The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (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 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 Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set (...) has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)
Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)
In this rare firsthand account of an individual's pursuit of sagehood, the early Ming dynasty scholar and teacher Wu Yubi chronicles his progress and his setbacks, as he strives to integrate the Neo-Confucian practices of self-examination and self-cultivation into everyday life. In more than three hundred entries, spanning much of his adult life, Wu paints a vivid picture, not only of the life of the mind, but also of the life of a teacher of modest means, struggling to make ends (...) meet in a rural community. This volume features M. Theresa Kelleher's superb translation of Wu's journal, along with translations of more than a dozen letters from his personal correspondence. A general Introduction discusses Neo-Confucianism and the Ming dynasty, and includes biographical information that puts the main work in context. A substantial commentary on the journal discusses the obstacles and supports Wu encounters in pursuit of his goal, the conflict between discipline and restraint of the self and the nurturing and expanding of the self, Wu's successes and failures, and Wu’s role as a teacher. Also included are a map of the Ming dynasty, a pronunciation guide, a chronology of Chinese dynasties, a glossary of names, a glossary of book titles, and suggestions for further reading. (shrink)
I use network models to simulate social learning situations in which the dominant group ignores or devalues testimony from the marginalized group. I find that the marginalized group ends up with several epistemic advantages due to testimonial ignoration and devaluation. The results provide one possible explanation for a key claim of standpoint epistemology, the inversion thesis, by casting it as a consequence of another key claim of the theory, the unidirectional failure of testimonial reciprocity. Moreover, the results complicate the understanding (...) and application of previously discovered network epistemology effects, notably the Zollman effect (Zollman 2007, 2010). (shrink)
In the spring of 1900, British archaeologist Arthur Evans began to excavate the palace of Knossos on Crete, bringing ancient Greek legends to life just as a new century dawned amid far-reaching questions about human history, art, and culture. With _Knossos and the Prophets of Modernism_, Cathy Gere relates the fascinating story of Evans’s excavation and its long-term effects on Western culture. After the World War I left the Enlightenment dream in tatters, the lost paradise that Evans offered in (...) the concrete labyrinth—pacifist and matriarchal, pagan and cosmic—seemed to offer a new way forward for writers, artists, and thinkers such as Sigmund Freud, James Joyce, Giorgio de Chirico, Robert Graves, and Hilda Doolittle. Assembling a brilliant, talented, and eccentric cast at a moment of tremendous intellectual vitality and wrenching change, Cathy Gere paints an unforgettable portrait of the age of concrete and the birth of modernism. (shrink)
Recent discussions of moral testimony have focused on the acceptability of forming beliefs on the basis of moral testimony, but there has been little acknowledgement of the limits to testimony's capacity to convey moral knowledge. In this paper I outline one such limit, drawing on Iris Murdoch's conception of private moral concepts. Such concepts, I suggest, plausibly play an important role in moral thought, and yet moral knowledge expressed in them cannot be testimonially acquired.
This book presents a systematic account of the role of the personal spiritual ideal of wu-wei--literally "no doing," but better rendered as "effortless action"--in early Chinese thought. Edward Slingerland's analysis shows that wu-wei represents the most general of a set of conceptual metaphors having to do with a state of effortless ease and unself-consciousness. This concept of effortlessness, he contends, serves as a common ideal for both Daoist and Confucian thinkers. He also argues that this concept contains within itself a (...) conceptual tension that motivates the development of early Chinese thought: the so-called "paradox of wu-wei," or the question of how one can consciously "try not to try." Methodologically, this book represents a preliminary attempt to apply the contemporary theory of conceptual metaphor to the study of early Chinese thought. Although the focus is upon early China, both the subject matter and methodology have wider implications. The subject of wu-wei is relevant to anyone interested in later East Asian religious thought or in the so-called "virtue-ethics" tradition in the West. Moreover, the technique of conceptual metaphor analysis--along with the principle of "embodied realism" upon which it is based--provides an exciting new theoretical framework and methodological tool for the study of comparative thought, comparative religion, intellectual history, and even the humanities in general. Part of the purpose of this work is thus to help introduce scholars in the humanities and social sciences to this methodology, and provide an example of how it may be applied to a particular sub-field. (shrink)
In this paper, we outline some of the connections between the literatures of organizational storytelling, spirituality in the workplace, organizational culture, and authentic leadership. We suggest that leader storytelling that integrates a moral and spiritual component can transform an organizational culture so members of the organization begin to feel connected to a larger community and a higher purpose. We specifically discuss how leader role modeling in authentic storytelling is essential in developing an ethically and spiritually based organizational culture. However, we (...) also acknowledge a potential dark side to leader storytelling. Implications for authentic storytelling research and practice are discussed. (shrink)
This article furthers the argument for a stakeholder theory that integrates into managerial decision-making the relationship between business organizations and the natural environment. The authors review the literature on stakeholder theory and the debate over whom or what should count as a stakeholder. The authors also critique and expand the stakeholder identification and salience model developed by Mitchell and Wood (1997) by reconceptualizing the stakeholder attributes of power, legitimacy, and urgency, as well as by developing a fourth stakeholder attribute: proximity. (...) In this way, the authors provide a stronger basis for arguing for the salience of the natural environment as the primary and primordial stakeholder of the firm. (shrink)
Behavioral ethics research has focused predominantly on how the attributes of individuals influence their ethicality. Relatively neglected has been how macro-level factors such as the behavior of firms influence members’ ethicality. Researchers have noted specifically that we know little about how a firm’s CSR influences members’ behaviors. We seek to better merge these literatures and gain a deeper understanding of the role macro-level influences have on manager’s ethicality. Based on agency theory and social identity theory, we hypothesize that a company’s (...) commitment to CSR shifts managers’ focus away from self-interests toward the interests of the firm, bolstering resistance to temptation. We propose this occurs through self-categorization and collective identification processes. We conduct a 2 × 2 factorial experiment in which managers make expense decisions for a company with commitment to CSR either present or absent, and temptation either present or absent. Results indicate that under temptation, managers make decisions consistent with self-interest. More importantly, we find when commitment to CSR is present, managers are more likely to make ethical decisions in the presence of temptation. Overall, this research highlights the interactive role of two key contextual factors—temptation and firm CSR commitment—in influencing managers’ ethical decisions. While limited research has highlighted the positive effects that a firm’s CSR has on its employees’ attitudes, the current results demonstrate CSR’s effects on ethical behavior and imply that through conducting and communicating its CSR efforts internally, firms can in part limit the deleterious effects of temptation on managers’ decisions. (shrink)
The Sea as Mirror traces the pressing and repressed material and symbolic presence of the Mediterranean Sea and the Atlantic Ocean from Plato to Heidegger. To do so, Wu Yi employs the maritime as a lens to understand the drive of philosophy as both a response to and moment within the impetus of Western colonization. Yi examines how philosophy has again and again constructed itself as a genre in opposition to the movement of deterritorialization and fluidity of mimesis. She does (...) so via the method (meta, “after” + hodos, “way, journey”) of a series of essayings (in the original sense of trial, measure, attempt) across a geopolitical topography of discourses. These include philosophical texts drawn from a constellation of historical topoi at the critical moments of their encounter with the maritime: Plato and Euripedes’s work from fifth-century Athens; Augustus and Plautus’s writings from republican and early imperial Rome; Shakespeare’s creations from Elizabethan England; Kant and Rousseau’s texts from enlightenment continental Europe; and the thinking of Husserl and Heidegger from interwar Germany of the twentieth century. For each historical topos, Yi juxtaposes different representations of and responses to the maritime through the reading of a philosophical text vis-à-vis the reading of a literary text. In so doing, she lays bare the deep political and moral ambiguity attributed to the ocean in Western philosophical and literary imaginaries. (shrink)
Contains over thirty essays which explore the complex contexts of political engagement--family and intimate relationships, friendships, neighborhood, community, work environment, race, religious, and other cultural groupings--that structure perceptions of women's opportunities for political participation.
In February 2015 the UK became the first country to legalise high-profile mitochondrial replacement techniques, which involve the creation of offspring using genetic material from three individuals. The aim of these new cell reconstruction techniques is to prevent the transmission of maternally inherited mitochondrial disorders to biological offspring. During the UK debates, MRTs were often positioned as a straightforward and unique solution for the ‘eradication’ of mitochondrial disorders, enabling hundreds of women to have a healthy, biologically-related child. However, many questions (...) regarding future applications and potential users remain. Drawing on a current qualitative study on reproductive choices in the context of mitochondrial disorders, this article illustrates how the potential limitations of MRTs have been obscured in public debates by contrasting the claims made about the future beneficiaries with insights from families affected by mitochondrial disorders and medical experts. The analysis illuminates the complex choices with which families and individuals affected by mitochondrial disorders are faced, which have thus far remained invisible. An argument is presented for improved information for the public as well as an intensification of critical empirical research around the complex and specific needs of future beneficiaries of new reproductive biotechnologies. (shrink)
We investigate in the frame of TTE the computability of functions of the measurable sets from an infinite computable measure space such as the measure and the four kinds of set operations. We first present a series of undecidability and incomputability results about measurable sets. Then we construct several examples of computable topological spaces from the abstract infinite computable measure space, and analyze the computability of the considered functions via respectively each of the standard representations of the computable topological spaces (...) constructed. (shrink)
This book is a result from a collective study on philosophy of scientific practice, which began around 2002 and still ongoing. There is an apparently increasing interest in scientific practice, influenced by the historicistic philosophy of science and the sociology of scientific knowledge. Prof. WU Tong and his research group believe that it is necessary for PSP to turn from the theory-dominant position to the practice dominance. PSP has also put forward the possibility of reinterpreting the epistemic status of local (...) knowledge in Chinese tradition, which provides the most significant motivation to participate this study. In this book, we have selected three main cases - namely, Chinese medicine, Fengshui, and Ethnobotany - to examine the effect of PSP. The aim of our collective study is not merely on theoretical construction of PSP, but also to consider the various applications of PSP, especially for re-interpreting and demonstrating the variety of local knowledge from traditional China, which seems to be a genuine contribution to the international enterprise of philosophy of science, particularly made by Chinese scholars. nterpreting and demonstrating the variety of local knowledge from traditional China, which seems to be a genuine contribution to the international enterprise of philosophy of science, particularly made by Chinese scholars. (shrink)
This article draws on the qualitative research component of a mixed-methods project exploring the Australian news media’s representation of violence against women. This critical discourse analysis is on print and online news reporting of the case of ‘Kings Cross Nightclub Rapist Luke Lazarus’, who in March 2015 was tried and convicted of raping a female club-goer in a laneway behind his father’s nightclub in Sydney, Australia. We explore the journalism discursive practices employed in the production of the news reports about (...) the Lazarus trial. Our analysis shows how some lexical features, quoting strategies and structuring elements serve to minimise the victim’s experience while emphasising the adverse effects of the trial on the accused. Furthermore, we demonstrate how such practices allow for the graphic representation of the attack in a salacious manner while minimising the impact of the crime on the victim by selectively referencing her victim impact statement. We found some differences between print and online news stories about this case, some of which may be attributable to the greater space available to the telling of news stories online. We conclude that in news reporting of the Lazarus case, routine journalism discursive practices, such as the inverted pyramid news-writing structure and decisions about who and what to quote, serve simultaneously to diminish the victim’s experience while objectifying her. These results build on international findings about media reporting practices in relation to violence against women and add substantially to what we know about these practices in Australia. (shrink)
A review of the literature on Corporate Codes of Ethics suggests that whilst there exists an informative body of literature concerning the prevalence of such codes, their design, implementation and promulgation, it is also evident that there is a relative lack of consideration of their impact upon members' everyday organizational behaviour. By drawing upon organizational sociology and psychology this paper constructs a contextualist and interpretive model which seeks to enable an analysis and evaluation of their effects upon individual, group and (...) organizational behaviour. (shrink)
In Religion in Secular Education Cathy Byrne explores the secular principle as a guiding compass for religions in state schools. Historical and contextual research and international comparisons explore the ideologies, policies, pedagogies and practices affecting national and individual religious identity.
Is calculation possible without language? Or is the human ability for arithmetic dependent on the language faculty? To clarify the relation between language and arithmetic, we studied numerical cognition in speakers of Mundurukú, an Amazonian language with a very small lexicon of number words. Although the Mundurukú lack words for numbers beyond 5, they are able to compare and add large approximate numbers that are far beyond their naming range. However, they fail in exact arithmetic with numbers larger than 4 (...) or 5. Our results imply a distinction between a nonverbal system of number approximation and a language-based counting system for exact number and arithmetic. (shrink)
This essay attempts to provide an alternative approach to the philosophy of religion through a new interpretation of Daoist philosophy in light of Husserl’s phenomenology. I argue that Lao-Zhuang’s wu-wei should be understood as a reduction of our existential and conceptual beliefs about the reality of this world. In Lao-Zhuang, wu-wei is related to the theme of decentering of the subject. In order to be a true self, we have to make space at the core of our being for Dao (...) to appear. The authentic selfhood is constituted in its correctrelation to Dao. In Daoist philosophy of religion, the center of gravity in the relation between Dao and the world is shifted from this world to Dao, and the problematic in the philosophy of religion is displaced from a truth-oriented issue to a receptivity issue. (shrink)
Background: One of the barriers to interprofessional ethics education is a lack of resources that actively engage students in reflection on living an ethical professional life. This project implemented and evaluated an innovative resource for interprofessional ethics education. Objectives: The objective of this project was to create and evaluate an interprofessional learning activity on professionalism, clinical ethics, and research ethics. Design: The Brewsters is a choose-your-own-adventure novel that addresses professionalism, clinical ethics, and research ethics. For the pilot of the book, (...) a pre-test/post-test design was used. Once implemented across campus, a post-test was used to evaluate student learning in addition to a student satisfaction survey. Participants and research context: A total of 755 students in six academic schools in a health science center completed the activity as part of orientation or in coursework. Ethical considerations: The project was approved as exempt by the university’s Committee for the Protection of Human Subjects. Findings: The pilot study with 112 students demonstrated a significant increase in student knowledge. The 755 students who participated in the project had relatively high knowledge scores on the post-test and evaluated the activity positively. Discussion: Students who read The Brewsters scored well on the post-test and had the highest scores on clinical ethics. Clinical ethics scores may indicate issues encountered in mass media. Conclusion: The Brewsters is an innovative resource for teaching interprofessional ethics and professionalism. Further work is needed to determine whether actual and long-term behavior is affected by the activity. (shrink)
Many recent philosophers have been tempted by epistemic partialism. They hold that epistemic norms and those of friendship constitutively conflict. In this paper, I suggest that underpinning this claim is the assumption that friendship is not an epistemically rich state, an assumption that even opponents of epistemic partiality have not questioned. I argue that there is good reason to question this assumption, and instead regard friendship as essentially involving knowledge of the other. If we accept this account of friendship, the (...) possibility of epistemic partialism does not arise. (shrink)
In China, political philosophy is still a comparatively new academic discipline. While there is no such phrase as "political philosophy" in ancient Chinese texts, there are elements within them that could be considered part of that field. Central questions of Chinese ancient political philosophy include the legitimacy of the source of political power, the foundation of moral rationality for the use of political power, and the purpose of political activities. This book explores the ideas of rights, the foundations of law, (...) transference of power, democracy and other topic as debated in ancient times. Focusing on important political thinkers in Chinese history, such as Kongzi, Laozi, Xu Fuguan, Liang Qichao and Li Dazhao, the book explains characteristics that are particular to China, such as the system of abdication, the general will of the people, and the society of Great Harmony. While making comparisons between Chinese and Western political philosophy, the book also discusses how to establish a Chinese modern state and how to promote Chinese culture today so that it can influence more and more people around the world. The book will be a valuable reference for scholars of Chinese philosophy, political philosophy and Chinese culture. (shrink)
There is no well-built theory on credit risk measurement and decision analysis for financial big data, and an effective and scientific evaluation system for them has not been formed. A review of them can contribute to grasping the abovementioned topics, understanding current issues, analyzing research problems, mastering research challenges, and predicting future research directions. Besides, this paper points out four research directions of credit risk measurement and decision analysis for financial big data. Moreover, this paper can provide some guidance directions (...) and insights for practitioners, researchers, financial institutions, and government departments who have an interest in complex decision-making in big data. (shrink)
