The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl. (shrink)
This paper is concerned with two theories of history—those of Hegel and of Marx. Its primary aim is to clarify. The writings of Hegel are notoriously obscure, and those of Marx have been variously interpreted, so there is room for a paper which tries to ensure that when the theories of history propounded by Marx and Hegel are criticized, what are criticized are views which they actually held. It is no part of this paper's thesis that, in his theory of (...) history, Marx consciously borrowed from Hegel. But it will be argued that there is more of Hegel in Marx than is sometimes supposed, and that if this fact is ignored one seriously distorts Marx. (shrink)
The concept of freedom is one which Hegel thought of very great importance; indeed, he believed that it is the central concept in human history. ‘Mind is free’, he wrote, ‘and to actualise this, its essence – to achieve this excellence – is the endeavour of the worldmind in world-history’ . Those who already have an interest in Hegel will doubtless be interested in his views on a topic which he thought so important; on the other hand, the many philosophers (...) who are either indifferent to or hostile to Hegel may point out that it does not follow that, because the subject of freedom interested Hegel, his views about this subject are of general interest. It will be the aim of this paper to show that they are of general interest; in the meantime, it may be recalled that Isaiah Berlin has argued that Hegel's concept of freedom is one of a type, called by him the concept of positive freedom, which is ‘at the heart of many of the nationalist, communist, authoritarian and totalitarian creeds of our day’. It will surely be worth while to see to what extent this is true of Hegel, and to what extent Hegel's views about freedom are true. (shrink)
Parkinson, Joseph Long after its publication in 1968, Pope Paul VI's encyclical letter on birth control Humanae Vitae continues to provoke great interest among Catholic bishops, clergy and faithful alike. At the time of its promulgation and in the years since, many Catholic couples struggled with the teaching contained in the document. Some couples apparently managed to adapt seamlessly to the continuing prohibition on contraception, but others encountered and continue to encounter major difficulties in receiving and living the teaching. (...) Birth control may no longer be an issue for that first generation of couples, yet many of them still view Humanae Vitae as a watershed in their journey in Catholic faith. (shrink)
Parkinson, Joseph Having taken all reasonable steps to make the best decision they can in conscience, a Catholic couple believe they have no real alternative but to use contraception for the time being. Can this couple continue to receive Holy Communion?
Parkinson, Joseph In September 2010, Western Australia's Legislative Council, the Upper House of that State's Parliament, voted down a Private Member's Bill to introduce voluntary euthanasia by a margin of 24 votes to 11. This article reviews the general context and content of the Bill and the public debate on euthanasia before offering more focused analysis.
Parkinson, Joseph Catholic health and aged care providers seeking new governance structures face a choice of embedding their ministry in either the local Church or the universal Church. This article asks how we view these ministries in the first place: in what sense are they truly 'ministries of the Church'?
Parkinson, Joseph Can a dead person conceive a child? Even if it is technically possible, should it be permitted? The legal system seems to have reached a position on this matter without obvious ethical reflection. Noting that a child should be able to know and relate to his or her parents, this article argues that a person's capacity to contribute to the conception of new life should cease with that person's death.
Parkinson, Joseph Near death experiences and the wisdom they produce are the stuff of countless novels, but when the story ends in the author's death, where is wisdom to be found? American neurosurgeon Paul Kalanithi has left an astonishingly eloquent and lucid account of his own dying and his inner journey to find meaning and even peace in that experience. As inspiring as it is tragic, "When Breath Becomes Air" rightly sits on The New York Times list of best (...) sellers, and is a must-read for anyone working in bioethics or health care. (shrink)
Parkinson, Joseph Bioethics at the bedside looks different from bioethics in the classroom, because the patient in the bed is a person with their own particular history, a unique experience of illness, and an unrepeatable future. In the context of Christian faith, bioethics must include far more than mere clinical data and academic prowess: there must be a central role for the God who is mystery. This article reflects on the rich perspective of leading American paediatrician and ethicist, Bioethics (...) has never been an exact science. Even when it strives for absolute objectivity by the application of the most rigorous philosophical discipline, clinical situations often escape our capacity to arrive at certain judgement. This should not surprise us, of course, since clinical situations are often extremely complex human dramas, and in such matters, as Aristotle reminds us, we should never expect greater certainty than our subject matter allows. (shrink)
Parkinson, Joseph Research shows that sexual orientation is neither well defined nor ultimately defining for adolescents seeking self-identity. Rather, the data on instability of sexual orientation among youth and young adults suggest that most of the time unquestioning affirmation of an adolescent's claimed same-sex attraction will do more long-term harm than good. This article explores this complexity and proposes more appropriate ways to provide excellent pastoral care in schools.
Spinoza's Ethics is a classic philosophy text but it is also one of the most difficult to understand. This latest text in the Oxford Philosophical Texts series includes a new, lucid translation of Ethics in which Parkinson provides a comprehensive guide to the understanding of Spinoza's work. An extensive introduction includes a short biography of Spinoza himself; the form of his writing including his own particular uses of definitions; an introductory guide through the philosophy of Ethics; and a summary (...) of the contents of Ethics itself. Further aids include a glossary of terms, notes to the text, and notes to the translation. (shrink)
In a series of related essays, Dr Parkinson argues that both science and religion are at a crossroads, because in both cases their current paradigms are breaking down. In science, Einstein’s General Relativity has left an unbridgeable gap between quantum physics and the new cosmology and, in the West, the gap between the story told by modern scholarship and “gospel truth” has become equally wide. What for two millennia has been considered to be historical fact is now seen often (...) to be not only pious myth but deliberate falsification. The author adds something new and positive – but controversial- to the debate, in arguing that a future science and religion must be symbiotic. That is to say, in being true to their most basic principles of truth-seeking, both will find themselves to be not merely harmonious but mutually supporting and illuminating. When the evidence for this is fully, and honestly, assessed, the “phoney war” between science and religion can be seen for what it is. The question under all the questions is this: if simple honesty is an essential part of both science and religion, can either continue to survive with what J. K. Galbraith called “institutional truth?”. (shrink)
This paper presents a new approach to the demarcation of social emotions, based on their dependence on social appraisals that are designed to assess events bearing on social concerns. Previous theoretical attempts to characterize social emotions are compared, and their inconsistencies highlighted. Evidence for the present formulation is derived from theory and research into links between appraisals and emotions. Emotions identified as social using our criteria are also shown to bring more consistent consequences for social behavior than nonsocial emotions. We (...) conclude by considering ways of validating and refining our classification. (shrink)
Objectives: The aims of this study were to: (1) investigate patients’ views on euthanasia and physician-assisted suicide (PAS), and (2) examine the impact of question wording and patients’ own definitions on their responses. Design: Cross-sectional survey of consecutive patients with cancer. Setting: Newcastle (Australia) Mater Hospital Outpatients Clinic. Participants: Patients over 18 years of age, attending the clinic for follow-up consultation or treatment by a medical oncologist, radiation oncologist or haematologist. Main Outcome Measures: Face-to-face patient interviews were conducted examining attitudes (...) to euthanasia and PAS. Results: 236 patients with cancer (24% participation rate; 87% consent rate) were interviewed. Though the majority of participants supported the idea of euthanasia, patient views varied significantly according to question wording and their own understanding of the definition of euthanasia. Conclusions: Researchers need to be circumspect about framing and interpreting questions about support of ‘euthanasia’, as the term can mean different things to different people, and response may depend upon the specifics of the question asked. (shrink)
The Routledge History of Philosophy, Volume 4 covers a period of three hundred and fifty years, from the middle of the fourteenth century to the early years of the eighteenth century and the birth of modern philosophy. The focus of this volume is on Renaissance philosophy and seventeenth-century rationalism, particularly that of Descartes, Spinoza, and Leibniz. Science was ascendant during the Renaissance and beyond, and the Copernican revolution represented the philosophical climax of the middle ages. This volume is unique in (...) its emphasis on the relationship between science and philosophy. Placing the philosophy of the age into its scientific, social and cultural context, it examines the scholastic thought which Renaissance philosophy both interacted with and reacted against. A grasp of the intellectual context of the rationalists is also critical to an understanding of this philosophical movement, and the writings of Bacon, Gassendi, Hobbes, and others are analyzed here. The Routledge History of Philosophy, Volume 4 provides a broad, scholarly introduction to this period for students of philosophy and related disciplines, as well as some original interpretations of these authors. It will be important reading both for the specialist and the general reader. It includes a glossary of over one hundred technical terms and a chronological table of philosophical, scientific, and other cultural events. (shrink)
Social responsibility on the part of business has various meanings, to some of which English law is more favourable than others. But the law could be changed. The author is a Solicitor and Lecturer in Law in the University of Bristol. His Corporate Power and Responsibility: Issues in the Theory of Company Law has recently been published by Oxford University Press.
This paper argues against the thesis of Professor Savan, that Spinoza's views about words and about the imagination are such that he could not consistently say, and indeed did not think, that philosophical truths can be expressed adequately in language. The evidence for this thesis is examined in detail, and it is argued that Spinoza should have distinguished between two types of imagination, corresponding roughly to Kant's transcendental and empirical imagination. Finally, it is suggested that the bulk of the argument (...) of the Ethics is conducted on the level of the ?second kind of knowledge?, reason, but that it also contains examples of the use of the first and third kinds of knowledge. (shrink)
The Cambridge Companion to Spinoza. Don Garrett (ed.). Cambridge University Press, 1996, pp. xiii, 465. ISBN 0-521-39235-7 (hb); ISBN 0-521-39865-7 (pb). 40.00 (hb) 12.95 (pb). Spinoza: The Enduring Questions. Graeme Hunter (ed.). University of Toronto Press, 1994, pp. xviii, 182. ISBN 0-8020-2876-4. 45.00. The Spinozistic Heresy: The Debate on the 'Tractatus Theologico-Politicus'. 1670-77. Paolo Cristofolini (ed.). APA-Holland University Press: Amsterdam and Maarssen, 1995, pp. viii, 260. ISBN 90-302-1502-X. Disguised and Overt Spinozism around 1700. Wiep van Bunge and Wim Klever (eds.). (...) Brill, Leiden, 1996, pp. ix, 378. ISBN 90-04-10307-4. Part of Nature: Self-Knowledge in Spinoza's 'Ethics', by Genevieve Lloyd. Cornell University Press, Ithaca and London, 1994, pp. 182. ISBN 0-8014-2999-4. 24.95. Spinoza and the 'Ethics', by Genevieve Lloyd. Routledge Philosophy Guidebooks, London, 1996, pp. x, 163. ISBN 0-415-10782-2 (pb). 6.99. Spinoza: The Way to Wisdom, by Herman de Dijn. Purdue University Press, West Lafayette, Indiana, 1996, pp. xii, 291. ISBN 1-55753-081-5. (shrink)
A computer can come to understand natural language the same way Helen Keller did: by using “syntactic semantics”—a theory of how syntax can suffice for semantics, i.e., how semantics for natural language can be provided by means of computational symbol manipulation. This essay considers real-life approximations of Chinese Rooms, focusing on Helen Keller’s experiences growing up deaf and blind, locked in a sort of Chinese Room yet learning how to communicate with the outside world. Using the SNePS computational (...) knowledge-representation system, the essay analyzes Keller’s belief that learning that “everything has a name” was the key to her success, enabling her to “partition” her mental concepts into mental representations of: words, objects, and the naming relations between them. It next looks at Herbert Terrace’s theory of naming, which is akin to Keller’s, and which only humans are supposed to be capable of. The essay suggests that computers at least, and perhaps non-human primates, are also capable of this kind of naming. (shrink)
Helen Frowe has recently offered what she calls a “practical” account of self-defense. Her account is supposed to be practical by being subjectivist about permissibility and objectivist about liability. I shall argue here that Frowe first makes up a problem that does not exist and then fails to solve it. To wit, her claim that objectivist accounts of permissibility cannot be action-guiding is wrong; and her own account of permissibility actually retains an objectivist (in the relevant sense) element. In (...) addition, her attempt to restrict subjectivism primarily to “urgent” situations like self-defense contradicts her own point of departure and is either incoherent or futile. Finally, the only actual whole-heartedly objectivist account she criticizes is an easy target; while those objectivist accounts one finds in certain Western European jurisdictions are immune to her criticisms. Those accounts are also clearly superior to hers in terms of action-guidingness. (shrink)
William Rapaport, in “How Helen Keller used syntactic semantics to escape from a Chinese Room,” (Rapaport 2006), argues that Helen Keller was in a sort of Chinese Room, and that her subsequent development of natural language fluency illustrates the flaws in Searle’s famous Chinese Room Argument and provides a method for developing computers that have genuine semantics (and intentionality). I contend that his argument fails. In setting the problem, Rapaport uses his own preferred definitions of semantics and syntax, (...) but he does not translate Searle’s Chinese Room argument into that idiom before attacking it. Once the Chinese Room is translated into Rapaport’s idiom (in a manner that preserves the distinction between meaningful representations and uninterpreted symbols), I demonstrate how Rapaport’s argument fails to defeat the CRA. This failure brings a crucial element of the Chinese Room Argument to the fore: the person in the Chinese Room is prevented from connecting the Chinese symbols to his/her own meaningful experiences and memories. This issue must be addressed before any victory over the CRA is announced. (shrink)
Despite intense academic debate in the recent past over the use of ‘sham surgery’ control groups in research, there has been a recent resurgence in their use in the field of neurodegenerative disease. Yet the primacy of ethical arguments in favour of sham surgery controls is not yet established. Preliminary empirical research shows an asymmetry between the views of neurosurgical researchers and patients on the subject, while different ethical guidelines and regulations support conflicting interpretations. Research ethics committees faced with a (...) proposal involving sham surgery should be aware of its ethical complexities. An overview of recent and current placebo-controlled surgical trials in the field of Parkinson's Disease is provided here, followed by an analysis of the key ethical issues which such trials raise. (shrink)
I am a philosopher with Parkinson’s Disease. Over the past several years I’ve been trying to write about my situation. I wrote about how I was forced to face the disease. I described how the disease twists and distorts my world. Then I asked myself, as a philosophy writer and teacher, whether I could say anything that might help myself or others facing life with Parkinson’s? I found ideas in the ancient Stoics and expanded them with ideas about (...) time, coming up with suggestions for living as excellently as possible despite the disease. Looking at those suggestions, I realized how the special awareness, resolve, and attention I was suggesting would be eaten away by dementia, and I know that a majority of Parkinson’s patients face dementia if they survive long enough. What can philosophy say to me or any person whose self and philosophy are being erased? Writing about such issues has helped me deal with my situation, and maybe my essay might be useful for others dealing with decline. (shrink)
What is characteristic of being aParkinson’s patient? This article intends toanswer this question by means of an analysis ofnovels about people with Parkinson’s disease,personal accounts, and scientific publications.The texts were analyzed from anexistential-phenomenological perspective, usingan adapted version of the existential analysis.Being a Parkinson’s patient is apparentlycharacterized by an existential paradox: lifeappears simultaneously immobile andunpredictably whimsical. This may manifestitself in the person’s corporeality, in hisbeing-in-time and in-space, in his relating tothings and events, his life-world, and in hisbeing-together-with-others as an (...) individual.Finally, some specific characteristics of beinga Parkinson’s patient are described that may berelevant for purposes of adequate care, as isto be specified by further research. (shrink)
One of the most contentious question in today’s discussions on the educational policies concerns the role and values of the humanities in contemporary society and education. Many see the humanities as empty, unnecessary, inefficient, phony and worthless. This paper offers a rundown of arguments adduced to support this view, followed by an overview of Helen Small’s The Value of the Humanities, which offers an exceptionally critical and insightful analysis into the current debate over the value of the humanities. The (...) paper ends by emphasizing further the need to recognize the contribution that the humanities make to the production of knowledge and enhancement of the quality of life, as well as to the much needed sense of purpose and meaning. (shrink)
Helen Dean King's scientific work focused on inbreeding using experimental data collected from standardized laboratory rats to elucidate problems in human heredity. The meticulous care with which she carried on her inbreeding experiments assured that her results were dependable and her theoretical explanations credible. By using her nearly homozygous rats as desired commodities, she also was granted access to venues and people otherwise unavailable to her as a woman. King's scientific career was made possible through her life experiences. She (...) earned a doctorate from Bryn Mawr College under Thomas Hunt Morgan and spent a productive career at the Wistar Institute of Anatomy and Biology in Philadelphia where she had access to the experimental subjects which made her career possible. In this paper I examine King's work on inbreeding, her participation in the debates over eugenics, her position at the Wistar Institute, her status as a woman working with mostly male scientists, and her involvement with popular science. (shrink)