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)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (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)

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; 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)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

Keith Ansell-Pearson, An Introduction to Nietzsche as Political Thinker (Cambridge: Cambridge University Press, 1994) hb: 0-521-41722-8. pb: 0-521-42721-5. Paul Patton, ed., Nietzsche, Feminism and Political Theory (London: Routledge. 1993) 0-4150-8256-0. Lester M. Hunt, Nietzsche and the Origin of Virtue (London: Routledge, 1993) 0-4150-9580-8. David Owen, Maturity and Modernity. Nietzsche, Weber, Foucault and the Ambivalence of Reason (London: Routledge, 1994) 0-4150-5398-6. Peter Lassmann and Ronald Spiers, eds., Weber: Political Writings (Cambridge: Cambridge University Press. 1994) hb: 0-521 -39312-4. pb: 0-521 -39719-7. Friedrich (...) Nietzsche, On the Genealogy of Morality and Other Writings, ed. Keith Ansell-Pearson, tr. Carol Diethe (Cambridge University Press, 1994) hb: 0-521-40459-2. pb: 0-521-40610-2. (shrink)

'Justice' and 'democracy' have alternated as dominant themes in political philosophy over the last fifty years. Since its revival in the middle of the twentieth century, political philosophy has focused on first one and then the other of these two themes. Rarely, however, has it succeeded in holding them in joint focus. This volume brings together leading authors who consider the relationship between democracy and justice in a set of specially written chapters. The intrinsic justness of democracy is challenged, the (...) relationship between justice, democracy and impartiality queried and the relationship between justice, democracy and the common good examined. Further chapters explore the problem of social exclusion and issues surrounding sub-national groups in the context of democracy and justice. Authors include Keith Dowding, Richard Arneson, Norman Schofield, Albert Weale, Robert E. Goodin, Jon Elster, David Miller, Phillip Pettit, Julian LeGrand and Russell Hardin. (shrink)

Book synopsis: Today the majority of philosophers in the English-speaking world adhere to the “naturalist” credos that philosophy is continuous with science, and that the natural sciences provide a complete account of all that exists—whether human or nonhuman. The new faith says science, not man, is the measure of all things. However, there is a growing skepticism about the adequacy of this complacent orthodoxy. This volume presents a group of leading thinkers who criticize scientific naturalism not in the name of (...) some form of supernaturalism, but in order to defend a more inclusive or liberal naturalism. The many prominent Anglo-American philosophers appearing in this book—Akeel Bilgrami, Stanley Cavell, Donald Davidson, John Dupré, Jennifer Hornsby, Erin Kelly, John McDowell, Huw Price, Hilary Putnam, Carol Rovane, Barry Stroud, and Stephen White—do not march in lockstep, yet their contributions demonstrate mutual affinities and various unifying themes. Instead of attempting to force human nature into a restricted scientific image of the world, these papers represent an attempt to place human nature at the center of renewed—but still scientifically respectful—conceptions of philosophy and nature. (shrink)

Acceptance of Humean Supervenience and thereductive Humean analyses that entail it leadsto a litany of inadequately explained conflictswith our intuitions regarding laws andpossibilities. However, the non-reductiveHumeanism developed here, on which law claimsare understood as normative rather than factstating, can accommodate those intuitions. Rational constraints on such norms provide aset of consistency relations that ground asemantics formulated in terms offactual-normative worlds, solving theFrege-Geach problem of construing unassertedcontexts. This set of factual-normative worldsincludes exactly the intuitive sets ofnomologically possible worlds associated witheach possible (...) set of laws. The extension ofthe semantics to counterfactual and subjunctiveconditionals is sketched. Potential objectionsinvolving subjectivity, mind-dependence, andnon-factuality are discussed. (shrink)

Abstract: This paper is an attempt to identify and to suggest reasons to reject those assumptions about the nature and scope of perceptual knowledge that appear to make an unacceptable scepticism the only strictly defensible answer to the philosophical problem of knowledge of the world in general. The suggestion is that our knowing things about the world around us by perception can be satisfactorily explained only if we can be understood to sometimes perceive that such-and-such is so, where what we (...) perceive to be so is the very state of the world that we thereby know to be so. This is not proposed as a better answer to the philosophical problem, but as a way of seeing how that problem as traditionally understood could not really present a threat to anyone who can think about the world at all. (shrink)

This book examines how ancient authors explored ideas of kingship as a political role fundamental to the construction of civic unity, the use of kingship stories to explain the past and present unity of the polis and the distinctive function or status attributed to kings in such accounts. -/- It explores the notion of kingship offered by historians such as Herodotus, as well as dramatists writing for the Athenian stage, paying particular attention to dramatic depictions of the unique capabilities of (...) Theseus in uniting the city in the figure of the ‘democratic king’. It also discusses kingship in Greek philosophy: the Socratics’ identification of an ‘art of kingship’, and Xenophon and Isocrates’ model of ‘virtue monarchy’. In turn, these allow a rereading of explorations of kingship and excellence in Plato’s later political thought, seen as a critique of these models, and also in Aristotle’s account of total kingship or pambasileia, treated here as a counterfactual device developed to explore the epistemic benefits of democracy. -/- This book offers a fascinating insight into the institution of monarchy in classical Greek thought and society, both for those working on Greek philosophy and politics, and also for students of the history of political thought. (shrink)

This paper considers two questions. First, what is the scope of the Equal Weight View? Is it the case that meeting halfway is the uniquely rational method of belief-revision in all cases of known peer disagreement? The answer is no. It is sometimes rational to maintain your own opinion in the face of peer disagreement. But this leaves open the possibility that the Equal Weight View is indeed sometimes the uniquely rational method of belief revision. Precisely what is the skeptical (...) import of this fact; is it the case that some form of skepticism triumphs in such cases? The answer to this question is also no. As it turns out, the situations in which it is most plausible that the Equal Weight view is a rational requirement are the ones in which meeting halfway with a disagreeing peer brings you closer to, and not farther from, knowledge. I argue for these theses in a novel way; by looking at the comparative reliability of belief- invariance and meeting halfway using measures of reliability for degrees of belief, and by drawing normative conclusions from such results. The conclusions here can have the effect of reframing the entire debate in the epistemology of disagreement. (shrink)

The book is both a call to action and a how-to guide to effective teaching.

A normative criterion identifying the conditions for a desirable corporate reputation, “reputational optimality,” or “reputational bliss,” is described, and a case developed for its utility and reasonableness as a criterion to apply to real world phenomena. The paper discusses some behavioral patterns under alternative moral positions taken by observers and the firm, critiques some alternative moral principles, and considers some dynamics of moving toward, defending and maintaining, and breaching or breaking reputational bliss.

Compilation of selected readings on the sociology of science - includes papers on the emergence and institutionalization of modern science and its relationships to society, structural and cultural factors, relations between science and technology, scientific entrepreneurship and the utilization of research, political aspects, science policy and its goals, the impact of science on social change, etc. References.

A defence of the idea that an agent's knowledge that he is intentionally doing such-and-such is not ‘based on’ or ‘derived from’ any ‘experience’ of the agent or any item or state he is aware of in acting as he does. The explanation of agents' knowing, in general, what they are intentionally doing lies in the capacity for self-ascription and self-knowledge that is a required for being a subject of any intentional attitudes, and so for competent intentional agency.

Prawitz proved a theorem, formalising ‘harmony’ in Natural Deduction systems, which showed that, corresponding to any deduction there is one to the same effect but in which no formula occurrence is both the consequence of an application of an introduction rule and major premise of an application of the related elimination rule. As Gentzen ordered the rules, certain rules in Classical Logic had to be excepted, but if we see the appropriate rules instead as rules for Contradiction, then we can (...) extend the theorem to the classical case. Properly arranged there is a thoroughgoing ‘harmony’, in the classical rules. Indeed, as we shall see, they are, all together, far more ‘harmonious’ in the general sense than has been commonly observed. As this paper will show, the appearance of disharmony has only arisen because of the illogical way in which natural deduction rules for Classical Logic have been presented. (shrink)