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)

"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.

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.

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)

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)

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)

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)

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.

One of Hume's most well-known works and a masterpiece of philosophy, A Treatise of Human Nature is indubitably worth taking the time to read.

Persons of diminished capacity, especially those who are still legally competent but are de facto incompetent should still be able to participate in moderately risky research projects that benefit the class of persons with similar diseases. It is argued that this view can be supported with a modified communitarianism, a philosophy ofmedicine that holds that health care is a joint responsibility that meets foundational human needs. The mechanism for obtaining a substituted consent I call ``community consent,'' and distinguish this from (...) the usual family or surrogate consent for treatment. Care givers are included in the community that might consent for an individual who has no identifiable family members. (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 two target articles in this issue draw an important connection between disability bioethics and geriatric bioethics. Dominic JC Wilkinson makes a pragmatic case for using frailty as a fa...

Populations around the world are aging at a very fast rate, so much so that care for the elderly will soon rupture even the most carefully planned, enlightened care provisions societies can offer. The demographics in advanced countries demonstrate this dilemma, even without projections based on antiaging medications that may be possible in the near future, and a healthier lifestyle that has preoccupied the yuppies for about 10 years.

Immunotoxins are hybrid molecules formed by coupling antibody molecules to powerful toxins of plant or bacterial origin. In experimental systems, immunotoxins have been found to kill cancer cells with great potency and specificity. This article reviews the current status of immunotoxins and some of the problems that have to be overcome before they can be used to treat human malignant disease.

Biologists and philosophers differ on whether selection should be analyzed at the level of the gene or of the individual. In Peter Godfrey-Smith’s book, Darwinian Populations and Natural Selection, he argues that individuals can be good members of Darwinian populations, whereas genes rarely can. I take issue with parts of this view, and suggest that Godfrey-Smith’s scheme for thinking about Darwinian populations is also applicable to populations of genes.

Does multilateral action always succeed in creating a Pax Universalis? On the contrary, it may lead to war. With arguments from the U.S. perspective and examples from the Gulf War, Hendrickson sees both collective and unilateral action as neither good nor bad.

In recent years, Bayesian probability theory has emerged not only as a powerful tool for building computational theories of vision, but also as a general paradigm for studying human visual perception. This book provides an introduction to and critical analysis of the Bayesian paradigm. Leading researchers in computer vision and experimental vision science describe general theoretical frameworks for modeling vision, detailed applications to specific problems and implications for experimental studies of human perception. The book provides a dialogue between different perspectives (...) both within chapters, which draw on insights from experimental and computational work, and between chapters, through commentaries written by the contributors on each other's work. Students and researchers in cognitive and visual science will find much to interest them in this thought-provoking collection. (shrink)

Acculturation is the process through which an individual's cultural behaviors and values change via contact with a majority or host culture. Although some individuals accomplish acculturation smoothly, most experience psychological stress during the acculturation process. When psychologists encounter individuals struggling to acculturate, they are mandated by ethical guidelines and principles to help through several steps: (a) recognize their own biases, beliefs, and attitudes that may influence their work with the acculturating individual; (b) develop competence to work with individuals whose cultural (...) beliefs and practices differ from their own; (c) counsel the acculturating individual using scientifically supported techniques; and (d) intervene without discrimination or disrespect. Two case studies are presented to illustrate how psychologists can ethically and effectively encourage mentally healthy acculturation. Keywords: acculturation, ethics, cultural differences. (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)

The relation between sex hormones and responses to partner infidelity was explored in two studies reported here. The first confirmed the standard sex difference in relationship jealousy, that males (n=133) are relatively more distressed by a partner’s sexual infidelity and females (n=159) by a partner’s emotional infidelity. The study also revealed that females using hormone-based birth control (n=61) tended more toward sexual jealousy than did other females, and reported more intense affective responses to partner infidelity (n=77). In study two, 47 (...) females were assessed four times across one month. Patterns of response to partner infidelity did not vary by week of menstrual cycle, but significant relations between salivary estradiol level and jealousy responses were obtained during the time of rising and high fertility risk. The implications, at least for females, are that any evolved psychological, affective, or behavioral dispositions regarding reproduction-related relationships are potentially moderated by estradiol, and that the use of synthetic hormones may disrupt this relation. (shrink)