This Is A New Release Of The Original 1903 Edition.

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)

Despite its strengths, Leech et al.'s model fails to address the important benefits that derive from self-explanation and task feedback in analogical reasoning development. These components encourage explicit, self-reflective processes that do not necessarily link to knowledge accretion. We wonder, therefore, what mechanisms can be included within a connectionist framework to model self-reflective involvement and its beneficial consequences.

The traditional college student of today is part of the Net Generation who has been raised in an era of instant access. Their communication and learning is complemented by the Internet, a major influence on this cohort. The regular method of contact is text messaging, instant messaging and cell phones. Learning methods for the Net Generation include Internet tools such as Web-CT, Blackboard, online courses, online journals and i-pod downloads. Are they ready to also change from print textbooks to Internet (...) based textbooks? This paper describes the attitudes of some Net Generation students towards the usage of electronic textbooks. Three case studies were conducted: one class used an online textbook and two other classes used e-chapter supplements. Students were questioned on their perceptions of using and learning with e-textbooks. Their views describe some changing thoughts towards network connected media that is the mantra of this generation. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

This article addresses five research questions: What specific behaviors are described in the literature as ethical or unethical? What percentage of business people are believed to be guilty of unethical behavior? What specific unethical behaviors have been observed by bank employees? How serious are the behaviors? Are experiences and attitudes affected by demographics? Conclusions suggest: There are seventeen categories of behavior, and that they are heavily skewed toward internal behaviors. Younger employees have a higher level of ethical consciousness than older (...) employees. The longer one works for a company, the more one may look to job security as a priority; this can lead to rationalizing or overlooking apparently unethical behaviors. More emphasis is needed on internal behaviors with particular attention on the impact that external behaviors have on internal behaviors. (shrink)

This essay contains material which will hopefully be of interest not only to philosophers, but also to those social scientists whose research concerns the analysis of communication, verbal or non-verbal. Although most of the topics taken up here are central to issues in the philosophy of language, they are, in my opinion, indistinguishable from topics in descriptive social psychology. The essay aims to provide a conceptual framework within which various key aspects of communication can be described, and it presents a (...) formal language, using techniques from modern modal logic, in which such descriptions can themselves be formulated. It is my hope that this framework, or parts of it, might also turn out to be of value in future empirical work. There are, therefore, essentially two sides to this essay: the development of a framework of concepts, and the construction of a formal language rich enough to express the elements of which that framework is composed. The first of these two takes its point of departure in the statement quoted from Lewis (1972) on the page preceding this introduction. The distinction drawn there by Lewis is accepted as a working hypothesis, and in one sense this essay may be seen as an attempt to explore some of the consequences of that hypothesis. (shrink)

The question of what makes someone the same person through time and change has long been a preoccupation of philosophers. In recent years, the question of what makes ordinary or lay people judge that someone is—or isn’t—the same person has caught the interest of experimental psychologists. These latter, empirically oriented researchers have sought to understand the cognitive processes and eliciting factors that shape ordinary people’s judgments about personal identity and the self. Still more recently, practitioners within an emerging discipline, experimental (...) philosophical bioethics or “bioxphi”—the focus of this chapter—have adopted a similar aim and employed similar methodologies, but with two distinctive features: (a) a special concern for enhanced ecological validity in the examples and populations studied; and (b) an interest in contributing to substantive normative debates within the wider field of bioethics. Our aim in this chapter is to sample illustrative work on personal identity in bioxphi, explore how it relates to studies in psychology covering similar terrain, and draw out the implications of this work for matters of bioethical concern. In pursuing these issues, we highlight recent work in bioxphi that includes the perceived validity of advance directives following neurodegeneration, the right of psychologically altered study participants to withdraw from research, how drug addiction may cause one to be regarded by others as “a completely different person,” the effect of deep-brain stimulation on perceptions of the self, and the potential influence of moral enhancement interventions on intuitive impressions of a person’s character. (shrink)

Sleep enhances integration across multiple stimuli, abstraction of general rules, insight into hidden solutions and false memory formation. Newly learned information is better assimilated if compatible with an existing cognitive framework or schema. This article proposes a mechanism by which the reactivation of newly learned memories during sleep could actively underpin both schema formation and the addition of new knowledge to existing schemata. Under this model, the overlapping replay of related memories selectively strengthens shared elements. Repeated reactivation of memories in (...) different combinations progressively builds schematic representations of the relationships between stimuli. We argue that this selective strengthening forms the basis of cognitive abstraction, and explain how it facilitates insight and false memory formation. (shrink)

Although death by neurologic criteria is legally recognized throughout the United States, state laws and clinical practice vary concerning three key issues: the medical standards used to determine death by neurologic criteria, management of family objections before determination of death by neurologic criteria, and management of religious objections to declaration of death by neurologic criteria. The American Academy of Neurology and other medical stakeholder organizations involved in the determination of death by neurologic criteria have undertaken concerted action to address variation (...) in clinical practice in order to ensure the integrity of brain death determination. To complement this effort, state policymakers must revise legislation on the use of neurologic criteria to declare death. We review the legal history and current laws regarding neurologic criteria to declare death and offer proposed revisions to the Uniform Determination of Death Act and the rationale for these recommendations. (shrink)

The ethical principle of ‘respect for persons’ in clinical research has traditionally focused on protecting individuals’ autonomy rights, but respect for participants also includes broader, although less well understood, ethical obligations to regard individuals’ rights, needs, interests and feelings. However, there is little empirical evidence about how to effectively convey respect to potential and current participants. To fill this gap, we conducted exploratory, qualitative interviews with participants in a clinical genomics implementation study. We interviewed 40 participants in English or Spanish (...) about their experiences with respect in the study and perceptions of how researchers in a hypothetical observational study could convey respect or a lack thereof. Most interviewees were female, identified as Hispanic/Latino or non-Hispanic white, reported annual household income under US$60 000 and did not have a Bachelor’s degree ; 30% had limited health literacy. We identified four key domains for demonstrating respect: personal study team interactions, with an emphasis on empathy, appreciation and non-judgment; study communication processes, including following up and sharing results with participants; inclusion, particularly ensuring materials are understandable and procedures are accessible; and consent and authorisation, including providing a neutral informed consent and keeping promises regarding privacy protections. While the experience of respect is inherently subjective, these findings highlight four key domains that may meaningfully demonstrate respect to potential and current research participants. Further empirical and normative work is needed to substantiate these domains and evaluate how best to incorporate them into the practice of research. (shrink)

Putnam and Laudan separately argue that the falsity of past scientific theories gives us reason to doubt the truth of current theories. Their arguments have been highly influential, and have generated a significant literature over the past couple of decades. Most of this literature attempts to defend scientific realism by attacking the historical evidence on which the premises of the relevant argument are based. However, I argue that both Putnam's and Laudan's arguments are fallacious, and hence attacking their premises is (...) unnecessary. The paper concludes with a discussion of the further historical evidence that would be required if the pessimistic induction is to present a serious threat to scientific realism. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

ABSTRACT:A wide range of research uses patterns of genetic variation to infer genetic similarity between individuals, typically referred to as genetic ancestry. This research includes inference of human demographic history, understanding the genetic architecture of traits, and predicting disease risk. Researchers are not just structuring an intellectual inquiry when using genetic ancestry, they are also creating analytical frameworks with broader societal ramifications. This essay presents an ethics framework in the spirit of virtue ethics for these researchers: rather than focus on (...) rule following, the framework is designed to build researchers’ capacities to react to the ethical dimensions of their work. The authors identify one overarching principle of intellectual freedom and responsibility, noting that freedom in all its guises comes with responsibility, and they identify and define four principles that collectively uphold researchers’ intellectual responsibility: truthfulness, justice and fairness, anti-racism, and public beneficence. Researchers should bring their practices into alignment with these principles, and to aid this, the authors name three common ways research practices infringe these principles, suggest a step-by-step process for aligning research choices with the principles, provide rules of thumb for achieving alignment, and give a worked case. The essay concludes by identifying support needed by researchers to act in accord with the proposed framework. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Metaphysicians should pay attention to quantum mechanics. Why? Not because it provides definitive answers to many metaphysical questions-the theory itself is remarkably silent on the nature of the physical world, and the various interpretations of the theory on offer present conflicting ontological pictures. Rather, quantum mechanics is essential to the metaphysician because it reshapes standard metaphysical debates and opens up unforeseen new metaphysical possibilities. Even if quantum mechanics provides few clear answers, there are good reasons to think that any adequate (...) understanding of the quantum world will result in a radical reshaping of our classical world-view in some way or other. Whatever the world is like at the atomic scale, it is almost certainly not the swarm of particles pushed around by forces that is often presupposed. This book guides readers through the theory of quantum mechanics and its implications for metaphysics in a clear and accessible way. The theory and its various interpretations are presented with a minimum of technicality. The consequences of these interpretations for metaphysical debates concerning realism, indeterminacy, causation, determinism, holism, and individuality are explored in detail, stressing the novel form that the debates take given the empirical facts in the quantum domain. While quantum mechanics may not deliver unconditional pronouncements on these issues, the range of possibilities consistent with our knowledge of the empirical world is relatively small-and each possibility is metaphysically revisionary in some way. This book will appeal to researchers, students, and anybody else interested in how science informs our world-view. (shrink)

Spontaneous collapse theories of quantum mechanics require an interpretation if their claim to solve the measurement problem is to be vindicated. The most straightforward interpretation rule, the fuzzy link, generates a violation of common sense known as the counting anomaly. Recently, a consensus has developed that the mass density link provides an appropriate interpretation of spontaneous collapse theories that avoids the counting anomaly. In this paper, I argue that the mass density link violates common sense in just as striking a (...) way as the fuzzy link, and hence should not be regarded as a problem-free alternative to the fuzzy link. Hence advocates of spontaneous collapse theories must accept some violation of common sense, although this is not necessarily fatal to their project. (shrink)

This dissertation examines the coherence and applicability of Whitehead's philosophy of organism insofar as that speculative scheme functions as a viable metaphysical basis for his philosophy of civilization. In short, what is offered is an inquiry concerning the metaphysical foundation of Whitehead's theory of civilized society. ;Overall, the metaphysical ground of civilized society is rooted in two tenets fundamental to Whitehead's philosophy: the paradigm of organism, exemplified in the becoming of an actual entity, and two, the essentially social character of (...) order, exemplified in the occurrences of natural events. Of the first, the primary ontological status of actual entities, each a self-creative process of many things in disjunction immanently related into one novel individual, sets the standard in terms of which all other existent things, human beings and civilized societies alike, are ultimately referent. Accordingly, the concepts of prehension and concrescence are most pertinent to the genesis and character of human experience, and thus to the advent of civilized society. The principle of creativity-one-many is likewise essential to the derivation of civilized society, inasmuch as the process of 'many' creatively united into 'one' is a universal archetype of Whitehead's philosophy, whether applied to cosmology or sociology. ;Equally fundamental to the metaphysical foundation of civilized society is Whitehead's conception of a composite organism, i.e., a "society" of actual entities, for it is upon this basis that the hierarchical social order of nature is established, and thereby the civilized order of human society. The occurrence of civilized society is, in this context, simply a highly specialized and unique form of social order made manifest by the impelling drive of creativity, actualized by way of the radical novelty of human mentality and the freedom of individual effort. Civilization is, as Whitehead so aptly puts it, an "adventure of ideas." So too, the question concerning the metaphysical status of civilized society, as an existent thing, as one or many, finds its resolution in conformity with the principles germane to the constitution of any such social organism. (shrink)

In an adaptive clinical trial , key trial characteristics may be altered during the course of the trial according to predefined rules in response to information that accumulates within the trial itself. In addition to having distinguishing scientific features, adaptive trials also may involve ethical considerations that differ from more traditional randomized trials. Better understanding of clinical trial experts’ views about the ethical aspects of adaptive designs could assist those planning ACTs. Our aim was to elucidate the opinions of clinical (...) trial experts regarding their beliefs about ethical aspects of ACTs. (shrink)