The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (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)

For historical epistemology to succeed, it must adopt a defensible set of categories to characterise scientific activity over time. In historically orientated philosophy of science during the twentieth century, the original categories of theory and observation were supplemented or replaced by categories like paradigm, research program and research tradition. Underlying all three proposals was talk about conceptual systems and conceptual structures, attributed to individual scientists or to research communities, however there has been little general agreement on the nature of these (...) structures. Recent experimental research in cognitive science has considerably refined the theory of concepts. Drawing upon the results of that research, philosophers can construct more concrete and empirically defensible representations of conceptual systems. I will suggest that this research supports a modest and useful sense of both normal and revolutionary science, not as epistemological continuities or discontinuities, but as particular patterns of conceptual change. (shrink)

Can hybridism about moral claims be made to work? I argue it can if we accept the conventional implicature approach developed in Barker (Analysis 2000). However, this kind of hybrid expressivism is only acceptable if we can make sense of conventional implicature, the kind of meaning carried by operators like ‘even’, ‘but’, etc. Conventional implictures are a form of pragmatic presupposition, which involves an unsaid mode of delivery of content. I argue that we can make sense of conventional implicatures, (...) but doing so requires we embrace a form of pure, non-hybrid expressivism. This is a cognitivist expressivism I have developed elsewhere. We need cognitivist expressivism to make sense of how we evaluate—judge as correct or incorrect—implicature-bearing sentences. Once we embraced the possibility of this pure expressivism, we might as well be pure expressivists about normative discourse too. I show how we can do that. The motivations for a specifically hybrid theory are dialectically undercut. (shrink)

Combining a Nietzschean framework with close attention to a wide range of carefully selected literary texts, Autoaesthetics presents a case for Nietzche's centrality in contemporary aesthetic and literary studies. Based on Nietzche's own practice of combining poetry and philosophy by transcending ressentiment and approaching life to its fullest, Autoaesthetics engages in a heated but intricate debate through and with Nietzche's re-articulation of the self as a strategic (and impossible) aesthetic creation." "Stephen Barker argues that all notions of self are (...) aesthetic, literary, strategic, and teleological, and must be seen not in the context of any essential self but as a complex series of self-articulations. He sets out a strategy of reading that combines Nietzschean "psychology" with subsequent theoretical investigations and shows how Nietzschean dialectics of the self are at work in all (self-defining) human experience in the (post)modern world. His book itself is a play of dialectics (again after Nietzche), designed for interdisciplinary scholars and graduate students interested in exploring the scope of literary and aesthetic theory and philosophy. (shrink)

Tragedy and Citizenship provides a wide-ranging exploration of attitudes toward tragedy and their implications for politics. Derek W. M. Barker reads the history of political thought as a contest between the tragic view of politics that accepts conflict and uncertainty, and an optimistic perspective that sees conflict as self-dissolving. Drawing on Aristotle's political thought, alongside a novel reading of the Antigone that centers on Haemon, its most neglected character, Barker provides contemporary democratic theory with a theory of tragedy. (...) He sees Hegel's philosophy of reconciliation as a critical turning point that results in the elimination of citizenship. By linking Hegel's failure to address the tragic dimensions of politics to Richard Rorty, John Rawls, and Judith Butler, Barkeroffers a major reassessment of contemporary political theory and a fresh perspective on the most urgent challenges facing democratic politics. Derek W. M. Barker is a program officer at the Kettering Foundation. (shrink)

Despite the burgeoning interest in new and more complex accounts of the organism-environment dyad by biologists and philosophers, little attention has been paid in the resulting discussions to the history of these ideas and to their deployment in disciplines outside biology—especially in the social sciences. Even in biology and philosophy, there is a lack of detailed conceptual models of the organism-environment relationship. This volume is designed to fill these lacunae by providing the first multidisciplinary discussion of the topic of organism-environment (...) interaction. It brings together scholars from history, philosophy, psychology, anthropology, medicine, and biology to discuss the common focus of their work: entangled life, or the complex interaction of organisms and environments. (shrink)

Drugs targeting a single TK/RTK in the treatment of solid cancers has not had the same success seen in blood cancers. This is, in part, due to acquired resistance in solid cancers arising from a range of mechanisms including the upregulation of compensatory RTK signalling. Rather than attempting to inhibit individual compensatory RTK—requiring knowledge of which RTKs are upregulated in any given tumour—strategies to universally inhibit signalling from multiple RTKs may represent an effective alternative. Endosomal trafficking of RTKs is a (...) common conduit that can regulate signalling from multiple RTKs simultaneously. As such, we posit that targeting endosomal trafficking—in particular, aberrant post‐translational modifications in cancers that contribute to dysregulated endosomal trafficking—could inhibit oncogenic signalling driven by multiple RTKs and pave the way for the development of a novel class of inhibitors that shift the trafficking of RTKs to inhibit tumour growth. (shrink)

The view that it is better for life to be created free of disability is pervasive in both common sense and philosophy. We cast doubt on this view by focusing on an influential line of thinking that manifests it. That thinking begins with a widely-discussed principle, Procreative Beneficence, and draws conclusions about parental choice and disability. After reconstructing two versions of this argument, we critique the first by exploring the relationship between different understandings of well-being and disability, and the second (...) by more briefly focusing on the idea of a significant reason. By placing these results against the broader historical and ongoing contexts in which the lives of those with disabilities have been deemed of inferior quality, we conclude with a call for greater humility about disability and well-being in thought and practice. (shrink)

Every thinking person wants to lead a life of meaning and purpose. For thousands of years, holy books have told us that such a life is available only through obedience and submission to some higher power. Today, the faithful keep popular devotionals and tracts within easy reach on bedside tables and mobile devices, all communicating this common message: "Life is meaningless without God." In this volume, former pastor Dan Barker eloquently, powerfully, and rationally upends this long-held belief. Offering words (...) of enrichment, emancipation, and inspiration, he reminds us how millions of atheists lead happy, loving, moral, and purpose-filled lives. Practicing what he preaches, he also demonstrates through his own personal journey that life is valuable for its own sake--that meaning and purpose come not from above, but from within. (shrink)

Are the sculpture and the mass of gold which permanently makes it up one object or two? In this article, we argue that the monist, who answers ‘one object’, cannot accommodate the asymmetry of material constitution. To say ‘the mass of gold materially constitutes the sculpture, whereas the sculpture does not materially constitute the mass of gold’, the monist must treat ‘materially constitutes’ as an Abelardian predicate, whose denotation is sensitive to the linguistic context in which it appears. We motivate (...) this approach in terms of modal analyses of material constitution, but argue that ultimately it fails. The monist must instead accept a deflationary, symmetrical use of ‘materially constitutes’. We argue that this is a serious cost for her approach. (shrink)

All over the globe, in both Western and Eastern traditions, philosophers have searched for answers to lifeʼs fundamental questions. Beginning with the Ancient Greeks and Chinese, through the founders of modern philosophy, to modern times, they have inspired legions of followers, some have generated fear, and many have made such an impact as to alter the course of history.\\Discover the life and work of more than 100 philosophers. Find out where and when they lived, review their accomplishments, and understand how (...) they transformed our world.\\An essential guide to 2,500 years of philosophical endeavor. \Learn about ancient philosophy, medieval philosophy, the foundations of modern philosophy, philosophy in Britain and America, Continental philosophy, and Eastern philosophy. \See philosophers in the context of their times.\Includes highlights of each philosopherʼs life and work, and an analysis of their contribution and legacy. (shrink)

This paper discusses the normative structure of principles that require belief-revision in the face of disagreement, the role of self-trust in our epistemic lives, and the tensions that arise between the two. Section 2 argues that revisionary principles of disagreement share a general normative structure such that they prohibit continued reliance upon the practices via which one came to hold the beliefs under dispute. Section 3 describes an affective mode of epistemic self-trust that can be characterised as one’s having an (...) attitude of optimism about the reliability of the practices via which one forms beliefs. The availability of affective self-trust is crucial to being able to rationally resist doubts about those practices. However, as argued in the final section of the paper, following revisionary principles of disagreement can render such trust psychologically unavailable. Consequently, attempts to follow such principles can have doxastic consequences that predictably exceed their normative implications. (shrink)

English ethologist, evolutionary biologist, and writer Richard Dawkins opens Chapter 2 of his bestseller The God Delusion by saying that the God of the Old Testament is "arguably the most unpleasant character in all fiction" and goes on to list nineteen negative character traits. Now in God : the Most Unpleasant Character in All Fiction, Dan Barker, a former ordained minister and current atheist, proves that Dawkins was right."--Jacket.

We argue that in contemporary business organizations, in which fundamental purpose is construed to be increased value—especially in ‘participative’ organizations, in which non–hierarchal interaction (for example, work teams) is the norm; and in ‘adaptive’ organizations, in which unpredictable change is the rule—a process of values covenanting will be much more valueable than just espoused values or even values covenants. We propose such a process model for organizational values covenanting and argue that such covenanting reflects an anthropomorphism of the human character (...) development process, validated in terms of the theory of viable systems. (shrink)

Against Transmission introduces the technical history and phenomenology of media, a field of study that explains the characteristics of contemporary life by looking to the technical properties of machines. By studying the engineering of signal processing, the book interrogates how the understanding of media-as-machine exposes us to a particular phenomenological relationship to the world, asking: what can the hardware of machines that segment information into very small elements tell us about experiences of time, memory and history? This book offers both (...) a detailed and radical investigation of the technical architecture of media such as television, computers, cameras, and cinematography. It achieves this through in-depth archive research into the history of the development of media technology, combined with innovative readings of key concepts from philosophers of media such as Harold A. Innis, Marshall McLuhan, Friedrich Kittler, Siegfried Zielinski and Wolfgang Ernst. Teaming philosophical inquiry with thorough technical and historical analysis, in a broad range of international case studies, from early experimental cinema and television to contemporary media art and innovative hardware developments, Barker shows how the technical discoveries made in these contexts have engineered the experiences of time in contemporary media culture. (shrink)

For over 40 years, Andrew Barker has been studying the ways in which ancient Greek philosophers, scientists and others analysed and discussed the structures underlying musical compositions; he has focused, in particular, on their methodologies, the conceptual frameworks within which their analyses were formed, and the various philosophical commitments they brought to their work. This volume contains a selection of the essays that Barker has published on these and related topics. The essays are preceded by an English version (...) of his book on 'psychomusicology', previously published only in Italian. It examines Greek writers' diverse and often influential speculations about correlations between musical structures and their counterparts in the soul, speculations which led them to striking conclusions about music's practical value in human affairs, and to recommendations for appropriate ways of employing it in such fields as, for example, moral education, psychotherapy, and the organization and governance of a healthy society. (shrink)

Living things are often plastic during their early development and are moulded by the environment. Many human fetuses have to adapt to a limited supply of nutrients, and in doing so they permanently change their physiology and metabolism. These programmed changes may be the origins of a number of diseases in later life, including coronary heart disease, stroke, diabetes and hypertension.

Aristocracy of sex -- Industrial aristocracy -- Expertocracy -- Mass and elite politics -- Democratic religion.

Do we have free will? And if we don't, why do we think we do? Scientists and philosophers have been battling with this issue for years. In this book, a former Christian minister who is now an internationally recognized authority on atheism addresses these questions."--Page 2 of cover.

Moral minds -- Fear morality -- Humanistic morality.

The Politics is one of the most influential texts in the history of political thought, and it raises issues which still confront anyone who wants to think seriously about the ways in which human societies are organized and governed. By examining the way societies are run--from households to city states--Aristotle establishes how successful constitutions can best be initiated and upheld. For this edition, Sir Ernest Barker's fine translation, which has been widely used for nearly half a century, has been (...) extensively revised to meet the needs of the modern reader. The accessible introduction and clear notes examine the historical and philosophical background of the work and discuss its significance for modern political thought. (shrink)

Some time ago, the editors of Monthly Review invited me to submit a short review of two recent books by Ellen Wood: The Pristine Culture of Capitalism, and Democracy Against Capitalism. I found myself, in the course of re-reading these books, filled with admiration for most of what the author said, and indeed, for the manner in which she presented her case. At various points, however, I found myself not fully satisfied. But a short review was not the place to (...) develop my concerns. (shrink)

Given the increasing need for solid organ and tissue transplants and the decreasing supply of suitable allographic organs and tissue to meet this need, it is understandable that the hope for successful xenotransplantation has resurfaced in recent years. The biomedical obstacles to xenotransplantation encountered in previous attempts could be mitigated or overcome by developments in immunosuppression and especially by genetic manipulation of organ source animals. In this essay we consider the history of xenotransplantation, discuss the biomedical obstacles to success, explore (...) recent developments in transgenic sourcing of organs and tissues, and analyze the problem of infectious disease resulting from xenotransplantation (xenosis). We then apply a model of risk analysis to these risks. The conclusions of this risk analysis are used in an ethical evaluation of informed consent in xenotransplantation, with an ethical foundation in Kantian autonomy and Levinasian heteronomic alterity. Our conclusion is that individual and collective informed consent to the infectious disease risks of xenotransplantation requires an open, participatory and dialogical public policy process not yet seen in the United States and Europe. Until that process is created, we propose caution in xenotransplantation in general and a postponement of solid organ xenotransplants in particular. (shrink)

In this paper I want to examine a view of the Darwinian theory of evolution which was put forward fairly recently by A. R. Manser. His approach is of interest not only in itself, but also because it may be expanded to raise some fundamental questions about the nature of the science of biology in general. I shall not consider these further implications here, but shall concentrate on an examination of his thesis in the context in which it is raised. (...) My paper falls into two sections. In the first I shall state Manser's thesis and some of the arguments with which he supports it, and shall try to show how a series of objections raised by A. G. N. Flew and K. Connolly may be answered. In the second I shall offer on my own account a positive argument to provide a possible basis for his point of view, with the aim of indicating why the theory should be of the kind he suggests, and what form the study of evolution must take. (shrink)

This volume presents new work in history and historiography to the increasingly broad audience for studies of the history and philosophy of science. These essays are linked by a concern to understand the context of early modern science in its own context.

Negative facts get a bad press. One reason for this is that it is not clear what negative facts are. We provide a theory of negative facts on which they are no stranger than positive atomic facts. We show that none of the usual arguments hold water against this account. Negative facts exist in the usual sense of existence and conform to an acceptable Eleatic principle. Furthermore, there are good reasons to want them around, including their roles in causation, chance-making (...) and truth-making, and in constituting holes and edges. (shrink)

This paper addresses the application of the ethical concept of trust and the legal and political concept of public trust to population genomics projects in Iceland, Estonia, and Tonga. Focusing on trust and public trust, the paper explores analogies between the genomics projects and the treatment of other common-pool resources, making use of the notion of trust as an ethical demand, derived from the works of Emmanuel Levinas and Knud Eljer Lgstrup. The paper discusses the degree to which the ethical (...) demands for trust and public trust have been established and maintained in the three national population genomics projects. (shrink)

Are the sculpture and the mass of gold which permanently makes it up one object or two? In this article, we argue that the monist, who answers ‘one object’, cannot accommodate the asymmetry of material constitution. To say ‘the mass of gold materially constitutes the sculpture, whereas the sculpture does not materially constitute the mass of gold’, the monist must treat ‘materially constitutes’ as an Abelardian predicate, whose denotation is sensitive to the linguistic context in which it appears. We motivate (...) this approach in terms of modal analyses of material constitution, but argue that ultimately it fails. The monist must instead accept a deflationary, symmetrical use of ‘materially constitutes’. We argue that this is a serious cost for her approach. (shrink)

Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...) and critique, it remains underdeveloped and is often misrepresented by its critics (section 8). (shrink)

Within recent feminist philosophy, controversy has developed over the desirability, and indeed, the possibility of defining the central terms of its analysis-"woman," "femininity," etc. The controversy results largely from the undertheorization of the notion of definition; feminists have uncritically adopted an Aristotelian treatment of definition as entailing metaphysical, rather than merely linguistic, commitments. A "discursive" approach to definition, by contrast, allows us to define our terms, while avoiding the dangers of essentialism and universalism.

This paper concerns virtue-based ethical principles that bear upon agricultural uses of technologies, such as GM crops and CRISPR crops. It does three things. First, it argues for a new type of virtue ethics approach to such cases. Typical virtue ethics principles are vague and unspecific. These are sometimes useful, but we show how to supplement them with more specific virtue ethics principles that are useful to people working in specific applied domains, where morally relevant domain-specific conditions recur. We do (...) this while still fulfilling the need for principles and associated practical reasoning to flexibly respect variation between cases. Second, with our more detailed approach we criticize and improve upon a commonly discussed principle about ecosystemic external goods that are crucial for human flourishing. We show this principle is far more conservative than appreciated, as it would prohibit many technology uses that are uncontroversially acceptable. We then replace this principle with two more specific ones. One identifies specific conditions in which ecosystem considerations are against a technology use, the other identifies favorable conditions. Third, we uncover a humility-based principle that operates within an influential “hubris argument” against uses of several biotechnologies in agriculture. These arguments lack a substantive theory of the nature of humility. We clarify such a theory, and then use it to replace the uncovered humility-based principle with our own more specific one that shifts focus from past moral failings, to current epistemic limits when deciding whether to support new technologies. (shrink)