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)

Background and Aims The study of intraspecific trait variation (ITV) in plants has a long history, dating back to the fourth century BC. Its existence was widely acknowledged by the end of the 18th century, although systematic and experimental studies commenced only a century later. However, the historiography of ITV has many gaps, especially with regard to early observations and visual documents. This note identifies an early depiction of plant ITV. -/- Methods The botanical works of Johann Wolfgang von (...) Goethe (1749–1832), a German writer and naturalist, were subjected to close reading. This included all publications and unpublished sources related to botany between 1785 and 1832 (e.g. notes, drafts, diaries, letters, drawings). This material is accessible in the multi-volume historical-critical edition of Goethe’s studies in natural science (Leopoldina-Ausgabe). -/- Key Results A diary entry from 9 September 1786 described changes in leaf morphology along an elevation gradient in the Bavarian Alps. The leaves of an unidentified species of willow (Spix sp.) and gentian (Gentiana sp.) were said to become narrower with increasing elevation; leaves also stood further apart on twigs, and the latter became thinner. A crude drawing of two willow twigs illustrated the differences. Goethe conjectured that the differences were due to environmental conditions. -/- Conclusions Goethe’s notes were anecdotal, and it is unclear whether the observed plant individuals actually belonged to the same species. Nevertheless, the notes represent an early and clear articulation of the hypothesis that changes in environmental conditions can cause ITV in a natural plant population. The drawing may be the earliest visual record of environmentally caused plant ITV in the wild. (shrink)

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)

There is a strong need to connect agricultural research to social movements and community-based food system reform efforts. Participatory research methods are a powerful tool, increasingly used to give voice to communities overlooked by academia or marginalized in the broader food system. Plant breeding, as a field of research and practice, is uniquely well-suited to participatory project designs, since the basic process of observing and selecting plants for desirable traits is accessible to participants without formal plant breeding (...) training. The challenge for plant breeders engaged in participatory research is to consider not only how their work incorporates farmer input in developing new varieties, but also how it interacts with broader questions of food sovereignty, food justice, diversity and democratization in the food system. This article examines these issues in the context of the Seed to Kitchen Collaborative, a participatory variety evaluation and breeding project at the University of Wisconsin-Madison. (shrink)

The article reevaluates the reception of Mendelism in France, and more generally considers the complex relationship between Mendelism and plant breeding in the first half on the 20th century. It shows on the one side that agricultural research and higher education institutions have played a key role in the development and institutionalization of genetics in France, whereas university biologists remained reluctant to accept this approach on heredity. But on the other side, plant breeders, and agricultural researchers, despite an (...) interest in Mendelism, never came to see it as the breeders' panacea, and regarded it instead as of only limited value for plant breeding. I account for this judgment in showing that the plant breeders and Mendelism designed two contrasting kinds of experimental systems and inhabited distinct experimental cultures. While Mendelian geneticists designed experimental systems that allowed the production of definite ratios of different forms that varied in relation to a few characters, plant breeders' experimental systems produced a wide range of variation, featuring combinations between hundreds of traits. Rather than breaking this multiple variation down into simple elements, breeders designed and monitored a genetic lottery. The gene was a unit in a Mendelian experimental culture, an "epistemic thing" as Rheinberger put it, that could be grasped by means of statistical regularities, but it remained of secondary importance for French plant breeders, for whom the strain or the variety -- not the gene -- was the fundamental unit of analysis and manipulation. (shrink)

The main point of our hypothesis “coloration undermines camouflage” is that many color patterns in plants undermine the camouflage of invertebrate herbivores, especially insects, thus exposing them to predation and causing them to avoid plant organs with unsuitable coloration, to the benefit of the plants. This is a common case of “the enemy of my enemy is my friend” and a visual parallel of the chemical signals that plants emit to call wasps when attacked by caterpillars. Moreover, this is (...) also a common natural version of the well‐known case of industrial melanism, which illustrates the great importance of plant‐based camouflage for herbivorous insects and can serve as an independent test for our hypothesis. We claim that the enormous variations in coloration of leaves, petioles and stems as well as of flowers and fruits undermine the camouflage of invertebrate herbivores, especially insects. We assume that the same principle might operate in certain animal–parasite interactions. Our hypothesis, however, does not contrast or exclude other previous or future explanations of specific types of plant coloration. Traits such as coloration that have more than one type of benefit may be selected for by several agents and evolve more rapidly than ones with a single type of advantage. BioEssays 26:1126–1130, 2004. © 2004 Wiley Periodicals, Inc. (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)

There is a strong need to connect agricultural research to social movements and community-based food system reform efforts. Participatory research methods are a powerful tool, increasingly used to give voice to communities overlooked by academia or marginalized in the broader food system. Plant breeding, as a field of research and practice, is uniquely well-suited to participatory project designs, since the basic process of observing and selecting plants for desirable traits is accessible to participants without formal plant breeding (...) training. The challenge for plant breeders engaged in participatory research is to consider not only how their work incorporates farmer input in developing new varieties, but also how it interacts with broader questions of food sovereignty, food justice, diversity and democratization in the food system. This article examines these issues in the context of the Seed to Kitchen Collaborative, a participatory variety evaluation and breeding project at the University of Wisconsin-Madison. (shrink)

Notre propos est ici d’examiner dans quelle mesure Aristote atteint son objectif. Pour ce faire, nous nous concentrerons sur l’approche explicative adoptée dans le traité De longitudine et brevitate vitae ( De la longévité et de la vie brève ), où Aristote se propose de rendre compte de la longévité, sans se limiter aux animaux. Nous discuterons des perspectives que peut ouvrir une telle étude commune aux animaux et aux plantes, mais aussi de ses éventuelles limites. Dans quelle mesure Aristote (...) est-il capable de traiter ensemble la question de la longévité des animaux et des plantes? La réponse à cette question est au cœur de notre article. (shrink)

This paper investigates how reticulate evolution contributes to a better understanding of human sociocultural evolution in general, and community formation in particular. Reticulate evolution is evolution as it occurs by means of symbiosis, symbiogenesis, lateral gene transfer, infective heredity, and hybridization. From these mechanisms and processes, we mainly zoom in on symbiosis and we investigate how it underlies the rise of (1) human, plant, animal, and machine interactions typical of agriculture, animal husbandry, farming, and industrialization; (2) diet-microbiome relationships; and (...) (3) host-virome and other pathogen interactions that underlie human health and disease. We demonstrate that reticulate evolution necessitates an understanding of behavioral and cultural evolution at a community level, where reticulate causal processes underlie the rise of synergistic organizational traits. (shrink)

There is an urgent need for novel protection strategies to sustainably secure crop production under changing climates. Studying microbial effectors, defined as microbe‐derived proteins that alter signalling inside plant cells, has advanced our understanding of plant immunity and microbial plant colonisation strategies. Our understanding of effectors in the establishment and beneficial outcome of plant symbioses is less well known. Combining functional and comparative interaction assays uncovered specific symbiont effector targets in highly interconnected plant signalling networks (...) and revealed the potential of effectors in beneficially modulating plant traits. The diverse functionality of symbiont effectors differs from the paradigmatic immuno‐suppressive function of pathogen effectors. These effectors provide solutions for improving crop resilience against climate stress by their evolution‐driven specification in host protein targeting and modulation. Symbiont effectors represent stringent tools not only to identify genetic targets for crop breeding, but to serve as applicable agents in crop management strategies under changing environments. (shrink)

This paper advances the development of a phylogeny-based psychology in which cognitive ability types are individuated as characters in the evolutionary biological sense. I explain the character concept and its utility in addressing (or dissolving) conceptual problems arising from discoveries of cognitive abilities across a wide range of species. I use the examples of stereopsis in the praying mantis, internal cell-to-cell signaling in plants, and episodic memory in scrub jays to show how anthropocentric cognitive ability types can be reformulated into (...) cognitive characters, thereby promoting the integration of psychology with other sciences of evolved traits. (shrink)

In his recent discussion of Nietzsche’s naturalism, Brian Leiter invokes examples from the world of plants to demonstrate that human behavior and values are causally determined by “heritable psychological and physiological traits,” or what he also refers to as “type-facts.”1 On this view, Nietzsche’s naturalistic project is concerned with explaining how and why a certain type of person comes to bear certain values and ideas just as “one might come to understand things about a certain type of tree by (...) knowing its fruits.”2 Leiter holds that “just as natural facts about the tree explain the fruit it bears, so too type-facts about a person will explain the ideas and values he comes to bear.”3 Nietzsche views the.. (shrink)

In his accounts of plant and animal generation Pierre Gassendi offers a mechanist story of how organisms create offspring to whom they pass on their traits. Development of the new organism is directed by a material “soul” or animula bearing ontogenetic information. Where reproduction is sexual, two sets of material semina and corresponding animulae meet and jointly determine the division, differentiation, and development of matter in the new organism. The determination of inherited traits requires a means of (...) combining or choosing among each parent's contributions, and towards this end, Gassendi outlines the nature of competition and dominance among animulae. Unlike his fellow mechanists, Gassendi can extend his mechanism to his heredity account, because his proposed vehicle for ontogenetic transmission is material. That proposal in turn relies on his atomist hypothesis. The relative uniformity of atoms allows animulae to operate equivalently across different modes of generation, spontaneous or otherwise. Further, his molecular model of atomic structures allows a material means of storing ontogenetic information received from the souls of parent organisms. These accounts—flawed and sketchy—unsurprisingly fail to specify how hereditary information might be borne physically, and in any case do not meet Gassendi's own empiricist standards. Yet this generation theory with pretensions to a materialist mechanism establishes Gassendi's firm commitment to a unity of the sciences through an atomist ontology that underlies all physical phenomena, including the organic. (shrink)

Research on early-divergent angiosperms, including Amborella, the putative sister to all other extant angiosperms, is increasingly used as a yardstick to infer the nature of the hypothetical ancestral angiosperm. Some traits are relatively diverse (and hence relatively labile) in this phylogenetic grade, compared with the more derived eudicot clade, in which developmental patterns have become increasingly canalized. One of the many mysteries surrounding the origin of the angiosperms is the evolutionary origin of the Polygonum-type embryo sac (monosporic, eight-nucleate and (...) seven-celled) that occurs in the majority of flowering plants. Observations on the megagametophyte of Amborella are conflicting, but a recent report of a supernumerary synergid in this genus1 raises the question of whether the Polygonum-type embryo sac is derived by duplication of a four-nucleate structure or by reduction from a multicellular structure. BioEssays 28: 1067–1071, 2006. © 2006 Wiley Periodicals, Inc. (shrink)

Public policy on the development and use of genetically modified organisms (GMOs) has mainly been concerned with defining proper strategies of risk management. However, surveys and focus group interviews show that although lay people are concerned with risks, they also emphasize that genetic modification is ethically questionable in itself. Many people feel that this technology “tampers with nature” in an unacceptable manner. This is often identified as an objection to the crossing of species borders in producing transgenic organisms. Most scientists (...) reject these opinions as based on insufficient knowledge about biotechnology, the concept of species, and nature in general. Some recent projects of genetic modification aim to accommodate the above mentioned concerns by altering the expression of endogenous genes rather than introducing genes from other species. There can be good scientific reasons for this approach, in addition to strategic reasons related to greater public acceptability. But are there also moral reasons for choosing intragenic rather than transgenic modification? I suggest three interrelated moral reasons for giving priority to intragenic modification. First, we should respect the opinions of lay people even when their view is contrary to scientific consensus; they express an alternative world-view, not scientific ignorance. Second, staying within species borders by strengthening endogenous traits reduces the risks and scientific uncertainty. Third, we should show respect for nature as a complex system of laws and interconnections that we cannot fully control. The main moral reason for intragenic modification, in our view, is the need to respect the “otherness” of nature. (shrink)

The flowers of the primitive angiosperm plants were radially symmetrical (actinomorphic). Flowers with bilateral symmetry (zygomorphic) evolved in several clades independently as an adaptation to specialized methods of pollination and played an important role in the diversification of flowering plants. In the model species Antirrhinum majus (snapdragon), the related genes CYCLOIDEA (CYC) and DICHOTOMA (DICH) are key in the development of this trait. This raises the question of whether they played a role in the evolution of floral bilateral symmetry. To (...) address this, the evolution of CYC in relation to the evolution of zygomorphy is being investigated. Phylogenetic and functional analyses of CYC‐like genes are being carried out in groups either closely related to Antirhinum or in families where zygomorphy evolved as an independent event. In addition, the origin of zygomorphy is being studied by comparing the function of CYC‐like genes in species with zygomorphic flowers with their function in species with radially symmetrical flowers. BioEssays 26:1175–1184, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The development of improved methods for genome‐wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k‐mers for GWAS has taken over as a (...) new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k‐mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker‐trait associations (MTAs) that are relevant to human healthcare and crop improvement. (shrink)

Darwin1 introduced the idea that ornamental secondary sexual traits have evolved in response to female preferences for showy males. Among such traits, yellow and red carotenoid‐based ornaments have been considered as particularly good candidates for explaining why and how females would benefit from mating with showy partners. Because carotenoids can be used for promotion of both health and appearance, colourful male ornaments should honestly reveal the vigour of the bearers. Two recent experiments with birds2,3 now show how allocation (...) of bodily carotenoids to sexual signalling is traded off against the use of carotenoids for boosting immune function. BioEssays 25:746–747, 2003. © 2003 Wiley Periodicals, Inc. (shrink)

In his theological explorations, suggests Raymond Plant in this illuminating new guide, Hegel tackled the issues of interest to us all.

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

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 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)

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)

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)

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

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

_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.

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)

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)