We have synthesized a 582,970-base pair Mycoplasma genitalium genome. This synthetic genome, named M. genitalium JCVI-1.0, contains all the genes of wild-type M. genitalium G37 except MG408, which was disrupted by an antibiotic marker to block pathogenicity and to allow for selection. To identify the genome as synthetic, we inserted "watermarks" at intergenic sites known to tolerate transposon insertions. Overlapping "cassettes" of 5 to 7 kilobases (kb), assembled from chemically synthesized oligonucleotides, were joined by in vitro recombination to produce intermediate (...) assemblies of approximately 24 kb, 72 kb ("1/8 genome"), and 144 kb ("1/4 genome"), which were all cloned as bacterial artificial chromosomes in Escherichia coli. Most of these intermediate clones were sequenced, and clones of all four 1/4 genomes with the correct sequence were identified. The complete synthetic genome was assembled by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae, then isolated and sequenced. A clone with the correct sequence was identified. The methods described here will be generally useful for constructing large DNA molecules from chemically synthesized pieces and also from combinations of natural and synthetic DNA segments. 10.1126/science.1151721. (shrink)

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 work explores an aspect of Yeats's writing largely ignored until now: namely, his wide-ranging absorption in S.T. Coleridge. Gibson explores the consistent and densely woven allusions to Coleridge in Yeats's prose and poetry, often in conjunction with other Romantic figures, arguing that the earlier poet provided him with both a model of philosopher - 'the sage' - and an interpretation of metaphysical ideas which were to have a resounding effect on his later poetry, and upon his rewriting of (...) A Vision. (shrink)

Books reviewed: The Literary Wittgenstein edited by John Gibson and Wolfgang Huerner, Routledge, London, 2004 (pp. xi + 356). Philosophy and Literature: A Book of Essays, M. W. Rowe, Ashgate, Aldershot, 2004 (pp xii + 238). Reviewed by M. H. Weston, University of Essex University of Essex Wivenhoe Park Colchester CO4 3SQ.

Ethics support staff help others to deal with moral challenges. However, they themselves can also experience moral challenges such as issues regarding (breaching) confidentiality when practicing ethics support. Currently there is no insight in these confidentiality issues and also no professional guidance for dealing with them. To gain insight into moral challenges related to Moral Case Deliberation (MCD), we studied a) beliefs and experiences of MCD facilitators regarding breaching confidentiality, b) considerations for (not) breaching confidentiality, and c) needs for an (...) ethics support tool. Data collection consisted of qualitative research methods: six semi-structured interviews; analyses of a) two recorded MCD sessions, and b) a focus group with MCD facilitators. Findings: MCD facilitators mention different conceptions and interpretations of confidentiality and various moral challenges. Questions concerning confidentiality ultimately cause reflections on roles and responsibilities of facilitators. Needs for ethics support vary from seeking advice to procedural and sometimes normative guidance for MCD facilitators. Education for MCD facilitators should focus on developing a concrete tool that stimulates awareness and reflection(skills). (shrink)

Using 94 published empirical articles in academic journals as a data base, this paper provides a critical review of the methodology employed in the study of ethical beliefs and behavior of organizational members. The review revealed that full methodological detail was provided in less than one half of the articles. Further, the majority of empirical research articles expressed no concern for the reliability or validity of measures, were characterized by low response rates, used convenience samples, and did not offer a (...) theoretic framework, hypotheses, or a definition of ethics. Several recommendations, including a reviewer rating form addressing methodological decisions and inclusion of methodologists on the review panel, are offered to improve methodological rigor in published ethics research. (shrink)

This chapter introduces the edited volume, The Oxford Handbook of Philosophy and Psychiatry. Published in 2013, the centenary of Karl Jaspers' General Psychopathology, the chapter draws lessons from the last hundred years for the coming century. No predictions are made. Instead, five 'conditions for flourishing' are set out: 1) Particular Problems - the importance of focussing on well-defined particular problems rather than general theory building, 2) Product- orientation - remaining always responsibly product oriented in the specific sense that both sides (...) put in the work necessary to 'go deep' with each other's fields, 3) Partnership - working in partnerships of one kind or another, 4) Process - constant reflection on process based on peer review but leaving scope for the occasional rogue voice to cut innovatively against the grain, and 5) Q - a condition of a different kind, Q is an empirically derived measure of the balance between in-group cohesion and out-group openness required to support creativity. Illustrations are given of how these five conditions for flourishing have underpinned the rapid expansion of philosophy and psychiatry in the closing decades of the twentieth century, and, correspondingly, are also reflected in the Handbook as a whole. Overviews and commentaries on individual contributions to the Handbook are given in extended editorial introductions to each of its eight sections. (shrink)

This chapter outlines the origins in ordinary language philosophy of a new skills-based approach to working with complex and conflicting values in medicine called values-based practice. Ordinary language philosophy focuses on our use of words as a useful first step in coming to a more complete understanding of their meanings. The theory of values-based practice was developed by applying ideas from ordinary language philosophy to the long-running debate about the "boundary problem" presented by the concept of mental disorder. Ordinary language (...) philosophy turns this debate topsy-turvy: it shows, that the concept of mental disorder instead of being the target problem is a resource for coming to a more complete understanding of the meanings of concepts of disorder as a whole including the concept of bodily disorder; and correspondingly, that the value-laden nature of mental disorder far from being part of the problem points to an evaluative element of meaning in concepts of disorder as a whole, again including concepts of bodily disorder. It is these topsy-turvy results that underpin the development of values-based practice. In a brief concluding section we indicate the potential for further development of values-based practice supported by ordinary language and other philosophies particularly through engagement with non-Western language groups representing diverse traditions of thought and practice in mental health. (shrink)

This Section examines several moral dilemmas and epistemological aporias in clinical practice and shows how clinicians can benefit from the introduction of philosophical methods and discourse. The authors develop these issues having in mind emblematic mental disorders and typical clinical situations. One important claim shared by the Authors is that a great effort has been made to ground psychiatry on evidence-based science, and to tie it to our growing understanding of the human brain. This is obviously an exceedingly important project, (...) but it would be a mistake to assume that the central questions of psychiatry can be completely resolved through scientific inquiry. Science offers guidance for clinical practice only in light of our concepts and normative judgments. (shrink)

In the editorial introduction the stage is set for the chapters in the section by a brief discussion of the relationship between the disciplines of philosophy and psychiatry. Then each chapter briefly is summarized or highlighted.

In this introduction to the Section II, the thrust of the component chapters is described. An important strand in the philosophy of psychiatry since its beginnings has been sociopolitical critiques: criticism which aims to improve and humanize psychiatric practice and mental health systems. From this standpoint, the introduction provides an overview of this tradition, including considerations of "postpsychiatry," value commitments in psychiatry, the recovery movement, racism and sexism in the field, and technology.

A cross-disciplinary discussion of the basis of interpersonal relating is of interest to philosophers and psychiatrists for several reasons. The development of successful clinical practice may depend, at least partly, on having an accurate understanding of the basic character of unimpaired interpersonal relating because such understanding can shed light on the nature and source of its disturbed forms. How we think about the basis of "mind-minding" competencies influences how we think about the prognosis and possible treatment of dysfunctional interpersonal relating. (...) Another reason is that philosophical frameworks influence the way we think about and evaluate possible psychiatric disorders and philosophical discussions may be of direct practical importance to psychiatry given that different theories suggest different potential ways of devising therapies. (shrink)

The editorial introduction sets the stage for the chapter by identifying the roles that concepts and categories play not just in the field of mental health medicine but in the human mind itself. Then, each chapter is summarized or highlighted.

Following on from Section IV on summoning concepts, this section of the Handbook presents theoretically informed descriptions of psychopathologies. The topics of the chapters range from anxiety, depression, and body image disorders, through emotion and affective disorders, to delusion, thought insertion, and the fragmentation of consciousness. These phenomena call, not only for assessment and diagnosis, but also for understanding on the part of both the engaged clinician and the philosophical commentator. They also provide case studies for general philosophical questions about (...) different levels of description and conceptualisation and the relationships between them, and about the contributions to psychological understanding that are made by phenomenology, clinical expert knowledge, and the sciences of the mind. (shrink)

In this introduction to Section VI, the thrust of the component chapters is described. The classification and diagnosis of mental disorders collects a number of philosophical challenges to the field that call for responses from a variety of philosophical resources: hermeneutics, phenomenology, philosophy of mind, narrative theory, philosophy of science, epistemology-to name a few. The authors in this section address the general challenges in the classification of psychopathology, as well as address particular kinds of mental disorders, including autism, dementia, mania, (...) psychotic disorders, and personality disorders. (shrink)

Decentralized clinical trials (DCTs) have the potential to advance the conduct of clinical trials, but raise several ethical issues, including obtaining valid informed consent. The debate on the ethical issues resulting from digitalization is predominantly focused on direct risks relating to for example data protection, safety, and data quality. We submit however, that a broader view on ethical aspects of DCTs is needed to touch upon the new challenges that come with the DCT practice. Digitalization has impacts that go beyond (...) its direct purposes, by shaping behaviors, experiences, social relations, and values. We examine four elements of the informed consent procedure that are affected by DCTs, while taking these soft impacts of technologies into account: (i) informing participants and testing understanding, (ii) freedoms in relation to responsibilities and burdens, (iii) trust in participant-researcher relations, and (iv) impacts on the concept of privacy. Our analysis reveals that a broad view is key for optimal conduct of DCTs. In addition, it provides insight into the ethical impacts of DCTs on informed consent. Technologies such as DCTs potentially have profound impacts which are not immediately addressed by the existing regulatory frameworks, but nonetheless important to recognize. These findings can guide future practices of DCTs to foster the important values of clinical research in this novel approach for conducting clinical trials. (shrink)

The present study applied Ajzen's (1985) theory of planned behavior to the explanation of ethical decision making. Nurses in three hospitals were provided with scenarios that depicted inadequate patient care and asked if they would report health professionals responsible for the situation. Study results suggest that the theory of planned behavior can explain a significant amount of variation in the intent to report a colleague. Attitude toward performing the behavior explained a large portion of the variance; subjective norms explained a (...) moderate amount of the variance; and, perceived behavioral control added little to the explanation of variance. Implications for research and practice are discussed. (shrink)