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)

Physics has been thought to truly represent reality since at least Galileo, and the foundations of physics are always established using philosophical ideas. In particular, the elegant naming of physical entities is usually very influential in the acceptance of physical theories. We here demonstrate (using current developments in thermodynamics as an example) that both the epistemology and the ontology of physics ultimately rest on poetic language. What we understand depends essentially on the language we use. We wish to establish our (...) knowledge securely, but strictly speaking this is impossible using only analytic language. Knowledge of the meanings of things must use a natural language designed to express meaning, that is, poetic language. Although the world is really there, and although we can indeed know it truly, this knowledge is never either complete or certain but ultimately must rest on intuition. Reading a recently discovered artefact with a palaeo-Hebrew inscription as from the first century, we demonstrate from it that this ontological understanding long predates the Hellenic period. Poetic language is primary, both logically and temporally. (shrink)

Main Response Topics ? Introduction ? Open display and public evaluation ? Publicity versus patient privacy ? Facial tissue donation ? Validity of Louisville Instrument for Risk Acceptance ? Patients' understanding of risk ? Face versus hand transplantation ? Rejection rates/risks ? Patient compliance ? Exit strategy ? Functional recovery ? Societietal implications ? Psychological implications ? Conclusion: Uncertainty likely to persist.

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)

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)

Transplantation continues to push the frontiers of medicine into domains that summon forth troublesome ethical questions. Looming on the frontier today is human facial transplantation. We develop criteria that, we maintain, must be satisfied in order to ethically undertake this as-yet-untried transplant procedure. We draw on the criteria advanced by Dr. Francis Moore in the late 1980s for introducing innovative procedures in transplant surgery. In addition to these we also insist that human face transplantation must meet all the ethical requirements (...) usually applied to health care research. We summarize the achievements of transplant surgery to date, focusing in particular on the safety and efficacy of immunosuppressive medications. We also emphasize the importance of risk/benefit assessments that take into account the physical, aesthetic, psychological, and social dimensions of facial disfiguration, reconstruction, and transplantation. Finally, we maintain that the time has come to move facial transplantation research into the clinical phase. (shrink)

Offering an engaging and accessible portrait of the current state of the field, Philosophy of Science: A New Introduction shows students how to think philosophically about science and why it is both essential and fascinating to do so. Gillian Barker and Philip Kitcher reconsider the core questions in philosophy of science in light of the multitude of changes that have taken place in the decades since the publication of C.G. Hempel's classic work, Philosophy of Natural Science —both in the (...) field and also in history and sociology of science and the sciences themselves. They explore how philosophical questions are connected to vigorous current debates—including climate change, science and religion, race, intellectual property rights, and medical research priorities—showing how these questions, and philosophers' attempts to answer them, matter in the real world. Featuring numerous illustrative examples and extensive further reading lists, Philosophy of Science: A New Introduction is ideal for courses in philosophy of science, history and philosophy of science, and epistemology/theory of knowledge. It is also compelling and illuminating reading for scientists, science students, and anyone interested in the natural sciences and in their place in global society today. (shrink)

Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do—i.e. their functional traits—within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological—i.e. epistemic—assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake (...) of an effective comparison and integration across domains, and for assessing whether or not to use functional diversity approaches for developing ecological management strategies. The objective of this contribution is to identify and critically analyze the most salient of these assumptions. To this aim, we provide an “epistemic roadmap” that pinpoints these assumptions along a set of historical, conceptual, empirical, theoretical, and normative dimensions. (shrink)

Interactive narratives are inextricable from the way that we understand our encounters with digital technology. This is based upon the way that these encounters are processually formed into a narrative of episodic events, arranged and re-arranged by various levels of agency. After describing past research conducted at the iCinema Research Centre at the University of New South Wales, this paper sets out a framework within which to build a relational theory of interactive narrative formation, outlining future research in the area.

This paper brings needed clarity to the influential view that species are cohesive entities held together by gene flow, and then develops an empirical argument against that view: Neglected data suggest gene flow is neither necessary nor sufficient for species cohesion. Implications are discussed. ‡I'm grateful to Rob Wilson, Alex Rueger and Lindley Darden for important comments on earlier drafts, and to Joseph Nagel, Heather Proctor, Ken Bond, members of the DC History and Philosophy of Biology reading group, and audience (...) members at the November 2006 meeting of the PSA, for helpful comments or discussion. Social Sciences and Humanities Research Council of Canada fellowship 752-2005-1208 supported research. †To contact the author, please write to: Philosophy Department, University of Wisconsin–Madison, 5185 Helen C. White Hall, 600 North Park Street, Madison, WI 53706; e-mail: mjbarker2@wisc.edu. (shrink)

The standard view about counterfactuals is that a counterfactual (A > C) is true if and only if the A-worlds most similar to the actual world @ are C-worlds. I argue that the worlds conception of counterfactuals is wrong. I assume that counterfactuals have non-trivial truth-values under physical determinism. I show that the possible-worlds approach cannot explain many embeddings of the form (P > (Q > R)), which intuitively are perfectly assertable, and which must be true if the contingent falsity (...) of (Q > R) is to be explained. If (P > (Q > R)) has a backtracking reading then the contingent facts that (Q > R) needs to be true in the closest P-worlds are absent. If (P > (Q > R)) has a forwardtracking reading, then the laws required by (Q > R) to be true in the closest P-worlds will be absent, because they are violated in those worlds. Solutions like lossy laws or denial of embedding won't work. The only approach to counterfactuals that explains the embedding is a pragmatic metalinguistic approach in which the whole idea that counterfactuals are about a modal reality, be it abstract or concrete, is given up. (shrink)

Athenaeus (637a) records these lines from the dithyrambHymenaios, along with a number of other snippets of poetry, in the course of an inconclusive discussion about the characteristics of the instrument (if it is an instrument) called the magadis. Athenaeus had good reasons for being puzzled; the wordfirst appeared in Greek, so far as we know, in the seventh centuryb.c., and its sense was already a matter of some doubt in the fourth. As to this particular fragment, even Telestes' original audience (...) might be forgiven some bafflement in the face of the third line, on which I shall initially focus here. What can be meant by ‘the five-rodded joining of the strings’? (shrink)

This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions are (...) rejected; rather it is main arguments for them that are the focus. (shrink)

Recent studies indicate that plakoglobin may have a similar function to that of β-catenin within the Wnt signaling pathway. β-catenin is known to be an oncogene in many forms of human cancer, following acquisition of stabilizing mutations in amino terminal sequences. Kolligs1 and coworkers show, however, that unlike β-catenin, plakoglobin induces neoplastic transformation of rat epithelial cells in the absence of such stabilizing mutations. Cellular transformation by plakoglobin also appears to be distinct from that of β-catenin in that it requires (...) activation of the proto-oncogene c-myc. Surprisingly, c-myc is activated more efficiently by plakoglobin than β-catenin, despite its previous identification as a target of Tcf/β-catenin.2 In contrast, a synthetic Tcf reporter gene is activated to a much greater extent by β-catenin than plakoglobin. Plakoglobin and β-catenin may therefore have different roles in Wnt signaling and cancer, which reflect their differential effects on target gene activity. BioEssays 22:961–965, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

In this paper we provide a reflexive account of fieldwork in out of school clubs in a range of localities across England and Wales. By reflecting upon our personal experiences of researching with c...

This letter was submitted to the Senate Standing Committee on Legal and Constitutional Affairs, Government of Canada, on 29th January, 2021, as final debate over Bill C-7 was being undertaken in the Senate regarding MAiD and the strong opposition to the legislation expressed across the Canadian disability community. It draws on our individual and joint work on eugenics, well-being, and disability.