The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)
Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)
The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)
The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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)
Translated and edited by Peter D. Arnott, this classic and highly popular edition contains two essential plays in the development of Greek tragedy-_Oedipus the King and Antigone_-for performance and study. The editor's introduction contains a brief biography of the playwright and a description of Greek theater. Also included are a list of principal dates in the life of Sophocles and a bibliography.
A historical perspective on the future of the car Content Type Journal Article Pages 1-3 DOI 10.1007/s11016-010-9479-z Authors Peter D. Norton, Department of Science, Technology and Society, University of Virginia, Charlottesville, VA 22904-4744, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.
This talk by Dr. Peter D. Hershock makes use of Buddhist conceptual resources to assess how the emerging global attention economy and the confluence of big data, machine learning, and artificial intelligence are reshaping the human experience. Like the Copernican revolution, which de-centered humanity in the cosmos, the intelligence revolution is dissolving once-foundational certainties and opening new realms of opportunity. The results are almost sure to be mixed. Smart cities will be more efficient and more livable; smart health care (...) can potentially reach and benefit the half of humanity that now lacks even basic health services. Yet, smart services and the algorithmic tailoring of individual experience have the potential to first supplement and eventually supplant intelligent human practices, rendering human intelligence superfluous. Focusing in particular on the karmic dimensions of these transformations, the talk will consider who we need to be present as in order to resist the allure of digital sirens and direct the intelligence revolution toward a truly equitable and ethical re-centering of the human. (shrink)
The Experiential Therapist steps outside of the medical model to explore alternative ways of thinking about mental health disorders. Peter D. Ladd argues that successful treatment results from an informed understanding of a patient’s experience, not an ability to name and categorize difficult experiences as classical disorders.
Over the last century, the world's urban population increased from 224 million to over 3.5 billion, and advances in manufacturing, transportation, and communication technologies brought virtually limitless lifestyle and identity options, as well as the greatest inequalities of wealth, risk, and opportunity in history. Yet, as momentous as these changes are, they are dwarfed by the fact that human activity is now affecting planetary processes like climate. Justice concerns about future generations are no longer academic curiosities; they are global ethical (...) imperatives. This talk by Dr. Peter D. Hershock builds on recent efforts to craft an ethics of global justice around the "social emotion" of compassion, making use of Buddhist conceptual resources to de-link justice from fictions of equality and conceive it, instead, as a dynamic function of relationally-achieved equity and diversity. (shrink)
This deeply informed book introduces the basic teachings and practices of Buddhism and their spread across Asia. Peter D. Hershock explores the history of the enduring Japanese tradition of Zen—from its beginnings as a form of Buddhist thought and practice imported from China to its reinvention in medieval Japan as a force for religious, political, and cultural change to its role in Japan’s embrace of modernity. He deftly blends historical detail with the felt experiences of Zen practitioners grappling with (...) the meanings of human suffering, personal freedom, and the integration of social and spiritual progress. (shrink)
The issues involved in decision making about the aggressiveness of future medical care for older persons are explored. They are related to population trends, the heterogeneity of older persons and a variety of factors involved in individual preferences. Case studies are presented to illustrate these points, as well as a review of pertinent literature. The argument is offered that, considering these many factors, a system of flexible, individualized care by informed patient preference, is more rational than the rationing of technological (...) services by age. (shrink)
This chapter is offered as a contribution to the logic of down below. We attempt to demonstrate that the nature of human agency necessitates that there actually be such a logic. The ensuing sections develop the suggestion that cognition down below has a structure strikingly similar to the physical structure of quantum states. In its general form, this is not an idea that originates with the present authors. It is known that there exist mathematical models from the cognitive science of (...) cognition down below that have certain formal similarities to quantum mechanics. We want to take this idea seriously. We will propose that the subspaces of von Neumann-Birkhoff lattices are too crisp for modelling requisite cognitive aspects in relation to subsymbolic logic. Instead, we adopt an approach which relies on projections into nonorthogonal density states. The projection operator is motivated from cues which probe human memory. (shrink)
Since 1991, sperm donors in the UK have had the legal right to withdraw consent for the use of their sperm in fertility treatment. This has the potential to adversely affect patients. It may mean that previous recipients of a donor’s sperm cannot have further children who are full biological siblings to an existing child, and that embryos created from the donor’s sperm and a patient’s eggs must be destroyed.
This paper considers the place of the capacity for sense perception in Plato's tripartite soul. It argues, against a common recent interpretation, that despite being a capacity of the soul's appetitive part, sense perception is not independent of the soul's rational capacities. On the contrary, the soul's ability to recognize the content that it receives through sense perception depends upon the objects and the activity of its rational capacities. Defending a position of this sort requires one to suppose that despite (...) its partition, the soul, for Plato, is, with respect to the activities of its various parts, substantially unitary. There are however passages in Plato that suggest that the capacities of the non-rational soul parts, in general, and sense perception, in particular, enjoy a certain degree of autonomy and independence from reason such that they, without the input of reason, can form beliefs about, and act on the basis of, their content. These passages have been read as belying this supposition. In this paper, however, I argue that these passages are perfectly consistent with the idea that the content of the non-rational capacities of the soul depends, for its intelligibility, on the soul's rational capacities. (shrink)
This paper addresses the question of whether, according to Plato, there are forms of sensible qualities; it is also addressed to the wider question of whether there are forms of physical and material things more generally. In particular, it considers the tension raised by the following theses: (1) a Platonic form is the essence of some thing; (2) for Plato, those essences that are forms are imperceptible and are knowable through reasoning alone; (3) knowing the essence of a particular color (...) (e.g., red) requires presentation with the relevant sensible quality and hence requires sense perception; (4) if a sensible quality has an essence, then that essence is a form. The solution I defend to this puzzle basically consists of accepting (1) through theses (3) but denying thesis (4). Sensible qualities, according to Plato, do have essences, but specifying their essences does not require that one postulate a separate form. (shrink)
This paper considers Berkeley’s use of Plato in Siris. Berkeley’s engagement with ancient thinkers in Siris has been a source of puzzlement for many readers. In this paper I focus on Siris § 266. In particular, I consider why Berkeley says of the Platonists that they “distinguished the primary qualities in bodies from the secondary” and why, given his own well-known misgivings about the distinction, he characterizes this as part of a “notion of the true system of the world.” I (...) argue that in Siris Berkeley accepts a distinctive form of corpuscularianism, and that he thinks a distinction between primary and secondary qualities follows from this. I further argue that in § 266, and elsewhere in Siris, Berkeley engages in a careful reading of Plato’s Timaeus, which he uses to bolster his defense of the compatibility between corpuscularianism and his immaterialist idealism. (shrink)
Speech act theory has taught us 'how to do things with words'. Arresting Language turns its attention in the opposite direction - toward the surprising things that language can undo and leave undone. In the eight essays of this volume, arresting language is seen as language at rest, words no longer in service to the project of establishing conventions or instituting legal regimes. Concentrating on both widely-known and seldom-read texts from a variety of philosophers, writers, and critics - from Leibniz (...) and Mendelssohn, through Kleist and Hebel, to Benjamin and Irigaray - the book analyzes the genesis and structure of interruption, a topic of growing interest to contemporary literary studies, continental philosophy, legal studies, and theological reflection. Arresting Language identifies critical moments in philosophical and literary texts during which language itself - without any identifiable speaker - arrests otherwise continuous processes and procedures, including the process of representation and procedures for its legitimization. (shrink)
As the Pyrrhonians made clear, reasons that adequately justify beliefs can have only three possible structures: foundationalism, coherentism, and infinitism. Infinitism—the view that adequate reasons for our beliefs are infinite and non-repeating—has never been developed carefully, much less advocated. In this paper, I will argue that only infinitism can satisfy two intuitively plausible constraints on good reasoning: the avoidance of circular reasoning and the avoidance of arbitrariness. Further, I will argue that infinitism requires serious, but salutary, revisions in our evaluation (...) of the power of reasoning. Thus, reasoning can not provide a basis for assenting to a proposition—where to assent to a proposition, p, means to believe that we know that p. A non-dogmatic form of provisional justification will be sketched. Finally, the best objections to infinitism, including those posed by the Pyrrhonians, will be shown (at least provisionally!) to be inadequate. (shrink)
As the Pyrrhonians made clear, reasons that adequately justify beliefs can have only three possible structures: foundationalism, coherentism, and infinitism. Infinitism—the view that adequate reasons for our beliefs are infinite and non-repeating—has never been developed carefully, much less advocated. In this paper, I will argue that only infinitism can satisfy two intuitively plausible constraints on good reasoning: the avoidance of circular reasoning and the avoidance of arbitrariness. Further, I will argue that infinitism requires serious, but salutary, revisions in our evaluation (...) of the power of reasoning. Thus, reasoning can not provide a basis for assenting to a proposition—where to assent to a proposition, p, means to believe that we know that p. A non-dogmatic form of provisional justification will be sketched. Finally, the best objections to infinitism, including those posed by the Pyrrhonians, will be shown to be inadequate. (shrink)
This chapter provides grounds for thinking that it is the quality of the reasons for the propositional content of our belief-states with true propositional contents, rather than the etiology of those belief-states, that determines whether the belief-state qualifies as knowledge. Normative epistemology rather than naturalized epistemology holds the key to understanding knowledge. This chapter delineates some important features of epistemic luck. It explores the etiology view and presents reasons for concluding that it cannot adequately account for epistemic luck. The chapter (...) then explores the reasons view and shows how it can account for some of the cases that are troublesome for the etiology view. There are many well-discussed and widely accepted counterexamples in the literature for each of the etiology views, with the exception of the virtue-views because those views are still relatively new. (shrink)
There are many things that could be wrong with foundationalism. For example, some have claimed that a so-called basic belief cannot be both 1) a reason for non-basic beliefs and 2) such that it cannot be provided with at least prima facie justification. If something is a reason, they say, then that something has to be a proposition and if it is a proposition, then it is the kind of thing that requires a reason in order to be even prima (...) facie justified. Another reason that some give for rejecting normative foundationalism is that it leads directly to skepticism. There is no way, they claim, to move from so-called basic propositions to “external world” propositions by employing normatively acceptable principles of reasoning. Still others have thought that the invention of a nonreasoned reason was as ad hoc as the invention of an unmoved mover. (shrink)