Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to (...) genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50, which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1, showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED. (shrink)

Conventional wisdom has had it that the naturalist Alfred Russel Wallace and his colleague Henry Walter Bates journeyed to the Amazon in 1848 with two intentions in mind: to collect natural history specimens, and to consider evidential materials that might reveal the causal basis of organic evolution. This understanding has been questioned recently by the historian John van Wyhe, who points out that with regard to the second matter, at least, there appears to be no evidence of a “smoking (...) gun” variety proving it so. In the present essay the circumstances of Wallace’s interest in the matter are reviewed, and van Wyhe is taken to task with alternate explanations for the facts he introduces in his argument. The conclusion is that Wallace almost certainly did have the second objective in mind when he left for both the Amazon, and the Far East. Keywords: Alfred Russel Wallace, Henry Walter Bates, evolution, natural selection. (shrink)

In 1967, the American Geographical Society awarded Marston Bates with one of its highest honors, the Charles P. Daly medal. In giving this award, they noted that Marston Bates wears an almost bewildering variety of scholarly hats, and all of them become him. He is at one and the same time biologist, zoologist, medical ecologist, naturalist, humanist, and, unquestionably, also geographer manqué.... He possesses a gift of clear and literate exposition; his style displays a philosophic bent, an (...) acuity of perception, and a spark of humor that together make for delightful reading. Bates was an early bioethicist, in the sense that he was one of the first thinkers in the 20th century to... (shrink)

Part I: The Life of Cognitive Science:. William Bechtel, Adele Abrahamsen, and George Graham. Part II: Areas of Study in Cognitive Science:. 1. Analogy: Dedre Gentner. 2. Animal Cognition: Herbert L. Roitblat. 3. Attention: A.H.C. Van Der Heijden. 4. Brain Mapping: Jennifer Mundale. 5. Cognitive Anthropology: Charles W. Nuckolls. 6. Cognitive and Linguistic Development: Adele Abrahamsen. 7. Conceptual Change: Nancy J. Nersessian. 8. Conceptual Organization: Douglas Medin and Sandra R. Waxman. 9. Consciousness: Owen Flanagan. 10. Decision Making: J. Frank (...) Yates and Paul A. Estin. 11. Emotions: Paul E. Griffiths. 12. Imagery and Spatial Representation: Rita E. Anderson. 13. Language Evolution and Neuromechanisms: Terrence W. Deacon. 14. Language Processing: Kathryn Bock and Susan M. Garnsey. 15. Linguistics Theory: D. Terence Langendoen. 16. Machine Learning: Paul Thagard. 17. Memory: Henry L. Roediger III and Lyn M. Goff. 18. Perception: Cees Van Leeuwen. 19. Perception: Color: Austen Clark. 20. Problem Solving: Kevin Dunbar. 21. Reasoning: Lance J. Rips. 22. Social Cognition: Alan J. Lambert and Alison L. Chasteen. 23. Unconscious Intelligence: Rhianon Allen and Arthur S. Reber. 24. Understanding Texts: Art Graesser and Pam Tipping. 25. Word Meaning: Barbara C. Malt. Part III: Methodologies of Cognitive Science:. 26. Artificial Intelligence: Ron Sun. 27. Behavioral Experimentation: Alexander Pollatsek and Keith Rayner. 28. Cognitive Ethology: Marc Bekoff. 29. Deficits and Pathologies: Christopher D. Frith. 30. Ethnomethodology: Barry Saferstein. 31. Functional Analysis: Brian Macwhinney. 32. Neuroimaging: Randy L. Buckner and Steven E. Petersen. 33. Protocal Analysis: K. Anders Ericsson. 34. Single Neuron Electrophysiology: B. E. Stein, M.T. Wallace, and T.R. Stanford. 35. Structural Analysis: Robert Frank. Part IV: Stances in Cognitive Science:. 36. Case-based Reasoning: David B. Leake. 37. Cognitive Linguistics: Michael Tomasello. 38. Connectionism, Artificial Life, and Dynamical Systems: Jeffrey L. Elman. 39. Embodied, Situated, and Distributed Cognition: Andy Clark. 40. Mediated Action: James V. Wertsch. 41. Neurobiological Modeling: P. Read Montague and Peter Dayan. 42. Production Systems: Christian D. Schunn and David Klahr. Part V: Controversies in Cognitive Science:. 43. The Binding Problem: Valerie Gray Hardcastle. 44. Heuristics and Satisficing: Robert C. Richardson. 45. Innate Knowledge: Barbara Landau. 46. Innateness and Emergentism: Elizabeth Bates, Jeffrey L. Elman, Mark H. Johnson, Annette Karmiloff-Smith, Domenico Parisi, and Kim Plunkett. 47. Intentionality: Gilbert Harman. 48. Levels of Explanation and Cognition Architectures: Robert N. McCauley. 49. Modularity: Irene Appelbaum. 50. Representation and Computation: Robert S. Stufflebeam. 51. Representations: Dorrit Billman. 52. Rules: Terence Horgan and John Tienson. 53. Stage Theories Refuted: Donald G. Mackay. Part VI: Cognitive Science in the Real World:. 54. Education: John T. Bruer. 55. Ethics: Mark L. Johnson. 56. Everyday Life Environments: Alex Kirlik. 57. Institutions and Economics: Douglass C. North. 58. Legal Reasoning: Edwina L. Rissland. 59. Mental Retardation: Norman W. Bray, Kevin D. Reilly, Lisa F. Huffman, Lisa A. Grupe, Mark F. Villa, Kathryn L. Fletcher, and Vivek Anumolu. 60. Science: William F. Brewer and Punyashloke Mishra. Selective Biographies of Major Contributors to Cognitive Science: William Bechtel and Tadeusz Zawidzki. (shrink)

First published in 2014. Routledge is an imprint of Taylor & Francis, an informa company.

This book is about the liberation of the concept of life from the bondage fashioned by the interpreters of life ever since biology began, and about the liberation of the life of humans and non-humans alike from the bondage of social structures and behaviour, which now threatens the fullness of life's possibilities if not survival itself. It falls into a tradition of writings about human problems from a perspective informed by biology. It rejects the mechanistic model of life dominant in (...) the Western world and develops an alternative 'ecological model' which is applicable to the life of the cell and the life of the human community. For the first time it brings together in one work the insights of modern biology with those of a modern holistic philosophy and a liberal theology in a way which challenges conventional approaches to science, agriculture, sociology, politics, economics, development and liberation movements. (shrink)

This essay discusses the difference between the concepts of multiculturalism and interculturalism, both concepts which are current on the Canadian scene. It argues that the difference between the two is not so much a matter of the concrete policies, but concerns rather the story that we tell about where we are coming from and where we are going. In some ways, we could argue that interculturalism is more suitable for certain European countries.

Reprint, in paper covers, of the Columbia U. Press edition of 1990. Annotation copyright by Book News, Inc., Portland, OR.

The psycho-social day-to-day experience of COVID-19 pandemic has shone some light on the wider scope of health vulnerability and has correspondingly enlarged the ethical debate surrounding the social implications of health and healthcare. This emerging paradigm is neither a single-handed problem of biomedical scientists nor of social analysts. It instead needs a strategically oriented collaborative and interdisciplinary preventive effort. To that effect, this article presents some socio-ethical reflections underscoring the judicious use of the insight from care ethics as an asset (...) in minimizing the possible propagation of the COVID-19 virus and the escalation of its vulnerability in the day-to-day human interaction. It further emphasizes that if this insight is overlooked, the effects of the diverse facets of the “shadow pandemics” of COVID-19—fallouts on both the affected and the infected—may equally be deadly. (shrink)

Are they needed? To be sure. The Darwinian industry, industrious though it is, has failed to provide texts of more than a handful of Darwin's books. If you want to know what Darwin said about barnacles (still an essential reference to cirripedists, apart from any historical importance) you are forced to search shelves, or wait while someone does it for you; some have been in print for a century; various reprints have appeared and since vanished." -Eric Korn,Times Literary Supplement (...) class='Hi'>Charles Robert Darwin (1880-1882) has been widely recognized since his own time as one of the most influential writers in the history of Western thought. His books were widely read by specialists and the general public, and his influence had been extended by almost continuous public debate over the last 130 years. New York University Press' edition makes it possible for the first time to review Darwin's public literary output as a whole, plus his scientific journal articles, his private notebooks, and his correspondence. This is the first complete edition containing all of Darwin's published books, featuring definitive texts recording original paginations with Darwin's indexes retained. All illustrations and plates are presented, inclucing 82 color plates of birds and mammals and several folding maps and plates. The set also features a general introduction and index, and textural introductions in each volume. (shrink)

ALTHOUGH I shall be attempting to examine the function of judgment, or what Aristotle called φρόνησις, in moral deliberation, I shall begin by discussing some previous opinions about what kind of importance examples have in moral experience. This strategy is only apparently circuitous. The role which one assigns to examples is symptomatic of the conception one has of judgment in moral decision-making, because the use of examples forms one way in which judgment is exercised. Indirectly, then, I shall be trying (...) to rehabilitate the significance of examples in moral deliberation. But the chief aim of this paper will be to determine both what is the function of judgment in moral deliberation and how we are to understand the activity of exercising it. (shrink)

Our paper contributes to Science, Technology and Society scholarship on the practices and technologies of containment. We build on existing work in STS that has analyzed containment as a performative sociotechnical system that generates and sustains new realities, new systems, and new relationships. Our contribution draws from the problem of containment in salmon aquaculture. The stakes for containing salmon are very high. Farmed salmon escapes are environmentally damaging to ecosystems and wild salmon populations, and they put additional pressure on an (...) industry that has a very poor environmental record. We consider in detail Newfoundland and Labrador’s “Code of Containment” that works to keep farmed salmon in cages and prevent them from escaping into the wild. Through our analysis of the Code, we argue that containment is not only about holding inside. It is also about holding together, an obsolete meaning of the term “to contain.” We add to STS scholarship by arguing that containment and its associated Code in Newfoundland holds together a large scale, industrial aquaculture sector that tolerates persistent farmed salmon escapes into the wild from ocean-based cages. We conclude by examining the broader implications of our analysis for STS scholarship on the practices and technologies of containment. (shrink)

David Sackett and Jack Wennberg have each introduced and developed ideas and methods that have had major impacts on how we think about and perform clinical research. Sackett is best known for his work in Evidence-Based Medicine (Sackett et al. 1997); Wennberg, upon noting wide geographic (and other) variations in best practices for the same conditions, stressed the importance of comparative effectiveness in clinical decision-making (Wennberg et al. 1993). When these two collaborated in an editorial about the current state of (...) the art and science of clinical research, it comes as no great surprise that they produced some truly memorable guidance. And, as is so often the case for inspired—and inspiring—advice, their .. (shrink)

A paradox, it is claimed, is a radical form of contradiction, one that produces gaps in meaning. In order to approach this idea, two senses of “separation” are distinguished: separation by something and separation by nothing. The latter does not refer to nothing in an ordinary sense, however, since in that sense what’s intended is actually less than nothing. Numerous ordinary nothings in philosophy as well as in other fields are surveyed so as to clarify the contrast. Then follows the (...) suggestion that philosophies which one would expect to have room for paradoxes actually tend either to exclude them altogether, or to dull them. There is a clear alternative, however, one that fully recognizes paradoxes and yet also strives to overcome them. (shrink)

Global Basic Rights brings together many of the most influential contemporary writers in political philosophy and international relations to explore some of the most challenging theoretical and practical questions provoked by Henry Shue's classic book Basic Rights.

Features the full text of "Wittgenstein and Kierkegaard: Religion, Individuality and Philosophical Method," by Charles L. Creegan. Discusses the works and theories of Danish philosopher Soren Kierkegaard (1813-1855) and British philosopher Ludwig Wittgenstein (1889-1951).

This book addresses the relevance of Timaeus’s cosmology to Socrates’ request for a speech about war. Charles Ives finds relevance in the dialogue’s concern for education apropos of the medical dimensions of Timaeus’ physics, the project of becoming like god, and the philosophical soul responsible for success on the battlefield.

On Thursday June 12th 2003, a press release concerning a Cabinet reshuffle declared as a footnote that the office of Lord Chancellor was to be abolished and that a new Supreme Court would replace the House of Lords as the highest court in the United Kingdom. In response to intense criticism of the Government for announcing these judicial reforms without holding any prior debate or consultation, Charles Banner and Alexander Deane have sought the views of several constitutional experts – (...) including judges, leading QCs, legal and political academics, commentators and MPs. This book is the product of their research: citing the interviewees at length, it critically analyses the Government’s proposals and looks at the various alternative models for appointing judges and for a new court of final appeal. The future of the QC system, which the Government has again indicated a desire to abolish, is also discussed in the book. (shrink)

Selon un récit aujourd'hui communément partagé, l'art depuis les années 1960 aurait définitivement abandonné le monde sensible pour se réfugier dans l'idée ou le concept, remisant ainsi l'expérience esthétique du côté des antiquités philosophiques. Dans ce livre, Charles Bobant tente de mettre au jour l'inactualité du sensible, c'est-à-dire la pertinence de la sensibilité pour rendre compte de notre commerce avec les œuvres d'art d'hier comme d'aujourd'hui."--Page 4 of cover.

Why, since happiness is so universally sought after, are so many people so miserable? The answer can be found by unpacking the wisdom of two of history's intellectual giants who set out to answer the question that has confounded man from time immemorial: What makes us happy? Aristotle and Thomas Aquinas existed sixteen centuries apart, yet each reached similar understandings about what makes a person happy and what makes him miserable. In these enlightening pages, Dr. Charles Nemeth synthesizes the (...) judgments of history's two greatest thinkers to present for you a life plan that inevitably leads to a happy human existence, whatever your ethnicity, religion, or citizenship. You will explore what it means to be happy and will come to understand the limitations of happiness. You'll learn how to live in accordance with your basic nature so that your inclinations will not conflict with that which makes you flourish. And you'll calibrate your compass so that you will be able to navigate your way into a state of life that makes you truly happy. Moreover, you'll discover why happiness is obtained through action and not mere desire and why wealth and fame do not -- and cannot -- buy happiness. You'll also learn why the body, despite providing avenues for sensory and intellectual pleasure, is incapable of providing true happiness. Strikingly, none of the suggestions in this book have ever been shown to be flawed. These timeless recommendations for a happy life never go out of favor and never change. Instead, they remain a constant, permanent, universal set of criteria on how to achieve a happy existence. You'll also learn: The benefits of moderation, sensibility, and equilibrium The source of ultimate happiness and the means to attain it The formula for fostering contentment -- what to strive for and what to avoid The essence of true goodness, happiness, and beauty Human excellence and different levels of happiness With this Rosetta stone of a book, you will find solutions to fortify your soul and bring you peace. You will be equipped with a new sense of direction, hope, and healing that will guide you closer to lasting happiness. (shrink)

Tomorrow has never looked better. Breakthroughs in fields like genetic engineering and nanotechnology promise to give us unprecedented power to redesign our bodies and our world. Futurists and activists tell us that we are drawing ever closer to a day when we will be as smart as computers, will be able to link our minds telepathically, and will live for centuries--or maybe forever. The perfection of a "posthuman" future awaits us. Or so the story goes. In reality, the rush toward (...) a posthuman destiny amounts to an ideology of human extinction, an ideology that sees little of value in humanity except the raw material for producing whatever might come next. In Eclipse of Man, Charles T. Rubin traces the intellectual origins of the movement to perfect and replace the human race. He shows how today's advocates of radical enhancement are--like their forebears--deeply dissatisfied with given human nature and fixated on grand visions of a future shaped by technological progress. Moreover, Rubin argues that this myopic vision of the future is not confined to charlatans and cheerleaders promoting this or that technology: it also runs through much of modern science and contemporary progressivism. By exploring and criticizing the dreams of post humanity, Rubin defends a more modest vision of the future, one that takes seriously both the limitations and the inherent dignity of our given nature. (shrink)

Analysts such as Steven Horwitz, with strong prior beliefs, are seldom impressed by mere fact and tend to explain away empirical deviations from their theories. The belief that markets are moved only by fundamentals and not by occasional faddism and overshooting rests on the assumption that market participants form their opinions independently, when in fact they are from time to time driven by emulation. The belief that markets are rational and well?informed but government officials and central bankers incompetent is implausible (...) on its face. The period since 1970 has seen bubble after bubble, some of which seemed likely to lead to financial crisis had it not been for the Federal Reserve. (shrink)