes. (shrink)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

Successful biomedical data mining and information extraction require a complete picture of biological phenomena such as genes, biological processes, and diseases; as these exist on different levels of granularity. To realize this goal, several freely available heterogeneous databases as well as proprietary structured datasets have to be integrated into a single global customizable scheme. We will present a tool to integrate different biological data sources by mapping them to a proprietary biomedical ontology that has been developed for the purposes of (...) making computers understand medical natural language. (shrink)

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

This paper argues that the historical conception of knowing as a presentational factive mental state (‘presentationalism’) is not best understood as an alternative to belief-based and knowledge-first epistemology, but rather as an account of epistemic architecture that is compatible with these paradigms. To defend this claim, the paper focuses on a challenge to presentationalism raised by inferential knowledge and argues that the problem can be solved only if presentationalism is understood as I suggest. The paper is structured as follows. §1 (...) explains presentationalism and its recent revival. §2 considers a flat-footed argument that presentationalism cannot get any cases of inferential knowledge right. §3 suggests that this problem can and should be solved by drawing a distinction between two kinds of epistemic priority, and by holding that inferential knowledge can be immediate in an epistemologically significant sense. But §4 argues that this only goes so far, since not all inferential knowledge is alike. This further problem can also be solved, but only if presentationalism is reframed as a proposal about epistemic architecture that does not compete with belief-based and knowledge-first accounts, §5 concludes. (shrink)

Despite the recent backlash against epistemic consequentialism, an explicit systematic alternative has yet to emerge. This paper articulates and defends a novel alternative, Epistemic Kantianism, which rests on a requirement of respect for the truth. §1 tackles some preliminaries concerning the proper formulation of the epistemic consequentialism / non-consequentialism divide, explains where Epistemic Kantianism falls in the dialectical landscape, and shows how it can capture what seems attractive about epistemic consequentialism while yielding predictions that are harder for the latter to (...) secure in a principled way. §2 presents Epistemic Kantianism. §3 argues that it is uniquely poised to satisfy the desiderata set out in §1 on an ideal theory of epistemic justification. §4 gives three further arguments, suggesting that it (i) best explains the objective normative significance of the subject's perspective in epistemology, (ii) follows from the kind of axiology needed to solve the swamping problem together with modest assumptions about the relation between the evaluative and the deontic, and (iii) illuminates certain asymmetries in epistemic value and obligation. §5 takes stock and reassesses the score in the debate. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

According to Veritism, true belief is the sole fundamental epistemic value. Epistemologists often take Veritism to entail that all other epistemic items can only have value by standing in certain instrumental relations—namely, by tending to produce a high ratio of true to false beliefs or by being products of sources with this tendency. Yet many value theorists outside epistemology deny that all derivative value is grounded in instrumental relations to fundamental value. Veritists, I believe, can and should follow suit. After (...) setting the stage in §1, I explain in §2 why Veritism should not take an Instrumentalist form. Instrumentalist Veritism faces a generalized version of the swamping problem. But this problem undermines Instrumentalism, not Veritism: granting Instrumentalism, similar problems arise for any economical epistemic axiology. I show in §3 how Veritism can take a less narrow form and solve the swamping problem. After answering some objections in §4, I consider in §5 what some would regard as a less radical alternative solution and argue that it either fails or collapses into mine. I close in §6 by taking stock and re-evaluating the overall prospects for Veritism, suggesting that it is a highly promising epistemic axiology when divorced from Instrumentalism. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

According to a view I’ll call Epistemic Normativism, knowledge is normative in the same sense in which paradigmatically normative properties like justification are normative. This paper argues against EN in two stages and defends a positive non-normativist alternative. After clarifying the target in §1, I consider in §2 some arguments for EN from the premise that knowledge entails justification. I first raise some worries about inferring constitution from entailment. I then rehearse the reasons why some epistemologists reject the Entailment Thesis (...) and argue that a non-normativist picture provides the best explanation of all the intuitions surrounding this thesis, favorable and unfavorable. On this picture, human knowledge is a structured non-normative complex that has as one of its parts a justification-making property, analogous in role to good-making properties like pleasurableness. After giving three arguments against EN in §3 and answering an objection in §4, I turn in §5 to further develop the positive view sketched in §2. In §6, I take stock and conclude. (shrink)

In this paper, I provide new foundations for experientialism about perceptual knowledge, the view that all perceptual knowledge derives from experience. §1 introduces the basic template for experientialism about perceptual knowledge and considers how recent work on perceptual justification encourages giving special attention to less intuitive ways of filling in the template. §2 and §3 draw attention to ways of filling in the template that are more compelling, including versions from the history of epistemology that are still taken seriously elsewhere (...) (e.g., in philosophy of mind and cognitive science). §4 spotlights one neglected kind of approach—anti-Humean experientialism—and highlights some of its attractive features. §5 concludes by noting how anti-Humean experientialism dissolves an influential problem for experientialism that originates in Sellars (1956). (shrink)

Ernest Sosa (1940-) is a central figure in contemporary epistemology. He is best known for pioneering the subfield of virtue epistemology, as well as developing across four decades his own distinctive framework in this tradition. Besides providing an overview of this work, this article offers a guide to Sosa’s other contributions to epistemology, stretching back to his first publication in 1964. The organization is as follows. §1 reviews Sosa’s distinctive brand of virtue epistemology and its development since 1980. §2 provides (...) a fuller synopsis of Sosa’s contributions to epistemology in five parts, covering his work on (i) the structure of justification and knowledge, (ii) the dawning of knowledge and understanding, (iii) skepticism and the possibility of empirical knowledge, (iv) methodology and the possibility of philosophy, and (v) the relationship between mind and world. Our aim is to encourage renewed appreciation of the full scope and depth of Sosa’s epistemology. We hope the reader will benefit from (re)exploring Sosa’s work guided by the map detailed below. (shrink)

It is often assumed that believing that p for a normative reason consists in nothing more than (i) believing that p for a reason and (ii) that reason’s corresponding to a normative reason to believe that p, where (i) and (ii) are independent factors. This is the Composite View. In this paper, we argue against the Composite View on extensional and theoretical grounds. We advocate an alternative that we call the Prime View. On this view, believing for a normative reason (...) is a distinctive achievement that isn’t exhausted by the mere conjunction of (i) and (ii). Its being an achievement entails that (i) and (ii) are not independent when one believes for a normative reason: minimally, (i) must hold because (ii) holds. Apart from its intrinsic interest, our discussion has important upshots for central issues in epistemology, including the analysis of doxastic justification, the epistemology of perception, and the place of competence in epistemology. (shrink)

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)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

This paper is an opinionated guide to the literature on normative epistemic reasons. After making some distinctions in §1, I begin in §2 by discussing the ontology of normative epistemic reasons, assessing arguments for and against the view that they are mental states, and concluding that they are not mental states. In §3, I examine the distinction between normative epistemic reasons there are and normative epistemic reasons we possess. I offer a novel account of this distinction and argue that we (...) in fact ought to acknowledge a threefold distinction between objective, possessed, and apparent normative epistemic reasons. In §4, I discuss the question of which normative reasons for doxastic attitudes are the epistemic ones, evaluating reasons against a simple evidentialist answer. Finally, in §5, I look at the role of reasons in epistemology, considering challenges to viewing reasons as the building blocks of epistemic normativity and maintaining that the challenges recommend a novel bi-level epistemology rather than a marginalization of reasons in epistemology. (shrink)

Ordinary thought recognizes many ways of knowing. Not all are epistemologically fundamental. Nevertheless, it is standard to think there is more than one fundamental way—call this view access pluralism. Access monism opposes access pluralism. This paper defends a version of access monism I call presentationalist monism (§1), on which the sole fundamental way of knowing is presentation. I defend presentationalist monism in three stages. Firstly (§2), I suggest that it is compelling about four central ways of knowing—viz., perceiving, episodically remembering, (...) introspecting, and intuiting. Then (§3) I argue that presentationalist monism also explains ostensibly less straightforward cases, including inference, testimony, semantic memory, and practical knowledge. After working through cases in this way, I show how this enumerative argument can be secured by understanding the view as a kind of formal foundationalism about ways of knowing. I conclude by addressing an objection (§4) and considering whether presentationalism about ways of knowing supports a presentational account of knowledge, cautioning against this inference (§5). (shrink)

The paper is an opinionated tour of the literature on the reasons for which we hold beliefs and other doxastic attitudes, which I call ‘operative epistemic reasons’. After drawing some distinctions in §1, I begin in §2 by discussing the ontology of operative epistemic reasons, assessing arguments for and against the view that they are mental states. I recommend a pluralist non-mentalist view that takes seriously the variety of operative epistemic reasons ascriptions and allows these reasons to be both propositions (...) and truth-making facts. In §3, I turn to consider what it takes for a consideration to be an operative epistemic reason, examining three conditions – the representational, treating, and explanatory conditions – that have been proposed. I offer a novel view about the explanatory condition. In §4, I discuss the special case of inferential operative reasons and examine attempts to understand them in terms of rule-following, sketching a competence-based spinoff of dispositionalism. Finally, in §5, I consider whether there are non-inferential operative reasons, observing that one needn't countenance them to be a foundationalist but then developing a view about what they are and how they do and don't differ from inferential reasons. (shrink)

We propose a domain-level ontology of plays for the facilitation of play-based collaborative autonomy among unmanned and manned-unmanned aircraft teams in the Army’s Unmanned Aircraft System (UAS) mission domain. We define a play as a type of plan that prescribes some pattern of intentional acts that are intended to reliably result in some goal in some competitive context, and which specifies one or more roles that are realized by those prescribed intentional acts. The ontology is well suited to be extended (...) to other types of military and nonmilitary unmanned vehicle operations. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Reasons fundamentalists maintain that we can analyze all derivative normative properties in terms of normative reasons. These theorists famously encounter the Wrong Kind of Reasons problem, since not all reasons for reactions seem relevant for reasons-based analyses. Some have argued that this problem is a general one for many theorists, and claim that this lightens the burden for reasons fundamentalists. We argue in this paper that the reverse is true: the generality of the problem makes life harder for reasons fundamentalists. (...) We do this in two stages. First, we show that reflection on the generality of the distinction between wrong-kind reasons and right-kind reasons shows that not all right-kind reasons are normative reasons. So, not only do reasons-based analyses require a distinction between right-kind reasons and wrong-kind reasons, they also need a distinction between normative right-kind reasons from nonnormative right-kind reasons. We call this the Right Kind of Reasons Problem. In the second stage of the paper, we argue that reasons fundamentalism places tight constraints on its proper solution: in particular, it forbids one from appealing to anything normative to distinguish normative RKRs from nonnormative RKRs. It hence seems that reasons fundamentalists can only appeal to natural facts to solve the problem, but it is unclear which ones can do the job. So, reflection on the generality of the distinction only multiplies the fundamentalist’s problems. We end by exploring several solutions to these problems, and recommend a form of constitutivism as the best. (shrink)

This paper considers the place of reasons in the metaphysics of epistemic normativity and defends a middle ground between two popular extremes in the literature. Against members of the ‘reasons first’ movement, we argue that reasons are not the sole fundamental constituents of epistemic normativity. We suggest instead that the virtue-theoretic property of competence is the key building block. To support this approach, we note that reasons must be possessed to play a role in the analysis of central epistemically normative (...) properties, and argue that the relation of possession must be analyzed in terms of competence. But while we diverge with reasons-firsters on this score, we also distance ourselves from those who deny reasons any important role in epistemology. For we maintain that possessed reasons do help to ground deontic facts in the epistemic domain (e.g., facts about what one epistemically ought to believe, may believe, or is justified in believing). Indeed, we present an argument that the possession of sufficient epistemic reasons is necessary and sufficient for propositional justification, and that proper basing on such reasons yields doxastic justification. But since possession and proper basing are themselves grounded in competence, reasons are not the end of the explanatory road: competence enables them to do their work, putting them—and us—in the middle. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Rationality requires us to respond to apparent normative reasons. Given the independence of appearance and reality, why think that apparent normative reasons necessarily provide real normative reasons? And if they do not, why think that mistakes of rationality are necessarily real mistakes? This paper gives a novel answer to these questions. I argue first that in the moral domain, there are objective duties of respect that we violate whenever we do what appears to violate our first-order duties. The existence of (...) these duties of respect, I argue, ensures that apparent moral reasons are exceptions to the independence of appearance and reality. I then extend these arguments to the domain of overall reason. Just as there are objective duties of respect for moral reasons that explain moral blameworthiness, so there are objective duties of respect for reasons that explain blameworthiness in the court of overall reason. The existence of these duties ensures that apparent reasons are exceptions to the independence of appearance and reality. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (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)

There is an emerging consensus within Natural Law that explains transgender identity as an “embodied misunderstanding.” The basic line of argument is that our sexual identity as male or female refers to our possible reproductive roles of begetting or conceiving. Since these two possibilities are determined early on by the presence or absence of a Y chromosome, our sexual identity cannot be changed or reassigned. I develop an argument from analogy, comparing gender and language, to show that this consensus is (...) premature. Language and gender imbue our body with further social meaning and so, I conclude, that just as we can learn multiple languages, so too can we learn multiple genders. Since language and gender each constitutively contribute to our wellbeing as a “second nature,” I argue against this consensus to show that the reason people who are transgender struggle to flourish is not because of a “troubled trans psyche,” but because there are conceptual, interpersonal, and institutional obstacles stacked against them. (shrink)

Many prominent proponents of Old and New Natural Law morally condemn sexual acts between people of the same sex because those acts are incapable of reproduction; they each offer a distinct set of supporting reasons. While some New Natural Law philosophers have begun to distance themselves from this moral condemnation, there are not many similarly ameliorative efforts within Old Natural Law. I argue for the bold conclusion that Old Natural Law philosophers can accept the basic premises of Old Natural Law (...) without also being committed to morally condemning sexual activity between people of the same sex. I develop an argument from analogy that shows how we can draw metaphysically distinct sub‐categories based on someone's capacity to experience the unitive goods of sex. This unitive capacity constitutes the sub‐category and provides a distinct principle for evaluating how members of that sub‐category (X) act as members of that sub‐category, rather than as acting as defective members of another category (Y). Even though my argument is ‘internal’ to Old Natural Law, I conclude by showing how these conclusions can also address some of the objections to same‐sex sex in New Natural Law. (shrink)

Philosophy and Phenomenological Research, EarlyView.

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

Categorization and memory for specific items are fundamental processes that allow us to apply knowledge to novel stimuli. This study directly compares categorization and memory using delay match to category (DMC) and delay match to sample (DMS) tasks. In DMC participants view and categorize a stimulus, maintain the category across a delay, and at the probe phase view another stimulus and indicate whether it is in the same category or not. In DMS, a standard item working memory task, participants encode (...) and maintain a specific individual item, and at probe decide if the stimulus is an exact match or not. Constrained Principal Components Analysis was used to identify and compare activity within neural networks associated with these tasks, and we relate these networks to those that have been identified with resting state-fMRI. We found that two frontoparietal networks of particular interest. The first network included regions associated with the dorsal attention network and frontoparietal salience network; this network showed patterns of activity consistent with a role in rapid orienting to and processing of complex stimuli. The second uniquely involved regions of the frontoparietal central executive network; this network responded more slowly following each stimulus and showed a pattern of activity consistent with a general role in role in decision-making across tasks. Additional components were identified that were associated with visual, somatomotor and default mode networks. (shrink)

We argue that we can avoid epistemic dilemmas by properly understanding the nature and epistemology of the suspension of judgment, with a particular focus on conflicts between higher-order evidence and first-order evidence.

The politics of climate change is marked by the fact that countries are dragging their heels in doing what they ought to do; namely, creating a binding global treaty, and fulfilling the duties assigned to each of them under it. Many different agents are culpable in this failure. But we can imagine a stylised version of the climate change case, in which no agents are culpable: if the bad effects of climate change were triggered only by crossing a particular threshold, (...) and it was reasonably, but mistakenly, believed by each country that insufficiently many other countries were willing to cooperate in order for that threshold to remain uncrossed, no country would be required to make a unilateral contribution. Yet even without culpability, we can diagnose a moral ill: the world has gone other than it should have. If not for the mistaken beliefs, there would have been a global climate treaty, and all the avoidance of future suffering that would come with it. In this article I argue that this moral ill has implications for the non-culpable agents, in that it generates duties to disgorge actual holdings over and above the counterpart holdings in the relevant counterfactual: those holdings the agents would have had, were the world to have gone as it should. (shrink)

Internalism holds that epistemic justification is determined by what is internal to the mind, not by facts about the mind-independent world. This paper introduces and defends a new kind of internalism that is rooted in rationalist ideas that have been neglected in recent epistemology, despite inspiring internalist projects in cognitive science. Ignoring rationalist insights has, I argue, damaged the prospects for internalism, by needlessly saddling internalists with empiricist burdens. Internalists can refuse these burdens by accepting a better philosophy of mind. (...) Rather than looking to 17th century rationalists, I look to Kant, and especially his idea that normativity is grounded in the constitution of agency and mind. A Kantian approach can avoid stock objections to internalism, I argue, and can also capture all the alleged benefits of externalism. The paper is structured as follows. In §2, I get back to basics and consider more ways to satisfy the core internalist template than have become standard. I draw attention to rationalist insights about how normativity could be grounded in the constitution of mind, and hypothesize that if internalism respects these insights, some problems disappear. I develop this hypothesis in §3 with a Kantian view. I further defend this view in §4. I conclude in §5 by explaining why Kantian internalism answers the latest challenges to internalism. (shrink)

On April 20, 1999, Eric Harris and Dylan Klebold shot and killed fifteen people at their high school in Columbine, Colorado. National media dubbed the event a “school shooting.” The term grimly expanded over the next several years to include similar events at army bases, movie theaters, churches, and nightclubs. Today, we commonly use the categories “mass shooter” and “mass shooting” to organize and classify information about gun violence. I will argue that neither category is an effective tool for reducing (...) gun violence and use empirical data to show how these categories perpetuate a moral panic that harms already vulnerable demographics. I conclude that we should instead favor a narrower description of individuals and events, (e.g., “X shot Y people at Z”) because we can talk about all of the relevant cases without contributing the undue harms. (shrink)