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)

Cooper, Austin Christian Spirituality can be approached from numerous points on the theological compass: Sacred Scripture is an obvious source, but so are almost any of the theological disciplines. This paper will be concerned with it as emanating from Church History.

Cooper, Austin John Henry Newman was born in 1801, converted to the Catholic Church in 1845 and died in 1890. That is, he spent the first half of his life in the Church of England. He was to exercise a profound influence on both Communions in Australia. The young Newman was elected a Fellow of Oriel College, Oxford, in April 1822. Despite the declining fortunes of his family, his own career was off to a promising start. Two years (...) later he was ordained Deacon at Christ Church Cathedral, Oxford on 13 June 1824. This was a very solemn commitment indeed. He thought he should give himself totally to the service of the Gospel. This attitude prompted him to write to the CMS (the Church Missionary Society) in London seeking information regarding service as a missionary. He followed up his letter with a visit to the CMS London Headquarters on July 3, 1824 - just two weeks after his ordination as deacon. (shrink)

Cooper, Austin Some years ago a priest who was dying told me that he had not had a spiritual director for years: he just kept reading St Teresa. Having a continuing conversation with a holy person by engaging with his or her writings would seem to conform to our beliefs: in the Apostles' Creed we affirm that the Holy Spirit enlivens the church and the communion of saints. And T. S. Eliot articulated the truth in poetic terms when (...) he wrote, 'the communication of the dead is tongued with fire beyond the language of the living'. (shrink)

Cooper, Austin More than a century ago The Australasian Catholic Record entered the Australasian scene, serving the church and over time quietly but substantially meeting changing circumstances. The journal was first established in 1895 by the then Archbishop of Sydney, Patrick Francis Cardinal Moran. With a typical Moran flourish it announced that this 'tiny barque' now departs the shore with the task of confronting the enemies of the church, 'Irreligion, Immorality and Anarchy'. The manifesto was something of a (...) war cry. In undertaking this objective the journal intended following the example of publications such as The American Catholic Quarterly Review, The Dublin Review and The Irish Ecclesiastical Record. (shrink)

Cooper, Austin Review(s) of: The Bloomsbury guide to Christian spirituality, by Richard Woods and Peter Tyler, eds. (London: Bloomsbury, 2012), pp. viii + 422, $65.00.

The Oxford or Tractarian Movement and later Ritualists and Anglo-Catholics schooled numerous converts in elements of the Catholic faith. Foremost among them was John Henry Cardinal Newman, one of the original founders of the Oxford Movement. Converts numbered in the hundreds and included another cardinal, Henry Edward Manning, the second Archbishop of Westminster, the religious foundress Cornelia Connelly, the priest novelist Robert Hugh Benson and later literary figures such as G.K. Chesterton, Evelyn Waugh and Mgr Ronald Knox. American historian, Patrick (...) Allitt, has argued that on both sides of the Atlantic converts dominated Catholic intellectual life between 1840 and 1960. While such 'Tractarian' converts have indeed greatly influenced Catholic life, many 'Tractarians' who never converted have also had a considerable impact on English-speaking Catholicism. C.S. Lewis is an obvious example. But there have been others, including author Charles Williams, poet T.S. Eliot and theologians John Macquarrie and Michael Ramsey. The author Dorothy L. Sayers also deserves to be counted among their number. (shrink)

Cooper, Austin Review of: Faith, Ireland and empire: The life of Patrick Joseph Clune CSSR 1864-1935, archbishop of Perth, Western Australia, by Christopher Dowd, Strathfield: St Pauls Publications, 2014, pp. xxiv + 416, paperback, $39.95.

Mixed lineage leukemia (MLL) fusion protein (FP)‐induced acute leukemia is highly aggressive and often refractory to therapy. Recent progress in the field has unraveled novel mechanisms and targets to combat this disease. Menin, a nuclear protein, interacts with wild‐type (WT) MLL, MLL‐FPs, and other partners such as the chromatin‐associated protein LEDGF and the transcription factor C‐Myb to promote leukemogenesis. The newly solved co‐crystal structure illustrating the menin–MLL interaction, coupled with the role of menin in recruiting both WT MLL and MLL‐FPs (...) to target genes, highlights menin as a scaffold protein and a central hub controlling this type of leukemia. The menin/WT MLL/MLL‐FP hub may also cooperate with several signaling pathways, including Wnt, GSK3, and bromodomain‐containing Brd4‐related pathways to sustain MLL‐FP‐induced leukemogenesis, revealing new therapeutic targets to improve the treatment of MLL‐FP leukemias. (shrink)

In this Article I argue that the emerging public/private nexus of surveillance involves the augmentation of state power and calls for new models of constitutional constraint. The key phenomenon is the role played by communications intermediaries in collecting the information that the state subsequently accesses. These intermediaries are not just powerful companies engaged in collecting and analyzing the information of users and the information they hold are not just business records. The key feature of these companies is that, through their (...) information practices and architecture, they mediate other relationships. I argue that this mediating function, and its underlying technological form, interacts with legal and social norms in ways that can lead to the erosion of constraints on state power. This Article maps two stories of erosion, rooted in two kinds of community displacement. The first involves the displacement of community participation in law enforcement and the emergence of “technological tattletales” where intermediaries cooperate with the state. Unlike citizen cooperation, this practice augments state power and undermines more traditional informal modes of constraint on state power. The second involves the displacement of national legal and political community. Communications intermediaries are often large multinational companies that operate in multiple jurisdictions and move their data to various datacenters across the world even as the individual data subject remains in one geographical location. Laws that treat nonresident aliens differently from residents and citizens can create “constitutional black holes” where the communications data of an individual is not protected by any constitutional constraints. (shrink)

This paper asks what it means to say that a disorder is a “real” disorder and then considers whether culture-bound syndromes are real disorders. Following J.L. Austin I note that when we ask whether some supposed culture-bound syndrome is a real disorder we should start by specifying what possible alternatives we have in mind. We might be asking whether the reported behaviours genuinely occur, that is, whether the culture-bound syndrome is a genuine phenomenon as opposed to a myth. We (...) might be wondering whether the condition should rightly be considered a disorder, as opposed to some sort of non-disorder condition. We might want to know whether the culture-bound syndrome is really a distinct disorder, in the sense that scientific classification systems should include it as a separate category, or whether it is just a variant of a universally occurring disorder. I argue that some specific difficulties can arise with determining whether a culture-bound syndrome is a real disorder in each of these three senses. However, the frequent assumption that real disorders will necessarily occur universally, and that those that occur only in certain environments are suspicious is not generally justified. (shrink)

Peter Abelard (1079–1142 ce) was the most wide‐ranging philosopher of the twelfth century. He quickly established himself as a leading teacher of logic in and near Paris shortly after 1100. After his affair with Heloise, and his subsequent castration, Abelard became a monk, but he returned to teaching in the Paris schools until 1140, when his work was condemned by a Church Council at Sens. His logical writings were based around discussion of the “Old Logic”: Porphyry's Isagoge, aristotle'S Categories and (...) On Interpretation and boethius'S textbook on topical inference. They comprise a freestanding Dialectica (“Logic”; probably c.1116), a set of commentaries (known as the Logica [Ingredientibus], c. 1119) and a later (c. 1125) commentary on the Isagoge (Logica Nostrorum Petititoni Sociorum or Glossulae). In a work Abelard called his Theologia, issued in three main versions (between 1120 and c.1134), he attempted a logical analysis of trinitarian relations and explored the philosophical problems surrounding God's claims to omnipotence and omniscience. The Collationes (“Debates,” also known as “Dialogue between a Christian, a Philosopher and a Jew”; probably c.1130) present a rational investigation into the nature of the highest good, in which the Christian and the Philosopher (who seems to be modeled on a philosopher of pagan antiquity) are remarkably in agreement. The unfinished Scito teipsum (“Know thyself,” also known as the “Ethics”; c.1138) analyses moral action. (shrink)

First published in 1962, contains the William James Lectures delivered at Harvard University in 1955. It sets out Austin's conclusions in the field to which he directed his main efforts for at least the last ten years of his life. Starting from an exhaustive examination of his already well- known distinction of performative utterances from statements, Austin here finally abandons that distinction, replacing it by a more general theory of 'illocutionary forces' of utterances which has important bearings on (...) a wide variety of philosophical problems. (shrink)

David Cooper explores and defends the view that a reality independent of human perspectives is necessarily indescribable, a "mystery." Other views are shown to be hubristic. Humanists, for whom "man is the measure" of reality, exaggerate our capacity to live without the sense of an independent measure. Absolutists, who proclaim our capacity to know an independent reality, exaggerate our cognitive powers. In this highly original book Cooper restores to philosophy a proper appreciation of mystery-that is what provides a (...) measure of our beliefs and conduct. (shrink)

A recent development in biology has been the growing acceptance that holobionts, entities comprised of symbiotic microbes and their host organisms, are widespread in nature. There is agreement that holobionts are evolved outcomes, but disagreement on how to characterize the operation of natural selection on them. The aim of this paper is to articulate the contours of the disagreement. I explain how two distinct foundational accounts of the process of natural selection give rise to competing views about evolutionary individuality.

For this second edition, the editors have returned to Austin's original lecture notes, amending the printed text where it seemed necessary.

From his own experience the author has found that searching and finding out that God has created a perfect world/universe relieves him of the stress and pressure of being in a world/universe of total confusion and turmoil while trying to make sense out of his daily struggles of living.

Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely (...) unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote “discontinuity.” Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was “special,” any such notion has more than rhetorical value. (shrink)

The influence of J. L. Austin on contemporary philosophy was substantial during his lifetime, and has grown greatly since his death, at the height of his powers, in 1960. Philosophical Papers, first published in 1961, was the first of three volumes of Austin's work to be edited by J. O. Urmson and G. J. Warnock. Together with Sense and Sensibilia and How to do things with Words, it has extended Austin's influence far beyond the circle who knew (...) him or read the handful of papers he published in journals. (shrink)

This book is the one to put into the hands of those who have been over-impressed by Austin 's critics....[Warnock's] brilliant editing puts everybody who is concerned with philosophical problems in his debt.

By re-examining the writings of Gadamer and Habermas and their views of earlier interpretive theorists, this book offers a radical challenge to their idea of the 'dialogue' between researchers and their subjects.

A British diplomat and foreign affairs expert presents his radical interpretation of the post-Cold War new world order and offers controversial advice on how civilized nations should deal with terrorism. Reprint.