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)

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)

Whether firms can be said to be moral agents and to have the capacity for moral responsibility has significant practical consequences. In most legal systems in the world, business firms are recognized as persons with the ability to own property, to maintain and defend lawsuits, and to self-organize governance structures. To recognize that these business persons can also act morally or immorally as organizations, however, would justify the imposition of other legal constraints and normative expectations on organizations. In the criminal (...) law, for example, the idea that an organized firm may itself have criminal culpability is accepted in many countries (such as the United States) but rejected in others (such as Germany). This book collects new contributions by leading business scholars in business ethics, philosophy, and related disciplines to extend our understanding of the moral responsibility of firms. (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)

From the time of Locke, discussions of personal identity have often ignored the question of our basic metaphysical nature: whether we human people are biological organisms, spatial or temporal parts of organisms, bundles of perceptions, or what have you. The result of this neglect has been centuries of wild proposals and clashing intuitions. What Are We? is the first general study of this important question. It beings by explaining what the question means and how it differs from others, such as (...) questions of personal identity and the mind-body problem. It then examines in some depth the main possible accounts of our metaphysical nature, detailing both their theoretical virtues and the often grave difficulties they face. The book does not endorse any particular account of what we are, but argues that the matter turns on more general issues in the ontology of material things. If composition is universal--if any material things whatever make up something bigger--then we are temporal parts of organisms. If things never compose anything bigger, so that there are only mereological simples, then we too are simples--perhaps the immaterial substances of Descartes--or else we do not exist at all (a view Olson takes very seriously). The intermediate view that some things compose bigger things and others do not leads almost inevitably to the conclusion that we are organisms. So we can discover what we are by working out when composition occurs. (shrink)

Consider the following three claims. (i) There are no truths of the form ‘p and ~p’. (ii) No one holds a belief of the form ‘p and ~p’. (iii) No one holds any pairs of beliefs of the form {p, ~p}. Irad Kimhi has recently argued, in effect, that each of these claims holds and holds with metaphysical necessity. Furthermore, he maintains that they are ultimately not distinct claims at all, but the same claim formulated in different ways. I find (...) his argument suggestive, if not entirely transparent. I do think there is at least an important kernel of truth even in (iii), and that (i) ultimately explains what’s right about the other two. Consciousness of an impossibility makes belief in the obtaining of the corresponding state of affairs an impossibility. Interestingly, an appreciation of this fact brings into view a novel conception of inference, according to which it consists in the consciousness of necessity. This essay outlines and defends this position. A central element of the defense is that it reveals how reasoners satisfy what Paul Boghossian calls the Taking Condition and do so without engendering regress. (shrink)

Concepts: Core Readings traces the develoment of one of the most active areas of investigation in cognitive science. This comprehensive volume brings together the essential background readings on concepts from philosophy, psychology, and linguistics, while providing a broad sampling of contemporary research. The first part of the book centers around the fall of the Classical Theory of Concepts in the face of attacks by W.V.O. Quine, Ludwig Wittgenstein, Eleanor Rosch, and others, emphasizing the emergence and development of the Prototype Theory (...) and the controversies it spurred. The second part surveys a broad range of contemporary theories—Neoclassical Theories, the Prototype Theory, the Theory-Theory, and Conceptual Atomism. (shrink)

I argue that to have an attitude is, primarily, (1.) to have a dispositional profile that matches, to an appropriate degree and in appropriate respects, a stereotype for that attitude, typically grounded in folk psychology, and secondarily, (2.) in some cases also to meet further stereotypical attitude-specific conditions. To have an attitude, on the account I will recommend here, is mainly a matter of being apt to interact with the world in patterns that ordinary people would regard as characteristic of (...) having that attitude. I contrast this view with alternative views that treat having an attitude as a matter of possessing some particular internally stored representational content or some other "deep" structural feature. (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)

Rationalization, in our intended sense of the term, occurs when a person favors a particular conclusion as a result of some factor (such as self-interest) that is of little justificatory epistemic relevance, if that factor then biases the person’s subsequent search for, and assessment of, potential justifications for the conclusion. Empirical evidence suggests that rationalization is common in people’s moral and philosophical thought. We argue that it is likely that the moral and philosophical thought of philosophers and moral psychologists is (...) also pervaded by rationalization. Moreover, although rationalization has some benefits, overall it would be epistemically better if the moral and philosophical reasoning of people, including professional academics, were not as heavily influenced by rationalization as it likely is. We discuss the significance of our arguments for cognitive management and epistemic responsibility. (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)

We present evidence that mainstream Anglophone philosophy is insular in the sense that participants in this academic tradition tend mostly to cite or interact with other participants in this academic tradition, while having little academic interaction with philosophers writing in other languages. Among our evidence: In a sample of articles from elite Anglophone philosophy journals, 97% of citations are citations of work originally written in English; 96% of members of editorial boards of elite Anglophone philosophy journals are housed in majority-Anglophone (...) countries; and only one of the 100 most-cited recent authors in the Stanford Encyclopedia of Philosophy spent most of his career in non-Anglophone countries writing primarily in a language other than English. In contrast, philosophy articles published in elite Chinese-language and Spanish-language journals cite from a range of linguistic traditions, as do non-English-language articles in a convenience sample of established European-language journals. We also find evidence that work in English has more influence on work in other languages than vice versa and that when non-Anglophone philosophers cite recent work outside of their own linguistic tradition it tends to be work in English. (shrink)

Unconscious logical inference seems to rely on the syntactic structures of mental representations (Quilty-Dunn & Mandelbaum 2018). Other transitions, such as transitions using iconic representations and associative transitions, are harder to assimilate to syntax-based theories. Here we tackle these difficulties head on in the interest of a fuller taxonomy of mental transitions. Along the way we discuss how icons can be compositional without having constituent structure, and expand and defend the “symmetry condition” on Associationism (the idea that associative links and (...) transitions are perfectly symmetric). In the end, we show how a BIT (“bare inferential transition”) theory can cohabitate with these other non-inferential mental transitions. (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)

Philosophers tend to be pretty impressed by human self-knowledge. Descartes (1641/1984) thought our knowledge of our own stream of experience was the secure and indubitable foundation upon which to build our knowledge of the rest of the world. Hume – who was capable of being skeptical about almost anything – said that the only existences we can be certain of are our own sensory and imagistic experiences (1739/1978, p. 212). Perhaps the most prominent writer on self-knowledge in contemporary philosophy is (...) Sydney Shoemaker. The central aim of much of his work has been to show that certain sorts of error are impossible (1963, 1988, 1994). David Chalmers has likewise attempted to show that, for a suitably constrained class of beliefs about one’s own consciousness, error is impossible (2003, sec. 4.1). Even philosophers most of the community thinks of as pessimistic about self-knowledge of consciousness seem to me, really, to be fairly optimistic. Paul Churchland, famous for his disdain of ordinary people’s knowledge about the mind, compares the accuracy of introspection to the accuracy of sense perception – pretty good, presumably, about medium-sized, nearby matters (1985, 1988). Dan Dennett, often cited as a pessimist about introspective report, actually says that we can come close to infallibility when charitably interpreted (2002). The above references concern knowledge of the stream of conscious experience, but philosophers have also tended to be impressed with our self-knowledge of our attitudes, such as our beliefs and desires. Consider this: Although I can be wrong about its being sunny outside, I can’t in the same way be wrong, it seems, about the fact that I think it’s sunny outside. Some.. (shrink)

In On Empirically Equivalent Systems of the World from 1975, Quine formulated a thesis of underdetermination roughly to the effect that every scientific theory has an empirically equivalent but logically incompatible rival, one that cannot be discarded merely as a terminological variant of the former. For Quine, the truth of this thesis was an open question. If true, some would argue that it undermines any belief in scientific theories that is based purely on their empirical success. But despite its potential (...) significance, surprisingly little has been done by way of establishing or refuting it. My aim is to establish the thesis for as large a class of theories as possible. Under various precisifications of the concepts involved, I show that it holds for all consistent and recursively axiomatizable theories that postulate infinitely many theoretical entities. (shrink)

On an intellectualist approach to belief, the intellectual endorsement of a proposition (such as “The working poor deserve as much respect as the handsomely paid”) is sufficient or nearly sufficient for believing it. On a pragmatic approach to belief, intellectual endorsement is not enough. Belief is behaviorally demanding. To really, fully believe, you must also “walk the walk.” This chapter argues that the pragmatic approach is preferable on pragmatic grounds: It rightly directs our attention to what matters most in thinking (...) about belief. (shrink)

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)

Eric Martin and Daniel N. Osherson present a theory of inductive logic built on model theory. Their aim is to extend the mathematics of Formal Learning Theory to a more general setting and to provide a more accurate image of empirical inquiry. The formal results of their study illuminate aspects of scientific inquiry that are not covered by the commonly applied Bayesian approach.

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)

Can large language models produce expert‐quality philosophical texts? To investigate this, we fine‐tuned GPT‐3 with the works of philosopher Daniel Dennett. To evaluate the model, we asked the real Dennett 10 philosophical questions and then posed the same questions to the language model, collecting four responses for each question without cherry‐picking. Experts on Dennett's work succeeded at distinguishing the Dennett‐generated and machine‐generated answers above chance but substantially short of our expectations. Philosophy blog readers performed similarly to the experts, while ordinary (...) research participants were near chance distinguishing GPT‐3's responses from those of an “actual human philosopher”. (shrink)

Once again available in paperback, Plato is the first half of Eric Voegelin's Plato and Aristotle, the third volume of his five-volume Order and History, which ...

In this book, Eric Havelock presents a challenging account of the development of the idea of justice in early Greece, and particularly of the way justice changed as Greek oral tradition gradually gave way to the written word in a literate society. He begins by examining the educational functions of poets in preliterate Greece, showing how they conserved and transmitted the traditions of society, a thesis adumbrated in his earlier book Preface to Plato. Homer, he demonstrates, has much to (...) say about justice, but since that idea is nowhere in the epics directly stated or expressed, it must be deduced from the speech and actions of the characters. Havelock's careful reading of the Iliad and the Odyssey is original and revealing; it sheds light both on Homeric notions of justice and on the Archaic Greek society depicted in the poems. As Havelock continues his inquiry from Hesiod to Aeschylus, his findings become more complex. The oral Greek world shades into a literate one. Words lose some kinds of meanings, gain others, and steadily become more suited to the conceptualization that Plato strove for and achieved. This evolution of language itself, Havelock shows, was one of the principal accomplishments of the Greek world. Lucidly written and forcefully argued, this book is a major contribution to our knowledge of ancient Greece--its politics, philosophy, and literature, from Homer to Plato. (shrink)

One big question in biology is what life is, but another is how life divides into living things. This is the problem of biological individuality. Proposed statements of the problem have been vague and incomplete. And proposed theories of biological individuality are not detailed enough to solve the problem even if they are correct. The root of these troubles is that their authors have not recognized the metaphysical claims presupposed in their statement of the problem. Making these claims explicit will (...) enable us to see better what the problem is and what form a solution to it would need to have. (shrink)

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

Trust me: my chair isn't big enough for two. You may doubt that every rational, conscious being is a person; perhaps there are beings that mistakenly believe themselves to be people. If so, read ‘rational, conscious being’ or the like for 'person'.

Preface -- Introduction -- How to value democracy -- Paper stones, the ethics of participation -- Philosophers-citizens -- Superdeliberators -- What is it like to be a citizen? -- Democracy's ethics of belief -- The division of democratic labor -- Representing principles -- Democratic complicity -- Not in my name, macrodemocratic design.

Introduction -- Sanctioning models : theories and their scope -- Methodology for a virtual world -- A tale of two methods -- When theories shake hands -- Models of climate : values and uncertainties -- Reliability without truth -- Conclusion.

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)