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)

This chapter contains sections titled: Sartre's Life Early Phenomenological Works Phenomenological Ontology: Being and Nothingness Phenomenological Marxism Conclusion.

In lieu of an abstract, here is a brief excerpt of the content:Camus’s Meursault and Sartrian IrresponsibilityDavid ShermanIn the wake of poststructuralism, with its glorification of the libidinal play of unaccountable, fragmented subjectivities, the concept of personal responsibility has been rehabilitated. From the French fascination with various forms of neo-Kantianism to the American interest in homey (albeit demagogic) books on the virtues, personal responsibility is regaining currency. But what, exactly, does it mean to be personally responsible? When Albert Camus suggested (...) in “Neither Victims Nor Executioners” that non-violence was the “responsible” position for intellectuals to take on the Algerian crisis, he was reproached for legalistically evading responsibility by his erstwhile friend Jean-Paul Sartre. Sartre, who offered up the concept of “absolute responsibility,” and viewed any attempt to obscure the nature of this ontological burden for oneself as “bad faith,” regarded Camus’s position as just such an attempt: “If you’re not victims when the government which you voted for, when the army in which your younger brothers are serving... have undertaken race murder, you are, without a shadow of a doubt, executioners.” 1 For Sartre, who tentatively advocated revolutionary violence, taking responsibility meant acknowledging that “bloodying one’s hands” is unavoidable.The concept of personal responsibility is well considered within the context of French existentialism, which made it one of its hallmarks. In this essay, however, I shall approach personal responsibility from the vantage point of its opposite, personal irresponsibility. Towards this end, I shall consider Meursault, the protagonist in Camus’s The Stranger, whom I take to be one of the most irresponsible characters in literature. The depths of Meursault’s irresponsibility can best be appreciated, fittingly enough, within Sartre’s psychoanalytic framework. [End Page 60]IIn Being and Nothingness, Sartre offers up the ontologically rooted phenomenon of bad faith, which, for present purposes, can be explicated as follows: consciousness, which is intentional (nothing more than that which it is conscious of), reflectively reconstitutes the Self, which does not exist in consciousness but as an object in the external world. There is no intrinsic Self, and the Self that does exist is perpetually being transcended. Despite this state of unremitting transcendence, however, at any point in time there are the undeniable facts of our particular existences, which (however we choose to interpret them) define the range of our possible projects. These brute facts, which are inexorable, constitute our facticity. Thus, Sartre tells us, there is a “double property of the human being, who is at once a facticity and a transcendence” (B&N, p. 98). 2 It is in a person’s approach to the relationship between these two properties, which is marked by an irresolvable tension, that bad faith arises: “Bad faith does not wish either to coordinate them or to surmount them in a synthesis. Bad faith seeks to affirm their identity while preserving their differences. It must affirm facticity as being transcendence and transcendence as being facticity, in such a way that at the instant when a person apprehends the one, he can find himself abruptly faced with the other” (B&N, p. 98).Sartre provides numerous illustrations of individuals who flee from either their facticity or transcendence. For example, there is the homosexual and his interlocutor, the “champion of sincerity.” The former, despite repeated homosexual encounters, refuses to draw the conclusion that he is a homosexual; instead, he sees both his past behavior and his present inclinations as part of a “restless search.” Conversely, the latter demands that the homosexual sincerely avow what he is, “a homosexual.” Both are in bad faith. The homosexual denies responsibility for all that he has done by perpetually pushing his conception of Self into the future, and thus perpetually beyond the reach of his ability to make judgments about himself—he makes a mockery of his past and present choices. The champion of sincerity, on the other hand, pushes the homosexual’s conception of Self into the past in order to make it a thing—he denies the homosexual’s (and perhaps his own) freedom to make future choices, which is what enables us to transcend what we presently are. The former flees facticity; the latter, transcendence.All persons in bad faith fall... (shrink)

Paul Weiss continues the brilliant analysis of art he began in _The World of Art _and _Nine Basic Arts_—here_ _in the medium of film, at which he takes a close and inde­pendent look. Writing in a vigorous, jargon-free style, and covering all aspects of films and film making, Mr. Weiss presents a fresh, new approach to the study of our newest art. During the course of writing _Cinematics_,_ _Mr. Weiss asked various writers, critics, scholars, and producers long involved with (...) film to read and remark on what he had written. Five of them—Eric Sherman, Joseph Williman, Arthur Knight, David Slavitt, and Robert Thom—provided comments which are incorporated in the text. Their remarks are often trenchant, and perceptively provocative. These men frequently comment on lines of inquiry suggested in the book and often take issue with what has been said. The result is a kind of dialogue crisscrossed with stimu­lating insights. While this book is aimed at the general reader, Mr. Weiss hopes that experts and practitioners of film making will benefit from this fresh, independent, and philo­sophically based inquiry. Readers already familiar with Mr. Weiss’s writings will delight in this distillation of his thought on an art so intimately a part of our cul­ture. (shrink)

This useful, introductory guide to Continental philosophy is another fine volume within the Blackwell Philosophy Guides series, whose editor is Steven M. Cahn. Robert Solomon teaches business and philosophy at the University of Texas at Austin, and David Sherman teaches philosophy at the University of Montana–Missoula.

Jeremy Sherman distills Terrence Deacon's breakthrough natural science hypothesis for the emergence of agents and agency, selves and aims in an otherwise aimless universe. The theory cuts a new path through the dualistic spirit vs. mechanism debate, unifying the hard and soft sciences and suggesting new solutions to philosophical mysteries.

Moral emotions are evolved mechanisms that function in part to optimize social relationships. We discuss two moral emotions— disgust and the “cuteness response”—which modulate social-engagement motives in opposite directions, changing the degree to which the eliciting entity is imbued with mental states (i.e., mentalized). Disgust-inducing entities are hypo-mentalized (i.e., dehumanized); cute entities are hyper-mentalized (i.e., “humanized”). This view of cuteness—which challenges the prevailing view that cuteness is a releaser of parental instincts (Lorenz, 1950/1971)—explains (a) the broad range of affiliative behaviors (...) elicited by cuteness, (b) the marketing of cuteness to children (by toy makers and animators) to elicit play, and (c) the apparent ease and frequency with which cute things are anthropomorphized. (shrink)

RésuméL'authenticité et la diversité font aujourd'hui figure de slogans dans les sociétés contemporaines de part et d'autre de l'Atlantique nord. En revanche, on a peu exploré les liens entre ces deux idées. À cette fin, cet article aborde les écrits tantôt convergents, tantôt divergents de Charles Taylor et Martin Heidegger pour prolonger leurs réflexions respectives sur l'authenticité et montrer en quoi elles peuvent servir defondement à une nouvelle forme de diversité culturelle. Pour tous deux, l'être-au-monde authentique nous permet d'accider au (...) tréfonds du matériel culturel dont nous devons disposer pour que se nouent des rapports fructueux avec les autres cultures. (shrink)

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work.This work is in the public domain in (...) the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work.As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Even among scholars who emphasize Nietzsche’s naturalism (“the naturalists”), what it actually involves is disputed. This article identifies the foundations of Nietzsche’s naturalism and then elaborates on these foundations through a critical analysis of the works of those naturalists who also identify them. Nietzsche is a methodological naturalist, who, epistemically, is a reliabilist, and while he acknowledges the innate limitations of our cognitive inheritance, which is reflected in his perspectivism, he sees no reason to conclude that we cannot grasp the (...) natural world truly. As to the primary issue in scientific explanation, causation, Nietzsche adopts a regularity theory as early as The Gay Science, and, on the basis of this theory, rejects determinism. One consequence of this analysis is that Nietzsche’s naturalism is not as restrictive as the naturalists tend to portray it, and this opens up new possibilities for interpreting many of his other commitments. (shrink)

This book develops an original and comprehensive theory of political liberalism. It defends bold new accounts of the nature of autonomy and individual liberty, the content of distributive justice, and the justification for the authority of the State. The theory that emerges integrates contemporary progressive and pluralistic liberalism into a broadly Aristotelian intellectual tradition. The early chapters of the book challenge the traditional conservative idea of individual liberty-the liberty to dispose of one's property as one wishes-and replace it with a (...) new one, according to which liberty is of equal value to all persons, regardless of economic position. The middle chapters present an original theory of socio-economic justice, arguing that a society in which every citizen enjoys an equal share of liberty should be the distributive goal of the State. It is argued that this goal is incompatible with the existence of large disparities in wealth and economic power, and that (contra conservative and libertarian economic arguments) such disparities are harmful to the overall health of national and global economies. The final chapters provide an original argument that the State has both a moral duty and a moral right to pursue this program of socio-economic justice (contra conservative and libertarian moral arguments), and that only the measures necessary to implement this program lie within the morally justifiable limits on the State's authority. Though primarily a political work, it spans most areas of practical philosophy-including ethical, social, and legal theory; and meta-ethics, moral psychology, and action theory. And though fundamentally a philosophical work, it incorporates research from a number of fields-including decision theory, economics, political science, and jurisprudence; primatology, neuroscience, and psychology; and history, anthropology, sociology, and ecology-and is sure to be of interest to a wide range of scholars and students. (shrink)

The essential guide to understanding what literary theory is and why it matters.

The Equal Weight View holds that, when we discover we disagree with an epistemic peer, we should give our peer’s judgment as much weight as our own. But how should we respond when we cannot tell whether those who disagree with us are our epistemic peers? I argue for a position I will call the Earn-a-Spine View. According to this view, parties to a disagreement can remain confdent, at least in some situations, by fnding justifable reasons to think their opponents (...) are less credible than themselves, even if those reasons are justifable only because they lack information about their opponents. (shrink)

Exploring the meeting of mystical and philosophical theology, Partakers of the Divine shows that Christian philosophical and contemplative practices arose together and that throughout much of Christian history, philosophy, theology and contemplation remained internal to one another. In this compelling volume, Jacob Holsinger Sherman demonstrates that the relation of philosophy, theology and contemplation to one another provides theologians and philosophers of religion today with a way forward beyond many of the stalemates that have beset discussions about faith and reason, (...) the role of religion in contemporary culture, and the challenges of modernity and postmodernity"--Page 4 of cover. (shrink)

Journal Name: Cognitive Linguistics Issue: Ahead of print.

Understanding Literary Theory is the essential guide for every reader looking to understand what literary theory is and why it matters. This concise and accessible text introduces today's foremost schools of literary theory, offering historical background and outlining the important ideas of each. The theories are then applied to a variety of classic short stories, demonstrating how the different theoretical approaches can yield diverse interpretations of the same literary works. This volume separates itself from similar texts by providing clear and (...) accurate explanations of theory's most challenging concepts. It examines all of the major schools of criticism, including ecocriticism, ethnic studies, feminism, formalism, Marxism, narratology, new historicism, postcolonialism, postmodernism, post-structuralism, psychoanalysis, queer theory, reader response, and structuralism. Each chapter begins with a straightforward summary that outlines the focus of the theoretical approach, its notable practitioners, its advantages and disadvantages, and a concise definition. The chapters then delve into each theory by explaining the key concepts and the ideas that led to them. This book is indispensable for anyone intimidated by words like deconstruction, differance, heteroglossia or hyperreality. Understanding Literary Theory shows readers the interpretative possibilities that literary theory can provide. It is the ideal introduction for those who want to get the most out of the literature they read. (shrink)

While Aristotle in the Nicomachean Ethics does not provide a guide for action in the form of rules for a decision process as deontological or consequentialistethical theories purport to do, he does present a description of the virtuous agent and the virtues that this agent exercises in his choices of action. In this paper Iargue that Aristotle’s mature virtuous agent characteristically exercises the virtue of wisdom (sophia) as well as the practical virtues of character and intelligence in his choices of (...) action and that students of virtue (those sincerely interested in becoming virtuous by acting as the virtuous agent does) can derive certain action-guiding rules from a description of these three virtues and how they are exercised by the mature virtuous agent in any given choice of action. (shrink)

Ever since Max Weber started an argument about the role of Protestantism in jump-starting northern Europe's economic development, scholars have clashed over the influence of religion and culture on a society's economic prospects. Today, many wonder whether the "explosion" of Protestantism in Latin America will effect a similar wave of growth and democratization. In this book, Sherman compiles the results of her field study and national survey of 1000 rural Guatemalan households. She offers persuasive evidence that, in Guatemala and (...) throughout the region, religious world-views significantly influence economic life. Sherman explains how the change in attitude and behavior that accompanies conversion from animism to a Biblically orthodox world-view has improved the domestic welfare and economic status of many families. Further, she asserts that this new attitude, sympathetic to democratic-capitalism, has created a "moral cultural soil" in which freedom, personal empowerment, an enhanced status for women, and a desire to get ahead can be nurtured. (shrink)

In some previous work, I tried to give a concept-based account of the nature of our entitlement to certain very basic inferences (see the papers in Part III of Boghossian 2008b). In this previous work, I took it for granted, along with many other philosophers, that we understood well enough what it is for a person to infer. In this paper, I turn to thinking about the nature of inference itself. This topic is of great interest in its own right (...) and surprisingly understudied by philosophers. A correct understanding of inference promises to shed light on a number of important topics. In particular, it threatens to undermine the sort of concept-based story about entitlement to which I had previously been attracted. (shrink)

This chapter contains sections titled: Life Before the Fall A Short Pre‐History of the Absurd Camus's Absurd Problematic One Giant Leap Back, One Small Step Forward: the Problem of Meaning Camus's Existential Phenomenology Camus's Sisyphean Ethics The Myth of Sisyphus notes further reading.