Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

In the mid-seventeenth century a movement of self-styled experimental philosophers emerged in Britain. Originating in the discipline of natural philosophy amongst Fellows of the fledgling Royal Society of London, it soon spread to medicine and by the eighteenth century had impacted moral and political philosophy and even aesthetics. Early modern experimental philosophers gave epistemic priority to observation and experiment over theorising and speculation. They decried the use of hypotheses and system-building without recourse to experiment and, in some quarters, developed a (...) philosophy of experiment. The movement spread to the Netherlands and France in the early eighteenth century and later impacted Germany. Its important role in early modern philosophy was subsequently eclipsed by the widespread adoption of the Kantian historiography of modern philosophy, which emphasised the distinction between rationalism and empiricism and had no place for the historical phenomenon of early modern experimental philosophy. The re-emergence of interest in early modern experimental philosophy roughly coincided with the development of contemporary x-phi and there are some important similarities between the two. (shrink)

In The Hobbit, J. R. R. Tolkien constructs middle-aged Bilbo Baggins as a sheltered and emotionally immature ‘child’ during the opening chapters before tracing his development into an autonomous, self-aware adult as the tale progresses. This article examines Tolkien’s novel qua bildungsroman through both a literary lens—considering setting, dialogue, and symbolism, among other techniques—and via a psychological framework, emphasizing an Eriksonian conception of development. Additionally, Peter Jackson’s three-part film adaptation of The Hobbit is discussed throughout with ways that Jackson (...) succeeds and fails at portraying Bilbo’s childlike attributes noted. I argue that Tolkien presents a sophisticated account of Bilbo’s childish persona growing into a mature adult worldview, and that Jackson appropriately reflects much, though not all, of this development in his films. (shrink)

The book presents the first comprehensive survey of limits of the intentional control of action from an interdisciplinary perspective. It brings together leading scholars from philosophy, psychology, and the law to elucidate this theoretically and practically important topic from a variety of theoretical and disciplinary approaches. It provides reflections on conceptual foundations as well as a wealth of empirical data and will be a valuable resource for students and researchers alike. Among the authors: Clancy Blair, Todd S. Braver, Michael W. (...) Cole, Anika Fäsche, Maayan Davidov, Peter Gollwitzer, Kai Robin Grzyb, Tobias Heikamp, Gabriele Oettingen, Rachel McKinnon, Nachschon Meiran, Hans Christian Röhl, Michael Schmitz, John R. Searle, Gottfried Seebaß, Gisela Trommsdorff, Felix Thiede, J. Lukas Thürmer, Frank Wieber. (shrink)

Martine Nida-Rümelin (1996) argues that color science indicates behaviorally undetectable spectrum inversion is possible and raises this possibility as an objection to functionalist accounts of visual states of color. I show that her argument does not rest solely on color science, but also on a philosophically controversial assumption, namely, that visual states of color supervene on physiological states. However, this assumption, on the part of philosophers or vision scientists, has the effect of simply ruling out certain versions of functionalism. While (...) Nida-Rümelin is quite right to search for empirical tests for claims about the nature of visual states, philosophical issues remain pivotal in determining the correctness of these claims. (shrink)

This paper presents a preliminary analysis of the first participatory budgeting experiment in the United States, in Chicago's 49th Ward. There are two avenues of inquiry: First, does participatory budgeting result in different budgetary priorities than standard practices? Second, do projects meet normative social justice outcomes? It is clear that allowing citizens to determine municipal budget projects results in very different outcomes than standard procedures. Importantly, citizens in the 49th Ward consistently choose projects that the research literature classifies as low (...) priority. The results are mixed, however, when it comes to social justice outcomes. While there is no clear pattern in which projects are located only in affluent sections of the ward, there is evidence of geographic clustering. Select areas are awarded projects like community gardens, dog parks, and playgrounds, while others are limited to street resurfacing, sidewalk repairs, bike racks, and bike lanes. Based on our findings, we offer suggestions for future programmatic changes. (shrink)

Skow ([2007]), and much more recently Callender ([2017]), argue that time can be distinguished from space due to the special role it plays in our laws of nature: our laws determine the behaviour of physical systems across time, but not across space. In this work we assess the claim that the laws of nature might provide the basis for distinguishing time from space. We find that there is an obvious reason to be sceptical of the argument Skow submits for distinguishing (...) time from space: Skow fails to pay sufficient attention to the relationship between the dynamical laws and the antecedent conditions required to establish a complete solution from the laws. Callender’s more sophisticated arguments in favour of distinguishing time from space by virtue of the laws of nature presents a much stronger basis to draw the distinction. By developing a radical reading of Callender’s view we propose a novel approach to differentiating time and space that we call temporal perspectivalism. This is the view according to which the difference between time and space is a function of the agentive perspective. (shrink)

I propose a strategy for a metaphysical reduction of perceived color, that is, an identification of perceived color with properties characterizable in non-qualitative terms. According to this strategy, a description of visual experience of color, which incorporates a description of the appearance of color, is a reference-fixing description. This strategy both takes color appearance seriously in its primary epistemic role and avoids rendering color as metaphysically mysterious. I’ll also argue that given this strategy, a plausible account of perceived color claims (...) that colors are physical properties of physical objects. (shrink)

I argue that phenomenal externalism is preferable to phenomenal internalism on the basis of externalism's explanatory power with respect to qualitative character. I argue that external qualities, namely, external physical properties that are qualitative independent of consciousness, are necessary to explain qualitative character, and that phenomenal externalism is best understood as accepting external qualities while phenomenal internalism is best understood as rejecting them. I build support for the claim that external qualities are necessary to explain qualitative character on the basis (...) of a model of color perception as a certain sort of information filter by which perceivers gain access to external qualities. (shrink)

Color subjectivists claim that, despite appearances to the contrary, the world external to the mind is colorless. However, in giving an account of color perception, subjectivists about the nature of perceived color must address the nature of perceived spatial location as well. The argument here will be that subjectivists’ problems with coordinating the metaphysics of perceived color and perceived location render color perception implausibly mysterious. Consequently, some version of color realism, the view that colors are (physical, dispositional, functional, sui generis, (...) or some other) properties of physical objects, is correct. (shrink)

There has been some recent optimism that addressing the question of how we distinguish sensory modalities will help us consider whether there are limits on a scientific understanding of perceptual states. For example, Block has suggested that the way we distinguish sensory modalities indicates that perceptual states have qualia which at least resist scientific characterization. At another extreme, Keeley argues that our common-sense way of distinguishing the senses in terms of qualitative properties is misguided, and offers a scientific eliminativism about (...) common-sense modalities which avoids appeal to qualitative properties altogether. I’ll argue contrary to Keeley that qualitative properties are necessary for distinguishing senses, and contrary to Block that our common-sense distinction doesn’t indicate that perceptual states have qualia. A non-qualitative characterization of perceptual states isn’t needed to avoid the potential limit on scientific understanding imposed by qualia. (shrink)

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

With the success of cognitive science's interdisciplinary approach to studying the mind, many theorists have taken up the strategy of appealing to science to address long standing disputes about metaphysics and the mind. In a recent case in point, philosophers and psychologists, including Robert Kane, Daniel C. Dennett, and Daniel M. Wegner, are exploring how science can be brought to bear on the debate about the problem of free will. I attempt to clarify the current debate by considering how empirical (...) research can be useful. I argue that empirical findings don't apply to one basic dimension of the problem, namely the dispute between compatibilism and incompatibilism. However, I show that empirical research can provide constraints in connection with another fundamental dimension, namely the dispute between libertarianism, which claims that indeterminacy is, in certain contexts, sufficient for freedom, and hard determinism and compatibilism, which deny this. I argue that the source of the most powerful constraint is psychological research into the accuracy of introspection. (shrink)

In Ruling Passions, Simon Blackburn contends that we should reject sensibility theory because it serves to support a conservative complacency. Blackburn's strategy is attractive in that it seeks to win this metaethical dispute – which ultimately stems from a deep disagreement over antireductionism – on the basis of an uncontroversial normative consideration. Therefore, Blackburn seems to offer an easy solution to an apparently intractable debate. We will show, however, that Blackburn's argument against sensibility theory does not succeed; it is no (...) more supportive of conservative complacency than Blackburn's noncognitivism. A victory for noncognitivism cannot be so easily won. (shrink)

This chapter examines the spectrum inversion hypothesis as an argument against certain kinds of account of what it’s like to be conscious of color. The hypothesis aims to provide a counterexample to accounts of what it’s like to be conscious of color in non-qualitative terms, as well as to accounts of what it’s like to be conscious of color in terms of the representational content of conscious visual states (which, according to some philosophers, is in turn given an account in (...) non-qualitative terms). I explain the hypothesis’s reasoning in sections 1 and 2. I then take up background issues: since the counterexample provided by the hypothesis is typically given as a possibility rather than an actuality, I briefly discuss the kind of possibility involved in section 3, and the methodologies used to evaluate the plausibility of possibilities in section 4. In section 5, I describe some general considerations that are commonly used against the spectrum inversion hypothesis. I take up attempts to support the hypothesis with findings from color science in section 6. I end with comments skeptical of both the motivation for the spectrum inversion hypothesis and the methodology used to support it. (shrink)

We initially characterize what we’ll call existence problems as problems where there is evidence that a putative entity exists and this evidence is not easily dismissed; however, the evidence is not adequate to justify the claim that the entity exists, and in particular the entity hasn’t been detected. The putative entity is elusive. We then offer a strategy for determining whether an existence problem is philosophical or scientific. According to this strategy (1) existence problems are characterized in terms of causal (...) roles, and (2) these problems are categorized as scientific or philosophical on the basis of the epistemic context of putative realizers. We argue that the first step of the strategy is necessary to avoid begging the question with regard to categorization of existence problems, and the second step categorizes existence problems on the basis of a distinction between two ways in which an entity can be elusive. This distinction between kinds of elusiveness takes as background a standard account of inference to the best explanation. Applying this strategy, we argue that the existence of a multiverse is a scientific problem. (shrink)

"The Location Problem for Color Subjectivism" response to commentators.

The selected effects or ‘etiological’ theory of Proper function is a naturalistic and realist account of biological teleology. It is used to analyse normativity in philosophy of language, philosophy of mind, philosophy of medicine and elsewhere. The theory has been developed with a simple and intuitive view of natural selection. Traits are selected because of their positive effects on the fitness of the organisms that have them. These ‘selected effects’ are the Proper functions of the traits. Proponents argue that this (...) analysis of biological teleology has the unique advantage that the selected effect function of a trait is also a causal explanation of the trait: the trait exists because it performs this function. We show, however, that selected effect functions as currently defined explain the existence of traits only under highly restrictive assumptions about evolutionary dynamics. In many common scenarios in which traits evolve by natural selection, selected effect functions do not explain those traits. This is because definitions of selected effect function extract from any evolutionary scenario only the information that would be explanatorily relevant in the simple evolutionary scenario implicit in those definitions. When applied to more complex scenarios selected effect functions omit the key information that is explanatorily relevant in those scenarios. The assumptions required for selected effect functions to be explanatory are particularly unlikely to hold in the domain that its proponents care most about - the evolution of representation. A more adequate selected effects theory of Proper functions may be possible, but will require much greater attention to the structure of actual evolutionary explanations. (shrink)

Martine Nida-Rümelin (1996) argues that color science indicates behaviorally undetectable spectrum inversion is possible and raises this possibility as an objection to functionalist accounts of visual states of color. I show that her argument does not rest solely on color science, but also on a philosophically controversial assumption, namely, that visual states of color supervene on physiological states. However, this assumption, on the part of philosophers or vision scientists, has the effect of simply ruling out certain versions of functionalism. While (...) Nida-Rümelin is quite right to search for empirical tests for claims about the nature of visual states, philosophical issues remain pivotal in determining the correctness of these claims. (shrink)

This thesis is a study of the notion of time in modern physics, consisting of two parts. Part I takes seriously the doctrine that modern physics should be treated as the primary guide to the nature of time. To this end, it offers an analysis of the various conceptions of time that emerge in the context of various physical theories and, furthermore, an analysis of the relation between these conceptions of time and the more orthodox philosophical views on the nature (...) of time. In Part II I explore the interpretation of nonrelativistic quantum mechanics in light of the suggestion that an overly Newtonian conception of time might be contributing to some of the difficulties that we face in interpreting the quantum mechanical formalism. In particular, I argue in favour of introducing backwards-in-time causal influences as part of an alternative conception of time that is consistent with the picture of reality that arises in the context of the quantum formalism. Moreover, I demonstrate that this conception of time can already be found in a particular formulation of classical mechanics. One might see that one of the central themes of Part II originates from a failure to heed properly the doctrine of Part I: study into the nature of time should be guided by modern physics and thus we should be careful not to insert a preconceived Newtonian conception of time unwittingly into our interpretation of the quantum mechanical formalism. Thus, whereas Part I is intended as a demonstration of methodology with respect to the study of time, Part II in a sense explores a confusion that can be seen as arising in the absence of this methodology. (shrink)

While several tests and strategies are recommended for colorectal cancer (CRC) screening, studies suggest that primary care providers often recommend colonoscopy without providing information about its risks or alternatives. These observations raise concerns about the quality of informed consent for screening colonoscopy.

Despite the ubiquity of inner speech in our mental lives, methods for objectively assessing inner speech capacities remain underdeveloped. The most common means of assessing inner speech is to present participants with tasks requiring them to silently judge whether two words rhyme. We developed a version of this task to assess the inner speech of a population of patients with aphasia and corresponding language production deficits. As expected, patients’ performance on the silent rhyming task was severely impaired relative to controls. (...) More surprisingly, however, patients’ performance on this task did not correlate with their performance on a variety of other standard tests of overt language abilities. In particular, patients who were generally unimpaired in their abilities to overtly name objects during confrontation naming tasks, and who could reliably judge when two words spoken to them rhymed, were still severely impaired (relative to controls) at completing the silent rhyme task. This seems to suggest that inner speech was more severely impaired in these patients than outer speech. However, these results should also cause us to critically reflect on the relation between inner speech and silent rhyme judgments more generally. (shrink)

In recent years, language has been shown to play a number of important cognitive roles over and above the communication of thoughts. One hypothesis gaining support is that language facilitates thought about abstract categories, such as democracy or prediction. To test this proposal, a novel set of semantic memory task trials, designed for assessing abstract thought non-linguistically, were normed for levels of abstractness. The trials were rated as more or less abstract to the degree that answering them required the participant (...) to abstract away from both perceptual features and common setting associations corresponding to the target image. The normed materials were then used with a population of people with aphasia to assess the relationship of abstract thought to language. While the language-impaired group with aphasia showed lower overall accuracy and longer response times than controls in general, of special note is that their response times were significantly longer as a function of a trial’s degree of abstractness. Further, the aphasia group’s response times in reporting their degree of confidence (a separate, metacognitive measure) were negatively correlated with their language production abilities, with lower language scores predicting longer metacognitive response times. These results provide some support for the hypothesis that language is an important aid to abstract thought and to metacognition about abstract thought. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Exposome research is put forward as a major tool for solving the nature-versus-nurture debate because the exposome is said to represent “the nature of nurture.” Against this influential idea, we argue that the adoption of the nature-versus-nurture debate into the exposome research program is a mistake that needs to be undone to allow for a proper bioethical assessment of exposome research. We first argue that this adoption is originally based on an equivocation between the traditional nature-versus-nurture debate and a debate (...) about disease prediction/etiology. Second, due to this mistake, exposome research is pushed to adopt a limited conception of agential control that is harmful to one's thinking about the good that exposome research can do for human health and wellbeing. To fully excise the nature-versus-nurture debate from exposome research, we argue that exposome researchers and bioethicists need to think about the exposome afresh from the perspective of actionability. We define the concept of actionability and related concepts and show how these can be used to analyze the ethical aspects of the exposome. In particular, we focus on refuting the popular “gun analogy” in exposome research, returning results to study participants and risk-taking in the context of a well-lived life. (shrink)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

This introduction to the Journal of Business Research special issue on anti-consumption briefly defines and highlights the importance of anticonsumption research, provides an overview of the latest studies in the area, and suggests an agenda for future research on anti-consumption.

This paper is about teaching philosophy to high school students through Lincoln-Douglas (LD) debate. LD, also known as “values debate,” includes topics from ethics and political philosophy. Thousands of high school students across the U.S. debate these topics in class, after school, and at weekend tournaments. We argue that LD is a particularly effective tool for teaching philosophy, but also that LD today falls short of its potential. We argue that the problems with LD are not inevitable, and we offer (...) strategic recommendations for improving LD as a tool for teaching philosophy. Ultimately, our aim is to create a dialogue between LD and academic philosophy, with the hope that such dialogue will improve LD’s capacity to teach students how to do philosophy. (shrink)

Common everyday materials such as textiles, foodstuffs, soil or skin can have complex, mutable and varied appearances. Under typical viewing conditions, most observers can visually recognize materials effortlessly, and determine many of their properties without touching them. Visual material perception raises many fascinating questions for vision researchers, neuroscientists and philosophers, yet has received little attention compared to the perception of color or shape. Here we discuss some of the challenges that material perception raises and argue that further philosophical thought should (...) be directed to how we see materials. (shrink)

This paper is, in part, a report on the conclusions reached at a retreat on Part One of Kant's Conflict of the Faculties, held at the Center for Insight into Philosophic Health, Education, and Renewal, in Mendocino, California. It argues that Kant's distinction between the public and private spheres does not remove but intensifies the philosopher's duty to influence the general public. I conclude with some reflections on how a Kantian philosopher might have a positive influence on religious communities. Includes (...) an appendix coauthored by Richard W. Mapplebeckpalmer. (shrink)

Although there is a growing recognition that older adults and those with extensive comorbid conditions undergo cancer screening too frequently, there is little information about patients’ perceptions regarding cessation of cancer screening. Information on older adults’ views of screening cessation would be helpful both for clinicians and for those designing interventions to reduce overscreening.

Vigorous debate over the moral propriety of cognitive enhancement exists, but the views of the public have been largely absent from the discussion. To address this gap in our knowledge, four experiments were carried out with contrastive vignettes in order to obtain quantitative data on public attitudes towards cognitive enhancement. The data collected suggest that the public is sensitive to and capable of understanding the four cardinal concerns identified by neuroethicists, and tend to cautiously accept cognitive enhancement even as they (...) recognize its potential perils. The public is biopolitically moderate, endorses both meritocratic principles and the intrinsic value of hard work, and appears to be sensitive to the salient moral issues raised in the debate. Taken together, these data suggest that public attitudes toward enhancement are sufficiently sophisticated to merit inclusion in policy deliberations, especially if we seek to align public sentiment and policy. (shrink)

In real-time, Twitter strongly imprints world events, popular culture, and the day-to-day; Twitter records an ever growing compendium of language use and change; and Twitter has been shown to enable certain kinds of prediction. Vitally, and absent from many standard corpora such as books and news archives, Twitter also encodes popularity and spreading through retweets. Here, we describe Storywrangler, an ongoing, day-scale curation of over 100 billion tweets containing around 1 trillion 1-grams from 2008 to 2020. For each day, we (...) break tweets into 1-, 2-, and 3-grams across 150+ languages, record usage frequencies, and generate Zipf distributions. We make the data set available through an interactive time series viewer, and as downloadable time series and daily distributions. We showcase a few examples of the many possible avenues of study we aim to enable including how social amplification can be visualized through ‘contagiograms’. (shrink)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: -/- The main aim of this review will be to assess the effects of changing practitioner empathy or patient expectations for all conditions. The main objective is to conduct a systematic review of randomised trials where the intervention involves manipulating either (a) practitioner empathy or (b) patient expectations, or (c) both.

This is, to the best of my knowledge, the first published attempt at a rigorous logical formalization of a passage in Leibniz's Monadology. The method we followed was suggested by Johannes Czermak.

Until recently, psychologists have conceptualised and studied trust in God (TIG) largely in isolation from contemporary work in theology, philosophy, history, and biblical studies that has examined the topic with increasing clarity. In this article, we first review the primary ways that psychologists have conceptualised and measured TIG. Then, we draw on conceptualizations of TIG outside the psychology of religion to provide a conceptual map for how TIG might be related to theorised predictors and outcomes. Finally, we provide a research (...) agenda for future empirical work in this area, as well as practical applications for counsellors and religious leaders. (shrink)

Co-authored letter to the APA to take a lead role in the recognition of teaching in the classroom, based on the participation in an interdisciplinary Conference on the Role of Advocacy in the Classroom back in 1995. At the time of this writing, the late Myles Brand was the President of Indiana University and a member of the IU Department of Philosophy.

There is growing interest in the use of technology to enhance the tracking and quality of clinical information available for patients in disaster settings. This paper describes the design and evaluation of the Wireless Internet Information System for Medical Response in Disasters (WIISARD).

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Psychopathy refers to a range of complex behaviors and personality traits, including callousness and antisocial behavior, typically studied in criminal populations. Recent studies have used self-reports to examine psychopathic traits among noncriminal samples. The goal of the current study was to examine the underlying factor structure of the Self-Report of Psychopathy Scale–Short Form (SRP-SF) across complementary samples and examine the impact of gender on factor structure. We examined the structure of the SRP-SF among 2,554 young adults from three undergraduate samples (...) and a high-risk young adult sample. Using confirmatory factor analysis, a four-correlated factor model and a four-bifactor model showed good fit to the data. Evidence of weak invariance was found for both models across gender. These findings highlight that the SRP-SF is a useful measure of low-level psychopathic traits in noncriminal samples, although the underlying factor structure may not fully translate across men and women. (shrink)

Loneliness in medicine is a serious problem not just for patients, for whom illness is intrinsically isolating, but also for physicians in the contemporary condition of medicine. We explore this problem by investigating the ideal physician-patient relationship, whose analogy with friendship has held enduring normative appeal. Drawing from Talbot Brewer and Nir Ben-Moshe, we argue that this appeal lies in a dynamic form of companionship incompatible with static models of friendship-like physician-patient relationships: a mutual refinement of embodied virtue that draws (...) both persons together. The ideal physician-patient relationship has a dialectical character that fosters each member's improvement of phenomenologically recognizing and embodying moral virtues. A key component of this dynamic is a commitment to the common goal of the patient's health, realized through joint interactivities and conversations over time. The physician's presence to the patient's suffering—understood best as an alienating phenomenological condition for the patient—orients and discloses possibilities for virtuous caregiving by structuring the meanings of the goals, conversations, and joint narrative constitutive of their relationship. Presence to suffering, paradoxically, is perhaps an important prerequisite for this dynamic partnership. These activities dialectically build an interpretive horizon of understanding through which moral goods and character refinement—in and for the other—may become revealed for both persons in their shared being-in-the-world. This analysis of suffering, mood, and revealing of (possible) moral goods has implications for addressing the modern problem of loneliness for patients and physicians, who are increasingly inhibited from building flourishing relationships with each other. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

Historically, scientific and engineering expertise has been key in shaping research and innovation policies, with benefits presumed to accrue to society more broadly over time. But there is persistent and growing concern about whether and how ethical and societal values are integrated into R&I policies and governance, as we confront public disbelief in science and political suspicion toward evidence-based policy-making. Erosion of such a social contract with science limits the ability of democratic societies to deal with challenges presented by new, (...) disruptive technologies, such as synthetic biology, nanotechnology, genetic engineering, automation and robotics, and artificial intelligence. Many policy efforts have emerged in response to such concerns, one prominent example being Europe's Eighth Framework Programme, Horizon 2020, whose focus on “Responsible Research and Innovation” provides a case study for the translation of such normative perspectives into concrete policy action and implementation. Our analysis of this H2020 RRI approach suggests a lack of consistent integration of elements such as ethics, open access, open innovation, and public engagement. On the basis of our evaluation, we suggest possible pathways for strengthening efforts to deliver R&I policies that deepen mutually beneficial science and society relationships. (shrink)

According to standard late medieval Christian thought, humans in heaven are unable to sin, having been “confirmed” in their goodness; and, nevertheless, are more free than humans are in the present life. The rise of voluntarist conceptions of the will in the late thirteenth century made it increasingly difficult to hold onto both claims. Peter Olivi suggested that the impeccability of the blessed was dependent upon a special activity of God upon their wills and argued that this external constraint (...) upon their wills did not eliminate their freedom. Later voluntarists largely agreed with Olivi in attributing the confirmation of the blessed to be dependent upon God’s activity in some way, but disputed the means by which and the extent to which the wills of those in heaven could be said to retain their freedom. This paper will examine various attempts made to either harmonize these two claims or else to soften the blow of rejecting one of them; among the authors surveyed will be Peter John Olivi, John Duns Scotus, Henry of Harclay, William of Ockham, Walter Chatton, and Margurite Porete. (shrink)

Although convinced by Frankfurt-style cases that moral responsibility does not require the ability to do otherwise, semicompatibilists have not wanted to accept a parallel claim about moral responsibility for omissions, and so they have accepted asymmetrical requirements on moral responsibility for actions and omissions. In previous work, I have presented a challenge to various attempts at defending this asymmetry. My view is that semicompatibilists should give up these defenses and instead adopt symmetrical requirements on moral responsibility for actions and omissions, (...) and in this paper I highlight three advantages of doing so: first, it avoids a strange implication of the truth of determinism; second, it allows for a principled reply to Philip Swenson’s recent ‘No Principled Difference Argument’; third, it provides a reason to reject a crucial inference rule invoked by Peter van Inwagen’s ‘Direct Argument’ for the incompatibility of moral responsibility and determinism. (shrink)

Tarihte herhalde çok az soru Tanrı’nın varlığı sorusu kadar sık sorulmuş, çok yanıtlanmış ve verilen birbirinden farklı onca yanıta rağmen kesin bir sonuca ulaştırılamayıp tartışılmaya devam etmiştir. Yine de geçmişe dönüp baktığımızda bu soruya verilen farklı yanıtların farklı uygarlıkların inşa edilmesine, bazılarının yıkılmasına, acımasız çatışmalara ve her şeye rağmen kucaklaşmalara da vesile olduğunu görüyoruz. Tanrı var mı? Varsa onu nasıl bilebiliriz? Tanrı yoksa her şey mubah mı? İnsan aklı ilahi olanı kavrayabilir mi? Tanrı’nın varlığı ahlaklı olmanın şartı mı? Evren akıllı (...) bir tasarımcının imzasını taşıyor mu? Bu kitapta felsefeci William David Beck, bu sorulara tarihte verilen yanıtları ve bu konudaki tartışmaları ele alarak meselenin genel ve tarihsel bir tablosunu bize sunuyor. Platon, Aristoteles, Marcus Aurelius gibi Eski Yunan ve Roma düşünürlerinden Anselmus, Thomas Aquinas, Augustinus ve Yahudi-Hıristiyan geleneğine, Doğu’nun bilgelerine, İbni Rüşd, Fârâbî ve Gazzâlî gibi İslam düşünürlerinden Alvin Plantinga, Graham Oppy, Sam Harris, Richard Dawkins, Max Tegmark gibi Batılı modern ilahiyatçılara, bilim insanlarına ve Yeni Ateizm hareketine kadar uzanan bir çizgide “Tanrı var mı?” sorusuna verilen çeşitli yanıtları ve bu yanıtlara sunulan akılcı gerekçeleri ortaya koyarak soruya felsefece bir yanıt vermenin nasıl bir iş olduğunu da gösteriyor. (shrink)