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)

Are the relations between the property of a thing and its related disposition to react in certain ways, and between the triggering of that disposition and the consequent effect, necessary? Harré and Madden, in their analysis of causal powers, said they are, but their arguments are not persuasive. Humeans like Simon Blackburn deny it. I criticize the Humean position, and argue afresh for their necessity. I note that David Lewis' analysis of causation requires their necessity, though as a (...) confessed Humean he has not admitted this. (shrink)

In their simplest form, hybrid languages are propositional modal languages which can refer to states. They were introduced by Arthur Prior, the inventor of tense logic, and played an important role in his work: because they make reference to specific times possible, they remove the most serious obstacle to developing modal approaches to temporal representation and reasoning. However very little is known about the computational complexity of hybrid temporal logics.In this paper we analyze the complexity of the satisfiability problem of (...) a number of hybrid temporal logics: the basic hybrid language over transitive trees; nominal Until logic; and referential interval logic. We discuss the effects of including nominals, the @ operator, the somewhere modality E, and the difference operator D. Adding nominals to tense logic leads for several frame-classes to an increase in complexity of the satisfiability problem from PSPACE to EXPTIME. On transitive trees, however, the satisfiability problem for this language can be decided in PSPACE. Along the way we make a detour through hybrid propositional dynamic logic: we establish upper bounds for a number of temporal logics by generalizing results due to Passy and Tinchev [29] and De Giacomo [16]. We conclude with some remarks on the relevance of our results to description logic, and draw attention to the utility of the spypoint technique for proving upper and lower bounds. (shrink)

This study evaluated the online privacy policies of business-to-consumer e-commerce firms in five industries of mainland China, Taiwan, and Hong Kong. Based on the neo-institutional theory, we also tested whether the four institutional factors, top management’s legal education, managerial ethics, rule of law in information privacy protection and peer practices, had any effects on e-information and e-communication content. Results from a content analysis of 229 websites found that the privacy policy contents that complied with generally accepted privacy standards were lesser (...) in mainland China firms than those of Taiwan and Hong Kong firms. There were also significant differences in the amount of contents among the five industries. The results of regression analyses showed the importance of all four factors on e-information content. They also showed the importance of coercive, mimetic, and normative isomorphisms on e-information content. The validation of normative isomorphism highlighted the importance of managerial ethics and legal education. Our findings supplemented extant literature which identified economic motive as the main factor in influencing privacy practice disclosures. (shrink)

"Dr. Rubin has brought cognitive psychology into a wholly unprecedented dialogue with studies in oral tradition. The result is a truly new perspective on memory and the processes of oral tradition." --John Miles Foley, University of Missouri.

Considerable debate has occurred about the proper role of philosophers when offering ethics consultations. Some argue that only physicians or clinical experienced personnel should offer ethics consultations in the clinical setting. Others argue still further that philosophers are ill-equipped to offer such advice, since to do so rests on no social warrant, and violates the abstract and neutral nature of the discipline itself.I argue that philosophers not only can offer such consultations but ought to. To be a bystander when one's (...) discipline does offer insights and methods of value discernment is pusillanimous. But this position requires a view of clinical medical ethics as one that arises out of the clinical practice of medicine, and not just from an application of general ethical principles to the practice of medicine. I conclude with some skills that trained philosophers can bring to the consultation service, and note that all consultations are in the form of recommendations that the patient, family, and physician are still free to accept or reject. Philosophers in the clinical setting do not make decisions. (shrink)

What task might a society undertake dearer to it than the cultivation of its teachers? And when it nurtures them, what should it seek but excellence, what should it transmit but the highest f its ideals, and what should it evoke but the richest expressions of its wisdom and love? As David C. Jones surveyed young teachers in preparation after nearly thirty years as an educator, he felt that many of them would benefit by hearing from those who have (...) advanced in the field, who have seen meaning in life and who have embraced life purposefully, wholeheartedly and affectionately. So what is a master teacher after? A heightened awareness of self and of the motives, virtues, and actions which fulfill it. Then a deepened recognition that love fulfills it, or more specifically, unconditional love. This long-awaited book begins and ends with ideals. In the middle is the interplay between hoping and doing as experienced by eleven outstanding mentors. Few stories of the search for teaching excellence are as compelling and insightful. (shrink)

The sciences use a wide range of visual devices, practices, and imaging technologies. This diversity points to an important repertoire of visual methods that scientists use to adapt representations to meet the varied demands that their work places on cognitive processes. This paper identifies key features of the use of visualization in a range of scientific domains and considers the implications of this repertoire for understanding scientists as cognitive agents.

The problem of developing a moral philosophy of medicine is explored in this essay. Among the challenges posed to this development are the general mistrust of moral philosophy and philosophy in general created by post-modernist philosophical and even anti-philosophical thinking. This reaction to philosophical systematization is usually called antifoundationalism. I distinguish different forms of antifoundationalism, showing that not all forms of their opposites, foundationalism, are alike, especially with regards to claims made about the certitude of moral thought. I conclude that (...) we are correct to mistrust absolutist principles in a moral philosophy of medicine, but can find some center within the practice of medicine itself for a moral foundation. (shrink)

This is the first book-length study of the development of civility in Chinese societies. Although some social scientists and political philosophers have discussed civility, none has defined it as an analytical tool to systematically measure attitudes and behavior, and few have applied it to a non-Western society. By comparing the development of civility in mainland China and Taiwan, Civility and Its Development: The Experiences of China and Taiwan analyzes the social conditions needed for civility to become established in a society. (...) Schak argues that the attempts to impose civility top-down from the state are ineffective. Civility appeared in Taiwan only after state efforts to impose it ceased at the end of the 1980s when Taiwan began to democratize, and the PRC government civility campaigns have so far had only limited success. The book concludes with an examination of various differences between Taiwan and the PRC relevant to Taiwan’s having become a society with civility while the PRC still encounters difficulties in doing so. The essential factor in developing civility in Taiwan, Schak contends, was its evolution from a place composed of myriad small, inward-looking communities to a society in which everyone shares a strong identity and civic consciousness, and people consider others as fellow members, not anonymous strangers. “This book represents the most thorough review of what social scientists once called ‘the civilizing process’ in Chinese society. David C. Schak builds on the earlier studies on this issue and goes well beyond the established literature.” —James Watson, Fairbank Professor of Chinese Society and Professor of Anthropology, Emeritus, Harvard University “This is a topic that people talk about all the time, and David C. Schak draws a lot of material together in a systematic and comprehensive way that can stimulate important discussions beyond the academy.” —Thomas Gold, Professor of Sociology, University of California, Berkeley. (shrink)

Participants with posttraumatic stress disorder and participants with a trauma but without PTSD wrote narratives of their trauma and, for comparison, of the most-important and the happiest events that occurred within a year of their trauma. They then rated these three events on coherence. Based on participants’ self-ratings and on naïve-observer scorings of the participants’ narratives, memories of traumas were not more incoherent than the comparison memories in participants in general or in participants with PTSD. This study comprehensively assesses narrative (...) coherence using a full two by two design. The results are counter to most prevalent theoretical views of memory for trauma. (shrink)

It is quite extraordinary, philosophically speaking, that according to the orthodox interpretation: (a) quantum mechanics is a complete and comprehensive theory of microphysics, and yet (b) the role of measurement, in quantum mechanics, cannot be analyzed in terms of the collective effects of the microphysical particles making up the apparatus. It follows that, if the orthodox interpretation is correct, the measurement apparatus and its quantum physical effects cannot be accounted for microreductively. This is significant because it is widely believed that (...) the relation between physical wholes and parts is microreductive. Indeed, many philosophers are persuaded of the inevitability of universal microreduction to the basic elements of microphysics. This is the viewpoint embodied in the program for the unity of science, espoused in recent years, most notably by Robert Causey (1977). (shrink)

At the end of the most violent century in human history, it is good to take stock of our commitments to human and other life forms, as well as to examine the rights and the duties that might flow from their biological makeup. Professor Thomasma and Professor Loewy have held a long-standing dialogue on whether there are moral differences between animals and humans. This dialogue was occasioned by a presentation Thomasma made some years ago at Loewy's invitation at the University (...) of Illinois, Peoria, Medical Center. During that presentation, Thomasma argued that human beings are sufficiently distinct from other animals genetically and otherwise to justify a moral difference in rights and obligations. In effect, he argued that there are species-specific rights. This essay will pick up the threads of that dialogue. (shrink)

Moral capacity is an important feature of what it means to be human. In this volume, the contributors have taken on the daunting task of trying to distinguish between legal and moral capacity. This distinction is difficult at times for clinicians, philosophers and legal scholars alike. Part of the challenge of defining moral capacity lies in the difficulty of adequately categorizing it. For this reason, the editors have chosen to divide the book into three parts. The first looks at the (...) concepts involved in the discussion of moral capacity; the second considers the role of moral capacity in the lives of professionals; and the final part reflects on case studies of moral capacity or incapacity illustrating the challenge that moral capacity presents - its definition lying between two seemingly incommensurable models, those of the threshold and continuum. This volume takes a multidisciplinary approach to the subject, and ties the disciplines of medicine, philosophy and law into the health context. It will be of interest to medical health professionals as well as researchers working in the areas of philosophy and law. (shrink)

While pain is common among seniors, it is not adequately treated or managed. In particular, pain in seniors with dementia is often undertreated and undermanaged. Although the undertreatment of pain among persons with cognitive impairments represents a serious ethical concern for pain clinicians, most writers in the area explain the undertreatment of pain by focusing on issues related to liability, fears of addiction to opioids, and erroneous beliefs that pain is a normal part of the ageing process. We argue that (...) the philosophical notion of personhood must also be given careful attention when considering the problem of pain undermanagement. In this paper, we consider the undertreatment of pain among seniors with dementia, while focusing on the ontology of relationships and on existential philosophy. Moreover, we outline a series of recommendations to help minimize the probability of pain undertreatment in this population and to encourage considerations relating to personhood when treating people with dementia. (shrink)

Despite its long tradition in social psychology, we consider that Cognitive Dissonance Theory presents serious flaws concerning its methodology which question the relevance of the theory, limit breakthroughs, and hinder the evaluation of its core hypotheses. In our opinion, these issues are mainly due to operational and methodological weaknesses that have not been sufficiently addressed since the beginnings of the theory. We start by reviewing the ambiguities concerning the definition and conceptualization of the term cognitive dissonance. We then review the (...) ways it has been operationalized and we present the shortcomings of the actual paradigms. To acquire a better understanding of the theory, we advocate a stronger focus on the nature and consequences of the cognitive dissonance state itself. Next, we emphasize the actual lack of standardization, both in the ways to induce cognitive dissonance and to assess it, which impairs the comparability of the results. Last, in addition to reviewing these limits, we suggest new ways to improve the methodology and we conclude on the importance for the field of psychology to take advantage of these important challenges to go forwards. (shrink)

The organism is one of the fundamental concepts of biology and has been at the center of many discussions about biological individuality, yet what exactly it is can be confusing. The definition that we find generally useful is that an organism is a unit in which all the subunits have evolved to be highly cooperative, with very little conflict. We focus on how often organisms evolve from two or more formerly independent organisms. Two canonical transitions of this type—replicators clustered in (...) cells and endosymbiotic organelles within host cells—demonstrate the reality of this kind of evolutionary transition and suggest conditions that can favor it. These conditions include co-transmission of the partners across generations and rules that strongly regulate and limit conflict, such as a fair meiosis. Recently, much attention has been given to associations of animals with microbes involved in their nutrition. These range from tight endosymbiotic associations like those between aphids and Buchnera bacteria, to the complex communities in animal intestines. Here, starting with a reflection about identity through time, we consider the distinctions between these kinds of animal–bacteria interactions and describe the criteria by which a few can be considered jointly organismal but most cannot. (shrink)

We investigate introduction and elimination rules for truth-functional connectives, focusing on the general questions of the existence, for a given connective, of at least one such rule that it satisfies, and the uniqueness of a connective with respect to the set of all of them. The answers are straightforward in the context of rules using general set/set sequents of formulae, but rather complex and asymmetric in the restricted (but more often used) context of set/formula sequents, as also in the intermediate (...) set/formula-or-empty context. (shrink)

Kin selection is a core aspect of social evolution theory, but a small number of critics have recently challenged it. Here I address these criticisms and show that kin selection remains an important explanation for much social evolution. I show how many of the criticisms rest on historical idiosyncrasies of the way the field happened to develop, rather than on the real logic and evidence.

According to Frankena, “the moral point of view is what Alison Wilde and Heather Badcock did not have.” Most of us, however, are not such extreme examples. We are capable of the moral point of view, but we fail to take the necessary time or make the required efforts. We resist pulling ourselves from other distractions to focus on the plight of others and what we might do to ameliorate their suffering. Perhaps compassion is rooted in understanding what it is (...) that connects us with others rather than what separates us, and rests on developing sufficient awareness, to internalize what our actions, or lack of them, mean in the lives of others. (shrink)

Two challenges face European philosophy of medicine. The first is to counterbalance what is seen as an overemphasis on social analysis of medicine with greater attention to its personal and individual dimensions. The second, related challenge, is to more fully understand the clinical realities of modern medicine, which in turn, give rise to the scope and limits of physician duties, patient obligations, and social concerns.

St. John of the Cross’ work, The Dark Night of the Soul, and Joseph Symonds’ work, The Case and Cure of a Deserted Soul, offer two compelling treatments on the subject of spiritual dryness. Moreover, these works represent two spiritual traditions which offer distinct but viable perspectives on the Christian life. This paper seeks to answer the following question: What is the degree of similarity between St. John of the Cross’ understanding of the dark night of the soul and Joseph (...) Symonds’ understanding of spiritual desertion? A secondary question is also addressed: What is the value of these resources for pastoral care today? Although notable differences exist between the two, their degree of similarity is significant considering the disconnection between the spiritual traditions that each represent. Moreover, these works are invaluable resources for contemporary pastoral care. (shrink)