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)

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)

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)

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.

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 article presents Schelling’s claim that nature has an evolutionary process and Hegel’s response that nature is the development of the concept. It then examines whether evolution is progressive. While many evolutionary biologists explicitly repudiate the suggestion that there is progress in evolution, they often implicitly presuppose this. Moreover, such a notion seems required insofar as the shape of life’s history consists in a directional trend. This article argues that, insofar as a notion of progress is indeed conceptually ineliminatable from (...) evolutionary biology or needed to articulate the shape of life’s history, progress should be viewed as constitutive. The section on “Why Schelling and .. (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)

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)

Organic chemists have been able to develop a robust, theoretical understanding of the phenomena they study; however, the primary theoretical devices employed in this field are not mathematical equations or laws, as is the case in most other physical sciences. Instead it is diagrams, and in particular structural formulas and potential energy diagrams, that carry the explanatory weight in the discipline. To understand how this is so, it is necessary to investigate both the nature of the diagrams employed in organic (...) chemistry and how these diagrams are used in the explanations of the discipline. I will begin this paper by characterizing some of the major ways that structural formulas used in organic chemistry. Next I will present a model of the explanations in organic chemistry and describe how both structural formulas and potential energy diagrams contribute to these explanations. This will be followed by several examples that support my abstract account of the role of diagrams in the explanations of organic chemistry. In particular, I will consider both the appeal to ‘hyperconjugation’ in the explanation of alkene stability and how the idea of ‘ring strain’ was developed to explain the relative stability of cyclic compounds. (shrink)

The death of Jesse Gelsinger in 1999 during a gene therapy trial raised many questions about the ethical review of medical research. Here, the author argues that the principle of justice is interpreted too narrowly and receives insufficient emphasis and that what we permit in terms of bodily invasion affects the value we place on individuals. Medical research is a societally supported activity. As such, the author contends that justice requires that invasive medical research demonstrates sufficiently compelling societal benefit. Many (...) consider this societal benefit to be self evident. However, medical research is a complex activity; it yields new treatments but also creates financial rewards and affects health resource allocation. As research evolves into a multibillion pound, multinational enterprise, justice requires a much broader analysis of societal benefit. Without such evaluation we risk undermining the value of bodily integrity and of research participants. (shrink)

In his pioneering work of moral phenomenology, K. E. Løgstrup offered a phenomenological articulation of a central moment of ethical life: the experience in which “one finds oneself with the life of another more-or-less in one’s hands”. In such circumstances we encounter what Løgstrup calls simply the ethical demand. Løgstrup’s preferred formulation of the content of that demand is taken from the Bible: Love thy neighbor. This neighborly love is expressed in the form of spontaneous, selfless care for the other. (...) We shall have occasion in what follows to return to the content that Løgstrup associates with the ethical demand, but my primary focus here is not its content but its distinctive modality. Løgstrup specifies that modality in a fourfold analysis: the ethical demand is radical, silent, one-sided, and unfulfillable. My concern in what follows will be with the fourth element in this analysis – or what I shall refer to simply as Løgstrup’s unfulfillability thesis. My discussion addresses three specific questions: Is it coherent to suppose that the ethical demand is unfulfillable? Why does Løgstrup hold that the ethical demand is unfulfillable? What kind of response is appropriate in the face of an unfulfillable ethical demand? (shrink)

THE PROBLEM OF THE INTERPRETATION OF HAMANN Johann Georg Hamann is an intriguing but poorly known figure in the contemporary intellectual world. Yet this is the man whom Kierkegaard saluted as "Emperor!", whose writings were to have been arranged for publication by none other than Goethe himself, and whom Dilthey numbered among the primordial figures in the rise of modern historical consciousness. There are reasons for the persistence of this general ignorance. Hamann is deep. And, in addition, there is his (...) forbidding style. The readers of Kierkegaard and Dilthey, two other giants who them selves achieved late recognition, have not had to face this kind of imposing obstacle. Not only does Hamann expect his readers to handle themselves in deep water, but to intuit their way between his ideas which bob up like islands with no visible connection between them. Like Kierkegaard too, Hamann has had his troubles with the public. He himself referred to the hope that he would be understood by a "better posterity". In fact only the last few years have seen the printing of some of his more controversial writings, in particular his theories on the nature of human sexuality. (shrink)

Ordinairement les manuels de biologie débutent par une exposition des caractéristiques qui distinguent la nature organique de la nature anorganique. En définissant et en limitant aussi exactement que possible son sujet, la biologie, le biologue ne fait pas autre chose que le mathématicien. La présente étude nous montre les obstacles presque insurmontables auxquels se heurtent le biologue et le mathématicien. A les bien considérer, les anciennes distinctions entre l'organisme d'une part et la matière non-organisée ou un système statique matériel, comme (...) la machine, d'autre part, se basant sur la nutrition, la respiration, les échanges vitaux et le mouvement ne tiennent plus debout. L'auteur allègue les expériences récentes de W. M. Stanley (Rockefeller Institute à Princeton) d'où il appert qu'il peut y avoir aussi génération dans les substances qui se secrètent sous la forme de cristaux (cristaux vivants), et s'en rapporte aux fameuses expériences de Driesch sur la régénération. Il y rattache les conceptions de Jordan (Utrecht) -- rapports entre les enchaînements des causes "d'après leur caractère amboceptor"; "le dessein des causes". Les vitalistes portent surtout leur attention sur "la totalité", les mécanistes sur "les parties". Le naturaliste qui se propose uniquement la recherche des causes physico-chimiques des phénomènes physico-chimiques serait parfaitement en droit de se contenter d'une conception mécaniste de la nature. Mais cette conception mécaniste ne suffirait pas à celui qui, comme l'auteur, aspire à comprendre l'organisme dans son ensemble. (shrink)