The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

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)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Historically, patients have deferred to physicians′ judgments about appropriate medical care, thereby limiting patient participation in treatment decisions. In this model of medical decision making, physicians typically decided upon the treatment plan. Communication with patients focused on securing their cooperation in accepting a treatment decision that essentially had already been made.

Laurel Schneider takes the reader on a vivid journey from the origins of "the logic of the One" - only recently dubbed monotheism - through to the modern day, where monotheism has increasingly failed to adequately address spiritual, scientific, and ethical experiences in the changing world. In Part I, Schneider traces a trajectory from the ancient history of monotheism and multiplicity in Greece, Israel, and Africa through the Constantinian valorization of the logic of the One, to medieval and modern (...) challenges to that logic in poetry and science. She pursues an alternative and constructive approach in Part II: a "logic of multiplicity" already resident in Christian traditions in which the complexity of life and the presence of God may be better articulated. Part III takes up the open-ended question of ethics from within that multiplicity, exploring the implications of this radical and realistic new theology for the questions that lie underneath theological construction: questions of belonging and nationalism, of the possibility of love, and of unity. In this groundbreaking work of contemporary theology, Schneider shows that the One is not lost in divine multiplicity, and that in spite of its abstractions, divine multiplicity is realistic and worldly, impossible ultimately to abstract. (shrink)

Laurel Schneider takes the reader on a vivid journey from the origins of "the logic of the One" - only recently dubbed monotheism - through to the modern day, where monotheism has increasingly failed to adequately address spiritual, scientific, and ethical experiences in the changing world. In Part I, Schneider traces a trajectory from the ancient history of monotheism and multiplicity in Greece, Israel, and Africa through the Constantinian valorization of the logic of the One, to medieval and modern (...) challenges to that logic in poetry and science. She pursues an alternative and constructive approach in Part II: a "logic of multiplicity" already resident in Christian traditions in which the complexity of life and the presence of God may be better articulated. Part III takes up the open-ended question of ethics from within that multiplicity, exploring the implications of this radical and realistic new theology for the questions that lie underneath theological construction: questions of belonging and nationalism, of the possibility of love, and of unity. In this groundbreaking work of contemporary theology, Schneider shows that the One is not lost in divine multiplicity, and that in spite of its abstractions, divine multiplicity is realistic and worldly, impossible ultimately to abstract. (shrink)

The key objectives of this book are to demonstrate the applicability of issues in the philosophy of science to problems in psychiatry and to show how the conceptual issues raised by psychiatry should be considered more closely by philosophers of science. These are worthy aims: the philosophy of psychiatry needs to draw more thoughtfully upon contemporary philosophical debates and stimulating interest within the philosophy of science is a good way to do this.Cooper's book succeeds for both of these desiderata. (...) The first five chapters discuss the central issues in the philosophy of psychiatry: whether mental illness is a disease/natural kind and what follows from this. There is a large literature on these questions, some of which …. (shrink)

421A REREADING OF THE PHAEDO Journal of the History of Philosophy, vol. 40, no. 4 421?36 [421] Have We Been Careless with Socrates? Last Words?: A Rereading of the Phaedo LAUREL A. MADISON* IN SECTION 340 OF THE GAY SCIENCE, Nietzsche offers what he believes will be received as a scandalous interpretation of Socrates? last words.?Whether it was death or the poison or piety or malice?something loosened his tongue at that moment and he said:?O Crito, I owe Asclepius a (...) rooster.? This ridiculous and terrible?last word? means for those who have ears:?O Crito, life is a disease.??1 Nietzsche might be surprised, however, to discover just how many readers?have ears? to hear the pessimism and resentment in Socrates? voice as he bids farewell to his life. Indeed, this interpretation has become standard among both Plato scholars and non-scholars, taking on the air of orthodoxy.2 Not only is this?Nietzschean? reading widespread, it also has a significant impact on how we understand Plato?s project in general and, ultimately, whether or * Laurel A. Madison is writing a dissertation on Plato and Nietzsche at Loyola University Chicago. 1 Friedrich Nietzsche, The Gay Science, Walter Kaufmann, trans.. 2 See, for example, C. J. Rowe, ed., Plato: Phaedo, 295?6, who sees two options for interpreting this passage. Either Socrates is referring to an actual debt or he is thanking the god of healing for... (shrink)

421A REREADING OF THE PHAEDO Journal of the History of Philosophy, vol. 40, no. 4 421?36 [421] Have We Been Careless with Socrates? Last Words?: A Rereading of the Phaedo LAUREL A. MADISON* IN SECTION 340 OF THE GAY SCIENCE, Nietzsche offers what he believes will be received as a scandalous interpretation of Socrates? last words. ?Whether it was death or the poison or piety or malice?something loosened his tongue at that moment and he said: ?O Crito, I owe (...) Asclepius a rooster.? This ridiculous and terrible ?last word? means for those who have ears: ?O Crito, life is a disease.??1 Nietzsche might be surprised, however, to discover just how many readers ?have ears? to hear the pessimism and resentment in Socrates? voice as he bids farewell to his life. Indeed, this interpretation has become standard among both Plato scholars and non-scholars, taking on the air of orthodoxy.2 Not only is this ?Nietzschean? reading widespread, it also has a significant impact on how we understand Plato?s project in general and, ultimately, whether or * Laurel A. Madison is writing a dissertation on Plato and Nietzsche at Loyola University Chicago. 1 Friedrich Nietzsche, The Gay Science, Walter Kaufmann, trans. . 2 See, for example, C. J. Rowe, ed., Plato: Phaedo , 295?6, who sees two options for interpreting this passage. Either Socrates is referring to an actual debt or he is thanking the god of healing for.. (shrink)

Philosophers have recently revived the study of the ancient Greek topics of virtue and the virtues—justice, honesty, temperance, friendship, courage, and so on as qualities of mind and character belonging to individual people. But one issue at the center of Greek moral theory seems to have dropped out of consideration. This is the question of the unity of virtue, the unity of the virtues. Must anyone who has one of these qualities have others of them as well, indeed all of (...) them—all the ones that really do deserve to be counted as virtues? Even further, is there really no set of distinct and separate virtuous qualities at all, but at bottom only a single one—so that the person who has this single condition of “virtue” is entitled also to the further descriptions “honest” and “well-controlled” and “just” and “friendly” and “courageous” and “fostering” and “supportive,” and so on, as distinguishable aspects or immediate effects of his unitary “virtue”? (shrink)

Dialectic and Dialogue is an insightful and illuminating study of what is perhaps the most important yet frequently ignored question in Plato scholarship, namely, what is Plato's conception of philosophy? In his Introduction, Gonzalez rightly notes that while every study of Plato presupposes a particular understanding of the nature and aim of philosophy, few scholars pause to consider whether their conception of philosophy, which they proceed to impose on Plato, is in fact Plato's. This unrefiective approach results in a great (...) variety of readings that run the risk of seriously misrepresenting Plato's project. Thus, the aim of Dia~ lectic and Dialogue is to address the following fundamental questions: What, in Plato's view, does it mean to philosophize? What kind of knowledge do we seek and by what means do we acquire it? Since Plato generally identifies philosophy with dialectic, Gonzalez's study is an investigation into the nature of dialectic. (shrink)

We hope—even as we doubt—that the environmental crisis can be controlled. Public awareness of our species’ self-destructiveness as material beings in a material world is growing—but so is the destructiveness. The practical interventions needed for saving and restoring the earth will require a collective shift of such magnitude as to take on a spiritual and religious intensity.This transformation has in part already begun. Traditions of ecological theology and ecologically aware religious practice have been preparing the way for decades. Yet these (...) traditions still remain marginal to society, academy, and church. With a fresh, transdisciplinary approach, Ecospirit probes the possibility of a green shift radical enough to permeate the ancient roots of our sensibility and the social sources of our practice. From new language for imagining the earth as a living ground to current constructions of nature in theology, science, and philosophy; from environmentalism’s questioning of postmodern thought to a garden of green doctrines, rituals, and liturgies for contemporary religion, these original essays explore and expand our sense of how to proceed in the face of an ecological crisis that demands new thinking and acting. In the midst of planetary crisis, they activateimagination, humor, ritual, and hope. (shrink)

This is the first sustained study examining how the emotions of remorse and regret were manifested in Greek and Roman public life. By discussing the standard lexical denotations of remorse, Fulkerson shows how it was not normally expressed by high-status individuals, but by their inferiors, and how it often served to show defect of character.

Science, Richard Holmes suc- ISBN 9780375422225. Paper, Harper, ceeds admirably in pursing the London, 2009. £9.99, C$21.95. ISBN latter meaning, though he has 9780007149537. Vintage, New York, ambitions also to explore the 2010. $17.95. ISBN 9781400031870. former. Holmes, a biographer of Shelley, Coleridge, and Dr. Johnson, has woven together several tales of English scientists who ventured to exotic lands, flung themselves into love affairs, and wrote sonnets to science. The likes of Joseph Banks, William and Caroline Herschel, Mungo Park, and (...) Humphry Davy displayed, in the calmer English manner, the kind of personalities that discovered the “beauty,” if not exactly the “terror,” of science. Holmes dishes up the faux terror in his chapter on Mary Shelley’s Frankenstein, although the wilder opinions of Samuel Taylor Coleridge, who passes through his pages in a drug-induced ramble, are unsettling enough. The lives of the individuals whose accomplishments Holmes depicts are bracketed by James Cook’s fi rst voyage to the South Pacifi c and Darwin’s Beagle adventure. With dexterity and considerable but unobtrusive scholarship, Holmes goes far to reveal “the scientifi c process by which a mind of acknowledged power actually proceeds in the path of successful enquiry.” That last line comes from David Brewster’s Life of Sir Isaac Newton. The minds Holmes depicts, however, stand deep in the shadow of the standard by which Brewster gauged scientifi c power. Joseph Banks, botanist and long-time president of the Royal Society, serves Holmes as his Virgil, helping to link together the lives of his other protagonists. Banks gained his scientifi c reputation as a botanist on Cook’s fi rst voyage, though Holmes only touches lightly on the botanical work. He rather lingers, as a deft biographer might, over the scientist’s. (shrink)

This article brings together two case studies that examine how nontransgender people, “gender normals,” interact with transgender people to highlight the connections between doing gender and heteronormativity. By contrasting public and private interactions that range from nonsexual to sexualized to sexual, the authors show how gender and sexuality are inextricably tied together. The authors demonstrate that the criteria for membership in a gender category are significantly different in social versus sexual circumstances. While gender is presumed to reflect biological sex in (...) all social interactions, the importance of doing gender in a way that represents the shape of one's genitals is heightened in sexual and sexualized situations. Responses to perceived failures to fulfill gender criteria in sexual and sexualized relationships are themselves gendered; men and women select different targets for and utilize gendered tactics to accomplish the policing of supposedly natural gender boundaries and to repair breaches to heteronormativity. (shrink)

Playing with correct intonation is one of the major challenges for a string player. A player must learn how to physically reproduce a target pitch, but before that, the player must learn what correct intonation is. This requires audiation- the aural equivalent of visualization- of every note along with self-assessment whether the pitch played matches the target, and if not, what action should be taken to correct it. A challenge for successful learning is that much of it occurs during practice, (...) typically without outside supervision. A student who has not yet learned to hear correct intonation may repeatedly practice out of tune, blithely normalising bad habits and bad intonation. The real-time reflective nature of intonation and its consistent demand on attention make it a ripe target for technological intervention. Using a violin augmented to combine fingerboard sensors with audio analysis for real-time pitch detection, we examine the efficacy of three methods of real-time feedback for improving intonation and pitch learning. The first, aural feedback in the form of an in-tune guide pitch following the student in real-time, is inspired by the tradition of students playing along with teachers. The second is visual feedback on intonation correctness using an algorithm optimised for use throughout normal practice. The third is a combination of the two methods, simultaneously providing aural and visual feedback. Twelve beginning violinists, including children and adults, were given four in-situ 20-30 minute lessons. Each lesson used one of the intonation feedback methods, along with a control lesson using no feedback. We collected data on intonation accuracy and conducted interviews on student experience and preference. The results varied by player, with evidence of some players being helped by the feedback methods but also cases where the feedback was distracting and intonation suffered. However interviews suggested a high level of interest and potential in having such tools to help during practice, and results also suggested that it takes time to learn to use the real-time aural and visual feedback. Both methods of feedback demonstrate potential for assisting self-reflection during individual practice. (shrink)

ABSTRACT Political scientist James Fishkin has devised?deliberative polling? as a means to better informed, more autonomous, and more reflective participant opinion. After a deliberative poll, this improved form of public opinion can be disseminated to the general public and to policy makers so as to influence public opinion and public policy. Close examination of the results of deliberative polling, however, suggests no evidence of a normatively desirable gain in informed, autonomous, or considered opinion?as opposed to minor gains in participants' general (...) political knowledge and in ideological constraint, which is likely attributable to the pre-packaged?expert? views set forth in the briefing materials provided to the participants. (shrink)

This collection reports on the latest research on an increasingly pivotal issue for evolutionary biology: cooperation. The chapters are written from a variety of disciplinary perspectives and utilize research tools that range from empirical survey to conceptual modeling, reflecting the rich diversity of work in the field. They explore a wide taxonomic range, concentrating on bacteria, social insects, and, especially, humans. -/- Part I (“Agents and Environments”) investigates the connections of social cooperation in social organizations to the conditions that make (...) cooperation profitable and stable, focusing on the interactions of agent, population, and environment. Part II (“Agents and Mechanisms”) focuses on how proximate mechanisms emerge and operate in the evolutionary process and how they shape evolutionary trajectories. Throughout the book, certain themes emerge that demonstrate the ubiquity of questions regarding cooperation in evolutionary biology: the generation and division of the profits of cooperation; transitions in individuality; levels of selection, from gene to organism; and the “human cooperation explosion” that makes our own social behavior particularly puzzling from an evolutionary perspective. (shrink)

An ongoing study examining the discursive negotiation of ethnic and gendered embodied identities of adolescent girls in Japan with Japanese and `white' mixed-parentage is extended to also investigate and compare boys. This study draws on Feminist Poststructuralist Discourse Analysis which views women and girls as `simultaneously positioned as relatively powerless within a range of dominant discourses on gender, but as relatively powerful within alternative and competing social discourses'. Here, this is taken further by also giving voice to boys. Furthermore, ethnic (...) discourses are examined alongside of gender discourses. Not only girls constructed the `idealized Other', within discourses of femininity, but boys similarly viewed their bodies against a model of idealized masculinity within discourses of masculinities. The boys revealed a feminized, narcissistic body consciousness where they struggled to resist a `discourse of foreign grotesqueness' and instead worked to embody themselves within a positive `discourse of foreign attractiveness', as did the girls. (shrink)

Aside from aperçus of Kant, Nietzsche, and of course, Aristotle, metaphor has not, until recently, received its due. The dominant view has been Hobbes': metaphors are an ‘abuse’ of language, less dangerous than ordinary equivocation only because they ‘profess their inconstancy’.

Both notional and grammatical number affect agreement during language production. To explore their workings, we investigated how semantic integration, a type of conceptual relatedness, produces variations in agreement (Solomon & Pearlmutter, 2004). These agreement variations are open to competing notional and lexical-grammatical number accounts. The notional hypothesis is that changes in number agreement reflect differences in referential coherence: More coherence yields more singularity. The lexical-grammatical hypothesis is that changes in agreement arise from competition between nouns differing in grammatical number: More (...) competition yields more plurality. These hypotheses make opposing predictions about semantic integration. On the notional hypothesis, semantic integration promotes singular agreement. On the lexical-grammatical hypothesis, semantic integration promotes plural agreement. We tested these hypotheses with agreement elicitation tasks in two experiments. Both experiments supported the notional hypothesis, with semantic integration creating faster and more frequent singular agreement. This implies that referential coherence mediates the effect of semantic integration on number agreement. (shrink)

Cedant arma togae, ‘let arms yield to the toga’. Thus begins the famous verse from Cicero's poem on his consulship that highlights the protagonist's suppression of the Catilinarian conspiracy by favourably contrasting this political achievement with success on the battlefield. But how does the line continue? Its conclusion is transmitted in two different versions,concedat laurea laudiandconcedat laurea linguae, and scholars have long been divided over which one is Cicero's original text. In this paper, we revisit the issue and not only (...) propose an answer to the question of what Cicero actually wrote, but also examine those attestations of the verse that date to the author's own lifetime, elucidating the contexts that account for the quotation of one variant rather than the other. (shrink)

The medieval computus was intended primarily for literate and numerate ecclesiastical users; reading the Latin computus required a good knowledge of technical Latin, while understanding its calculations presupposed some formal education in arithmetic and astronomy. By the mid-thirteenth century, users would have included a small group of literate and numerate laymen; by the mid-fifteenth century, users would have included the less educated and even semiliterate, as a consequence of a more extensive range of computus material made available for the purpose (...) in the vernacular. (shrink)

The evolutionary origins of complex capacities such as musicality are not simple, and likely involved many interacting steps of musicality-specific adaptations, exaptations, and cultural creation. A full account of the origins of musicality needs to consider the role of ancient adaptations such as credible singing, auditory scene analysis, and prediction-reward circuits in constraining the emergence of musicality.

The ABA has adopted four model policies that address, in one way or another, the issue of foreign lawyer mobility. These policies are the ABA Model Foreign Legal Consultant Rule, which is commonly known as the FLC rule, the ABA Model Rule for Temporary Practice by Foreign Lawyers, which is commonly known as the FIFO rule, ABA Model Rule of Professional Conduct 5.5, which permits foreign lawyers to serve as in-house counsel, and the ABA Model Rule on Pro Hac Vice (...) Admission. All four of the ABA's foreign lawyer mobility recommendations include a requirement that the mobile foreign lawyer is “ subject to effective regulation and discipline by a duly constituted professional body or a public authority .” In other words, these rules set forth requirements regarding the nature of the regulatory system in the foreign lawyer's home jurisdiction. A number of US states have included this requirement in their foreign lawyer mobility provisions, but a number have not. Although the ABA model rules and a number of state rules include this requirement, neither the ABA Model Rules nor any of the state rules have defined what it means for a foreign lawyer to come from a system with “effective regulation and discipline.” Nor is there any evidence that this requirement has been enforced in those states that have included this requirement. This article suggests that the “effective regulation and discipline” requirement has been an elephant in the room that no one has been willing to talk about. The article argues that the time has come to confront this issue head-on. It asserts that either efforts should be undertaken to define and enforce this requirement or that the requirement should be abandoned. The article reviews two “threshold” issues that jurisdictions might want to consider when deciding whether to adopt or retain an “effective regulation and discipline” requirement. It also identifies cross-cultural and cross-professional resources that might be consulted for “benchmarking” purposes if and when US regulators decide to add “meat to the bones” by defining and enforcing the “effective regulation and discipline” requirement found in foreign lawyer mobility provisions. (shrink)