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)

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)

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 (...) class='Hi'>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)

This paper examines classification practices in the domain of plant data semantics, and particularly methods used to label plant traits to foster the collection, management, linkage and analysis of data about crops across locations—which crucially inform research and interventions on plants and agriculture. The efforts required to share data place in sharp relief the forms of diversity characterizing the systems used to capture the biological and environmental characteristics of plant variants: particularly the biological, cultural, scientific and semantic (...) diversity affecting the identification and description of plant traits, the methods used to generate and process data, and the goals and skills of those with relevant expertise—including farmers and breeders. Through a study of the Crop Ontology (which explicitly recognizes and negotiates diversity) and its application to cassava breeding, I argue for a process-sensitive approach to the naming of plant traits that focuses on documenting environmental processes instead of biological products. I claim that this approach can foster reliable linkage and robust re-use of plant data, while at the same time facilitating dialogue between data scientists, plant researchers, breeders, and other relevant experts in ways that crucially inform agricultural interventions. I conclude that the study of data semantics and related descriptors constitutes a productive and underexplored way to think about the epistemic import of naming traits within plant science. The effort to articulate semantic differences among plant varieties and methods of data processing can generate newly inclusive ways to develop and communicate biological knowledge. In turn, such practices have the potential to defy existing understandings of systematisation and hierarchies of expertise in biology, thus bolstering the extent to which plant science can support biodiversity and sustainable agriculture. (shrink)

Philosophy is one of the most intimidating and difficult of disciplines, as any of its students can attest. This book is an important entry in a distinctive new series from Routledge: "The Great Philosophers." Breaking down obstacles to understanding the ideas of history's greatest thinkers, these brief, accessible, and affordable volumes offer essential introductions to the great philosophers of the Western tradition from Plato to Wittgenstein.In just 64 pages, each author, a specialist on his subject, places the philosopher and his (...) ideas into historical perspective. Each volume explains, in simple terms, the basic concepts, enriching the narrative through the effective use of biographical detail. And instead of attempting to explain the philosopher's entire intellectual history, which can be daunting, this series takes one central theme in each philosopher's work, using it to unfold the philosopher's thoughts. (shrink)

A stimulating introduction to central issues of political theory, including liberty, rights and the state, and the claims of need and politics.

Simone Weil (1909-1943) was one of the most original philosophers & political thinkers of this century. Coming to Christianity late in her short life, she offered a refreshing creativity & a rare ability to confront theological complacencies. In introducing her writings & thoughts, this book emphasizes her never-ending search for truth, a search that epitomizes twentieth-century spirituality.

A short book combining extracts from the work of one of the world's greatest thinkers with commentary from one of Britain's most distinguished writers on philosophy.

There are long-standing doubts about whether data from subjective scales—for instance, self-reports of happiness—are cardinally comparable. It is unclear how to assess whether these doubts are justified without first addressing two unresolved theoretical questions: how do people interpret subjective scales? Which assumptions are required for cardinal comparability? This paper offers answers to both. It proposes an explanation for scale interpretation derived from philosophy of language and game theory. In short: conversation is a cooperative endeavour governed by various maxims (Grice 1989); (...) because subjective scales are vague and individuals want to make themselves understood, scale interpretation is a search for a focal point (Schelling 1960). A specific focal point it hypothesised; if this hypothesis is correct, subjective data will be cardinally comparable. Four individually necessary and jointly sufficient conditions for cardinal comparability are specified. The paper then argues this hypothesis can be empirically be tested, makes an initial attempt to do so using subjective well-being data, and concludes it is supported. Numerous areas for further research are identified including, at the end of the paper, how certain tests could be used to ‘correct’ subjective data if they are not cardinal. (shrink)

While life satisfaction theories (LSTs) of well-being are barely discussed in philosophy, they are popular among social scientists and wider society. When philosophers have discussed LSTs, they are taken to be a distinct alternative to the three canonical accounts of well-being—hedonism, desire theories, the objective list. This essay makes three main claims. First, on closer inspection, LSTs are indistinguishable from a type of desire theory—the global desire theory. Second, the life satisfaction/global desire theories are the only subjectivist accounts of well-being (...) in the sense that they maintain individuals decide what makes their lives go well for them; hedonism and other desire theories are subjectivist only in some alternative senses. Third, subjectivism is implausible, although for different reasons from those that are usually given. I examine what I take to be the two main current objections to LSTs and argue that they are unproblematic. I then raise two different, challenging objections. The first is novel. The second has been noted in passing, but its seriousness underestimated. I close by sketching some non-obvious difficulties that subjectivists will face if they attempt to show rival objectivist theories suffer even more counterintuitive implications. Although subjectivism has a strong intuitive pull, we should be ready to abandon it in favour of an objectivist theory—although it is not my purpose here to say which one. (shrink)

First published in 1980. Routledge is an imprint of Taylor & Francis, an informa company.

In "Culture and Value" Wittgenstein remarks that the truly "religious man" thinks himself to be, not merely "imperfect" or "ill," but wholly "wretched." While such sentiments are of obvious biographical interest, in this paper I show why they are also worthy of serious philosophical attention. Although the influence of Wittgenstein's thinking on the philosophy of religion is often judged negatively (as, for example, leading to quietist and/or fideist-relativist conclusions) I argue that the distinctly ethical conception of religion (specifically Christianity) that (...) Wittgenstein presents should lead us to a quite different assessment. In particular, his preoccupation with the categorical nature of religion suggests a conception of "genuine" religious belief which disrupts both the economics of eschatological-salvationist hope, and the traditional ethical precept that "ought implies can." In short, what Wittgenstein presents is a sketch of a religion without recompense. (shrink)

There is a world-wide debate at the moment about the appropriate role for the state in modern societies in the light of the world financial crisis. This book provides a comprehensive analysis and critique of Neo-liberal or economic liberal ideas on this issue.

Widespread and lasting consensus has not been philosophy's fate. Indeed, one of philosophy's most striking features is its ability to accommodate “not only different answers to philosophical questions” but also “total disagreement on what questions are philosophical” (Rorty 1995, 58). It is therefore hardly surprising that philosophers' responses to this metaphilosophical predicament have been similarly varied. This article considers two recent diagnoses of philosophical diversity: Kornblith and Rescher (respectively) claim that taking philosophical disagreement seriously does not lead to metaphilosophical scepticism. (...) The article argues that their confidence is misplaced in so far as both wrongly assume that ordinary, first-order philosophical practice and second-order metaphilosophical reflection are separate enterprises. We can say that the universe consists of a substance, and this substance we will call “atoms,” or else we will call it “monads.” Democritus called it atoms. Leibniz called it monads. Fortunately, the two men never met, or there would have been a very dull argument. (Allen 1997, 171) When will philosophers learn to be less pretentious and arrogant in their claims? One would imagine that the philosophic experiences of twenty-five centuries would have taught them the fallacy of self-esteem! (Schilpp 1935, 233). (shrink)

Mark Dooley has recently argued (principally against Simon Critchley) that the attempt to establish too strong a ‘connection’ between Jacques Derrida and Emmanuel Levinas not only distorts crucial disparities between their respective philosophies, it also contaminates Derrida’s recent work with Levinas’s inherent ‘political naivety’. In short, on Dooley’s reading, Levinas is only of ‘inspirational value’ for Derrida. I am not concerned with defending Critchley’s own reading of the ‘Derrida–Levinas connection’. My objective is rather to demonstrate, first, the way in which (...) Dooley’s argument hinges upon a misreading of Levinas and Derrida, and, second, why Derrida’s recent thinking is in fact fundamentally Levinasian. Key Words: contingency • guilt • Holocaust • hospitality • institutions • nature • suffering • third party • violence. (shrink)

In Culture and Value Wittgenstein remarks: ‘Thoughts that are at peace. That's what someone who philosophizes yearns for’. The desire for such conceptual tranquillity is a recurrent theme in Wittgenstein's work, and especially in his later ‘grammatical-therapeutic’ philosophy. Some commentators (notably Rush Rhees and C. G. Luckhardt) have cautioned that emphasising this facet of Wittgenstein's work ‘trivialises’ philosophy – something which is at odds with Wittgenstein's own philosophical ‘seriousness’ (in particular his insistence that philosophy demands that one ‘Go the bloody (...) hard way’). Drawing on a number of correlations between Wittgenstein's conception of philosophy and that of the Pyrrhonian Sceptics, in this paper I defend a strong ‘therapeutic’ reading of Wittgenstein, and show how this can be maintained without ‘trivialising’ philosophy. (shrink)

Grondin situates Gadamer's concerns in the context of traditional philosophical issues, showing, for example, how Gadamer both continues and significantly modifies Descartes' approach to the philosophical problem of method and advances rather than simply follows Heidegger's treatment of the relationship of thinking to language. In doing this Grondin shows that the issues of philosophical hermeneutics are relevant to contemporary concerns in science and history.

This article argues for four interrelated claims: Metaphilosophy is not one sub-discipline of philosophy, nor is it restricted to questions of methodology. Rather, metaphilosophical inquiry encompasses the general background conditions of philosophical practice. These background conditions are of various sorts, not only those routinely considered “philosophical” but also those considered biographical, historical, and sociological. Accordingly, we should be wary of the customary distinction between what is proper and merely contingent to philosophy. “What is philosophy?” is best understood as a practical (...) question concerning how members of different philosophical sub-communities identify what is pertinent to their respective activities and self-conceptions. Given –, understanding what philosophy is requires us to take more seriously the social-institutional dimension of contemporary philosophical practice. (shrink)

The paper explicates Bonhoeffer's dense statement, made in a 1932 lecture, that `Reality is the sacrament of [the ethical] command'. It begins with a summary of William T. Cavanaugh's rich description of the Eucharist as that act which makes the Church Christ's body, thereby constituting the true res publica. A comparison is drawn with Bonhoeffer's account of the sacramental foundation of the Church's public proclamation of God's ethical command. Bonhoeffer differs from Cavanaugh, I suggest, not only in his conviction that (...) the Church speaks God's command penultimately and with humility, but in regarding the state as one of the means by which God acts within the penultimate to preserve creation. (shrink)

A phenome occurs through the many pathways of the complex net of interaction between the phenome and its environment; therefore researching and understanding how it arises requires investigation into many possible causes that are in constant interaction with each other. The most comprehensive investigations in biology are the ones in which many biologists from different sub-areas—evolutionary biology, developmental biology, molecular biology, physiology, genetics, epigenetics, ecology—have collaborated. Still, biologists do not always need to collaborate or look for the most (...) comprehensive explanations. A more standard investigation in biology occurs within a single subarea, and uses well-defined experiments with very specific conditions. This paper is about causation and related explanation in plant phenome research and its relevance to Aristotle’s Theory of Four Causes. I argue that there are causes which resemble Aristotle’s formal, material, and efficient causes in phenotype explanation and occurrence; but causes which resemble Aristotle’s final causes occur in phenotype explanation only, not in the occurrence. (shrink)

_Wittgenstein and Levinas_ examines the oft-neglected relationship between the philosophies of two of the most important and notoriously difficult thinkers of the twentieth century. By bringing the work of each philosopher to bear upon the other, Plant navigates between the antagonistic intellectual traditions that they helped to share. The central focus on the book is the complex yet illuminating interplay between a number of ethical-religious themes in both Wittgenstein's mature thinking and Levinas's distinctive account of ethical responsibility.

IN his running debate with Fr Joseph Owens, Dr Joseph Bobik at one point raises this issue.

First published in 1973 this volume demonstrates the interconnection between Hegel's political and metaphysical writings. This book provides a point of entry into Hegel's system of ideas. Condemned unread, and when read far too often misunderstood, Hegel's thought has once more begun to make its impact on contemporary ideas with many of today's most important social and political thinkers.

In 1981, after 20 years of teaching and writing philosophy, Derrida claimed that ‘less than ever’ did he ‘know what philosophy is’. Indeed, his ‘knowledge of what ... constitutes the essence of philosophy’ remained ‘at zero degree’. 1 These were not flippant remarks. Rather, Derrida’s avowed uncertainty is part of a more general metaphilosophical view; namely, that ‘Philosophy has a way of being at home with itself that consists in not being at home with itself’. 2 In this article I (...) will critically reconstruct and develop this view, paying particular attention to the ‘institutional’ dimension of contemporary philosophy. (shrink)

Wittgenstein’s remarks on religious and magical practices are often thought to harbour troubling fideistic and relativistic views. Unsurprisingly, commentators are generally resistant to the idea that religious belief constitutes a ‘language‐game’ governed by its own peculiar ‘rules’, and is thereby insulated from the critical assessment of non‐participants. Indeed, on this fideist‐relativist reading, it is unclear how mutual understanding between believers and non‐believers (even between different sorts of believers) would be possible. In this paper I do three things: (i) show why (...) the fideist‐relativist reading of Wittgenstein is not wildly implausible (Sections 1–2); (ii) argue that, despite its initial plausibility, this reading fails to take into account Wittgenstein’s naturalism (Sections 3–4); and (iii) explain what sort of naturalism this is, and how it sheds light on Wittgenstein’s remarks on religious belief (Sections 5–6). (shrink)

According to Levinas, the history of western philosophy has routinely ‘assimilated every Other into the Same’. More concretely stated, philosophers have neglected the ethical significance of other human beings in their vulnerable, embodied singularity. What is striking about Levinas’ recasting of ethics as ‘first philosophy’ is his own relative disregard for non-human animals. In this article I will do two interrelated things: (1) situate Levinas’ (at least partial) exclusion of the non-human animal in the context of his markedly bleak conception (...) of ‘the state of nature’, and (2) drawing on Orwell, Wittgenstein and Gaita, argue that, despite his more positive evaluation of animality (specifically a dog named Bobby), Levinas is guided by a number of anthropomorphic prejudices; not least that the epithet ‘the animal’ can be used in the general singular. (shrink)

In "The History of Sexuality", Foucault maintains that "Western man has become a confessing animal" (1990, 59), thus implying that "man" was not always such a creature. On a related point, Wittgenstein suggests that "man is a ceremonial animal" (1996, 67); here the suggestion is that human beings are, by their very nature, ritualistically inclined. In this paper I examine this crucial difference in emphasis, first by reconstructing Foucault's "genealogy" of confession, and subsequently by exploring relevant facets of Wittgenstein's later (...) thinking. While there are significant correlations between Foucault and Wittgenstein, an important disparity emerges in relation to the question of the "natural." By critically analyzing this, I show how Wittgenstein's minimal naturalism provides an important corrective to Foucault's more extravagant claims. By implication, we see why any radical relativist, historicist, and/or constructivist position becomes untenable on Wittgensteinian grounds, even though Wittgenstein himself is often read as promoting such views. (shrink)

I review MacAskill's book What We Owe The Future, which makes the case for longtermism, the idea that positively influencing the longterm future is a key moral priority of our time. After summarising it, I raise four challenges to the nature or presentation of his case. First, I point out MacAskill's stated three-premise 'case' for longtermism is not a valid argument. Second, I argue his case is not, as he describes it, 'simple' and 'uncontroversial'; MacAskill brushes over crucial subtleties and (...) mauls a strawman. Third, I am unpersuaded by the argument that we can influence the longterm future; the book does not contain a single example that shows this has happened before, so we should be sceptical we can do so. Fourth, I question the practical importance of longtermism. MacAskill argues we should do more to prevent global catastrophic risks from e.g. AI and nuclear war. Longtermism may give us more reason to care about them but it is neither necessary nor sufficient to make those the priorities. (shrink)

Notwithstanding his own spiritual inadequacies, Wittgenstein has a profound respect for those capable of living a genuinely religious life; namely, those whose “passionate,” “loving” faith demands unconditional existential commitment. In contrast, he disapproves of those who see religious belief as hypothetical, reasonable, or dependent on empirical evidence. Drawing primarily on Culture and Value, “Lectures on Religious Belief,” and On Certainty, in this essay I defend two claims: (1) that there is an unresolved tension between Wittgenstein's later descriptive-therapeutic approach and the (...) implicit normativity of his conception of genuine/passionate religious belief; and (2) that the demarcation between the latter and its pseudo-religious counterpart is itself problematic. To illustrate these claims I argue that apocalyptic Christian fundamentalism presents a significant challenge to Wittgenstein's taxonomy. Despite these shortcomings, however, I conclude by suggesting that his characterization of religious belief as a “passion” or “love” remains valuable. (shrink)

The formulae "perhaps" and "perhaps not," [] we adopt in place of "perhaps it is and perhaps it is not" []. But here again we do not fight about phrases [] these expressions are indicative of non-assertion. Sextus Empiricus, Outlines of Pyrrhonism One could spend years on [] the perhaps [] whose modality will render fictional and fragile everything that follows []. One does not testify in court and before the law with "perhaps." Jacques Derrida, Demeure: Fiction and Testimony.