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)

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)

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)

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)

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/) 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)

Jerry L. Walls, the author of books on hell and heaven, completes his tour of the afterlife with a philosophical and theological exploration and defense of purgatory, the traditional teaching that most Christians require a period of postmortem cleansing and purging of their sinful dispositions and imperfections before they will be fully made ready for heaven. He examines Protestant objections to the doctrine and shows that the doctrine of purgatory has been construed in different ways, some of which are (...) fully compatible with Protestant theology. In particular, while purgatory has often been understood as matter of punishment in order to make satisfaction for sins that have not been fully remitted, it can also be seen as the completion of the sanctification process, an account of the doctrine that is fully consistent with the Protestant doctrine of justification by faith. Purgatory assumes not only continuity of personal identity but also gradual moral and spiritual growth between death and resurrection. Different theories of personal identity are examined and assessed in light of these assumptions. Walls also shows that the traditional doctrine of purgatory is not understood as a second chance for salvation, but goes on to argue that it should be modified to allow for postmortem repentance. He concludes with an examination of C.S. Lewis's writings on purgatory, and suggests that Lewis can be a model for evangelicals and other Protestants to engage the doctrine of purgatory in a way that is true to their theology. (shrink)

Jerry L. Walls argues that the doctrine of heaven is ripe for serious reconsideration. He contends not only that the orthodox view of heaven can be defended from objections commonly raised against it, but also that heaven is a powerful resource for addressing persistent philosophical problems, not the least of which concern the ground of morality and the meaning of life. Walls shows how heaven is integrally related to central Christian doctrines, particularly those related to salvation, and tackles (...) the difficult problem of why faith in Christ is necessary to save us from our sins. In addition, heaven is shown to illumine thorny problems of personal identity and to be an essential component of a satisfactory theodicy. Walls goes on to examine data from near-death experiences from the standpoint of some important recent work in epistemology and argues that they offer positive evidence for heaven. He concludes that we profoundly need to recover the hope of heaven in order to recover our very humanity. (shrink)

Seeks to illuminate Beckett's world view and the philosophical ramifications of Waiting for Godot by examining characterization and such themes as communication, memory, and identity.

Naturalistic ethics is the reigning paradigm among contemporary ethicists; in God and Cosmos, Baggett and Walls argue that this approach is seriously flawed. This book canvasses a broad array of secular and naturalistic ethical theories in an effort to test their adequacy in accounting for moral duties, intrinsic human value, prospects for radical moral transformation, and the rationality of morality. In each case, the authors argue, although various secular accounts provide real insights and indeed share common ground with theistic (...) ethics, the resources of classical theism and orthodox Christianity provide the better explanation of the moral realities under consideration. Among such realities is the fundamental insight behind the problem of evil, namely, that the world is not as it should be. Baggett and Walls argue that God and the world, taken together, exhibit superior explanatory scope and power for morality classically construed, without the need to water down the categories of morality, the import of human value, the prescriptive strength of moral obligations, or the deliverances of the logic, language, and phenomenology of moral experience. This book thus provides a cogent moral argument for God's existence, one that is abductive, teleological, and cumulative. (shrink)

Vesicovaginal fistula was a catastrophic complication of childbirth among 19th century American women. The first consistently successful operation for this condition was developed by Dr J Marion Sims, an Alabama surgeon who carried out a series of experimental operations on black slave women between 1845 and 1849. Numerous modern authors have attacked Sims’s medical ethics, arguing that he manipulated the institution of slavery to perform ethically unacceptable human experiments on powerless, unconsenting women. This article reviews these allegations using primary historical (...) source material and concludes that the charges that have been made against Sims are largely without merit. Sims’s modern critics have discounted the enormous suffering experienced by fistula victims, have ignored the controversies that surrounded the introduction of anaesthesia into surgical practice in the middle of the 19th century, and have consistently misrepresented the historical record in their attacks on Sims. Although enslaved African American women certainly represented a “vulnerable population” in the 19th century American South, the evidence suggests that Sims’s original patients were willing participants in his surgical attempts to cure their affliction—a condition for which no other viable therapy existed at that time. (shrink)

David Hume's philosophy is notoriously naturalistic. It is an attempt to give an account of man and his world relying only on evidence which can be gleaned from sense observation and introspection. Whatever can be inferred from this evidence is a proper philosophical conclusion.

Jerry L. Walls aims to demonstrate in his book Hell: The Logic of Damnation that some traditional views of hell are still defensible and can be believed with intellectual and moral integrity. Focusing on the issues from the standpoint of philosophical theology, Walls explores the doctrine of hell in relation to both the divine nature and human nature. He argues, with respect to the divine nature, that some traditional versions of the doctrine are compatible not only with God's (...) omnipotence and omniscience, but also with a strong account of His perfect goodness. The concept of divine goodness receives special attention since the doctrine of hell is most often rejected on moral grounds. (shrink)

We theoretically discuss and empirically show how CEO power based on environmental expertise and formal influence over executives and directors, in the absence and presence of shareholder activism, spurs firms toward greener strategies. Our results support the idea that CEOs with informal power, grounded in expertise, reduce corporate environmental impact and this relationship is amplified when the CEO also enjoys formal power over the board of directors. Additionally, we found that any source of CEO power, whether informal or formal, is (...) a good catalyst for transforming shareholder activism into corporate greening. However, in the absence of such activism, only CEOs’ informal environmental expert power acts as a determinant of firm environmental performance. (shrink)

Jerry L. Walls argues that the doctrine of heaven is ripe for serious reconsideration. He contends not only that the orthodox view of heaven can be defended from objections commonly raised against it, but also that heaven is a powerful resource for addressing persistent philosophical problems, not the least of which concern the ground of morality and the meaning of life. Walls shows how heaven is integrally related to central Christian doctrines, particularly those related to salvation, and tackles (...) the difficult problem of why faith in Christ is necessary to save us from our sins. In addition, heaven is shown to illumine thorny problems of personal identity and to be an essential component of a satisfactory theodicy. Walls goes on to examine data from near-death experiences from the standpoint of some important recent work in epistemology and argues that they offer positive evidence for heaven. He concludes that we profoundly need to recover the hope of heaven in order to recover our very humanity. (shrink)

This volume will be the primary resource for students, scholars, and others interested in questions of our ultimate existence.

Jerry L. Walls argues that the doctrine of heaven is ripe for serious reconsideration. He contends not only that the orthodox view of heaven can be defended from objections commonly raised against it, but also that heaven is a powerful resource for addressing persistent philosophical problems, not the least of which concern the ground of morality and the meaning of life. Walls shows how heaven is integrally related to central Christian doctrines, particularly those related to salvation, and tackles (...) the difficult problem of why faith in Christ is necessary to save us from our sins. In addition, heaven is shown to illumine thorny problems of personal identity and to be an essential component of a satisfactory theodicy. Walls goes on to examine data from near-death experiences from the standpoint of some important recent work in epistemology and argues that they offer positive evidence for heaven. He concludes that we profoundly need to recover the hope of heaven in order to recover our very humanity. (shrink)

I argue that no classical theist, and even more no orthodox Christian, should affirm compatibilism in our world. However plausible compatibilism may be on atheistic assumptions, bringing God into the equation should radically alter our judgment on this ongoing controversy. In particular, if freedom and determinism are compatible, then God could have created a world in which all persons freely did only the good at all times. Given this implication of compatibilism, three issues that are already challenging become extraordinarily more (...) difficult, if not insuperable, namely: moral responsibility, the problem of evil, and the orthodox doctrine of eternal damnation. (shrink)

The director of the Center for Ethics and Public Life presents a series of essays on the philosophical implications of the Narnia series, exploring Lewis's ...

In the target article, we presented the hypothesis that parasite-stress variation was a causal factor in the variation of in-group assortative sociality, cross-nationally and across the United States, which we indexed with variables that measured different aspects of the strength of family ties and religiosity. We presented evidence supportive of our hypothesis in the form of analyses that controlled for variation in freedom, wealth resources, and wealth inequality across nations and the states of the USA. Here, we respond to criticisms (...) from commentators and attempt to clarify and expand the parasite-stress theory of sociality used to fuel our research presented in the target article. (shrink)

Weeter and Duvall were good friends and philosophical colleagues. Their friendship was served by the fact that they shared a number of important philosophical commitments. Both, for instance, were theists. Both also devoutly believed in possible worlds, propositions, and essences. And furthermore, both were ardent libertarians.

Joseph Blado critiqued my probabilistic arguments against Roman papal doctrines by deploying probability arguments, particularly Bayesian arguments, in favor of the papacy. He contends that there are good C-inductive arguments for papal doctrine that, taken together, add up to a good P-inductive argument. I argue that his inductive arguments fail, and moreover that there are three good C-inductive arguments against papal doctrine in the neighborhood of his failed arguments. I conclude by critiquing his retreat to what he calls ‘skeptical papalism’ (...) as a last ditch sort of move to defend papal doctrine. (shrink)

John Wesley explained the existence of evil in moral rather than metaphysical terms. His understanding of the fall was fairly typical of western theology and he also enthusiastically embraced a version of the felix culpa theme as essential for theodicy. Unlike many influential western theologians, he also relied heavily on libertarian freedom to account for evil. His most striking proposal for theodicy involves his eschatalogical vision of the future in which he believed the entire world living then will be converted. (...) I argue that his theodicy is implicitly universalist, especially in its eschatalogical speculations, and show that this is in tension with his strong libertariancommitments. (shrink)

Whether you play basketball, coach it, or just love to watch it, this book will forever enrich your understanding and appreciation of the game.

This article discusses the doctrine of hell. It covers traditional versus contemporary defences of hell, challenges to freedom accounts of hell, and the coherence of eternal hell. The article then argues that the doctrine of heaven has not received as much attention from philosophers as hell has and identifies some interesting challenges raised against the Christian hope of eternal joy.

Individual choice and freedom are repeatedly invoked in contemporary policy debates, including those with a focus on risk behaviors such as smoking and health insurance coverage. The idea of making the right choice with regard to health and well-being has been fortified by the neoliberal discourse of self-reliance, personal autonomy, and responsibility. This neoliberal view, stemming from the conceptualization of freedom of philosopher John Stuart Mill justifying the freedom of the individual in opposition to unlimited state control, holds that success, (...) good health, and favorable educational outcomes are largely due to individual effort. Correspondingly, so too is failure, including failure of.. (shrink)

In this paper, I respond to the central points of Steve Cowan and Greg Welty’s response to my 2011 article in which I argued that theists, especially Christian theists, should not be compatibilists. I contend that their counterexamples fail to undermine my “provenance principle” as my “evil manipulator principle.” Their counterexamples are not convincing cases of determinism, and thus tacitly rely on libertarian freedom to make moral sense. I also argue that their appeal to skeptical theism fails to undercut my (...) argument from appalling moral evil. Finally, I argue that the resources provided by libertarian freedom better makes sense of damnation than does compatibilism. (shrink)

This essay examines how C. S. Lewis, in Till We Have Faces, illustrates the Christian’s journey of sanctification through the pre-Christian story of his main character, Orual. She must gain two ‘faces’ in this process that correspond to the two books she writes. First, she must gain the face of self-knowledge through humility. The key components to this face are her memory and the act of writing of her first book, which together create a mirror to reflect her sin back (...) to her. Second, Orual must gain the face of transformation through divine agape love. The humility she learned from her first face now allows her to enter what Lewis describes as the dance of self-giving, which is a crucial element to the second face of transformation in its mortification of Orual’s sin and selfishness. In the second face, Orual gains access to an ‘actual language’ that transcends merely verbal words and involves worshipping the god with her whole being, as do we in being transformed to reflect Christ more clearly. Orual’s writing is a form of this ‘actual language’, and her second book that shares her personal encounter with the god of the mountain reflects to others the beauty of the divine. Similarly, Christians should reflect Jesus with their lives and their art, which are inextricably intertwined because a life lived for Him is the highest form of artwork they can create. (shrink)

This paper considers the use of textual analysis of oral histories as a method for historians of nursing. Fifty‐three oral histories of retired nurses in midwestern USA were analyzed for the purpose of historical reconstruction of past education experiences in nursing. Textual analysis was used to determine how nurses made sense of their educational experiences, and it involved gathering data, analyzing the information, and using a different method of interpreting the data. Although the participants responded to specific questions, the oral (...) histories in this study are more than mere answers to the researchers’ queries. The participants’ memories are narratives that are the joint product of both the historian and the participant. As such, the oral history becomes a text to be stored along with other primary sources for future historians’ use. The research also suggests decentering oral histories from an exclusively academic agenda and focusing more on what the participants choose to remember and why they make those choices. (shrink)