Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

"The Quattrocento Dialogue" discussed by David Marsh was produced by Leonardo Bruni, Poggio Bracciolini, Lorenzo Valla, Leon Battista Alberti, and Giovanni Pontano. Their dialogues "examine philosophical questions in a contemporary setting," and since that setting is one of emerging modernity, the development of the genre of dialogue "illustrates the development of emerging modern thought". Marsh’s book is a mixture of intellectual and literary history, unburdened or unenlivened with fashionable theorizing, and directed more toward establishing the existence of (...) a genre of Quattrocento dialogue than toward defining modernity. (shrink)

Increasingly, the world seems to shrink due to our ever-expanding technological and communication capacities. Correspondingly, our awareness of other cultures increases. This is especially true in the field of bioethics because the technological progress of medicine throughout the world is causing dramatic and challenging intersections with traditionally held values. Think of the use of pregnancy monitoring technologies like ultrasound to abort fetuses of the “wrong” sex in India, the sale of human organs in and between countries, or the disjunction between (...) the haves and the have-nots in South America when it comes to bone marrow transplants, while thousands of other children die for want of fundamental goods and services like clean water, basic inoculations, and food itself. (shrink)

Plagiarism has been a long standing concern within higher education. Yet with the rapid rise in the use and availability of the Internet, both the research literature and media have raised the notion that the online environment is accelerating the decline in academic ethics. The majority of research that has been conducted to investigate such claims have involved self-report data from students. This study sought to collect empirical data to investigate the potential influence the prevalence of the Internet has had (...) on significant higher education artifacts by comparing dissertations written prior to widespread use of the Internet with those written in a period in ubiquitous Internet use. Due to the prestige associated with the doctoral degree and the fact that the majority of the effort necessary to achieve such a degree resides within the dissertation, this study utilized Doctor of Philosophy dissertations written in English and published by accredited universities in the U.S. and Canada. A sample of 384 dissertations were analyzed by Turnitin plagiarism detection software. The mean similarity indices for pre-Internet and post-Internet eras were 14.5 and 12.3 %, respectively. A Mann Whitney U test indicated that the differences between groups was significant, however opposite than has been purported within the exigent literature. When comparing the counts of dissertations for each time era considering those with plagiarism versus those that had little/no evidence thereof, there was no statistically significant difference. The findings of this study suggest that the Internet may not be significantly impacting the prevalence of plagiarism in advanced levels of higher education. (shrink)

I argue that thought experiments are a form of experimental reasoning similar to real experiments. They require the same ability to participate by following a narrative as real experiments do. Participation depends in turn on using what we already know to visualize, manipulate and understand what is unfamiliar or problematic. I defend the claim that visualization requires embodiment by an example which shows how tacit understanding of the properties of represented objects and relations enables us to work out how such (...) objects might behave in a postulated world. This knowledge is that of embodied agents. That thought experiments require embodied participation is what makes them experiments rather than arguments. Unlike real experiments, from which ordinary perception has been displaced by instrumentation, thought experiments still appeal to relatively unmediated common sense, even when their purpose is to criticize or subvert common sense notions. (shrink)

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)

We explore ways in which purely qualitative belief change in the AGM tradition throws light on options in the treatment of conditional probability. First, by helping see why it can be useful to go beyond the ratio rule defining conditional from one-place probability. Second, by clarifying what is at stake in different ways of doing that. Third, by suggesting novel forms of conditional probability corresponding to familiar variants of qualitative belief change, and conversely. Likewise, we explain how recent work on (...) the qualitative part of probabilistic inference leads to a very broad class of 'proto-probability' functions. (shrink)

Book reviewed in this article: Balancing Act: The New Medical Ethics of Medicine's New Economics. By E. Haavi Morreim.

This book reviews the latest research in the field of autobiographical memory.

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)

I argue that in four important respects locke's views on faith and reason are similar to aquinas' position. However, Locke drew some conclusions from these views with which thomas would not have agreed, And it was concerning these matters that locke was accused of unorthodoxy. I suggest that in the 17th century context some of those charges were justified and that locke's views in any event are inadequate.

Our global knowledge of different cultures and the diversity of values increases almost daily. New challenges arise for ethics. This is especially true in the field of bioethics because the technological progress of medicine throughout the world is causing dramatic interactions with traditionally held values. Science and technology are rapidly advancing beyond discussions and corresponding political struggles over human rights, leaving those debates behind. This rapid development of science is at odds with the principle of sustained development that calls for (...) measured and thoughtful planning, such that no new idea should rupture the delicate fabric of communities, environment, and cultural evolution. (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)

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)

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)

There are several branches of ethics. Clinical ethics, the one closest to medical decisionmaking, can be seen as a branch of medicine itself. In this view, clinical ethics is a unitary hermeneutics. Its rule is a guideline for unifying other theories of ethics in conjunction with the clinical context. Put another way, clinical ethics interprets the clinical situation in light of a balance of other values that, while guiding the decisionmaking process, also contributes to the very weighting of those values. (...) The case itself originates ideas, not only about which value ought to predominate in its resolution, but also provides the origin of clinical rules that can be used in other cases. These are interpretive rules. Some examples of these rules are presented as well. (shrink)

We (Patterson & Plaut, 2009) argued that cognitive neuropsychology has had a limited impact on cognitive science due to a nearly exclusive reliance on (a) single‐case studies, (b) dissociations in cognitive performance, and (c) shallow, box‐and‐arrow theorizing, and we advocated adopting a case‐series methodology, considering associations as well as dissociations, and employing explicit computational modeling in studying “how the brain does its cognitive business.” In reply, Coltheart (2010) claims that our concern is misplaced because cognitive neuropsychology is concerned only with (...) studying the mind, in terms of its “functional architecture,” without regard to how this is implemented in the brain. In this response, we do not dispute his characterization of cognitive neuropsychology as it has typically been practiced over the last 40 years, but we suggest that our understanding of brain structure and function has advanced to the point where studying the mind without regard to the brain is unwise and perpetuates the field’s isolation. (shrink)

A position has been advanced by a number of philosophers, notably by Burnham and Skilleås, that certain knowledge is required to aesthetically appreciate a fine wine. They further argue that pleasure is not an integral part of aesthetically appreciating wine. Their position implies that a novice cannot aesthetically appreciate a fine wine. This paper draws on research into tasting and psychology to rebut these claims. I argue that there is strong evidence from both the average consumer and from wine experts (...) that they are unable to separate enjoyment from aesthetic evaluation; secondly, I argue that wine knowledge may actually preclude tasting of the wine as it exists in the glass due to perceptual bias. I conclude by arguing that it is unclear how exactly knowledge of things like terroir is supposed to affect the taste, as well as question what role conforming to a certain style plays in aesthetic success, as arguments that require knowledge for appreciation typically emphasize knowledge of styles of wine. (shrink)

William James is frequently considered one of America's most important philosophers, as well as a foundational thinker for the study of religion. Despite his reputation as the founder of pragmatism, he is rarely considered a serious philosopher or religious thinker. In this new interpretation David Lamberth argues that James's major contribution was to develop a systematic metaphysics of experience integrally related to his developing pluralistic and social religious ideas. Lamberth systematically interprets James's radically empiricist world-view and argues for an (...) early dating for his commitment to the metaphysics of radical empiricism. He offers a close reading of Varieties of Religious Experience; and concludes by connecting James's ideas about experience, pluralism and truth to current debates in philosophy, the philosophy of religion, and theology, suggesting James's functional, experiential metaphysics as a conceptual aid in bridging the social and interpretive with the immediate and concrete while avoiding naive realism. (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.

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)

To achieve the goals of ethics education, students must have oportunities to develop both moral capacities (imagination, responsibility, and perseverance) and intellectual capacities (critical thinking). This article contends that service-based learning represents an important opportunity for integrative ethics education. It describes a program of leadership internships at North Central College in Naperville, Illinois, in which faculty members conduct a for-credit reflection seminar with students involved in service internships. The seminar is based upon student-written cases about ethical issues they face in (...) their work settings. (shrink)

The mammalian pineal gland contains two types of N‐acetyltransferases which act on aromatic amines. One type preferentially acetylates arylamines such as phenetidine and aniline, whereas the other preferentially acetylates arylalkylamines such as tryptamine and phenylethylamine. The two enzymes can be distinguished by (1) molecular size, (2) regulation, and (3) inactivation characteristics. Arylalkylamine N‐acetyltransferase is involved in the regulation of melatonin synthesis in the pineal gland. A specific function of pineal arylamine N‐acetyltransferase has not been established; it may function as a (...) nonspecific detoxification mechanism. (shrink)

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)