Religious faith may manifest itself, among other things, as a mode of seeing the ordinary world, which invests that world imaginatively (or inspiredly) with an unseen depth of divine intention and spiritual significance. While such seeing may well be truthful, it is also unavoidably constructive, involving the imagination in its philosophical sense of the capacity to organize underdetermined or ambiguous sense date into a whole or gestalt. One of the characteristic ways in which biblical narratives inspire and teach is by (...) renewing their characters’ and readers’ imagination. The texts do so not inexorably but in a similar way as (other) works of art. This paper therefore investigates the ways in which works of art engage and develop the imagination, and thereby enable renewed perceptual and cognitive engagement with the world. The paper introduces predictive processing as a helpful psychological theory for analyzing this dynamic, and outlines questions for further research. (shrink)

Philosophical treatments of natural kinds are embedded in two distinct projects. I call these the philosophy of science approach and the philosophy of language approach. Each is characterized by its own set of philosophical questions, concerns, and assumptions. The kinds studied in the philosophy of science approach are projectible categories that can ground inductive inferences and scientific explanation. The kinds studied in the philosophy of language approach are the referential objects of a special linguistic category—natural kind terms—thought to refer directly. (...) Philosophers may hope for a unified account addresses both sets of concerns. This paper argues that this cannot be done successfully. No single account can satisfy both the semantic objectives of the philosophy of language approach and the explanatory projects of the philosophy of science approach. After analyzing where the tensions arise, I make recommendations about assumptions and projects that are best abandoned, those that should be retained, and those that should go their separate ways. I also recommend adopting the disambiguating terminology of “scientific kinds” and “natural kinds” for the different notions of kinds developed in these different approaches. (shrink)

This paper explains the metaphysical implications of the view that species are individuals (SAI). I first clarify SAI in light of the separate distinctions between individuals and classes, particulars and universals, and abstract and concrete things. I then show why the standard arguments given in defense of SAI are not compelling. Nonetheless, the ontological status of species is linked to the traditional "species problem," in that certain species concepts do entail that species are individuals. I develop the idea that species (...) names are rigid designators and show how this provides additional motivation for SAI. (shrink)

This paper presents and defends an account of the coincidence of biological organisms with mereological sums of their material components. That is, an organism and the sum of its material components are distinct material objects existing in the same place at the same time. Instead of relying on historical or modal differences to show how such coincident entities are distinct, this paper argues that there is a class of physiological properties of biological organisms that their coincident mereological sums do not (...) have. The account answers some of the most pressing objections to coincidence, for example the so-called grounding problem , that material coincidence seems to require that coinciding objects have modal differences that do not supervene on any other properties. (shrink)

Philosophical arguments regarding academic freedom can sometimes appear removed from the real conflicts playing out in contemporary universities. This paper focusses on a set of issues at the front line of these conflicts, namely, questions regarding sex, gender and gender identity. We document the ways in which the work of academics has been affected by political activism around these questions and, drawing on our respective disciplinary expertise as a sociologist and a philosopher, elucidate the costs of curtailing discussion on fundamental (...) demographic and conceptual categories. We discuss some philosophical work that addresses the conceptual distinction between academic freedom and free speech and explore how these notions are intertwined in significant ways in universities. Our discussion elucidates and emphasises the educational costs of curtailing academic freedom. (shrink)

This chapter defends a pluralist understanding of species on which a normative species concept is viable and can support natural goodness evaluations. The central question here is thus: Since organisms are to be evaluated as members of their species, how does a proper understanding of species affect the feasibility of natural goodness evaluations? Philippa Foot has argued for a form of natural goodness evaluation in which living things are evaluated by how well fitted they are for flourishing as members of (...) their species, in ways characteristic of their species. She has further argued that assessments of moral goodness in humans are of the same evaluative form. However, natural goodness evaluations and, by extension, the natural goodness approach, do not garner justification in virtue of employing a scientifically privileged conception of species. The natural goodness approach is only justified given particular metaethical and normative commitments that are independent of naturalism, since the approach does not depend upon naturalism alone. (shrink)

Locke is often cited as a precursor to contemporary natural kind realism. However, careful attention to Locke’s arguments show that he was unequivocally a conventionalist about natural kinds. To the extent that contemporary natural kind realists see themselves as following Locke, they misunderstand what he was trying to do. Locke argues that natural kinds require either dubious metaphysical commitments (e.g., to substantial forms or universals), or a question-begging version of essentialism. Contemporary natural kind realists face a similar dilemma, and should (...) not appeal to Locke in their defense. (shrink)

: New genetic technologies continue to emerge that allow us to control the genetic endowment of future children. Increasingly the claim is made that it is morally "irresponsible" for parents to fail to use such technologies when they know their possible children are at risk for a serious genetic disorder. We believe such charges are often unwarranted. Our goal in this article is to offer a careful conceptual analysis of the language of irresponsibility in an effort to encourage more care (...) in its use. Two of our more important sub-claims are: A fair judgment of genetic irresponsibility necessarily requires a thick background description of the specific reproductive choice; and there is no necessary connection between an act's being morally wrong and its being irresponsible. These are distinct judgments requiring distinct justifications. (shrink)

In Ethics 1p5, Spinoza asserts that “In Nature there cannot be two or more substances of the same nature or attribute”. This claim serves as a crucial premise in Spinoza’s argument for substance monism, yet Spinoza’s demonstration of the 1p5 claim is surprisingly brief and appears to have obvious difficulties. This paper answers the principle difficulties that have been raised in response to Spinoza’s argument for 1p5. The key to understanding the 1p5 argument lies in a proper understanding of the (...) substance-attribute relationship and the principles of metaphysical individuation that Spinoza accepts. (shrink)

This paper analyses the opposing accounts of ‘the ordinary’ given by Jacques Derrida and Stanley Cavell, beginning with their competing interpretations of J. L. Austin¹s thought on ordinary language. These accounts are presented as mutually critiquing: Derrida¹s deconstructive method poses an effective challenge to Cavell¹s claim that the ordinary is irreducible by further philosophical analysis, while, conversely, Cavell¹s valorisation of the human draws attention to a residual humanity in Derrida¹s text which Derrida cannot account for. The two philosophers’ approaches are, (...) in fact, predicated on each other like the famous Gestalt-image of a vase and two faces: they cannot come into focus at the same time, but one cannot appear without the other to furnish its background. (shrink)

It has been argued that some animals are moral subjects, that is, beings who are capable of behaving on the basis of moral motivations. In this paper, we do not challenge this claim. Instead, we presuppose its plausibility in order to explore what ethical consequences follow from it. Using the capabilities approach, we argue that beings who are moral subjects are entitled to enjoy positive opportunities for the flourishing of their moral capabilities, and that the thwarting of these capabilities entails (...) a harm that cannot be fully explained in terms of hedonistic welfare. We explore the implications of this idea for the assessment of current practices involving animals. (shrink)

Bioethicists appearing in the media have been accused of "shooting from the hip" (Rachels, 1991). The criticism is sometimes justified. We identify some reasons our interactions with the press can have bad results and suggest remedies. In particular we describe a target (fostering better public dialogue), obstacles to hitting the target (such as intrinsic and accidental defects in our knowledge) and suggest some practical ways to surmont those obstacles (including seeking out ways to write or speak at length, rather than (...) in sound bites). We make use of our own research into the way journalists quote bioethicists. We end by suggesting that the profession as a whole look into this question more fully. (shrink)

This paper has two aims. The first is to describe several sources of the moral responsibility to remedy or alleviate global poverty—reasons why an agent might have such a responsibility. The second is to consider what sorts of agents bear the responsibilities associated with each source—in particular, whether they are collective agents like states, societies, or corporations, on the one hand, or individual human beings on the other. We often talk about our responsibilities to the poorest people in the world, (...) or what we owe them. So the question is who this we is. I shall argue that the answer depends on the source of the responsibility. Some responsibilities—one species of causal responsibilities—belong in the first instance to collectives, although they will also trickle down to at least some individuals within the collective. Other responsibilities—humanitarian responsibilities, and a different species of causal responsibilities—belong in the first instance to individuals, but can, I shall argue, “trickle up” to collectives of which individuals are members. (shrink)

When people act to aid others, they get something in return—at the very least, the satisfaction of having their desire to help fulfilled. Some conclude from this and other puzzles about motivation that people always act simply to benefit themselves. But this is an error: there is altruism in the world, although it is often inextricably linked with the well-being of the agent who does good.

Moral distress is the sense that one must do, or cooperate in, what is wrong. It is paradigmatically faced by nurses, but it is almost a universal occupational hazard.

Business Ethics and medical ethics are in principle compatible: In particular, the tools of business ethics can be useful to those doing healthcare ethics. Health care could be conducted as a business and maintain its moral core.

A discussion of the ethics of stem cell research, and attempts to regulate it.

Elderhood—or old age, if one prefers—is a stage of life without much cultural meaning. It is generally viewed simply as a time of regrettable decline. Paying more attention to it, to its special pleasures and developmental achievements, will be helpful not only to elders but to those younger as well. I will argue that three existential tasks are central in elderhood, but also important at every other stage of adult life. I identify three: cherishing the present, accepting the past, and (...) investing in a future broader than one’s own. Articulating these tasks is intellectually interesting, useful to elders, and should be enlightening (as well as reassuring) to younger adults. (shrink)

Margaret Urban Walker argues that hospital ethics committees should think of their task as "keeping moral space open." I develop her suggestion with analogies: Enlarge the windows (i.e., expand what counts as an ethical issue); add rooms and doors (i.e., choose particular issues to engage). Examples include confidentiality defined as information flow, and moral distress in the healthcare workplace.

As feminist theory explicates its fundamental principles – justice for the oppressed – it can lose its essential focus on the situation of women. One example is the inattention to nurses within feminist bioethics. Nurses deserve attention because most are women, but also because their lack of power is paradigmatic of patriarchy. Those examining ethics consultations should discuss whether nurses are allowed to request them. But feminists also need to imagine ways in which nurses can be heard when, for instance, (...) their worklives are “redesigned.” Doing so would also allow attention to other classes of the disempowered. (shrink)

Tradução do artigo "What is Critique? An Essay on Foucault's Virtue.".

Faculty resistance to Writing Across the Curriculum (WAC) is an issue that has been recognized by WAC program directors and practitioners for decades, yet it remains unresolved. Perhaps the problem is not resistance per se, but how we interpret and react to it. Faculty resistance is typically viewed as an impediment to the pedagogical change WAC programs hope to achieve. Moreover, the label of "resistance" is often used without further examination of the underlying causes. Based on research and experience as (...) doctoral Writing Fellows in the Borough of Manhattan Community College WAC Program, we argue that so-called resistances are often justified concerns in regard to implementing WAC under given institutional, disciplinary, departmental, and personal constraints. We also suggest that if we listen and respond to these concerns, they become means to facilitate faculty engagement with WAC. By working through their concerns and adapting WAC to their context, faculty can take ownership of WAC and further develop the practice. Thus, what at first appears to be an impediment to deep-rooted pedagogical change ”resistance” can be used to encourage faculty to make WAC their own. (shrink)

The UK Government's Higher Education (Freedom of Speech) Bill is currently progressing through Parliament. The bill is designed to strengthen free speech and academic freedom in higher education, in response to what former Education Secretary Gavin Williamson describes as ‘the rise of intolerance and cancel culture upon our campuses’. But is there really a crisis of academic freedom in British universities?To see that there is, say Judith Suissa and Alice Sullivan, we need only look at the contemporary reality of (...) suppression of debate on sex and gender. The evidence they catalogue of suppression of research, of blacklisting, harassment and smear campaigns, of no-platforming, disinvitations and shutting down of events, is incontrovertible. The recent experience of scholars and students wishing to discuss the material reality and political salience of sex makes complacency about academic freedom a luxury we cannot afford.Suissa and Sullivan set out a powerful argument for the role of academic freedom in pursuing truth within the academy and developing democracy beyond it. They effectively counter attempts to narrow the scope of academic freedom so as to render it compatible with no-platforming. And they lay out a series of practical steps administrators can take to ensure that universities are places where an expansive and pluralistic intellectual climate prevails.This is a timely and compelling intervention in a vexed but urgent public debate. For their clear-sighted diagnosis of where and how academic freedom has been eroded in our universities, and for their judicious account of what must be done to rebuild it, Suissa and Sullivan deserve a wide and attentive hearing. (shrink)

“Postularse como un ser radicalmente autogenerado, ser el autor de la propia voluntad y conocimiento, es negar que uno está constituido en y por lo que es infinitamente más grande que el individuo humano. Kierkegaard llamará a esta fuente más grande que todo lo humano 'Dios' o 'el infinito'. Negar que uno está constituido en lo que es más grande que uno mismo es, para Kierkegaard, estar en una especie de desesperación”.

Friedrich Wilhelm Joseph von Schelling (1775-1854) is often thought of as a “philosopher’s philosopher,” with a specialist rather than generalist appeal. One reason for Schelling’s lack of popularity is that he is something of a problem case for traditional narratives about the history of philosophy. Although he is often slotted in as a stepping stone on the intellectual journey from Kant to Hegel, any attention to his ideas will show that he does not fit this role very well. His later (...) philosophy suggests a materialism and empiricism that puts him outside of idealism proper; his connection with the romantic movement suggests an aestheticism that challenges traditional philosophy as such; and his mysticism allies him with medieval, pre-critical philosophies considered antiquated by the 19th century. And if Schelling was not entirely at home with his contemporaries, he seems, on the face of it, to have fared little better with his future: there has been no Schelling school, he has had no followers. No historical trajectory announces Schelling as its point of departure. -/- And yet Schelling’s influence has been an extraordinary one. He has inspired physicists, physicians, theologians, historians and poets. A wildly diverse set of philosophers have claimed that their ideas have resonance with his. Perhaps the question of Schelling’s influence can be approached by looking at what Kant says about works of genius -- that they should give rise to inspiration, not imitation. Paradoxically, to imitate genius is not to produce an imitation but a new creative work. Whether or not Schelling should be strictly viewed as a genius, Kant’s notion suggests a sense in which Schelling should be understood as a “philosopher’s philosopher”; he inspired creativity, not repetition. In this perspective, the lack of a “Schelling school” is a sign of strength; Schelling is continually being rediscovered, and his works have retained a fresh and untimely character. If Schelling does not have any obvious historical successors, it is because his influence cannot be charted by the usual methods. New philosophical tools are needed in order to understand his philosophical significance, his impact on contemporary thought and relevance for contemporary concerns. (shrink)

The work under consideration addresses a fundamental problem in cognitive neuroscience and social science. Although both aim to explain and understand human action, their explanatory tools are so divergent that our theories are riddled with conceptual gaps. Both fields are moreover permeated by old-fashioned action theory and folk psychology, which explain and understand action in terms of mind-reading and attributing beliefs, desires, and intentions to others. While these theories may work pragmatically in navigating our social world, they are increasingly questioned (...) as a basis for our theorizing. These and other problems within both disciplines have long held back a much-needed multidisciplinary approach to human action from gaining traction. Turner’s book aims to set it free. In this review I assess the book based on the key argumentative steps in Turner’s analysis, rather than providing a chapter-by-chapter overview. (shrink)

Schopenhauer is famously abusive toward his philosophical contemporary and rival, Friedrich William Joseph von Schelling. This chapter examines the motivations for Schopenhauer’s immoderate attitude and the substance behind the insults. It looks carefully at both the nature of the insults and substantive critical objections Schopenhauer had to Schelling’s philosophy, both to Schelling’s metaphysical description of the thing-in-itself and Schelling’s epistemic mechanism of intellectual intuition. It concludes that Schopenhauer’s substantive criticism is reasonable and that Schopenhauer does in fact avoid Schelling’s errors: (...) still, the vehemence of the abuse is best perhaps explained by the proximity of their philosophies, not the distance. Indeed, both are developing metaphysics of will with full and conflicted awareness of the Kantian epistemic strictures against metaphysics. In view of this, Schopenhauer is particularly concerned to mark his own project as legitimate by highlighting the manner in which he avoids Schelling’s errors. (shrink)

Humans interact with animals in numerous ways and on numerous levels. We are indeed living in an “animal”s world,’ in the sense that our lives are very much intertwined with the lives of animals. This also means that animals, like those dogs we commonly refer to as our pets, are living in a “human’s world” in the sense that it is us, not them, who, to a large degree, define and manage the interactions we have with them. In this sense, (...) the human-animal relationship is nothing we should romanticize: it comes with clear power relations and thus with a set of responsibilities on the side of those who exercise this power. This holds, despite the fact that we like to think about our dogs as human’s best friend. Dogs have been part of human societies for longer than any other domestic species. Like no other species they exemplify the role of companion animals. Relationships with pet dogs are both very widespread and very intense, often leading to strong attachments between owners or caregivers and animals and to a treatment of these dogs as family members or even children. But how does this relationship look from the dogs’ perspective? How do they perceive the humans they engage with? What responsibilities and duties arise from the kind of mutual understanding, attachment, and the supposedly “special” bonds we form with them? Are there ethical implications, maybe even ethical implications beyond animal welfare? The past decades have seen an upsurge of research from comparative cognition on pet dogs’ cognitive and social skills, especially in comparison with and reference to humans. We will therefore set our discussion about the nature and ethical dimensions of the human–dog relationship against the background of the current empirical knowledge on dog (social) cognition. This allows us to analyze the human–dog relationship by applying an interdisciplinary approach that starts from the perspective of the dog to ultimately inform the perspective of humans. It is our aim to thereby identify ethical dimensions of the human–dog relationship that have been overlooked so far. (shrink)

The focus of this study was to investigate "principals' administrative competence and teachers work performance" in Calabar Education zone. Four null hypotheses were tested in the course of the study. Correlational research design was adopted, while purposive sampling technique was used in selecting a sample of 800 teachers. Two instruments were used for data collection including "Principals' Administrative Competence Questionnaire (PACQ)," and Teachers' Work Performance Questionnaire (TWPQ)." Pearson Product Moment Correlation Analysis (r) and multiple regression (R) analysis were employed to (...) test the hypotheses at.05 level of significance were applicable, with the aid of SPSS v21. Findings from the study revealed that; principals' supervisory, leadership and communication competences are significantly related to teachers' work performance in terms of instructional delivery, attendance to classes, notes writing, and record keeping respectively. It was also revealed that; principals' supervisory, leadership and communication competences have significant composite influence on teachers' work performance in terms of instructional delivery (p <.05; F = 26.764), attendance to classes (p <.05; F = 109.122), notes writing (p <.05; F = 228.118), and record keeping (P <.05; F = 468.793). Based on these findings, it was recommended amongst others that; such techniques as close supervision of teachers, good leadership styles, and effective communication should be jointly practiced by secondary school principals in order to improve teachers' work performance. (shrink)

‘Romanticism’ is one of the more hotly contested terms in the history of ideas. There is a singular lack of consensus as to its meaning, unity, and historical extension, and many attempts to fix the category of romanticism very quickly become blurry. As a result, the great historian of ideas, Arthur Lovejoy, famously concludes that: ‘the word ‘romantic’ has come to mean so many things that, by itself, it means nothing. It has ceased to perform the function of a verbal (...) sign’ But his pessimistic advice has not stopped scholars from trying to define romanticism. If anything, it has brought renewed vigour to the determination with which critics try to pinpoint the term. There are several approaches to take, for those who attempt to do so. One class of critics tries to enumerate the features shared by the authors and texts generally considered romantic. An alternative approach would try to identify the fundamental unity that informs romanticism and gives rise to the empirical commonalities. But what would this essential feature be? Both of these approaches take an external perspective on romanticism, seeing it as the object of inquiry. An alternative approach, which we will pursue, looks at romantic subjects, and romanticism as a self-constituting category, rather than merely as an externally imposed one. In other words, we will take as basic neither an (empirical) array of candidate properties constituting romanticism, nor a supposed underlying (rationalist) essence from which properties can be derived, but rather we will focus on how the romantics themselves took up the idea of romanticism and transformed it into a self-conscious movement. We will treat the question of romanticism with respect to England, but above all Germany. Although romantic movements arose and flourished elsewhere in Europe (and in France in particular), German and English romanticism were uniquely theoretically sophisticated and philosophically nuanced. (shrink)

It is sometimes claimed that as members of the species Homo sapiens we have a responsibility to promote the good of Homo sapiens itself (distinct from the good of its individual members). Lawrence Johnson has recently defended this claim as part of his approach to resolving the problem of future generations. We show that there are several difficulties with Johnson's argument, many of which are likely to attend any attempt to establish the moral considerability of Homo sapiens or species generally. (...) Further, even if Homo sapiens were morally considerable, this would not ground an adequate response to the problem of future generations. The sort of moral considerability that would be appropriate to Homo sapiens, or species generally, would not be as robust nor have the implications that many have supposed. (shrink)

Religious faith may manifest itself, among other things, as a mode of seeing the ordinary world, which invests that world imaginatively with an unseen depth of divine intention and spiritual significance. While such seeing may well be truthful, it is also unavoidably constructive, involving the imagination in its philosophical sense of the capacity to organize underdetermined or ambiguous sense date into a whole or gestalt. One of the characteristic ways in which biblical narratives inspire and teach is by renewing their (...) characters’ and readers’ imagination. The texts do so not inexorably but in a similar way as works of art. This paper therefore investigates the ways in which works of art engage and develop the imagination, and thereby enable renewed perceptual and cognitive engagement with the world. The paper introduces predictive processing as a helpful psychological theory for analyzing this dynamic, and outlines questions for further research. (shrink)

This paper examined the relationship between tertiary students’ social media management attitudes and their academic performance in Cross River State, with a specific focus on Facebook, WhatsApp, and Instagram. To achieve this purpose, three null hypotheses were formulated accordingly. The study adopted a correlational research design. Cluster and simple random sampling techniques were used to select a sample of 1000 students from the entire population. The instrument used for data collection was a questionnaire titled: Tertiary Students’ Social Media Management and (...) Academic Performance Questionnaire (TESSMMAPQ). The reliability of the instrument was established through Cronbach alpha and estimate of .93 was obtained indicating that the instrument was internally consistent in measuring what it purports to measure. Pearson Product Moment Correlation Analysis used to analyze data and to test the hypotheses at .05 level of significance. Findings revealed that there is no significant relationship between tertiary students Facebook management attitudes (r. cal.0.032 < crit. r.0.062), WhatsApp management attitudes (r. cal.0.038 < crit. r.0.062), and Instagram management attitudes (r. cal.-0.009 < crit. r.0.062) respectively, with their academic performance. Based on these findings it was recommended among others that; tertiary students' social media usage should be regulated by smartphones producers and internet service providers; in such a way that a maximum monthly login interval (MMLI) is provided that will restrict users to a limited number of login chances. This will ensure that students maintain focus when they have been barred. (shrink)

How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, Symbiosis and Individuality: Conceptual and Philosophical Issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of (...) incorporating into meetings experts from other disciplines, such as philosophy and history of science. (shrink)

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

The empirical phenomenon at the center of this paper is projection, which we define (uncontroversially) as follows: (1) Definition of projection An implication projects if and only if it survives as an utterance implication when the expression that triggers the implication occurs under the syntactic scope of an entailment-cancelling operator. Projection is observed, for example, with utterances containing aspectual verbs like stop, as shown in (2) and (3) with examples from English and Paraguayan Guaraní (Paraguay, Tupí-Guaraní).1 The Guaraní example in (...) (2) and its English translation have at least the following implications: (i) Carla has previously smoked, and (ii) Carla stopped smoking. The first but not the second of these implications is also conveyed by the question version of sentence (2), as in (3a), or when (2) is embedded under entailment-cancelling sentential operators, such as negation, as in (3b), the antecedent of a conditional, as in (3c), or an epistemic modal, as in (3d). Hence, by the definition in (14), the first but not the second implication of (2) projects. (shrink)

This project continues our interdisciplinary research into computational and cognitive aspects of narrative comprehension. Our ultimate goal is the development of a computational theory of how humans understand narrative texts. The theory will be informed by joint research from the viewpoints of linguistics, cognitive psychology, the study of language acquisition, literary theory, geography, philosophy, and artificial intelligence. The linguists, literary theorists, and geographers in our group are developing theories of narrative language and spatial understanding that are being tested by the (...) cognitive psychologists and language researchers in our group, and a computational model of a reader of narrative text is being developed by the AI researchers, based in part on these theories and results and in part on research on knowledge representation and reasoning. This proposal describes the knowledge-representation and natural-language-processing issues involved in the computational implementation of the theory; discusses a contrast between communicative and narrative uses of language and of the relation of the narrative text to the story world it describes; investigates linguistic, literary, and hermeneutic dimensions of our research; presents a computational investigation of subjective sentences and reference in narrative; studies children’s acquisition of the ability to take third-person perspective in their own storytelling; describes the psychological validation of various linguistic devices; and examines how readers develop an understanding of the geographical space of a story. This report is a longer version of a project description submitted to NSF. This document, produced in May 2007, is a L ATEX version of Technical Report 89-07 (Buffalo: SUNY Buffalo Department of Computer Science, August 1989), with slightly.. (shrink)

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

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

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

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)