The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

in Values and Morals, eds. Alvin Goldman and Jaegwon Kim (Reidel, 1978), pp. 186-214.

Contemporary science presents us with the remarkable theory that the universe began to exist about fifteen billion years ago with a cataclysmic explosion called "the Big Bang." The question of whether Big Bang cosmology supports theism or atheism has long been a matter of discussion among the general public and in popular science books, but has received scant attention from philosophers. This book sets out to fill this gap by means of a sustained debate between two philosophers, William Lane (...) Craig and Quentin Smith, who defend opposing positions. Craig argues that the Big Bang that began the universe was created by God, while Smith argues that the Big Bang has no cause. Alternating chapters by the two philosophers criticize and attempt to refute preceding arguments. Their arguments are based on Einstein's theory of relativity and include a discussion of the new quantum cosmology recently developed by Stephen Hawking and popularized in A Brief History of Time. (shrink)

This is a book symposium on Steffen Borge’s The Philosophy of Football. It has contributions from William Morgan, Murray Smith and Brian Weatherson with replies from Borge.

It is often presumed that effects of neural tissue transplants are due to release of neurotransmitter. In many cases, however, effects attributed to transplants may be related to phenomena such as trophic effects mediated by glial cells or even tissue reactions to injury. Any conclusion regarding causation of graft effects must be based on the control groups or other comparisons used. In human clinical studies, for example, comparing the same subject before and after transplantation allows for many interpretations of the (...) causes of clinical changes. (shrink)

What determines whether an action is right or wrong? Morality, Rules, and Consequences: A Critical Reader explores for students and researchers the relationship between consequentialist theory and moral rules. Most of the chapters focus on rule consequentialism or on the distinction between act and rule versions of consequentialism. Contributors, among them the leading philosophers in the discipline, suggest ways of assessing whether rule consequentialism could be a satisfactory moral theory. These essays, all of which are previously unpublished, provide students in (...) moral philosophy with essential material and ask key questions on just what the criteria for an adequate moral theory might be. (shrink)

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

In this chapter we explain what the no-difference challenge is, focusing in particular on act consequentialism. We talk about how different theories of causation affect the no-difference challenge; how the challenge shows up in real-world cases including voting, global labour injustice, global poverty, and climate change; and we work through a number of the solutions to the challenge that have been offered, arguing that many fail to actually meet it. We defend and extend one solution that does, and present a (...) further solution of our own. (shrink)

UK-based research conducted within a healthcare setting generally requires approval from the National Research Ethics Service. Research ethics committees are required to assess a vast range of proposals, differing in both their topic and methodology. We argue the methodological benchmarks with which research ethics committees are generally familiar and which form the basis of assessments of quality do not fit with the aims and objectives of many forms of qualitative inquiry and their more iterative goals of describing social processes/mechanisms and (...) making visible the complexities of social practices. We review current debates in the literature related to ethical review and social research, and illustrate the importance of re-visiting the notion of ethics in healthcare research. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

The topic of this book is a fundamental philosophical question: why should I be moral? Philosophers have long been concerned with the legitimacy of morality's claim on us, especially with morality's ostensible aim to motivate certain actions of all persons unconditionally. While the problem of moral normativity - that is, the justification of the binding force of moral claims - has received extensive treatment analytic moral theory, little attention has been paid to the potential contribution that phenomenology might make to (...) this central debate in metaethics. -/- In The Phenomenology of Moral Normativity, William H. Smith takes up the question of morality's legitimacy anew, drawing contemporary moral philosophers, particularly Christine Korsgaard and Stephen Darwall, into conversation with present-day phenomenologists like John Drummond and the phenomenological philosophy of Edmund Husserl, Martin Heidegger, and Emmanuel Levinas. -/- The results of this juxtaposition are surprising: utilizing a two-part account of moral normativity, Smith contends that the ground of morality itself is second-personal, rooted in the ethical demand intrinsic to other persons, while the ground for particular moral-obligations is first-personal, rooted in the subject's avowal or endorsement of certain moral norms within a concrete historical situation. Thus, Smith argues that phenomenological analysis allows us to make sense of an idea that has long held intuitive appeal, but that modern moral philosophy has been unable to render satisfactorily, namely, that the normative source of valid moral claims is simply other persons and what we owe to them. (shrink)

This symposium collects together five essays reflecting on The Phenomenology of Moral Normativity by William H. Smith. This work is an original monograph bridging the phenomenological tradition and contemporary moral theory in an attempt to articulate a phenomenological theory of moral normativity. The first piece in the symposium, by Smith, offers a précis of the book’s argumentative structure, including its central theses, methodological commitments, and pluralistic orientation. The next three pieces provide critical assessments of the book’s major (...) narrative turns: Therese Cory writes in defense of moral realism and the third-person perspective, in response to Smith’s use of Korsgaard in the opening chapters of his book; Apple Igrek wonders whether the post-modern radicality of Levinas’s ethics have been compromised by Smith’s appropriation of Levinas; and Matthew Rellihan contends that Smith’s purported phenomenological theory of morality is inconsistent with a rigorous application of the phenomenological method. In the final piece, Smith responds to each critic in turn. This last offering defends Smith’s two-fold grounding of morality in a phenomenological account of the self and our responsibility to others, a reimagining of Heidegger’s fundamental ontology in light of Levinas’s ethical metaphysics. The theory unites authenticity with the face-to-face encounter, resoluteness with first-person reflective endorsement, and infinite responsibility to the other with second-personal address. These essays were first delivered at an author-meets-critics session hosted at Seattle University in the winter of 2012, then substantially revised and updated for this publication. (shrink)

Skepticism about ethical expertise has grown common, raising concerns that bioethicists’ roles are inappropriate or depend on something other than expertise in ethics. While these roles may depend on skills other than those of expertise, overlooking the role of expertise in ethics distorts our conception of moral advising. This paper argues that motivations to reject ethical expertise often stem from concerns about elitism: either an intellectualist elitism, where some privileged elite have supposedly special access in virtue of expertise in moral (...) theory; or an authoritarian elitism, where our reliance on experts in ethics risks violation of autonomy and democracy. The paper sketches an anti-elitist conception of ethics expertise in bioethics as continuous with an anti-elitist conception of ethics expertise in common moral practice, undercutting the intellectualism, and then uses this anti-elitist conception to reject arguments that ethical expertise violates autonomy or democracy. An anti-elitist picture of ethical expertise both renders it consistent with our general moral practice and allows us to resist skeptical concerns. (shrink)

In this paper I explore various grounds on which wilderness can be regarded as something which we should value, and I draw attention to the problems of resolving conftict which are generated by these diverse grounds. I conclude that our attitudes toward nature are partially determined by a background of metaphysical assumptions which derive in particular from the philosophy of Descartes. Thesemetaphysical preconceptions lead to the misconception that various alternative views about the natural environment are mystical or occult. Thus, an (...) alternative non-Cartesian mode ofconception involving holistic or systemic modes of-thought is required in order to develop a satisfactory basis for our attitude toward the natural world. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)