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)
Background Genuine uncertainty on superiority of one intervention over the other is called equipoise. Physician-investigators in randomized controlled trials need equipoise at least in studies with more than minimal risks. Ideally, this equipoise is also present in patient-participants. In pediatrics, data on equipoise are lacking. We hypothesize that 1) lack of equipoise at enrolment among parents may reduce recruitment; 2) lack of equipoise during participation may reduce retention in patients assigned to a less favoured treatment-strategy. Methods We compared preferences of (...) parents/patients at enrolment, documented by a questionnaire, with preferences developed during follow-up by an interview-study to investigate equipoise of child-participants and parents in the BeSt-for-Kids-study. This trial in new-onset Juvenile Idiopathic Arthritis-patients consists of three strategies. One strategy comprises initial treatment with a biological disease-modifying-antirheumatic-drug, currently not standard-of-care. Semi-structured interviews were conducted with 23 parents and 7 patients, median 11 months after enrolment. Results Initially most parents and children were not in equipoise. Parents/patients who refused participation, regularly declined due to specific preferences. Many participating families preferred the biological-first-strategy. They participated to have a chance for this initial treatment, and would even consider stopping trial-participation when not randomized for it. Their conviction of superiority of the biological-first strategy was based on knowledge from internet and close relations. According to four parents, the physician-investigator preferred the biological-first-strategy, but the majority stated that she had no preferred strategy. In phase 2, preferences tended to change to the treatment actually received. Conclusions Lack of equipoise during enrolment did not reduce study recruitment, mainly due to the fact that preferred treatment was only available within the study. Still, when developing a trial it is important to evaluate whether the physicians’ research question is in line with preferences of the patient-group. By exploring so-called ‘informed patient-group’-equipoise, successful recruitment may be enhanced and bias avoided. In our study, lack of equipoise during trial-participation did not reduce retention in those assigned to a less favoured option. We observed a change for preference towards treatment actually received, possibly explained by comparable outcomes in all three arms. (shrink)
G.E. Moore, more than either Bertrand Russell or Ludwig Wittgenstein, was chiefly responsible for the rise of the analytic method in twentieth-century philosophy. This selection of his writings shows Moore at his very best. The classic essays are crucial to major philosophical debates that still resonate today. Amongst those included are: * A Defense of Common Sense * Certainty * Sense-Data * External and Internal Relations * Hume's Theory Explained * Is Existence a Predicate? * Proof of an External World (...) In addition, this collection also contains the key early papers in which Moore signals his break with idealism, and three important previously unpublished papers from his later work which illustrate his relationship with Wittgenstein. (shrink)
The paper describes and discusses unethical behavior in organizations, as a result of (interacting) disputable leadership and ethical climate. This paper presents and analyzes the well-known bond trading scandal at Salomon Brother to demonstrate the development of an unethical organizational culture under the leadership of John Gutfreund. The paper argues that leaders shape and reinforce an ethical or unethical organizational climate by what they pay attention to, how they react to crises, how they behave, how they allocate rewards, and how (...) they hire and fire individuals. (shrink)
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)
The contributions to this volume offer a rich, detailed, and in some respects innovative and remarkable account of that uniquely fecund and philosophically revolutionary epoch known as German Idealism. The epoch’s historical context, its driving ideas, its post-Kantian development, and its repercussions in post-Hegelian philosophy are all presented competently and concisely. The editor also included essays on some of the philosophical ideas underlying the parallel phenomenon of German Romanticism, for good reasons, since some of the foremost poets and literary theorists (...) of the age were philosophers in their own right, whose influence on the development of German Idealism was not insignificant. What emerges from this collection is the picture of a multifaceted philosophical movement embedded in and influenced by and in turn influencing a complex intellectual and literary environment. The reader of this volume will be in no danger of reducing German Idealism to a linear development that started with Kant and that was preordained to culminate in Hegel’s system. (shrink)
In this paper the moral responsibility of a Healthcare Organization (HCO) is conceived as an inextricable aspect of the identity of the HCO. We attempt to show that by exploring this relation a more profound insight in moral responsibility can be gained. Referring to Charles Taylor we explore the meaning of the concept of identity. It consists of three interdependent dimensions: a moral, a dialogical, and a narrative one. In section two we develop some additional arguments to apply his concept (...) of personal identity to organizations. The final section works out the relationship of three dimensions of identity to some actual issues in contemporary HCOs: the tension between care and justice, the importance of dialogues about the diversity of goods, and the relevance of becoming familiar with the life-story of the HCO. Identity of an HCO is established and developed in commitments to and identification with certain goods that are central for a HCO. However, many of these goods are interwoven with everyday practices and policies. Therefore, moral responsibility asks for articulation of goods that often stay implicit and should not be reduced to a merely procedural approach. However difficult this articulation may be, if it is not tried at all HCOs run the risk of drifting away from their very identity as healthcare institutions: to offer care to patients and to do this in accordance with demands of social justice. (shrink)
Solidarity belongs to the basic principles of Catholic Social Teaching (CST) and is part of the ethical repertoire of European moral traditions and European healthcare systems. This paper discusses how leaders of Catholic healthcare organizations (HCOs) can understand their institutional moral responsibility with regard to the preservation of solidarity. In dealing with this question, we make use of Taylor's philosophy of modern culture. We first argue that, just as all HCOs, Catholic ones also can embody and strengthen solidarity by just (...) doing their quintessential job, that is, to care for people with ill health. Second, we focus on the Catholic identity of these organizations and argue that this characteristic can empower a radical commitment to solidarity. Finally, we argue that CST provides a critical ethical framework for approaching solidarity from the perspective of the common good. (shrink)
Is God's foreknowledge compatible with human freedom? One of the most attractive attempts to reconcile the two is the Ockhamistic view, which subscribes not only to human freedom and divine omniscience, but retains our most fundamental intuitions concerning God and time: that the past is immutable, that God exists and acts in time, and that there is no backward causation. In order to achieve all that, Ockhamists distinguish ‘hard facts’ about the past which cannot possibly be altered from ‘soft facts’ (...) about the past which are alterable, and argue that God's prior beliefs about human actions are soft facts about the past. (shrink)
An important contribution to the foundations of probability theory, statistics and statistical physics has been made by E. T. Jaynes. The recent publication of his collected works provides an appropriate opportunity to attempt an assessment of this contribution.
The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)
How could the self be a substance? There are various ways in which it could be, some familiar from the history of philosophy. I shall be rejecting these more familiar substantivalist approaches, but also the non-substantival theories traditionally opposed to them. I believe that the self is indeed a substance—in fact, that it is a simple or noncomposite substance—and, perhaps more remarkably still, that selves are, in a sense, self-creating substances. Of course, if one thinks of the notion of substance (...) as an outmoded relic of prescientific metaphysics—as the notion of some kind of basic and perhaps ineffable stuff —then the suggestion that the self is a substance may appear derisory. Even what we ordinarily call ‘stuffs’—gold and water and butter and the like—are, it seems, more properly conceived of as aggregates of molecules or atoms, while the latter are not appropriately to be thought of as being ‘made’ of any kind of ‘stuff’ at all. But this only goes to show that we need to think in terms of a more sophisticated notion of substance—one which may ultimately be traced back to Aristotle's conception of a ‘primary substance’ in the Categories , and whose heir in modern times is W. E. Johnson's notion of the ‘continuant’. It is the notion, that is, of a concrete individual capable of persisting identically through qualitative change, a subject of alterable predicates that is not itself predicable of any further subject. (shrink)
Human research ethics has developed in both theory and practice mostly from experiences in medical research. Human participants, however, are used in a much broader range of research than ethics committees oversee, including both basic and applied research at technical universities. Although mandated in the United States, the United Kingdom, Canada, and Australia, non-medical research involving humans need not receive ethics review in much of Europe, Asia, Latin America, and Africa. Our survey of the top 50 technical universities in the (...) world shows that, where not specifically mandated by law, most technical universities do not employ ethics committees to review human studies. As the domains of basic and applied sciences expand, ethics committees are increasingly needed to guide and oversee all such research regardless of legal requirements. We offer as examples, from our experience as an ethics committee in a major European technical university, ways in which such a committee provides needed services and can help ensure more ethical studies involving humans outside the standard medical context. We provide some arguments for creating such committees, and in our supplemental article, we provide specific examples of cases and concerns that may confront technical, engineering, and design research, as well as outline the general framework we have used in creating our committee. (shrink)
What is a natural kind ? As we shall see, the concept of a natural kind has a long history. Many of the interesting doctrines can be detected in Aristotle, were revived by Locke and Leibniz, and have again become fashionable in recent years. Equally there has been agreement about certain paradigm examples: the kinds oak, stickleback and gold are natural kinds, and the kinds table, nation and banknote are not. Sadly agreement does not extend much further. It is impossible (...) to discover a single consistent doctrine in the literature, and different discussions focus on different doctrines without writers or readers being aware of the fact. In this paper I shall attempt to find a defensible distinction between natural and non-natural kinds. (shrink)
In this philosophy classic, which was first published in 1951, E. R. Dodds takes on the traditional view of Greek culture as a triumph of rationalism. Using the analytical tools of modern anthropology and psychology, Dodds asks, "Why should we attribute to the ancient Greeks an immunity from 'primitive' modes of thought which we do not find in any society open to our direct observation?" Praised by reviewers as "an event in modern Greek scholarship" and "a book which it would (...) be difficult to over-praise," _The Greeks and the Irrational _was Volume 25 of the Sather Classical Lectures series. (shrink)
The strong weak truth table (sw) reducibility was suggested by Downey, Hirschfeldt, and LaForte as a measure of relative randomness, alternative to the Solovay reducibility. It also occurs naturally in proofs in classical computability theory as well as in the recent work of Soare, Nabutovsky, and Weinberger on applications of computability to differential geometry. We study the sw-degrees of c.e. reals and construct a c.e. real which has no random c.e. real (i.e., Ω number) sw-above it.
The prevailing view among historians of science holds that Charles Darwin became a convinced transmutationist only in the early spring of 1837, after his Beagle collections had been examined by expert British naturalists. With respect to the fossil vertebrate evidence, some historians believe that Darwin was incapable of seeing or understanding the transmutationist implications of his specimens without the help of Richard Owen. There is ample evidence, however, that he clearly recognized the similarities between several of the fossil vertebrates he (...) collected and some of the extant fauna of South America before he returned to Britain. These comparisons, recorded in his correspondence, his diary and his notebooks during the voyage, were instances of a phenomenon that he later called the “law of the succession of types.” Moreover, on the Beagle, he was following a geological research agenda outlined in the second volume of Charles Lyell’s Principles of Geology, which implies that paleontological data alone could provide an insight into the laws which govern the appearance of new species. Since Darwin claims in On the Origin of Species that fossil vertebrate succession was one of the key lines of evidence that led him to question the fixity of species, it seems certain that he was seriously contemplating transmutation during the Beagle voyage. If so, historians of science need to reconsider both the role of Britain’s expert naturalists and the importance of the fossil vertebrate evidence in the development of Darwin’s ideas on transmutation. (shrink)
O presente texto procura acompanhar alguns aspectos da reconstrução sartreana das relações entre indivíduo e história, tentando mostrar que a fenomenologia e o materialismo dialético comparecem nessa proposta de conhecimento e que é a convergência das duas perspectivas que permite, contemplando adequadamente a universalidade e a singularidade, descrever e compreender dialeticamente o modo histórico de produção da identidade individual.
In this paper I shall venture into an area with which I am not very familiar and in which I feel far from confident; namely into phenomenology. My main motive is not to get away from standard, boring, methodological questions like those of induction and demarcation; but the conviction that a phenomenological account of the empirical basis forms a necessary complement to Popper's falsificationism. According to the latter, a scientific theory is a synthetic and universal, hence unverifiable proposition. In fact, (...) in order to be technologically useful, a scientific hypothesis must refer to future states-of-affairs; it ought therefore to remain unverified. But in order to be empirical, a theory must bear some kind of relation to factual statements. According to Popper, such a relation can only be one of potential conflict. Thus a theory T will be termed scientific if and only if T is logically incompatible with a so-called basic statement b, where b is both empirically verifiable and empirically falsifiable. In other words: T is scientific if it entails ¬b; where b, hence also ¬b, is an empirically decidable proposition. (shrink)
Why does the problem of free will seem so intractable? I surmise that in large measure it does so because the free will debate, at least in its modern form, is conducted in terms of a mistaken approach to causality in general. At the heart of this approach is the assumption that all causation is fundamentally event causation. Of course, it is well-known that some philosophers of action want to invoke in addition an irreducible notion of agent causation, applicable only (...) in the sphere of intelligent agency. But such a view is generally dismissed as incompatible with the naturalism that has now become orthodoxy amongst mainstream analytical philosophers of mind. What I want to argue is that substances, not events, are the primary relata of causal relations and that agent causation should properly be conceived of as a species of substance causation. I shall try to show that by thus reconceiving the nature of causation and of agency, the problem of free will can be made more tractable. I shall also argue for a contention that may seem even less plausible at first sight, namely, that such a view of agency is perfectly compatible with a volitionist theory of action. (shrink)
Plagiarism detection services are a powerful tool to help encourage academic integrity. Adoption of these services has proven to be controversial due to ethical concerns about students’ rights. Central to these concerns is the fact that most such systems make permanent archives of student work to be re-used in plagiarism detection. This computerization and automation of plagiarism detection is changing the relationships of trust and responsibility between students, educators, educational institutions, and private corporations. Educators must respect student privacy rights when (...) implementing such systems. Student work is personal information, not the property of the educator or institution. The student has the right to be fully informed about how plagiarism detection works, and the fact that their work will be permanently archived as a result. Furthermore, plagiarism detection should not be used if the permanent archiving of a student’s work may expose him or her to future harm. (shrink)
E-Z Reader 7 is a processing model of eye-movement control. One constraint imposed on the model is that high-level cognitive processes do not influence eye movements unless normal reading processes are disturbed. I suggest that this constraint is unnecessary, and that the model provides a sensible architecture for explaining how both low- and high-level processes influence eye movements.
The concept of âhumane healthcareâ cannot and may not be limited to a personal virtue. For elucidating its meaning and making it functional as a critical ethical criterion for healthcare as a social institution, it is necessary to reflect on the social, cultural, and historical conditions in which modern healthcare finds its offspring and its further development. Doing this is the object and aim of social ethics. Social ethics in itself covers a broad area of different approaches. A main division (...) can be made between a liberal and a communitarian approach. This article focuses on the latter and concentrates on one of its representatives, Charles Taylor. The paper starts with two clarifying paragraphs: one about the terms humane and human, a second about the scope of social ethics. Next, because the term humane presupposes a certain view of man, attention will be paid to the lack of consensus in this respect within modernity, using some reflections of Taylor. In his view, resigning in this lack is a threat for one of the main motives behind modernity: the pursuit of a good and meaningful life. In the following section Taylor's analysis is applied to contemporary healthcare, by means of two examples. At the end the question is raised how to promote humane healthcare? In a short and conclusive sketch, three suggestions are offered for further research: scrutiny of goals and meanings within healthcare and culture, the broadening of the concept of autonomy and the upholding of human dignity as an intrinsic and imperative value. (shrink)
If one is an egalitarian, what should one want to equalize? Opportunities or outcomes? Resources or welfare? These positions are usually conceived to be very different. I argue in this paper that the distinction is misconceived: the only coherent conception of resource equality implies welfare equality, in an appropriately abstract description of the problem. In this section, I motivate the program which the rest of the paper carries out.
Hume's famous discussion of miracles in the Enquiry Concerning Human Understanding is curious both on account of the arguments he does deploy and on account of the arguments he does not deploy, but might have been expected to. The first and second parts of this paper will be devoted to examining, respectively, these two objects of curiosity. The second part I regard as the more important, because I shall there try to show that the fact that Hume does not deploy (...) an argument that he might have been expected to deploy in fact reflects a weakness in the view of natural laws that has come to be associated with Hume's name. I shall argue, in fact, that it is a symptom of the defectiveness of the ‘Humean’ view of natural laws that on that view it is only too easy to rule out the possibility of a miracle ever occurring. In the third part of the paper, I shall show how another view of laws can overcome this problem. (shrink)