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)

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)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (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)

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

In this volume, Julinna Oxley and Ramona Ilea bring together essays that examine and defend the use of experiential learning activities to teach philosophical terms, concepts, arguments, and practices. Experiential learning emphasizes the importance of student engagement outside the traditional classroom structure. Service learning, studying abroad, engaging in large-scale collaborative projects such as creating blogs, websites and videos, and practically applying knowledge in a reflective, creative and rigorous way are all forms of experiential learning. Taken together, the contributions to (...) Experiential Learning in Philosophy argue that teaching philosophy is about doing philosophy with others. The book is divided into two sections: essays that engage in the philosophical debate about defining and implementing experiential learning, and essays that describe how to integrate experiential learning into the teaching of philosophy. Experiential Learning in Philosophy provides a timely reflection on best practices for teaching philosophical ideals and theories, an examination of the evolution of the discipline of philosophy and its adoption of active modes of learning, and an anticipation of the ways in which pedagogical practices will continue to evolve in the 21 st century. (shrink)

The question of why Plato censored poetry in his Republic has bedeviled scholars for centuries. In Exiling the Poets, Ramona A. Naddaff offers a strikingly original interpretation of this ancient quarrel between poetry and philosophy.

By 2050, global livestock production is expected to double—growing faster than any other agricultural sub-sector—with most of this increase taking place in the developing world. As the United Nation’s four-hundred-page report, Livestock’s Long Shadow: Environmental Issues and Options , documents, livestock production is now one of three most significant contributors to environmental problems, leading to increased greenhouse gas emissions, land degradation, water pollution, and increased health problems. The paper draws on the UN report as well as a flurry of other (...) recently published studies in order to demonstrate the effect of intensive livestock production on global warming and on people’s health. The paper’s goal is to outline the problems caused by intensive livestock farming and analyze a number of possible solutions, including legislative changes and stricter regulations, community mobilizing, and consumers choosing to decrease their demand for animal products. (shrink)

The presence of agriculture is diminishing in today’s society: it provides only a small percentage of jobs, and the number of visible farms that can provide exposure to agricultural processes is continuously decreasing. We hypothesize that the direct involvement with farm activities or interaction with farmers and visual appreciation of agricultural processes of all kinds, influences rural inhabitants’ relationship to agriculture. We assume that the latter plays a role in how far inhabitants are attached to their place, and more specifically, (...) perceive rural place. In this paper, we aim to initiate a discussion on this complex social relationship and suggest a model to capture fine interactions between relationship to agriculture and rural place attachment. We examine the direct and indirect effects from the density of resident farmers on these interactions. We set up a model using data from empirical research in Germany conducted in 2016. We surveyed rural inhabitants and interviewed farmers in villages purposefully sampled based on high and low density of resident farmers. To reveal underlying relationships among the latent constructs and more directly measurable indicators, as well as the indirect effect of farm presence on place attachment through its effect on forming perceptions about agriculture, we operationalized our analysis using a structural equation model. Besides a good model fit, our initial results indicate that rural inhabitants form stronger relationship to agriculture when the density of resident farmers is higher. Further, farm presence and attachment to rural place are positively related, but needs to be better captured. (shrink)

W.S.F. Pickering, Durkheim’s Sociology of Religion. Themes and Theories, Cambridge: James Clarke & Co, 2009, 576 pages.

Teachers’ job satisfaction has been the subject of many studies that tried to identify its main sources. Based on the social cognitive career theory, the present study aimed to investigate the relationships between personality traits, goals orientation, and teachers’ job satisfaction. A total of 321 Romanian teachers completed an online questionnaire. The results demonstrated new insights regarding the relationships between psychological variables and teachers’ job satisfaction. Cognitive rigidity, as a mechanism to resistance to change, mediates between conscientiousness and teachers’ job (...) satisfaction. Moreover, the moderation role of learning goals orientation manifests in the relation between conscientiousness and job satisfaction. These findings emphasize that school management needs to offer teachers information and explain the change’s benefits if they want to prevent individual resistance to change and decrease satisfaction related to their work. (shrink)

An evaluation was made of theassociations between self-reported healthconscious consumerism, body-mass index (BMI),and consumer beliefs, attitudes, intentions,and behaviors regarding sustainably producedfoods. Self-administered surveys were completedby adult consumers (n = 550) in threemetropolitan Minnesota grocery stores. Selecteddemographic and psychographic differencesbetween health conscious consumers andnon-health conscious consumers were evaluated.Compared to non-health conscious consumers,health conscious consumers were more likely tobe female, older, more educated, higher incomeearners, more active, healthier, and possess ahealthier body mass index. They also held moresupportive beliefs, attitudes, and intentionswith regard (...) to sustainably produced foods. Inconclusion, some consumers are interested insupporting sustainable production practices andtheir support may be linked to improvedpersonal, environmental, and communityhealth. (shrink)

One of the major themes of discussion in the art and especially the literature of the 18th and 19th centuries was the body rather than the soul. In the beginning this seemed to be the case mostly because of the natural processes related to the transforming events of maturation and death of the human body and mind. However, towards the end of the 18th century and well into the 19th century, a certain shift took place from the common perspective on (...) the body to a rather scientific literary approach. Our attempt is to notice and make the necessary connections between the concepts of nature (both human and external/physical nature) and the innovative technologies implemented in the then society, with a later reference to the new accidental and commercial facets of death felt as destruction of nature especially in the work of the American Romantic writers Ralph Waldo Emerson and Henry David Thoreau. Being aware that they are highly spoken of in view of their transcendentalism as a particular philosophy dealing with the bond between man and nature, we will slowly come to terms with this type of concerns and connect them to the conflicting reality of industrialization as a sudden and repressive phenomenon within the society of men. Finally our point is that this very phenomenon caused the two writers to make a historical detour and use their formation as naturalist thinkers in order to make sense of their century’s deaths and diseases. This is to say that even from a Romantic perspective, the concern for the body is surprisingly concrete, while these writers’ transcendentalist concerns for the soul are prolix though without substance. (shrink)

Written for a series of case studies titled “In the Humanities Classroom,” this contribution describes an undergraduate course on ancient rhetoric at Berkeley, in which Professor Ramona Naddaff was accused by a male student of demeaning women during a lecture and of causing him trauma in the process. He threatened to bring charges against her to campus authorities, claiming the support of fellow students. In her lecture, she had discussed the classical figuration of rhetoric—persuasive speech—as violence and sometimes rape. (...) In a discussion the following week, some students requested the use of “trigger warnings” before the utterance of words like rape. The instructor and her teaching assistant Katharine Wallerstein individually give their views of this disconcerting experience and comment on the difficulties of teaching critical thinking in the current political and cultural climate. They conclude that the language of personal rights and the demand for self-protection tend to come at the expense of teaching and learning alike. (shrink)

In this study, I examine the online discourse of the European refugee crisis on the micro-blogging platform, Twitter. Specifically, I analyze 100 tweets that include #refugeesnotwelcome, and explore how this hashtag is used to express negative feelings, beliefs and ideologies toward refugees and migrants in Europe. Guided by critical discourse studies, I focus on Twitter users’ discursive strategies as well as form and function of semiotic resources and multimodality. Twitter users who include this particular hashtag use a rhetoric of inclusion (...) and exclusion to depict refugees as unwanted, criminal outsiders. These tendencies align with current trends in Europe where nationalist-conservative and xenophobic right-wing groups gain power and establish a socially accepted discourse of racism. (shrink)

Inconsistent information between an organization’s corporate social responsibility (CSR) commitments and perceived CSR (in-)action is a big challenge for organizations because this is typically associated with perceptions of corporate hypocrisy and related negative stakeholder reactions. However, in contrast to the prevailing corporate hypocrisy literature we argue that inconsistent CSR information does not always correspond to perceptions of corporate hypocrisy; rather, responses depend on individual predispositions in processing CSR-related information. In this study, we investigate how an individual’s moral identity shapes reactions (...) to inconsistent CSR information. The results of our three studies show that individuals who symbolize—i.e., display—their moral identity to the public more than they internalize moral values react less negatively to inconsistent CSR information. We also show that this weakens their anger and willingness to change company behavior. Furthermore, we find that this effect is amplified for extraverted but weakened for neurotic individuals. Our findings underline the importance of individual predispositions in processing CSR information. (shrink)

Book review of Martha Nussbaum's book Frontiers of Justice.

Processuality as refusal to “freeze,” “eternize,” and fragment reality is an attempt to deconstruct the I’s main mechanism, which is, as it was named in psychoanalysis, the compulsion of repetition. Through this deceit and illusion fabrication mechanism, the knowing I tries to “freeze”, to “fixate” and to fragment reality, through “catching” it in different images, formulae, dogmas, theories, ideologies, symbols and systems which become just as many “icons” or graven images of reality. This attempt of deconstruction is made from the (...) perspective of a philosophy/vision of process, quite sporadic in the Western space, bringing arguments from the perspective of Henri Bergson and Emil Cioran’s intuitionist philosophy, as well as from that of the new scientific paradigm of quantum mechanics. All these philosophies could be seen as philosophies of process, demanding as it were an understanding of reality in terms of process, and not of result. This understanding of process takes place with the help of intuition, the only one which can grasp, beyond the static, rigid and artificial concepts or categories of the intellect, the movement, “verb” or interior pulsation of things within the framework of an integration process which reveals the unity, non-separability, intercorrelation and mutual interconnectivity of things. (shrink)

Review of Pr. Ioan Chirilă, Scara cuvântului. Eseuri omiletice [ The Ladder of the Word. Homiletic Essays ],.

Review of Joseph Kim, Reformed Epistemology and the Problem of Religious Diversity.

This paper is an inquiry into Edward Schillebeeckx’ concept of resurrection, though it is fairly different from a thorough analysis of the meaning of resurrection per se. The difference comes from the fact that we will not simply view his take on the concept as a peculiar experiment, but the question of the importance of resurrection today receives special attention. This does not mean that certain attempts at defining and elaborating on the significance of Schillebeeckx’s concept of resurrection have been (...) overlooked. Still, the main purpose of this study is to literally put this concept to the test and see the tradition associated with it over the years. A final purpose is to determine Schillebeeckx’s place at the end of this experiment, as he is associated with the two poignant interpretations of resurrection today, namely the radical and liberal positions. The aim of this experiment is to decide whether we still need to talk about resurrection today and how critical it is to ask serious questions about it in this human history facing its end. This paper explores the concept of resurrection based on its impact on the humanum or the potential of human history always with an eye to its future, where in Schillebeeckx’s thought the perfect human state will be attained. (shrink)

This paper offers an analysis of Edward Schillebeeckx’s insights on different perceptions of revelation as related to concepts like salvation, God, church, human experience and creation in the work Jesus in Our Western Culture. The incentive of Schillebeeckx’s hermeneutical method in nowadays Western phenomenology, upon which God “breathed his breath of life”, triggered our interest in meanings which Schillebeeckx ascribes to human history as the realm of God’s work for the benefit of men and women. This meaning is suggested in (...) the very beginning of the book by its original Dutch title If Politics is not Everything. As stated in this work’s introduction, Schillebeeckx’s main theme is the origin of salvation in the humanum, from the Abba experience to nowadays revelatory events. Our attempt is to see how Schillebeeckx’s humanum, which is the embodiment of human experience of consciousness, becomes relevant for the Christian doctrines and why Schillebeeckx reckons that bringing them together would impact both his worldview and Western culture. (shrink)

The framers of the U.S. Constitution believed that intellectual property rights were crucial to scientific advancement. Yet, the framers also recognized the need to balance innovation, privatization, and public use. The courts’ expansion of patent protection for biotechnology innovations in the last 30 years raises the question whether the patent system effectively balances these concerns. While the question is not new, only through a thorough and thoughtful examination of these issues can the current system be evaluated. It is then a (...) policy decision for Congress if any change is necessary. (shrink)

800x600 Normal 0 21 false false false RO X-NONE X-NONE MicrosoftInternetExplorer4 st1:*{behavior:url(#ieooui) } /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabel Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman","serif";} Review of Joseph Steiff (ed.), Sherlock Holmes and Philosophy. The Footprints of a Gigantic Mind (Chicago and La Salle, Illinois: Open Court, 2011), 376 pages.

Objective: Theory and research suggest that the pursuit of personal goals that do not fit a person's affect-based implicit motives results in impaired emotional well-being, including increased symptoms of depression. The aim of this study was to evaluate an intervention designed to enhance motive-goal congruence and study its impact on well-being. Method: Seventy-four German students (mean age = 22.91, SD = 3.68; 64.9% female) without current psychopathology, randomly allocated to 3 groups: motivational feedback (FB; n = 25; participants learned about (...) the fit between their implicit motives and explicit goals), FB + congruence-enhancement training (CET; n = 22; participants also engaged in exercises to increase the fit between their implicit motives and goals), and a no-intervention control group (n = 27), were administered measures of implicit motives, personal goal commitments, happiness, depressive symptoms, and life satisfaction 3 weeks before (T1) and 6 weeks after (T2) treatment. Results: On two types of congruence measures derived from motive and goal assessments, treated participants showed increases in agentic (power and achievement) congruence, with improvements being most consistent in the FB+CET group. Treated participants also showed a trend-level depressive symptom reduction, but no changes on other well-being measures. Although increases in overall and agentic motivational congruence were associated with increases in affective well-being, treatment-based reduction of depressive symptoms was not mediated by treatment-based agentic congruence changes. Conclusion: These findings document that motivational congruence can be effectively enhanced, that changes in motivational congruence are associated with changes in affective well-being, and they suggest that individuals’ implicit motives should be considered when personal goals are discussed in the therapeutic process. (shrink)

This interactive book is designed to help readers deepen their relationship with the Divine by connecting to the vibrancy of life. This cosmic message of hope is meant to be read without hurry, while taking time to ponder and absorb the wisdom of these great mystics.