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)

In this study we seek to determine whether catastrophic events lead to corporate charitable giving unrelated to levels of firm profitability. We examine the issue relative to the corporate philanthropic response to the 9/11 terrorist attacks of 2001. Based on a sample of 489 Fortune 500 companies, we find that differences in the extent of corporate contributions following 9/11 are positively and significantly associated with differences in firms' profitability. Further, while the degree of connection to the catastrophic event led to (...) higher levels of giving in comparison to the contributions of less connected firms, differences in the extent of philanthropy are still␣related to short-term profitability for the more connected firms. The study thus provides evidence suggesting that even in the wake of catastrophic events, corporate philanthropic giving is constrained by economic concerns. (shrink)

Bertolt Brecht’s poem “A Worker’s Speech to a Doctor” is frequently cited as a means to raise awareness among health workers of the health effects of living and working conditions. Less cited is his Call to Arms trilogy of poems, which calls for class-based action to transform the capitalist economic system that sickens and kills so many. In this article, we show how “A Worker’s Speech to a Doctor,” with its plea for empathy for the ill, contrasts with the more (...) activist and often militant tone of the Call to Arms trilogy: “Call to a Sick Communist,” “The Sick Communist’s Answer to the Comrades,” and “Call to the Doctors and Nurses.” We also show that, while “A Worker’s Speech to a Doctor” has been applied in the training of health workers, its accusatorial tone towards health workers’ complicity in the system the poem is critiquing risks alienating such workers. In contrast, the Call to Arms trilogy seeks common ground, inviting these same workers into the broader political and social fight against injustice. While we contend that the description of the sick worker as a “Communist” risks estranging these health workers, our analysis of the Call to Arms poems nevertheless indicates that their use can contribute to moving health workers’ educational discourse beyond a laudable but fleeting elicitation of empathy for the ill towards a structural critique and deeper systemic understanding in order to prompt action by health workers to reform or even replace the capitalist economic system that sickens and kills so many. (shrink)

UK-based research conducted within a healthcare setting generally requires approval from the National Research Ethics Service. Research ethics committees are required to assess a vast range of proposals, differing in both their topic and methodology. We argue the methodological benchmarks with which research ethics committees are generally familiar and which form the basis of assessments of quality do not fit with the aims and objectives of many forms of qualitative inquiry and their more iterative goals of describing social processes/mechanisms and (...) making visible the complexities of social practices. We review current debates in the literature related to ethical review and social research, and illustrate the importance of re-visiting the notion of ethics in healthcare research. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Women do most of the parenting. To provide a stable and healthier setting for children they must sublimate their own interests and feelings, which puts greater pressures on women to communicate needs clearly or to be deceptive when the occasion demands. The likely advantage in communication skills and self-control may ameliorate the impact of disorders like ADHD where the most serious deficit is in self-inhibition. This would account for the strikingly uneven male to female sex ratio of 2:1 (in epidemiological (...) samples) to 10:1 (in clinical settings), the higher threshold for females, and the sex difference in the pattern of associated mental disorders. (shrink)

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

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

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

In searching for appropriate business ethics for the 21st century, it is necessary to embrace a range of inter-related disciplines such as psychology and ethics, but also areas including philosophy, politics and religion. This text acts as an example of interdisciplinary scholarship.

In lieu of an abstract, here is a brief excerpt of the content:Philosophy of Music Education Review 12.1 (2004) 67-70 [Access article in PDF] Response to Mary J. Reichling, "Intersections: Form, Feeling, and Isomorphism" David Stevenson Vassalboro, Maine Mary J. Reichling's essay regarding the three concepts, form, feeling, and isomorphism, is lucid, well structured, and aptly supported by research of other music education philosophers. She states her purpose in the opening paragraph: "to examine and to elucidate various aspects of (...) these three concepts in her [Susanne Langer's] writing, as they are fundamental to an understanding of her aesthetic theory and to the construction of a philosophy of music and music education."A philosophy of music education must be the focus in all ensuing debate, and must remain of paramount importance. Arguments, especially dialectic arguments, are not won or lost; they merely strip away the outer garments until more and more of the truth is exposed. My thoughts regarding Reichling's essay are offered in this vein.Reichling amply makes the point that music is a dynamic moving form. She asserts that "Langer argues that form is not separable from content," clarifying further by saying that "By content Langer is designating the form's import or meaning." And she offers other examples of dynamic, moving forms, among them, "forms created by movements of clouds or fog through the mist and early light." [End Page 67]At this point, perhaps interjecting the notion of perception is in order. I would suggest that the cloud formations offer no content or meaning outside of the viewer's perceptions or imagination. Music (art), being the nebulous subject that it is, ensconced in subjectivity and steeped in perception, both interpersonal and intrapersonal at the same time, exists to be taken by individuals, each at his or her own level of accomplishment, understanding, and interest. Therefore, does the meaning inhere in the form, as Langer and Reichling assert, or is it assigned by the listener (in the case of music) or by the viewer (in the case of the cloud formation)? "If the doors of perception were cleansed every thing would appear to man as it is: infinite."1 William Blake's observation notwithstanding, the truth is that perception is the only thing that we have with which to view our existence. I believe that there is such a thing as absolute truth, and that reality does exist. However, we mere mortals lack the ability to view the world through anything other than our own perceptions. The knowledge or meaning gained through contemplation of the form is, in all likelihood, quite different for each observer.Likewise, imagination and conceptual ability play a role in interpreting what the senses have perceived. Langer, and by quotation, Reichling, offers the notion of a red dot placed on the rim of a spinning wheel that appears to the viewer as a red circle. "When the spinning stops, the form, the red circle, evaporates. Did it really exist? Does it have ontological status? Is it merely an illusion?" I asked my students to close their eyes and imagine a spinning wheel with a red dot placed on the rim. I asked them, "As the wheel spins, do you see the dot?" The answer was that they saw a red circle. Did they really see a red circle, or even a spinning wheel? Of course not, we were in a music classroom. Yet they were able to conceptualize or imagine the image, and I would suggest that that carries more weight in the realm of art than does actual ontological status.The problem with the experiment of the preceding paragraph is that "Langer argues that form is not separable from content, writing that it is not possible 'to divorce the logical form from its one embodiment or expression.'" In the subsequent paragraph Reichling states, When the music stops, when the ballet is concluded, when the play ends, when the wheel stops spinning, memory may remain but the content (content as meaning-my parenthetical interjection), the feeling, the red circle, the image the dancer created is gone. Is this illogical or has knowledge... (shrink)

This article constructs and deploys a set of autoethnographic narratives from the author’s experience as a Baptist minister to critically retrieve the category of ‘women’s experience’ for feminist theological construction. Autoethnography, as a response to the crisis of representation in the Humanities, uses personal narratives of the self to reveal, critique and transform wider cultural trends. It therefore provides helpful tools for analysing, critiquing and transforming theological thought and practice. Following the article’s methodological sections, the constructive sections use the crafted (...) autoethnographies to re-frame Rowan Williams’s vision for how church and world co-constitute each other towards God’s just ends. Whereas Williams argues that this co-constitution occurs through processes of interactive transformative judgment, the feminist theological understanding argued for here founds the process instead on interactive, transformative grace. (shrink)

In _The Search for Meaning: A Short History, _Dennis Ford explores eight approaches human beings have pursued over time to invest life with meaning and to infuse order into a seemingly chaotic universe. These include myth, philosophy, science, postmodernism, pragmatism, archetypal psychology, metaphysics, and naturalism. In engaging, companionable prose, Ford boils down these systems to their bare essentials, showing the difference between viewing the world from a religious point of view and that of a naturalist, and comparing a scientific worldview (...) to a philosophical one. Ford investigates the contributions of the Greeks, Kant, and William James, and brings the discussion up to date with contemporary thinkers. He proffers the refreshing idea that in today's world, the answers provided by traditional religions to increasingly difficult questions have lost their currency for many and that the reductive or rationalist answers provided by science and postmodernism are themselves rife with unexamined assumptions. (shrink)

The paper attempts to provide a basis for exploring the continued relevance of Catholic social teaching to business ethics, byinterpreting the historic development of a Catholic work ethic and the traditions of Catholic social teaching in light of contemporary discussions of economic globalization, notably those of Robert Reich and Peter Drucker. The paper argues that the Catholic work ethic and the Church’s tradition of social teaching has evolved dynamically in response to the structural changes involved in the history of modern (...) economic development, and thus is well poised to speak to the ethical challenges implicit in the advent of a knowledge-based society. In order to test this thesis, the author sketches an approach to the ethical challenge of corporate downsizing that he believes illustrates the continued relevance of Catholic social teaching to business ethics. (shrink)

In _The Search for Meaning: A Short History, _Dennis Ford explores eight approaches human beings have pursued over time to invest life with meaning and to infuse order into a seemingly chaotic universe. These include myth, philosophy, science, postmodernism, pragmatism, archetypal psychology, metaphysics, and naturalism. In engaging, companionable prose, Ford boils down these systems to their bare essentials, showing the difference between viewing the world from a religious point of view and that of a naturalist, and comparing a scientific worldview (...) to a philosophical one. Ford investigates the contributions of the Greeks, Kant, and William James, and brings the discussion up to date with contemporary thinkers. He proffers the refreshing idea that in today's world, the answers provided by traditional religions to increasingly difficult questions have lost their currency for many and that the reductive or rationalist answers provided by science and postmodernism are themselves rife with unexamined assumptions. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Kiyozawa Manshi’s Two Theories of Evolution and Their Western InspirationDennis PROOIIntroductionIf one solely were to confine the scope of one’s inquiry into the defining trait of a “Tokyo School of Philosophy” to the years immediately following the founding of Tokyo University in 1877, it would be hard to escape the conclusion that philosophy there at the time was determined almost entirely by the dominant intellectual wind blowing through its (...) lecture halls, namely that of evolutionary theory. Katō Hiroyuki (1836–1916), president of the university from 1890 to 1893, was one of its staunchest advocates, doing much to foster the spread of ideas that would today be typified as “Social-Darwinian.”1 Inoue Enryō (1858–1919), undoubtedly the Meiji period’s most successful public philosopher, came to embrace many Spencerian ideas on evolution under the influence of Toyama Masakazu (1848–1900), a devout Spencerian, during his time as a student there (from 1881 to 1885).2 Ernest F. Fenollosa (1853–1908), an American philosopher who exerted great influence over the university’s young philosophical minds, was working on a synthesis of the Spencerian and Hegelian philosophical systems.3 He had been brought to Tokyo University by the Darwinian zoologist Edward S. Morse (1838–1925), who was himself instrumental in the spread of evolutionary ideas. This quick survey of Tokyo notables serves not only to establish the dominance of evolutionary theory, but also to show how in the context of late nineteenth-century Japan, “evolutionary theory” (shinkaron 進化論) is best understood as an umbrella term that could refer to a wide array of ideas—including, but certainly not limited to, Darwinian, Social-Darwinian, Spencerian, and Hegelian ones, or a mix of these—on the nature of (individual and social) change, development, and progress.Although the impact of 1859’s The Origin of Species made Darwin a figure impossible to ignore, by no means was evolutionary theory [End Page 77] equated with his theory of natural selection. For their ideas of evolution, many looked to Herbert Spencer (1820–1903), regarded by the Victorian English as the philosopher of evolution and whose system of synthetic philosophy presented positivist-leaning Meiji-era Japanese intellectuals with a definitive model of philosophical achievement. Spencer prided himself in having been the first to formulate the principle of evolution, remarking in the revised version of Social Statics (1892) that he had arrived at the general idea as early as 1850, many years before The Origin of Species had appeared in print.4 From Spencer’s point of view, Darwin had done no more than confirm a posteriori for biological organisms what was in fact an a priori law of evolution, established by Spencer in First Principles (1867) both inductively and deductively as the universal tendency of phenomena to pass from “an indefinite, incoherent homogeneity to a definite, coherent heterogeneity,” a process accompanied by “an integration of matter and concomitant dissipation of motion.”5 Spencer’s nod to the materialist tradition by formulating his conception of evolution in terms of matter in motion in his own self-understanding placed him in the camp of English philosophy, which did not let itself be deluded by the wrong use of language and spurned the invocation of what from its perspective was superfluous metaphysics. The opposing camp of German philosophy—following William Hamilton (1788–1856), derided by Spencer as “absolute theorisers”—made abundant use of such metaphysics to defend a teleological understanding of evolution—the kind of understanding Darwin (with his emphasis on the non-teleological character of natural selection) and Spencer (with his focus on matter in motion) attempted to render obsolete.6Under the influence of Fenollosa, many students of philosophy at Tokyo University became attracted to the alternative German teleological model of evolution, the history of which via the German Romantics goes back to Leibniz’s attempt to reintroduce into physics the idea of final causes after these in that domain had been eliminated by Descartes.7 Descartes, to begin with, was the one to revolutionize natural philosophy by reducing the physical world to one of matter in motion ruled by efficient causation, imagining, much like Spencer two centuries later, that such a minimalist view of... (shrink)

"A work of major importance for the interpretation of Descartes's development and for the understanding of the function of the imagination in Descartes's early works. Descartes's Imagination will be a must in Descartes and imagination studies. It is long overdue."--Eva T. H. Brann, author of The World of Imagination: Sum and Substance "A significant contribution to our understanding of the development of Descartes's philosophy."--William R. Shea, author of The Magic of Numbers and Motion: The Scientific Career of Rene Descartes.

The significance of A. N. Whitehead’s contribution to 20th century metaphysics has become widely recognized. The focus on the novelty of his process ontology, however, has led to a view that isolates him from the mainstream of the tradition of Western philosophy. Hence, it is often overlooked that on the methodological level Whitehead is a pragmatist, whose much quoted indebtedness to William James is reflected in the project of his speculative metaphysics. A detailed analysis of the respective theories of (...) truth and knowledge in James and Whitehead illustrates their common methodological approach and allows us to assess the role of Whiteheadian thinking within the pragmatist tradition. James advances a form of epistemic conservatism that supplements the pragmatic idea of a concept’s cash-value with the demand for internal consistency. New beliefs have to fit in the totality of all previously accepted convictions in order to become accepted as true. James argues his case on three levels – a psychological, an epistemological and a pragmatic one – and develops a theory of truth that comprises an empirical and a rational dimension. Whitehead takes up this two-sided approach, but modifies the idea of genetic consistency into that of systematic coherence. The fundamental concepts of an ontological theory must not be isolated from each other to allow for a cosmology which is both rational and satisfies the pragmatic test of applicability. With the close relation of James and Whitehead in mind, the latter can be identified as the ‘missing link’ that bridges the gap between the so-called classical pragmatism and its more analytic versions as advanced by Quine, Lewis and Rescher. (shrink)

This article explores and critically assesses the metaxological account of a philosophy of God professed by William Desmond. Postmodern reflection on the philosophy of God has a tendency to focus on the 'signs' of God and urges for a passive acceptance of these signs. Desmond argues, contrary to this tendency, for a mindful togetherness of philosophical activity and religious passivity. After exploring Desmond's thought on this topic, I move to assess his 'metaxological yes' to God as the agapeic origin (...) from an existential point of view. Initially it seems that his 'yes' is somewhat strained as it burdens itself with an excessive task of having faith into something that is beyond determination. I illustrate this insight by referring to Friedrich Nietzsche’s 'Thus Spoke Zarathustra.' Nietzsche's existential 'No' toward transcendence is a consequence of a mindful confrontation with the excesses as play. (shrink)