Unintended consequences of existential quantifications in biomedical ontologies

<p>Abstract</p> <p>Background</p> <p>The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors.</p> <p>Results</p> <p>We analyzed ontologies and ontology cross products available via the OBO Foundry site <url>http://www.obofoundry.org</url> for existential restrictions (<it>someValuesFrom</it>), from which we examined a random sample of 2,836 clauses.</p> <p>According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' <it>κ </it>= 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (<it>κ </it>= 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations.</p> <p>Conclusions</p> <p>The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints.</p

Philosophical Issues From Kripke's 'Semantical Considerations on Modal Logic'

In ‘Semantical Considerations on Modal Logic’, Kripke articulates his project in the discourse of “possible worlds”. There has been much philosophical discussion of whether endorsement of the Kripke semantics brings ontological commitment to possible worlds. However, that discussion is less than satisfactory because it has been conducted without the necessary investigation of the surrounding philosophical issues that are raised by the Kripke semantics. My aim in this paper is to map out the surrounding territory and to commence that investigation. Among the surrounding issues, and my attitudes to them, are these: (1) the potential of the standard distinction between pure and impure versions of the semantic theory has been under-exploited; (2) there has been under-estimation of what is achieved by the pure semantic theory alone; (3) there is a methodological imperative to co-ordinate a clear conception of the purposes of the impure theory with an equally clear conception of the content the theory; (4) there is a need to support by argument claims about how such a semantic theory, even in an impure state, can fund explanations in the theory of meaning and metaphysics; (5) greater attention needs to be paid to the crucial advance that Kripke makes on the precursors of possible-worlds semantics proper (e.g. Carnap 1947) in clearly distinguishing variation across the worlds within a model of modal space from variation across such models and, finally, (6) the normative nature of the concept of applicability, of the pure semantic theory, is both of crucial importance and largely ignored

Structural Parsimony

Many metaphysicians often appeal to Hume’s dictum (HD), according to which there are no necessary connections between distinct entities (or states of entities), in order to resist theories that commit us to such connections. Some have argued that HD is an unsupported dogma of metaphysics. But theories that commit us to necessary connections between distinct goings-on can also be resisted by invoking a normative twist on HD, which I call the Humean Solvent (HS): “Do not connect distinct entities (or states of entities) beyond necessity”. HS is a principle of structural parsimony – assuming that a theory is structurally more parsimonious than another when the latter is committed to a more connected ontology than the former is. Just as Ockham’s ‘razor’ encourages us to cut down superfluous ontological commitments, the Humean ‘solvent’ encourages us to dissolve dispensable metaphysical glue: we ought not to glue elements of our ontology beyond necessity. HS has both a qualitative and a quantitative dimension: qualitatively, it encourages us to avoid using metaphysical glues that are unnecessarily strong, the strongest of which being metaphysically necessary connections; quantitatively, it encourages us not to metaphysically glue things that need no gluing. Thus, given HS, other things being equal, what is worst is a theory that entails that everything is metaphysically necessarily connected to anything else and what is best is a theory that leaves all things loose and separable. In this paper, I will first compare HD and HS as grounds for paradigmatic Humean doctrines in contemporary metaphysics, then I will argue that structural parsimony is neither a variety of ontological nor of ideological parsimony; finally, I will offer an argument for HS

Where constructionism and critical realism converge: interrogating the domain of epistemological relativism

The paper interrogates the status, nature and significance of epistemological relativism as a key element of constructionism and critical realism. It finds that epistemological relativism is espoused by authorities in critical realism and marginalized or displaced in the field of management and organization studies, resulting in forms of analysis that are empirically, but not fully critically, realist. This evaluation prompts reflection on the question of whether, how and with what implications epistemological relativism might be recast at the heart of critical realist studies of management and organization

Rhetorical contestation involving disputed organizational and ontological categories

In this dissertation, through three articles, I explore rhetorical contestation of disputed organizational and ontological categories. In the first article, I analyze connections between some categories of the Department of Homeland Security (DHS) and the Federal Emergency Management Agency (FEMA) involving conflicting interpretations on the part of the two organizations and issues of structure, agency, and power in the two organizations as they responded to Hurricane Katrina. In the second and the third articles, I explore ontological categories of science and non-science in a boundary-work dispute (Gieryn, 1983; Taylor, 1996) at Iowa State University between proponents of teaching only evolution and proponents of teaching Intelligent Design as well. My analysis of DHS and FEMA\u27s disputed categories shows a shift in organizational power unaccounted for by previous rhetorical studies. Specifically, legitimated or dominant categories (Giddens, 1984) of DHS came to be delegitimated through kairotic agency (Herndl & Licona, 2007) of a FEMA agent and unintended consequences (Giddens, 1984) of these categories. In the first article involving the debate at Iowa State, I show how the main rhetorical basis for boundary-work between evolution and its opponents has changed from Popper\u27s falsification theory to methodological naturalism. The change throws light on rhetorical core of these disputes and provides an illustration of science as an institutional category (Kinsella, 2005). In the second article, I explore a relatively underexplored basis for boundary-work--academic freedom--in a relatively underexplored setting--higher education. My analysis suggests that differences in academic freedom in settings of public schools and higher education are key to different boundary-work by proponents and opponents of evolution in these two types of settings

Constructing futures: a social constructionist perspective on foresight methodology

The aim of this paper is to demonstrate the relationship between a particular epistemological perspective and foresight methodology. We draw on a body of social theory concerned with the way that meaning is produced and assimilated by society; specifically, the social construction of knowledge, which is distinguished from its nearneighbour constructivism by its focus on inter-subjectivity. We show that social constructionism, at least in its weak form, seems to be implicit in many epistemological assumptions underlying futures studies. We identify a range of distinctive methodological features in foresight studies, such as time, descriptions of difference, participation and values, and examine these from a social constructionist perspective. It appears that social constructionism is highly resonant with the way in which knowledge of the future is produced and used. A social constructionism perspective enables a methodological reflection on how, with what legitimacy, and to what social good, knowledge is produced. Foresight that produces symbols without inter-subjective meaning neither anticipates, nor produces futures. Our conclusion is that foresight is both a social construction, and a mechanism for social construction. Methodologically, foresight projects should acknowledge the socially constructed nature of their process and outcomes as this will lead to greater rigour and legitimacy

From "Infant Hercules" to "Ghost Town":Industrial collapse and social harm on Teesside

This article explicates the harms associated with deindustrialization in Teesside in the North East of England in the context of neoliberalism. Drawing on in-depth qualitative interviews (n = 25), the article explores how ongoing industrial collapse, typified by Sahaviriya Steel Industries’ (SSI) closure in 2015, has generated various harms. First, the article examines industrialism’s socioeconomic security and stability. It then explores the negative impact of SSI’s closure in 2015, including a sense of loss and unemployment. Next, it demonstrates how the absence of economic stability produces harmful outcomes, namely insecurity, mental health problems and bleak visions of the future. The article concludes by casting industrial ruination as an impediment to human flourishing; the normal functioning of capitalism represents a “negative motivation to harm” that prevents the stability and security necessary for individual and collective flourishin

Warts and all: using student portfolio outcomes to facilitate a faculty development workshop

In 2004, the Department of Writing Studies at Roger Williams University in Bristol, Rhode Island, the U.S., began an assessment of student outcomes for two first-year writing courses (Fall 04 to Fall 05) to evaluate performance on previously established criteria. A study of the students’ Portfolio Assessment Sheets concluded that one pervasive problem was “Development” as determined partly by low A grades in the two courses. To engage the faculty (full-time and adjunct), the grades from Fall 04, Spring 05, and Fall 05 were presented during a SummerWorkshop in June 2006. After analyzing a sample student essay, the 28 faculty participants discussed the implications of “Development” and evaluated the presentation itself. This case study of one college’s participatory exercise in improving writing found some faculty resistance and some unintended results

Social Objects

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.