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)

Medical technologies and assistive devices such as ventilators and power wheelchairs are designed to sustain life and/or improve functionality but they can also contribute to stigmatization and social exclusion. In this paper, drawing from a study of ten men with Duchenne muscular dystrophy, we explore the complex social processes that mediate the lives of persons who are dependent on multiple medical and assistive technologies. In doing so we consider the embodied and emplaced nature of disability and how life is lived (...) through bodies coupled with technologies and experienced as 'techno-body-subjects in situ'. Normative implications for theory and research, including bioethics research, are discussed. (shrink)

Medical technologies and assistive devices such as ventilators and power wheelchairs are designed to sustain life and/or improve functionality but they can also contribute to stigmatization and social exclusion. In this paper, drawing from a study of ten men with Duchenne muscular dystrophy, we explore the complex social processes that mediate the lives of persons who are dependent on multiple medical and assistive technologies. In doing so we consider the embodied and emplaced nature of disability and how life is lived (...) through bodies coupled with technologies and experienced as ‘techno-body-subjects in situ’. Normative implications for theory and research, including bioethics research, are discussed. (shrink)

A collection of personal narratives and essays, Living Professionalism is designed to help medical students and residents understand and internalize various aspects of professionalism. These essays are meant for personal reflection and above all, for thoughtful discussion with mentors, with peers, with others throughout the health care provider community who care about acting professionally.

There are two mutually indispensable ways of doing it. The first is to study the development of Plato's literary style. The second is to follow the sequence of his thought from one dialogue to another. Neither test is infallible; that is why Platonic scholarship goes happily on and on. In the course of a brilliant article concerning the place of the Timaeus in the order of the dialogues, Mr. G. E. L. Owen has shown how a merely statistical study of (...) stylistic mannerisms may seriously mislead; and as for thought sequences, they notoriously depend on hypothetical intuitions and vary widely from one critic to another. But along both lines a certain advance is possible. Since Owen, mechanical stylometry is discredited; and no one would now do what Schleiermacher did in his time--place the Phaedrus chronologically first among the dialogues on the ground that it contains in brief the whole of Plato's philosophy. There is progress in these matters, if not finality. (shrink)

Linguistic dependencies between non‐adjacent words have been shown to cause comprehension difficulty, compared with local dependencies. According to one class of sentence comprehension accounts, non‐local dependencies are difficult because they require the retrieval of the first dependent from memory when the second dependent is encountered. According to these memory‐based accounts, making the first dependent accessible at the time when the second dependent is encountered should help alleviate the difficulty associated with the processing of non‐local dependencies. In a dual‐task paradigm, participants (...) read sentences that did or did not contain a non‐local dependency (i.e., object‐ and subject‐extracted cleft constructions) while simultaneously remembering a word. The memory task was aimed at making the word held in memory accessible throughout the sentence. In an object‐extracted cleft (e.g., It was Ellen whom John consulted…), the object (Ellen) must be retrieved from memory when consulted is encountered. In the critical manipulation, the memory word was identical to the verb's object (ELLEN). In these conditions, the extraction effect was reduced in the comprehension accuracy data and eliminated in the reading time data. These results add to the body of evidence supporting memory‐based accounts of syntactic complexity. (shrink)

The recent genome sequencing of a non‐vertebrate deuterostome, the ascidian tunicate Ciona intestinalis, makes a substantial contribution to the fields of evolutionary and developmental biology.1 Tunicates have some of the smallest bilaterian genomes, embryos with relatively few cells, fixed lineages and early determination of cell fates. Initial analyses of the C. intestinalis genome indicate that it has been evolving rapidly. Comparisons with other bilaterians show that C. intestinalis has lost a number of genes, and that many genes linked together in (...) most other bilaterians have become uncoupled. In addition, a number of independent, lineage‐specific gene duplications have been detected. These new results, although interesting in themselves, will take on a deeper significance once the genomes of additional invertebrate deuterostomes (e.g. echinoderms, hemichordates and amphioxus) have been sequenced. With such a broadened database, comparative genomics can begin to ask pointed questions about the relationship between the evolution of genomes and the evolution of body plans. BioEssays 25:529–532, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

In this article, we describe the influence of violations of community standards of fairness (Kahneman, Knetsch, and Thaler, 1986a) on subsequent ethical decision-making and emotions. Across two studies, we manipulated explanations for a common action, and we find that explanations that violate community standards of fairness (e.g., by taking advantage of an in crease in market power) lead to greater intentions to behave unethically than explanations that are consistent with community standards of fairness (e.g., by passing along a price increase). (...) We find that perceptions of justifiability mediate this relationship. We also find that individuals derive significant psychological benefits (greater satisfaction, greater happiness, and reduced anger) from engaging in unethical behavior following perceived violations of fairness. (shrink)

Two self-paced reading experiments investigated several factors that influence the comprehension complexity of singly-embedded relative clauses (RCs) in English. Three factors were manipulated in Experiment 1, resulting in three main effects. First, object-extracted RCs were read more slowly than subject-extracted RCs, replicating previous work. Second, RCs that were embedded within the sentential complement of a noun were read more slowly than comparable RCs that were not embedded in this way. Third, and most interestingly, object-modifying RCs were read more slowly than (...) subject-modifying relative clauses. This result contradicts one of the central tenets of complexity research: that nested sentences are harder to understand than their right-branching equivalents (e.g., Miller and Chomsky 1963). It is hypothesized that this result followed from a combination of two information-flow factors: (1) background information is usually presented early in a sentence; and (2) restrictive RCs—the form of the RCs in Experiment 1—usually convey background information. Experiment 2 tested this hypothesis by comparing restrictive and non-restrictive RCs— which generally provide new information—in both subject- and objectmodifying positions. The results of the experiment were as predicted by the information-flow account: Only restrictive RCs were read more slowly when modifying objects. It is concluded that both resource and information-flow factors need to be considered in explaining RC complexity effects. (shrink)

In this paper I argue against three leading accounts of self-deception in the philosophical literature and propose a heretofore overlooked route to self-deception. The central problem with extant accounts of self-deception is that they are unable to balance two crucial desiderata: (1) to make the dynamics of self-deception (e.g., the formation of self-deceptive beliefs) psychologically plausible and (2) to capture self-deception as an intentional phenomenon for which the self-deceiver is responsible. I argue that the three leading views all fail on (...) one or both counts. However, I claim that many or most cases of self-deception conform to a different model, which I call ‘Self-deception as Omission’. In these cases, the process of self-deceptive belief formation and the intentional act for which the self-deceiver is responsible come apart, allowing us to meet both desiderata. Self-deceptive beliefs are often formed by unconscious mechanisms closely analogous to the 'System 1' processes of dual-systems psychology, or by other mechanisms of motivated reasoning. The nascently self-deceptive subject then acquiesces in the comforting belief and commits an epistemic failure by allowing it to persist. If this is done for motivationally biased reasons — e.g., preferring that the belief in question be true — then the subject is self-deceived and is blameworthy for her epistemic omission. (shrink)

Describing someone as disabled means evaluating their relationship with their environment, body, and self. Such descriptions pivot on the person’s perceived limitations due to their atypical embodiment. However, impairments are not inherently pathological, nor are disabilities necessarily deviations from biological normality, a discrepancy often articulated in science fiction via the presentation of radically altered environments. In such settings, non-impaired individuals can be shown to be unsuited to the world they find themselves in. One prime example of this comes courtesy of (...) H. G. Wells’s “The Country of the Blind.” This paper demonstrates science fiction’s capacity to decouple disability’s normative quality from classical medical models stemming from the medical Enlightenment movement by challenging the idea of the biologically normal. It first provides a brief account of disability before exploring the concept of medical normality. It then problematizes the biologically consistent being, arguing that health is only understandable when environmentally situated. Next, the paper provides an overview of “The Country of the Blind” before analyzing how it challenges the idea of biological normality, framing it as a social product rather than a universal constant. Finally, the paper concludes that science fiction narratives effectively interrogate our world’s seemingly consistent trends by envisioning (un)desirable alternatives. (shrink)

Nature of the problem: Testimony from scientists. Reflex action and theism (1881) by W. James. The organization of thought (1916) by A.N. Whitehead. The changing scientific scene 1900-1950 (1952) by J.B. Conant. A note on methods of analysis (1943) by H.J. Muller. The way things are (1959) by P.W. Bridgman. A definition of style (1948) by J.R. Oppenheimer.--Consequences of the problem: Testimony from artists and writers. Existentialism (1947) by J.-P. Sartre. The testimony of modern art (1957) by W. Barrett. Parts (...) of speech and punctuation (1935) by G. Stein. The waves (1931) by V. Woolf. The imperfect paradise, by W. Stevens. A note on style and the limits of language, by W. Gibson. (shrink)

The quantifier “some” often elicits a scalar implicature during comprehension: “Some of today's letters have checks inside” is often interpreted to mean that not all of today's letters have checks inside. In previous work, Goodman and Stuhlmüller (G&S) proposed a model that predicts that this implicature should depend on the speaker's knowledgeability: If the speaker has only examined some of the available letters (e.g., two of three letters), people are less likely to infer that “some” implies “not all” than if (...) the speaker has examined all of the available letters. G&S also provided behavioral evidence in support of their model. In this paper, we first show that a simple extension of G&S's model (1) predicts G&S's knowledgeability effects, and in addition, (2) predicts that the knowledgeability effect will be reduced when the speaker's usage indicates numeral alternatives are available. We tested the new model's predictions in four preregistered experiments. All experiments supported the first model prediction, replicating G&S's finding of a main effect of the speaker's knowledge. Further, Experiments 2 and 4 supported the second model prediction showing that the words that a speaker tends to use affect the strength of scalar implicature that comprehenders make. In particular, when the speaker has partial knowledge (e.g., has only examined two of three letters), comprehenders think that “some” is more likely to mean “not all” when the speaker also tends to produce number words in similar sentences (e.g., “2 of today's rooms have working smoke detectors.”). These results have important ramifications for theories of meaning: the context beyond the sentence (e.g., the speaker's tendency to use particular words) affects the set of alternatives that comprehenders consider when inferring meaning. (shrink)

This volume is fifth in a series, Monuments of Western Thought. Most of the book consists of excerpts from the works of Bacon and Descartes The selections from Bacon are the preface and plan of The Great Instauration, parts of the New Organon, a bit of Advancement of Learning, and all of The New Atlantis. The selections from Descartes are a short passage from the Discourse on Method and all of the Meditations. The text is introduced by a historical sketch (...) of the intellectual, social, and political context in which Bacon and Descartes lived, and by brief intellectual biographies. The volume closes with short critical selections, pointing up and commenting on important issues in the source material. On Bacon: A. N. Whitehead deals with Bacon's concept of matter, the justification of induction, and Bacon's emphasis on quality; C. D. Broad discusses Bacon's concept of "Form" and its relation to the principle of limited variety; R. F. Jones discusses the Idols, especially the Idol of the Market-place, and Bacon's stress on experimentation; B. Farrington interprets Bacon's rejection of scholasticism as part of the contemporary effort to return to the Hebrew origins of Christianity. On Descartes: A. Koyré deals with consequences of the Cartesian identification of matter with extension; S. V. Keeling discusses the importance of the cogito and interprets it as giving knowledge of the existence of a substantival self; A. B. Gibson interprets Cartesian personalism as the foundation of a realism; M. Versfeld interprets Cartesian personalism as an error making knowledge impossible. Each section is followed by a few questions designed to force the student to think about what he has read and to return to the text.--L. G. (shrink)