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)

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 (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)

What is the self? And how does it relate to the body? In the second edition of Personal Identity, Harold Noonan presents the major historical theories of personal identity, particularly those of Locke, Leibniz, Butler, Reid and Hume. Noonan goes on to give a careful analysis of what the problem of personal identity is, and its place in the context of more general puzzles about identity. He then moves on to consider the main issues and arguments which are the (...) subject of current debate, including the work of Bernard Williams and Derek Parfit, and makes new and challenging interpretations of them. This new edition contains additional material assessing the biological approach which has become increasingly popular in recent years, and extends the treatment of indeterminate identity to take account of the epistemic view of vagueness. This book covers the problem of personal identity from its origin in Locke's work to the most recent debates in the philosophical literature, and will be invaluablereading for any student of the topic. (shrink)

Thats logic. LEWIS CARROLL, Through the Looking Glass 1-1. The fundamental problem of this work is the question of the nature of scientific inference.

My purpose is to explore the possible lines of reply available to a defender of the neo‐Lockean position on personal identity in response to the recently popular ‘animalist’ objection. I compare the animalist objection with an objection made to Locke by Bishop Butler, Thomas Reid and, in our own day, Sydney Shoemaker. I argue that the only possible response available to a defender of Locke against the Butler–Reid–Shoemaker objection is to reject Locke's official definition of a person as a thinking, (...) intelligent thing and replace it with the concept of the self– the object of self‐reference – and that this response is equally obligatory for the neo‐Lockean in replying to the animalist. I explore other possibilities, including the position that there is no sense in talking about personal identity at all. (shrink)

One of three distinct approaches to his famous ‘Trust’ argument, this paper written by Garfinkel in 1960, and never before published, proposed a rethinking of rules, games and linguistic classifications in interactional terms consistent with Wittgenstein’s language games. Garfinkel had been working in collaboration with Parsons since 1958 to craft an approach to culture that would replace conceptual classification with the constitutive expectancies of interaction and systems of interaction. The argument challenged the work of cultural anthropologists influenced by zoology and (...) biology, who called themselves ‘ethnoscientists’ and studied culture in terms of linguistic classification systems. Garfinkel had proposed an alternative sociological ‘ethnoscience’ of culture and language that would focus on how culture was made, on how linguistic events are achieved, and on the rules of their making. This ‘Language Games’ approach followed Wittgenstein in seeking what Garfinkel called a literal description of cultural/linguistic events: meaning by ‘literal’, a step-by-step account of the constitutive and preferred rules participants use to create a recognizable event-in-a-language. Made famous three years later in version associated with Schutz, Garfinkel’s Trust argument also appears in a 1962 text (Parsons’ Primer, published in 2019) in a version built on Parsons. (shrink)

Considered ahead of its time since the first publication in 1981, Medical Choices, Medical Chances provides a telescope for viewing how developments in the fields of medical research, medical technology, and health care organization are likely to influence the doctor-patient relationship in the 21st Century. The book explores this intricate web of relationships among doctors, patients, and families and offers a new framework for mastering the emotional and intellectual challenges of uncertainty, while at the same time providing tools for all (...) concerned to regain control from managed care. It is a must-read for all those interested in medicine and where it is headed in the new millennium. (shrink)

This paper argues that realism issue in the social sciences is not one that can be decided by general philosophical arguments that evaluate entire domains at once. The realism issue is instead many different empirical issues. To defend these claims, I sort issues that are often run together, explicate and criticize several standard realist and antirealist arguments about the social sciences, and use the example of the productive/nonproductive distinction to illustrate the approach to realism questions that I favor.

Personal Identity is a comprehensive introduction to the nature of the self and its relation to the body. Harold Noonan places the problem of personal identity in the context of more general puzzles about identity, discussing the major historical theories and more recent debates. The second edition of Personal Identity contains a new chapter on 'animalism' and a new section on vagueness.

general, abstract situation. On the other side, I know that graduate students and all mathematicians sometimes falter because their intuitive, ..

Coward (religious studies, U. of Calgary) explores the similarities and differences between the language theories of modern French philosopher Jacques Derrida and several traditional Indian schools of thought.

Carnap, R. Empiricism, semantics, and ontology.--Quine, W. V. Two dogmas of empiricism. Meaning and translation.--Sellars, W. Empiricism and the philosophy of mind.--Putnam, H. Brains and behaviour.--Popper, K. R. Science: conjectures and refutations.--Feyerabend, P. K. Science without experience. How to be a good empiricist--a plea for tolerance in matters epistemological.--Kuhn, T. S. Incommensurability and paradigms.--Hesse, M. Duhem, Quine and a new empiricism.--Chomsky, N. Recent contributions to the theory of innate ideas.--Putnam, H. The innateness hypothesis and explanatory models in linguistics.--Goodman, N. The (...) epistemological argument.--Quine, W. V. Linguistics and philosophy.--Edgley, R. Chomsky's theory of innate ideas.--Fodor, J. A. Methodological arguments for behaviorism.--Chomsky, N. Some empirical assumptions in modern philosophy of language.--Annotated bibliography (p. 319-326). (shrink)

Tarrant examines whether the relationship between Socrates and his young followers could ever have been treated by Plato in the same fashion as it is treated in the Platonic Theages, where the terminology of synousia is repeatedly applied to it. In minimizing the part played by knowledge and maximizing the role of the divine and of eros, the work creates a "Socrates" who conforms to the educational ideology of the Academy of Polemo in the period 314-270 BC.

I think it is important to try to make sense of these thoughts concerning the justificatory role of experiences, for I suspect that we are losing the ability to see why philosophers have traditionally been attracted to such thoughts. Coherentism and reliabilism, perhaps the two most currently popular theories of epistemic justification, appear simply to reject the idea that experiences can justify beliefs. Thus according to coherentism, the view that ‘a belief is justified by its coherence with other beliefs one (...) holds,’ it is only other beliefs, not experiences, that can justify beliefs. Although there is little consensus as to how the notion of coherence should be explicated, it is generally agreed that experiences are not the sort of thing that can cohere with beliefs. Reliabilism, by contrast, holds that ‘a belief is justified if and only if it is “well-formed,” i.e., it has an ancestry of reliable and/or conditionally reliable cognitive operations.’ In other words, according to reliabilism beliefs are justified, not by experiences, but by being caused by reliable belief-forming processes. Experiences may be formed in the course of such processes, but they need not be, and even when they are, they make no contribution to the justification of the beliefs that are formed as the result of those processes. What makes a belief-forming process justification-conferring, according to reliabilism, is simply that it is reliable, not that it gives rise to experiences. So neither coherentism nor reliabilism seems to allow any room for the traditional thought that experiences justify beliefs. (shrink)

Mysteries: remains of a hidden life -- Words on paper -- In search of a person behind the words -- A France of broken families -- Families -- Politiques -- Breaking with his father -- Aristocratic Paris -- Libertine Paris -- A political education -- Gearing up for war: mathematical inspirations -- Breda -- Military engineering -- Meeting Isaac Beeckman -- The Holy Roman empire -- Anxious dreams -- Curious meetings -- War and diplomacy in Europe -- Into Bohemia -- (...) To Hungary and disaster -- The Baltic and return to the Netherlands -- Again in France -- Paris and the rosicrucian scare -- The Valtellina and Rome -- The struggle for France -- Problems with the cardinal -- The campaign for La Rochelle -- Confrontation and departure -- The meetings -- Confrontation and conversation -- Becoming a sectarian -- Feeling threatened -- Exile -- Not yet concluded. (shrink)

In recent years empiricism has been under persistent attack, and serious questions have been raised about the ability of empiricism to provide the basis for a viable philosophy of science. The attack has been sufficiently vigorous, and in some quarters sufficiently successful, that many now maintain that empiricism is dead. My aim in this paper is to argue that, rather than being ready for embalmment and emplacement in the museum of philosophic oddities, empiricism is very much alive, and the central (...) thesis of empiricism remains the cornerstone for any viable philosophy of science. This is not to say that the recent attacks on empiricism have been without a point, rather, they have put anyone who would defend empiricism in the position of having to rethink many datails of the empiricist viewpoint. But it is the details, the way in which empiricism has been elaborated by its proponents, not the central empiricist insight, that must be reconsidered. (shrink)

Philosophy of science is still, in the minds of many, identified with positivism. This is understandable since twentieth century philosophy of science originates with the work of the Vienna Circle. Positivism is most famous for the verification theory of meaning, the doctrine that the meaning of any proposition is the method by which it is verified, and that any nonanalytic locution which cannot be proven or disproven by some empirical test has no cognitive significance. Positivism is an attempt to construct (...) a “scientific philosophy” in the worst sense: it is maintained that (with the exception of propositions which are analytic and thus vacuous) only those propositions which occur in the sciences are meaningful, all other discourse having at best some emotive value, but no cognitive content, and all of this is maintained within the confines of an exceedingly narrow notion of scientific knowledge. This notion is so narrow that its advocates found themselves in danger of having to relegate most of physics to the realm of nonsense since physics contains many statements which are strictly universal and thus cannot be conclusively verified. (shrink)

A belief must have justification if it is to count as knowledge. And it is a commonplace thought that in certain circumstances experiences can serve as justifications for beliefs. Moreover, many have thought that there is something distinctive about the wayin which experiences justify beliefs, and that there is something distinctive about experiences which accounts for the distinctive way in which they justify beliefs. In this paper, I seek to elucidate views about experience and justification that can make sense of (...) these thoughts and that can show us why so many have been attracted to them.I think it is important to try to make sense of these thoughts concerning the justificatory role of experiences, for I suspect that we are losing the ability to see why philosophers have traditionally been attracted to such thoughts. Coherentism and reliabilism, perhaps the two most currently popular theories of epistemic justification, appear simply to reject the idea that experiences can justify beliefs. (shrink)

The novel has always provided a vehicle for commenting on various aspects of human existence. We are familiar with the political novel, the historical novel, or the metaphysical novel, and in this sense Sorrentino's Mulligan Stew, with its running commentary on novels, novelists, critics and publishers, may be viewed as a critical novel. A critical novel, however, has a striking feature which it does not share with the other sorts of novels mentioned above in that a critical novel is itself (...) a novel, and a member of the class of objects on which it is commenting. This is a structure that logicians call “self-reference” and the phenomenon of self-reference has provided a central theme in twentieth century logic and philosophy. (shrink)

“There is, in addition, a second reason for doubting that scientists reject paradigms because confronted with anomalies or counterinstances. In developing it my argument will itself foreshadow another of this essay's main theses. The reasons for doubt sketched above were purely factual; they were, that is, themselves counterinstances to a prevalent epistemological theory. As such, if my present point is correct, they can at best help to create a crisis or, more accurately, to reinforce one that is already very much (...) in existence. By themselves they cannot and will not falsify that philosophical theory, for its defenders will do what we have already seen scientists doing when confronted by anomaly. They will devise numerous articulations and ad hoc modifications of their theory in order to eliminate any apparent conflict. Many of the relevant modifications and qualifications are, in fact, already in the literature. If, therefore, these epistemological counterinstances are to constitute more than a minor irritant, that will be because they help to permit the emergence of a new and different analysis of science within which they are no longer a source of trouble. Furthermore, if a typical pattern, which we shall later observe in scientific revolutions, is applicable here, these anomalies will then no longer seem to be simply facts. From within a new theory of scientific knowledge, they may instead seem very much like tautologies, statements of situations that could not conceivably have been otherwise.”. (shrink)