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)

One of the many claims about the value of local food is that local food exchanges generate trust between producers and consumers. To what degree is this actually the case and how does such trust develop? Drawing on interview and fieldwork data in one local food system in the Northeastern U.S., I show how local food participants build trust and reciprocity with one another in order to mitigate the challenges imposed by the conventional system. This trust and reciprocity builds primarily (...) through three mechanisms: reliable, positive relationships; demonstrations of good will toward one another; and a shared understanding of the value of locally-oriented food. Through these mechanisms, local food operators are able to build a healthy, stable local food system, able to better resist the pressures of the conventional system in which it must continually operate. (shrink)

This paper addresses the question of how local can be defined in practice. It contributes to the growing literature on local food systems and particularly our understanding of what counts as local and the elements that influence those contours. While most of our conceptions of local food tend to rely on an articulation of either proximity traveled or relationship between entities, I argue that a more nuanced and complete understanding must take account of both of these aspects. I draw on (...) a dataset of locally oriented farm and food-related establishments in southern New England to identify how far local food travels in this region and how interconnected local food establishments are with one another and use these and other measures to tease out the tension between proximity and relationship as measures of local. I find that these two aspects not only are connected to each other in a complex dynamic, but also are bound up with other structural factors as well. (shrink)

One of the many claims about the value of local food is that local food exchanges generate trust between producers and consumers. To what degree is this actually the case and how does such trust develop? Drawing on interview and fieldwork data in one local food system in the Northeastern U.S., I show how local food participants build trust and reciprocity with one another in order to mitigate the challenges imposed by the conventional system. This trust and reciprocity builds primarily (...) through three mechanisms: reliable, positive relationships; demonstrations of good will toward one another; and a shared understanding of the value of locally-oriented food. Through these mechanisms, local food operators are able to build a healthy, stable local food system, able to better resist the pressures of the conventional system in which it must continually operate. (shrink)

As local food activities expand and grow, an important question to answer is how various participants contribute to a local food system’s overall vitality and strength. This paper does so by focusing on the relationships between locally-oriented farm and retail actors and assessing what the configuration of these relationships tells us about the workings of the broader local food system. Such an analysis reveals two things. Empirically, it shows the important role food retailers play in the overall vibrancy of local (...) food exchanges: food retailers form crucial links holding the broader system together and significantly expanding consumer access to local foods. Further, different retailer types have distinct impacts on network configurations, each serving particular roles in the development and maintenance of local food systems. Methodologically, this paper shows the value of applying social network analysis techniques to the study of local food systems: such an approach yields insights that may not be as readily assessable from other strategies. In this paper, I overview common network analysis techniques and apply them to a case study of local food activities in New England, suggesting how such an approach might be applied to local food systems in other places. (shrink)

The term “exploitation” has gained wide currency in recent discussions of biomedical and research ethics. This is due in no small measure to the influence of Alan Wertheimer’s path-breaking work on the topic (Wertheimer 1999, 2011). Wertheimer presented a clear and compelling non-Marxist account of the concept of exploitation—one that stressed the connection between exploitation and unfair distributive outcomes. On this account, when one party exploits another, she takes advantage of the other to gain unfairly. A number of contemporary bioethicists (...) have accepted Wertheimer’s account of exploitation and have proceeded to apply it to a range of issues in research ethics (Hawkins and Emanuel 2008; Miller and Brody .. (shrink)

In this paper, we defend the ethics of clinical research against the charge of paternalism. We do so not by denying that the ethics of clinical research is paternalistic, but rather by defending the legitimacy of paternalism in this context. Our aim is not to defend any particular set of paternalistic restrictions, but rather to make a general case for the permissibility of paternalistic restrictions in this context. Specifically, we argue that there is no basic liberty-right to participate in clinical (...) research and that considerations of distributive fairness justify some paternalistic protections of research subjects. (shrink)

Drawing the line on physician assistance in physician-assisted death continues to be a contentious issue in many legal jurisdictions across the USA, Canada and Europe. PAD is a medical practice that occurs when physicians either prescribe or administer lethal medication to their patients. As more legal jurisdictions establish PAD for at least some class of patients, the question of the proper scope of this practice has become pressing. This paper presents an argument for restricting PAD to the terminally ill that (...) can be accepted by defenders as well as critics of PAD for the terminally ill. The argument appeals to fairness-based paternalism and the social meaning of medical practice. These two considerations interact in various ways, as the paper explains. The right way to think about the social meaning of medical practice bears on fair paternalism as it relates to PAD and vice versa. The paper contends that these considerations have substantial force when directed against proposals to extend PAD to non-terminally ill patients, but considerably less force when directed against PAD for the terminally ill. The paper pays special attention to the case of non-terminally ill patients who suffer from treatment-resistant depression, as these patients present a potentially strong case for extending PAD beyond the terminally ill. (shrink)

The allocation of vaccines and therapeutics for Covid‐19 obviously raises ethical questions, and physicians and ethicists have begun to address them. Writers have identified various criteria that should guide allocation decisions, but the criteria often conflict and need to be balanced against one another. This article proposes a model for thinking about how different considerations that are relevant to the distribution of vaccines and scarce treatments for Covid‐19 could be integrated into an allocation procedure. The model employs the construct of (...) a weighted lottery, which is a construct that has been employed in other contexts that involve the distribution of scarce resources. The article highlights the advantages of applying a weighted lottery to the Covid‐19 context and offers an illustration for how it might work in practice. The primary aim of the article is to articulate the structural features of a weighted lottery for this context and to bring out its advantages over other methods for allocating Covid‐19 medications. (shrink)

The ethical standards that regulate clinical research have multiple rationales. Among them is the need to protect potential subjects from making imprudent decisions, which extends beyond the soft paternalistic concern to protect people from making uninformed decisions to participate in trials. This article argues that a plausible risk/benefit restriction on clinical trials is presumptively justified by hard paternalism, which in turn is supported by a deeper fairness-based rationale. This presumptive case for hard paternalism in research is not defeated by the (...) alleged right to participate in clinical trials, by concerns about insult or status, by the need to conduct early phase trials that promise little to no benefit to participants, or by the recognition that some potential subjects are altruistically motivated. (shrink)

We studied collaborative skill acquisition in a dynamic setting with the game Co-op Space Fortress. While gaining expertise, the majority of subjects became increasingly consistent in the role they adopted without being able to communicate. Moreover, they acted in anticipation of the future task state. We constructed a collaborative skill acquisition model in the cognitive architecture ACT-R that reproduced subject skill acquisition trajectory. It modeled role adoption through reinforcement learning and predictive processes through motion extrapolation and learned relevant control parameters (...) using both a reinforcement learning procedure and a new to ACT-R supervised learning procedure. This is the first integrated cognitive model of collaborative skill acquisition and, as such, gives us valuable insights into the multiple cognitive processes that are involved in learning to collaborate. (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)

This book is a collection of secondary essays on America's most important philosophic thinkers—statesmen, judges, writers, educators, and activists—from the colonial period to the present. Each essay is a comprehensive introduction to the thought of a noted American on the fundamental meaning of the American regime.

Social referencing informs and regulates one’s relation with the environment as a function of the perceived appraisals of social partners. Increased emphasis on relational and social contexts in the study of emotion makes this interpersonal process particularly relevant to the field. However, theoretical conceptualizations and empirical operationalizations of social referencing are disjointed across domains and populations of study. This article seeks to unite and refine the study of this construct by providing a clear and comprehensive definition of social referencing. Our (...) perspective presents social referencing and social appraisal as coterminous processes and emphasizes the importance of a relational and interpersonal approach to the study of emotion. We conclude by outlining possible lines of research on this construct. (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)

POHLMAN S, CIBULKA NJ, PALMER JL, LORENZ RA and SMITHBATTLE L. Nursing Inquiry 2013; 20: 71–81 The placebo puzzle: examining the discordant space between biomedical science and illness/healingThe placebo response presents an enigma to biomedical science: how can ‘inert’ or ‘sham’ procedures reduce symptoms and produce physiological changes that are comparable to prescribed treatments? In this study, we examine this puzzle by explicating the discordant space between the prevailing biomedical paradigm, which focuses on a technical understanding of diagnosis and treatment, (...) and a broader understanding of illness and healing as relational and embodied. Although biomedical achievements are impressive, the knowledge resulting from this paradigm is limited by its ontological and epistemological assumptions. When the body and world are objectified, illness meanings, therapeutic relationships, and healing practices are dismissed or distorted. In spite of a robust critique of the tenets of biomedicine for guiding practice, the biomedical paradigm retains a tenacious hold on evidence-based medicine and nursing, downplaying our clinical understanding of the sentient body, patients’ life-worlds, and illness and healing. In reality, skilled nurses rely on multiple forms of knowledge in providing high-quality care to particular patients. Clinically wise nurses integrate their experience and knowledge of patients’ priorities, fears, and illness trajectories along with biomedical findings to make astute judgments and promote health and healing. (shrink)

To date, emotion research has primarily focused on the experience and display of the emoter. However, of equal, if not more, importance is how such displays impact and guide the behavior of an observer. We incorporate a functionalist framework of emotion to examine the development of differential responding to discrete emotion, theorize on what may facilitate its development, and hypothesize the functions that may underlie such behavioral responses. Although our review is focused primarily on development, the theoretical and methodological ideas (...) laid out are relevant for researchers of emotion at all ages. (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)

Attempts to explain emotion typically emphasize the interaction of evolutionary and socialization processes. However, in describing this interplay the role of the person is typically underemphasized or unaccounted for. This paper lays out empirical and theoretical rationale for considering the person as a major contributor to emotion generation and development.

We are encouraged by the attention paid to fundamental aspects relating to the interpersonal functions of emotion. In continuing this discussion, we consider two arguments used to distinguish social referencing and social appraisal, namely the role of ostension and the absence of prior appraisals of the individual. We contend that neither element is essential to social referencing.

Growth in CSR-washing claims in recent decades has been dramatic in numerous academic and activist contexts. The discourse, however, has been fragmented, and still lacks an integrated framework of the conditions necessary for successful CSR-washing. Theorizing successful CSR-washing as the joint occurrence of five conditions, this paper undertakes a literature review of the empirical evidence for and against each condition. The literature review finds that many of the conditions are either highly contingent, rendering CSR-washing as a complex and fragile outcome. (...) This finding runs counter to the dominant perception in the general public, among activists, and among a vocal contingent of academics that successful CSR-washing is rampant. (shrink)

There appears to be few, if any, limits on what sorts of logical connectives can be added to a given logic. One source of potential limitations is the motivating ideology associated with a logic. While extraneous to the logic, the motivating ideology is often important for the development of formal and philosophical work on that logic, as is the case with intuitionistic logic. One family of logics for which the philosophical ideology is important is the family of relevant logics. In (...) this paper, I explore the limits of what a relevant connective is, showing how some basic criteria motivated by the ideology of relevant logicians provide robust limits on potential connectives. These criteria provide some plausible necessary conditions on being a relevant connective. (shrink)

Will stakeholder theory continue to transform how we think about business and society? On the occasion of this journal’s 60th anniversary, this review article examines the journal’s role in shaping stakeholder theory to date and suggests that it still has transformative potential. We conducted a bibliometric analysis of co-citations in the literature from 1984 to 2020. Reporting these results, we examine the field’s evolving structure. Contextualized theoretically as an accomplishment of institutional work—the creation of a meaningful and innovative field ideology—this (...) structure is remarkable for how it integrates ethical and behavioral arguments, invites engagement from adjacent domains, and arrives at important insights for business and society. We advance a research agenda consistent with this larger institutional project. (shrink)

The ability to reason and think in a logical manner forms the basis of learning for most mathematics, computer science, philosophy and logic students. Based on the author's teaching notes at the University of Maryland and aimed at a broad audience, this text covers the fundamental topics in classical logic in an extremely clear, thorough and accurate style that is accessible to all the above. Covering propositional logic, first-order logic, and second-order logic, as well as proof theory, computability theory, and (...) model theory, the text also contains numerous carefully graded exercises and is ideal for a first or refresher course. (shrink)

Psychologists and philosophers who pose moral dilemmas to understand moral judgment typically specify outcomes as certain to occur in them. This contrasts with real-life moral decision-making, which is almost always infused with probabilities (e.g., the probability of a given outcome if an action is or is not taken). Seven studies examine sensitivity to the size and location of shifts in probabilities of outcomes that would result from action in moral dilemmas. We find that moral judgments differ between actions that result (...) in an equal increase in probability of harm (equal size), but have different end-states (e.g., an increase in harm probability from 25% to 50% or from 50% to 75%). This deviation from expected value is robust under separate evaluation, and increases when the comparison between shifts is made explicit under simultaneous evaluation. Consistent with the centrality of perceived harm in some models of moral judgment, perceived harm partially mediates sensitivity to location of harm probability shift. Unlike for shifts in harm probabilities, participants are insensitive to the location of shifts in probability of beneficial outcomes. They are also insensitive to the location of shifts in probability of analogous monetary losses and gains, suggesting an asymmetry between harm and benefit in moral reasoning, as well as an asymmetry between moral and monetary decision-making more broadly. Implications for normative philosophical theory and moral psychological theory, as well as practical applications, are discussed. (shrink)

A full understanding of emotion necessitates the bridging of disciplinary perspectives and methodological approaches. This special section uses emotional development as a foil to illustrate how suc...

Emotion regulation is one of the major foci of study in the fields of emotion and emotional development. This article proposes that to properly study emotion regulation, one must consider not only an intrapersonal view of emotion, but a relational one as well. Defining properties of intrapersonal and relational approaches are spelled out, and implications drawn for how emotion regulation is conceptualized, how studies are designed, how findings are interpreted, and how generalizations are drawn. Most research to date has been (...) conducted from an intrapersonal perspective, and the shortcomings of this approach for understanding emotion regulation are highlighted. The article emphasizes major conceptual and methodological steps required for a fuller description of the process of emotion regulation. (shrink)

Originally published in 1944, this book was originally intended as a continuation of the 1943 publication Nautical Mathematics, which is also reissued in this series. In it, the principles set out in Nautical Mathematics are given practical applications, and the text is supplied with exercises to test and clarify the lessons. This book will be of value to anyone with an interest in the history of education in the forces during WWII.

Although a personal god of mixed moral character is logically possible, no personal god that has been represented as less than wholly good has gained more than a strictly local appeal. The Judaeo-Christian god is no exception. The god is represented as merciful, kind, longsuffering, forgiving, loving - in a word, wholly good. Of course, representing a god as wholly good is one thing; providing a convincing defence of his goodness is quite another. Indeed, many would contend that of all (...) the defences provided within the Judaeo-Christian system, the defence of the goodness of God is the least convincing. (shrink)

Empathy is an extensively studied construct, but operationalization of effective empathy is routinely debated in popular culture, theory, and empirical research. This article offers a process-focused approach emphasizing the relational functions of empathy in interpersonal contexts. We argue that this perspective offers advantages over more traditional conceptualizations that focus on primarily intrapsychic features. Our aim is to enrich current conceptualizations and empirical approaches to the study of empathy by drawing on psychological, philosophical, medical, linguistic, and anthropological perspectives. In doing so, (...) we highlight the various functions of empathy in social interaction, underscore some underemphasized components in empirical studies of empathy, and make recommendations for future research on this important area in the study of emotion. (shrink)

According to the response-dependence view of moral responsibility, a person is morally responsible just in case, and in virtue of the fact that, she is an appropriate target for reactive attitudes. This paper raises a new puzzle regarding response-dependence: there is a mismatch between the granularity of the reactive attitudes and of responsibility facts. Whereas the reactive attitudes are comparatively coarse-grained, responsibility facts can be quite fine-grained. This poses a challenge for response-dependence, which seeks to ground facts about responsibility in (...) facts about the reactive attitudes. Specifically, reactive attitudes are not enough for grounding facts about degrees of moral responsibility. The responsedependence view thus requires significant revisions or supplementations. (shrink)

In this paper, we build on earlier work by Standefer (Logic J IGPL 27(4):543–569, 2019) in investigating extensions of substructural logics, particularly relevant logics, with the machinery of justification logics. We strengthen a negative result from the earlier work showing a limitation with the canonical model method of proving completeness. We then show how to enrich the language with an additional operator for implicit commitment to circumvent these problems. We then extend the logics with axioms for D, 4, and 5, (...) which requires additional justification term operators, following the work of Pacuit (in proceedings of the fifth panhellenic logic symposium, 2005) and Rubtsova (in Grigoriev D, Harrison J (eds) Computer science—theory and applications, CSR 2006; J Logic Comput 16(5):671–684, 2006), and present the required modifications to the frame semantics. We present a simplification of the neighborhood frames from the earlier work and we close by investigating the distinctive contribution of the + operator to the logic. (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)