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)

Meta‐analysis: the glass eye of evidence‐based practice?Meta‐analysis was developed as a technique for combining the results of many different quantitative studies: it is often used to produce quantitative estimates of causal relations and/or association between variables. Meta‐analysis is sometimes regarded as a central component of evidence‐based practice. We draw attention to an incompatibility in the epistemology and methods of reasoning in quantitative meta‐analysis and the epistemology and reasoning implicit in expert practice. We argue that this may be because the (...) common perception of meta‐analysis appeals to truth as correspondence; we suggest that rejecting the naïve realism that underpins truth as correspondence allows meta‐analysis to be understood in terms of truth as coherence. We can then develop an account of meta‐analysis that does not depend upon reduction to a mathematical procedure but is an attempt to maximise coherence in beliefs about what works that is consistent with clinical reasoning in expert practice. (shrink)

Dramatic events involving dangerous microbes often focus attention on isolation and quarantine as policy instruments. The incident in May-June 2007 involving Andrew Speaker and drug-resistant tuberculosis joins other communicable disease crises that have forced contemplation or actual application of quarantine powers. Implementation of quarantine powers, which encompasses authority for both isolation and quarantine actions, is important not only for the handling of a specific event but also because the use of such authority provides a window on broader issues of (...) public health and the legal rules, ethical principles, and governance systems that support it. Debates about quarantine powers reflect political and social attitudes about public health that often tell us more about this policy endeavor than acts of isolation and quarantine themselves. (shrink)

This paper argues that the dominance of linear models has led many sociologists to construe the social world in terms of a "general linear reality." This reality assumes (1) that the social world consists of fixed entities with variable attributes, (2) that cause cannot flow from "small" to "large" attributes/events, (3) that causal attributes have only one causal pattern at once, (4) that the sequence of events does not influence their outcome, (5) that the "careers" of entities are largely independent, (...) and (6) that causal attributes are generally independent of each other. The paper discusses examples of these assumptions in empirical work, consider standard and new methods addressing them, and briefly explores alternative models for reality that employ demographic, sequential, and network perspectives. (shrink)

In this paper I shall examine how the pragmatists regarded the context of a single self in time (the problem of personal development over the life course) and the context of a single self in social space (the problem not only of surrounding individuals but also of surrounding and fundamentally different groups). After a quick glance at the ontologies of the earlier pragmatists, I discuss the problems of individual development and social difference as they emerged society-wide during and after the (...) first pragmatist generation. Having specified these problems, I can set the second pragmatist generation in the context they provide. The paper concludes with a discussion of the centrality of accounts of development and difference in a processualized social ontology. (shrink)

Buchanan highlighted the inconsistencies that arise when public services are financed by general taxation. Citizens increase their demand for services, even though citizens are reticent to increase taxation. Buchanan invited readers to explore the impact of different assumptions of politicians’ behaviour. In this chapter, attention focuses on the way that vote maximising governments are likely to respond to the divorce between receipt and payment for services. Buchanan illustrated his analysis with reference to the National Health Service in the UK. Predictions (...) are tested with reference to the pattern of excess demand in the National Health Service between 1970 and 2012. (shrink)

The first edition was awarded the '2005 Textbook Award of the Association of University Professors of Management (Verband der Hochschullehrer fur ...

Building on the success of the bestselling first edition, the second edition of this textbook provides a comprehensive and accessible introduction to the major issues in Principles and Parameters syntactic theory, including phrase structure, the lexicon, case theory, movement, and locality conditions. Includes new and extended problem sets in every chapter, all of which have been annotated for level and skill type. Features three new chapters on advanced topics including vP shells, object shells, control, gapping and ellipsis and an additional (...) chapter on advanced topics in binding. Offers a brief survey of both Lexical-Functional Grammar and Head-Driven Phrase Structure Grammar. Succeeds in strengthening the reader's foundational knowledge, and prepares them for more advanced study. Supported by an instructor's manual and online resources for students and instructors, available at www.blackwellpublishing.com/carnie. (shrink)

This paper develops a theory of analog representation. We first argue that the mark of the analog is to be found in the nature of a representational system’s interpretation function, rather than in its vehicles or contents alone. We then develop the rulebound structure theory of analog representation, according to which analog systems are those that use interpretive rules to map syntactic structural features onto semantic structural features. The theory involves three degree-theoretic measures that capture three independent ways in which (...) a system can be more or less analog. We explain how our theory improves upon prior accounts of analog representation, provides plausible diagnoses for novel challenge cases, extends to hybrid systems that are partially analog and partially symbolic, and accounts for some of the advantages and disadvantages of representing analogically versus symbolically. (shrink)

Vagueness is the study of concepts that admit borderline cases. The epistemology of vagueness concerns attitudes we should have towards propositions we know to be borderline. On this basis Andrew Bacon develops a new theory of vagueness in which vagueness is fundamentally a property of propositions, explicated in terms of its role in thought.

Conscious experiences are characterized by mental qualities, such as those involved in seeing red, feeling pain, or smelling cinnamon. The standard framework for modeling mental qualities represents them via points in geometrical spaces, where distances between points inversely correspond to degrees of phenomenal similarity. This paper argues that the standard framework is structurally inadequate and develops a new framework that is more powerful and flexible. The core problem for the standard framework is that it cannot capture precision structure: for example, (...) consider the phenomenal contrast between seeing an object as crimson in foveal vision versus merely as red in peripheral vision. The solution I favor is to model mental qualities using regions, rather than points. I explain how this seemingly simple formal innovation not only provides a natural way of modeling precision, but also yields a variety of further theoretical fruits: it enables us to formulate novel hypotheses about the space and structures of mental qualities, formally differentiate two dimensions of phenomenal similarity, generate a quantitative model of the phenomenal sorites, and define a measure of discriminatory grain. A noteworthy consequence is that the structure of the mental qualities of conscious experiences is fundamentally different from the structure of the perceptible qualities of external objects. (shrink)

The voluntary and informed consent of subjects has been the central focus of concern in research reviews, overshadowing the importance of all other considerations. The Nuremberg Code, with its rights-based protection of the subject's autonomy above all else, made it difficult to justify research with no intended benefit when subjects are incompetent to make a valid informed choice to participate. Subsequent codes providing for research with incompetent subjects followed the lead of Nuremberg, substituting the informed authorization of a proxy for (...) the informed consent of the subject. (shrink)

In a new study, Ben-Haim et al. use subliminal stimuli to separate conscious and unconscious perception in macaques. A programme of this type, using a range of cognitive tasks, is a promising way to look for conscious perception in more controversial cases.

This three-part chapter explores a higher-order logic we call ‘Classicism’, which extends a minimal classical higher-order logic with further axioms which guarantee that provable coextensiveness is sufficient for identity. The first part presents several different ways of axiomatizing this theory and makes the case for its naturalness. The second part discusses two kinds of extensions of Classicism: some which take the view in the direction of coarseness of grain (whose endpoint is the maximally coarse-grained view that coextensiveness is sufficient for (...) identity), and some which take the view in the direction of fineness of grain (whose endpoint is the maximally fine-grained theory containing all distinctness claims compatible with Classicism). The third part introduces some techniques for constructing models of Classicism, and uses them to prove the consistency of many of the extensions of Classicism introduced in the second part. (shrink)

Liberalism, or at least twentieth century liberalism, is today out of fashion amongst the electorate of the United States and Britain. Even within the academy—often, contrary to liberalism itself, one of the last institutions to reflect major shifts in ideology—it appears to be losing its grip. The rise of neo-contractarianism in social and political philosophy and neo-conservatism in economics are only two pieces of evidence of its demise. Nevertheless, reports of its death have been greatly exaggerated in some quarters of (...) social philosophy; in particular, it still thrives as the received opinion whenever the issue of paternalism is raised. And, of course, the single most important liberal standard-bearer here is John Stuart Mill. (shrink)

In this wide-ranging interview Andrew Sayer discusses how he became a realist and then the development of his work over the subsequent decades. He comments on his postdisciplinary approach, his early work on economy and its influences, how he came to write Method in Social Science and the transition in Realism and Social Science to normative critical social science and moral economy. The interview concludes with discussion of his three most recent books and the themes that connect them, not (...) least the ongoing problem of a ‘diabolical double crisis’ of capitalism: extreme inequality and climate change. (shrink)

We consider the relationship between neural and behavioural evidence for animal consciousness. We critically examine two recent studies: one neural and one behavioural. The first, on crows, finds different neural activity depending on whether a stimulus is reported as seen or unseen. However, to implicate this neural activity in consciousness, we must assume that a specific conditioned behaviour is a report of conscious experience. The second study, on macaques, records behaviours strikingly similar to patterns of conscious and unconscious perception in (...) humans. However, confounds are only ruled out in human subjects, presupposing substantial neural similarity between humans and macaques. Taken together, the two studies reveal a sense in which neural and behavioural research rely on each other. Looking ahead, these two types of evidence could prove to be either mutually reinforcing or mutually undermining. The science of animal consciousness needs both neural and behavioural evidence, ideally obtained as part of a single coordinated programme. (shrink)

Some philosophers think that life is worth living not merely because of the goods and the bads within it, but also because life itself is good. I explain how this idea can be formalized by associating each version of such of a view with a function from length of life to the value generated by life itself. Then I argue that every version of the view that life itself is good faces some version of the following dilemma: either (1) good (...) human lives are worse than very long lives wholly devoid of pleasure, desire-satisfaction, knowledge, or any other goods, or (2) very short lives containing nothing but suffering are worth living. Since neither result is plausible, we ought to reject the view that life itself is good. On the view I favor, any given life may be worth living because of the goods that it contains, but life itself is neutral. (shrink)

J. L. Schellenberg's argument from hiddenness against the existence of God is simple. The primary argument is as follows.The Main Argument from Hiddenness If God exists, then no one would be epistemically rational for not believing in God. Some people are epistemically rational for not believing in God. Therefore, God does not exist.However, much of the issue concerning this argument surrounds the support for premise. As many have noted, Schellenberg's first premise does not demand an undeniable, incontrovertible proof for God's (...) existence. He merely claims that God would provide evidence sufficient for rational belief, and presumably this would entail that the only people who do not believe are culpable for their nonbelief. Their nonbelief would be their own fault. (shrink)

A reply to contemporary skepticism about intuitions and a priori knowledge, and a defense of neo-rationalism from a contemporary Kantian standpoint, focusing on the theory of rational intuitions and on solving the two core problems of justifying and explaining them.

The Foundations of Positive and Normative Economics: A Handbook is the first book in a new series by Andrew Caplin and Andrew Schotter. There is currently no guide available on the rapidly changing methodological frontiers of the field of economics. Economists have been introducing new theories and new sources of data at a remarkable rate in recent years, and there are widely divergent views both on how productive these expansions have been in the past, and how best to (...) make progress in the future. The speed of these changes has left economists ill at ease, and has created a backlash against new methods. The series will debate these critical issues, allowing proponents of a particular research method to present proposals in a safe yet critical context, with alternatives being clarified. This first volume, written by some of the most prominent researchers in the discipline, reflects the challenges that are opened by new research opportunities. The goal of the current volume and the series it presages, is to formally open a dialog on methodology. The editors' conviction is that such a debate will rebound to the benefit of social science in general, and economics in particular. The issues under discussion strike to the very heart of the social scientific enterprise. This work is of tremendous importance to all who are interested in the contributions that academic research can make not only to our scientific understanding, but also to matters of policy. (shrink)

Despite the enormous influence of Michel Foucault in gender studies, social theory, and cultural studies, his work has been relatively neglected in the study of politics. Although he never published a book on the state, in the late 1970s Foucault examined the technologies of power used to regulate society and the ingenious recasting of power and agency that he saw as both consequence and condition of their operation. These twelve essays provide a critical introduction to Foucault's work on politics, exploring (...) its relevance to past and current thinking about liberal and neo-liberal forms of government. Moving away from the great texts of liberal political philosophy, this book looks closely at the technical means with which the ideals of liberal political rationalities have been put into practice in such areas as schools, welfare, and the insurance industry. This fresh approach to one of the seminal thinkers of the twentieth century is essential reading for anyone interested in social and cultural theory, sociology, and politics. (shrink)

Higher-order logic augments first-order logic with devices that let us generalize into grammatical positions other than that of a singular term. Some recent metaphysicians have advocated for using these devices to raise and answer questions that bear on many traditional issues in philosophy. In contrast to these 'higher-order metaphysicians', traditional metaphysics has often focused on parallel, but importantly different, questions concerning special sorts of abstract objects: propositions, properties and relations. The answers to the higher-order and the property-theoretic questions may coincide (...) sometimes but will often come apart. I argue that when they do, the higher-order questions are closer to the metaphysical action and so it would be better for these debates to proceed in higher-order terms. (shrink)

Many philosophers accept both of the following claims: (1) consciousness matters morally, and (2) species membership doesn’t matter morally. In other words, many reject speciesism but accept what we might call 'sentientism'. But do the reasons against speciesism yield analogous reasons against sentientism, just as the reasons against racism and sexism are thought to yield analogous reasons against speciesism? This paper argues that speciesism is disanalogous to sentientism (as well as racism and sexism). I make a case for the following (...) asymmetry: (a) some non-humans clearly have interests, but (b) no non-conscious entities clearly have interests. This asymmetry, I argue, renders sentientism resistant to the standard argument against speciesism. (shrink)

Recent studies show that returning global health trainees often report having felt inadequately prepared to deal with ethical dilemmas they encountered during outreach clinical work. While global health training guidelines emphasize the importance of developing ethical and cultural competencies before embarking on fieldwork, their practical implementation is often lacking and consists mainly of recommendations regarding professional behavior and discussions of case studies. Evidence suggests that one of the most effective ways to teach certain skills in global health, including ethical and (...) cultural competencies, is through service learning. This approach combines community service with experiential learning. Unfortunately, this approach to global health ethics training is often unattainable due to a lack of supervision and resources available at host locations. This often means that trainees enter global health initiatives unprepared to deal with ethical dilemmas, which has the potential for adverse consequences for patients and host institutions, thus contributing to growing concerns about exploitation and “medical tourism.” From an educational perspective, exposure alone to such ethical dilemmas does not contribute to learning, due to lack of proper guidance. We propose that the tension between the benefits of service learning on the one hand and the respect for patients’ rights and well-being on the other could be resolved by the application of a simulation-based approach to global health ethics education. (shrink)

The ArgumentThe last two plates of Aby Warburg's unpublished picture-atlasMnemosyne, which is thought today to be among Warburg's most innovative contributions to the study of art history, are here analyzed in detail. These plates were assembled in the summer before his death in 1929; they reflect experiences of the time he spent in Rome during 1928 and 1929 and are here understood as Warburg's attempt to visualize his theory of the symbol.TheBilderatlaswas to have a two-fold function: Warburg planned it to (...) be a summary of his life's work; he also wanted its plates to reflect his theory of pictures and images. I argue here that particularly plate 79 is indeed an attempt tovisualizethe theoretical foundation of Warburg's view of the representational function of pictures. It refers to the origin of the power of images in sacrificial rituals and to the limits of this power. Warburg singles out the Eucharist and the doctrine of transsubstantiation to illustrate the role of the symbol in rituals.With this emphasis on ritual as a necessary complement for the functioning of the symbol, Warburg reaffirms his theory of the image to include the social act. This inclusion can be shown to be motivated by contemporary political concerns. (shrink)

Introduction: the age of reflexion Part I. Romanticism: 1. Romanticism and the sciences David Knight 2. Schelling and the origins of his Naturphilosophie S. R. Morgan 3. Romantic philosophy and the organization of the disciplines: the founding of the Humboldt University of Berlin Elinor S. Shaffer 4. Historical consciousness in the German Romantic Naturforschung Dietrich Von Engelhardt 5. Theology and the sciences in the German Romantic period Frederick Gregory 6. Genius in Romantic natural philosophy Simon Shaffer Part II. Sciences of (...) the Organic: 7. Doctors contra clysters and feudalism: the consequences of a Romantic revolution Nelly Tsouyopoulos 8. Morphotypes and the historical-genetic method in Romantic biology Timothy Lenoir 9. ’Metaphorical mystifications’: the Romantic gestation of nature in British biology Evelleen Richards 10. Transcendental anatomy Philip F. Rehbock 11. Romantic thought and the origins of cell theory L. S. Jacyna 12. Alexander von Humbolt and the geography of vegetation Malcolm Nicholson Part III. Sciences of the Inorganic: 13. Goethe, colour, and the science of seeing Dennis L. Sepper 14. Johann Wilhelm Ritter: Romantic physics in Germany Walter D. Wetzels 15. The power and the glory: Humphrey Davy and Romanticism Christopher Lawrence 16. Oersted’s discovery of electromagnetism H. A. M. Snelders 17. Caves, fossils and the history of the earth Nicholas A. Rupke Part IV. Literature and the Sciences: 18. Goethe’s use of chemical theory in his Elective Affinities Jeremy Adler 19. Kleist’s bedlam: abnormal psychology and psychiatry in the works of Heinrich von Kleist Nigel Reeves 20. Coleridge and the sciences Trevor H. Levere 21. Nature’s book: the language of science in the American Renaissance David van Leer 22. The shattered whole: Georg Buchner and Naturphilosophie John Reddick. (shrink)

Clinicians have good moral and professional reasons to contribute to pragmatic clinical trials (PCTs). We argue that clinicians have a defeasible duty to participate in this research that takes place in usual care settings and does not involve substantive deviation from their ordinary care practices. However, a variety of countervailing reasons may excuse clinicians from this duty in particular cases. Yet because there is a moral default in favor of participating, clinicians who wish to opt out of this research must (...) justify their refusal. Reasons to refuse include that the trial is badly designed in some way, that the trial activities will violate the clinician’s conscience, or that the trial will impose excessive burdens on the clinician. (shrink)

For more than 100 years, anthropologists have collected ethnographic research among communities who assert that the spirits, animal allies, and other entities of the unseen world are “really real,” yet we have historically contextualized this information under the umbrella of cultural relativism rather than taking the veracity of these claims seriously. In the last decade, some anthropologists claim that our discipline has finally undergone an ontological turn, which opens a door for anthropologists to finally take claims of nonhuman sentience seriously (...) under the umbrella of ontological, rather than cultural, relativism. This paper takes issue with ontological relativism as just one more frame for explaining away the stories of other-than-human consciousness that ethnographers report and suggests that there is an urgent need to consider the relevance, rather than the relativism, of other-than-human consciousness. It looks to Michael Harner's work as a welcome alternative to ontological relativism and encourages opening our minds to a reconsideration of what is “really real.”. (shrink)

Andrew Youpa offers an original reading of Spinoza's moral philosophy, arguing it is fundamentally an ethics of joy. Unlike approaches to moral philosophy that center on praiseworthiness or blameworthiness, Youpa maintains that Spinoza's moral philosophy is about how to live lovingly and joyously. His reading expands to examinations of the centrality of education and friendship to Spinoza's moral framework, his theory of emotions, and the metaphysical foundation of his moral philosophy.

Nicolas Malebranche is one of the most important philosophers of the 17th Century after Descartes. A pioneer of Rationalism, he was one of the first to champion and to further Cartesian ideas. Andrew Pyle places Malebranche's work in the context of Descartes and other philosophers, and also in its relation to ideas about faith and reason. He examines the entirety of Malebranche's writings, including the famous The Search After Truth , which was admired and criticized by both Leibniz and (...) Locke. Pyle presents an integrated account of Malebranche's central theses, occasionalism and 'vision in God', before exploring and assessing Malebranche's contribution to debates on physics and biology, and his views on the soul, self-knowledge, grace, and the freedom of the will. This penetrating and wide-ranging study will be of interest to not only philosophers, but also to historians of science and philosophy, theologians, and students of the Enlightenment or 17th Century thought. (shrink)

The result of combining classical quantificational logic with modal logic proves necessitism – the claim that necessarily everything is necessarily identical to something. This problem is reflected in the purely quantificational theory by theorems such as ∃x t=x; it is a theorem, for example, that something is identical to Timothy Williamson. The standard way to avoid these consequences is to weaken the theory of quantification to a certain kind of free logic. However, it has often been noted that in order (...) to specify the truth conditions of certain sentences involving constants or variables that don’t denote, one has to apparently quantify over things that are not identical to anything. In this paper I defend a contingentist, non-Meinongian metaphysics within a positive free logic. I argue that although certain names and free variables do not actually refer to anything, in each case there might have been something they actually refer to, allowing one to interpret the contingentist claims without quantifying over mere possibilia. (shrink)