The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (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)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

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)

Upshot: In our response we focus on five questions that point to important common themes in the commentaries: why start in wicked problems, what kind of system is a scientific perspective, what is the nature of second-order research processes, what does this mean for understanding interdisciplinary work, and how may polyocular research help make real-world decisions.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

A brief examination of the self-negating quality of the precautionary principle within the context of environmental ethics, and its consequent failure, as an ethical guide, to justify large-scale regulation of atmospheric cabon dioxide emissions.

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey- (...) class='Hi'>Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

I argue, first, that the deprived individuals whose predicaments Nussbaum cites as examples of "adaptive preference" do not in fact prefer the conditions of their lives to what we should regard as more desirable alternatives, indeed that we believe they are badly off precisely because they are not living the lives they would prefer to live if they had other options and were aware of them. Secondly, I argue that even where individuals in deprived circumstances acquire tastes for conditions that (...) we regard as bad, they are typically better off having their acquired preferences satisfied. If they are badly off it is because they cannot get what we and they, would regard as more desirable alternatives. Preference utilitarianism explains why individuals in such circumstances are badly off whether they have adapted to their deprived circumstances or not. Even if they prefer the conditions of their lives to all other available alternatives, most would prefer alternatives that are not available to them which would, on the preferentist account, make them better off. And that, on the preferentist account, is the basis for a radical critique of unjust institutions that limit people's options and prevent them from getting what they want. (shrink)

Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...) form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future. (shrink)

Women in the labor force are at a disadvantage not only because of continuing discrimination in hiring and promotion, but because of factors extrinsic to the labor market hence adjusting conditions within the labor market will not completely eliminate women's disadvantage. Because, unlike most men, most women do not have spouses to take on the major responsibility of running their homes and caring for their children, the costs of working outside the home, particularly in a professional or managerial capacity, are (...) greater for women than they are for men. Thus, even if ongoing discrimination in the labor market were eliminated, through affirmative action policies or other such remedies, women would still be as a disadvantage relative to men.For women, the costs and benefits of behaving like men are different than they are for their male counterparts. To the extent that the costs and benefits of various policies of action are not the same for women as they are for men, men and women are not equal, therefore, arguably, it is not fair to treat them equally. (shrink)

I argue on utilitarian grounds that while traditional constraints on heterosexual activity, including the prohibition of pre-marital sex and divorce may be justified by appeal to purely secular principles, no comparable prohibitions are justified as regards homosexual activity. Homosexuality is in this respect.

What role does the wild duck play in Ibsen's famous drama? I argue that, besides mirroring the fate of the human cast members, the duck is acting as animal subject in a quasi-experiment, conducted in a private setting. Analysed from this perspective, the play allows us to discern the epistemological and ethical dimensions of the new scientific animal practice (systematic observation of animal behaviour under artificial conditions) emerging precesely at that time. Ibsen's play stages the clash between a scientific and (...) a romantic understanding of animals that still constitutes the backdrop of most contemporary debates over animals in research. Whereas the scientific understanding reduces the animal's behaviour, as well as its environment, to discrete and modifiable elements, the romantic view regards animals as being at one with (or violently disconnected from) their natural surroundings. (shrink)

Presence as ordinarily understood requires spatio-temporal proximity. If however Christ’s presence in the Eucharist is understood in this way it would take a miracle to secure multiple location and an additional miracle to cover it up so that the presence of Christ where the Eucharist was celebrated made no empirical difference. And, while multiple location is logically possible, such metaphysical miracles—miracles of distinction without difference, which have no empirical import—are problematic. I propose an account of Eucharist according to which Christ (...) is indeed really and objectively present in the religiously required sense, without benefit of metaphysical miracles. According to the proposed account, which draws upon Searle’s discussion of “social ontology” in The Construction of Social Reality and The Making of the Social World, the presence of Christ in the Eucharist is an institutional fact. I argue that such an account satisfies the requirements for a real presence doctrine. (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)

The doctrine that Christ is really present in the Eucharist appears to entail that Christ's body is not only multiply located but present in different ways at different locations. Moreover, the doctrine poses an even more difficult meta-question: what makes a theological explanation of the Eucharist a ‘real presence’ account? Aquinas's defence of transubstantiation, perhaps the paradigmatic account, invokes Aristotelian metaphysics and the machinery of Scholastic philosophy. My aim is not to produce a ‘rational reconstruction’ of his analysis but rather (...) to suggest a metaphysically innocent alternative that will ‘save the phenomena’ of religious belief and practice.Send article to KindleTo send this article to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle. Note you can select to send to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply. Find out more about the Kindle Personal Document Service.The real presenceVolume 49, Issue 1H. E. BABER DOI: https://doi.org/10.1017/S0034412512000121Your Kindle email address Please provide your Kindle [email protected]@kindle.com Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Dropbox To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Dropbox. The real presenceVolume 49, Issue 1H. E. BABER DOI: https://doi.org/10.1017/S0034412512000121Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Send article to Google Drive To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about sending content to Google Drive. The real presenceVolume 49, Issue 1H. E. BABER DOI: https://doi.org/10.1017/S0034412512000121Available formats PDF Please select a format to send. By using this service, you agree that you will only keep articles for personal use, and will not openly distribute them via Dropbox, Google Drive or other file sharing services. Please confirm that you accept the terms of use. Cancel Send ×Export citation Request permission. (shrink)

This paper examines the justice of unconditional basic income (UBI) through the lens of the Hegel-inspired recognition-theory of justice. As explained in the first part of the paper, this theory takes everyday social roles to be the primary subject-matter of the theory of justice, and it takes justice in these roles to be a matter of the kind of freedom that is available through their performance, namely ‘social’ freedom. The paper then identifies the key criteria of social freedom. The extent (...) to which the introduction of an UBI would meet these criteria is then examined, with a focus on the social role that stands to be most affected by an UBI, namely that of the worker-earner. It is argued that while an UBI is likely to be only partially effective as an instrument of specifically social freedom, its main justification lies not here, but in securing a basis for the subjective freedom that social freedom presupposes. (shrink)

Table of contents for MONSTERS AND PHILOSOPHY, edited by Charles T. Wolfe (London 2005) -/- List of Contributors iii Acknowledgments vii List of Abbreviations ix -/- Introduction xi Charles T. Wolfe The Riddle of the Sphinx: Aristotle, Penelope, and 1 Empedocles Johannes Fritsche Science as a Cure for Fear: The Status of Monsters in 21 Lucretius Morgan Meis Nature and its Monsters During the Renaissance: 37 Montaigne and Vanini Tristan Dagron Conjoined Twins and the Limits of our Reason 61 Annie (...) Bitbol-Hespériès Degeneration and Hybridism in the Early Modern Species 109 Debate: Towards the Philosophical Roots of the Creation-Evolution Controversy Justin E. H. Smith Leibniz on the Unicorn and Various other Curiosities 131 Roger Ariew The Creativity of God and the Order of Nature: 153 Anatomizing Monsters in the Early Eighteenth Century Anita Guerrini The Status of Anomalies in the Philosophy of Diderot 169 Annie Ibrahim The Materialist Denial of Monsters 187 Charles T. Wolfe Cerebral Assymetry, Monstrosities and Hegel. 205 On the Situation of the Life Sciences in 1800 Michael Hagner The Lady Knight of the Perilous Place 217 Elfriede Jelinek Monster: More than a Word. . . From Portent to Anomaly, 231 the Extraordinary Career of Monsters Beate Ochsner Index 281 . (shrink)

I suggest that the post-Hegelian tradition presents us with three contrasting normative models of work. According to the first model, the core norms of work are those of means-ends rationality. In this model, the modern world of work is constitutively a matter of deploying the most effective means to bring about given ends. The rational kernel of modern work, the core norm that has shaped its development, is on this view instrumental reason, and this very same normative core, in the (...) shape of advanced technology and more efficient, time-saving production, can help to liberate it. The second model, by contrast, takes the core norms of work to be internal to working activity. Rather than work gaining its normativity from something external to it, from ends to which the work is a contingent means, on this second view the core norms of work are expressions of values or meanings that are immanent to working practices themselves. The expressive model of work regards the actual world of work to be constituted historically by work-specific norms, norms which working subjects themselves have invoked and mobilised around in the course of their struggles for emancipation. According to the third model, the core norms of work have to do neither with instrumental rationality nor authentic self-expression. Rather they concern norms that relate either to individual achievement or contribution through work (in the form of esteem) or to the conditions that must in place for individuals to participate in the exchange of services by which market societies reproduce themselves (in the form of mutual respect). (shrink)

I compare Bratman’s theory with Gilbert’s. I draw attention to their similarities, query Bratman’s claim that his theory is the more parsimonious, and point to one theoretical advantage of Gilbert’s theory.

I begin by picking up on Brandom’s suggestion that expressivism follows American pragmatism in seeking to advance the cause of the Enlightenment. This provides us with a first point of contrast with Taylor’s understanding of expressivism, since Taylor takes expressivism to be inseparably bound up with the Romantic critique of the Enlightenment and as fundamentally opposed to Enlightenment naturalism. I then distinguish two features of what we ordinarily mean by the term ‘expression’, one of which provides an intuitive basis for (...) understanding Brandom’s expressivist program, the other of which provides an interpretive key for understanding Taylor’s version of expressivism. After looking briefly at the main tenets of Taylor’s expressivism, I conclude by considering its relation to Romanticism on the one hand, and to Brandom’s expressivist renewal of the Enlightenment project on the other. (shrink)

Animal ethicists have recently debated the ethical questions raised by disenhancing animals to improve their welfare. Here, we focus on the particular case of breeding hens for commercial egg-laying systems to become blind, in order to benefit their welfare. Many people find breeding blind hens intuitively repellent, yet ‘welfare-only’ positions appear to be committed to endorsing this possibility if it produces welfare gains. We call this the ‘Blind Hens’ Challenge’. In this paper, we argue that there are both empirical and (...) theoretical reasons why even those adopting ‘welfare-only’ views should be concerned about breeding blind hens. But we also argue that alternative views, which (for example) claim that it is important to respect the telos or rights of an animal, do not offer a more convincing solution to questions raised by the possibility of disenhancing animals for their own benefit. (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)

Friedrich Engels’ dialectical assessment of modern science resulted from his fascination with the natural sciences in combination with his resurging interest in the work of “old Hegel.” Engels became especially interested in what he saw as the molecular essence of life, namely proteins or, more specifically, albumin, seeing life as the mode of existence of these enigmatic substances. Hegelian dialectics is crucial for a dialectical materialist understanding of contemporary technoscience. The dialectical materialist understanding of technoscience as a research practice builds (...) on Engels, but also on later authors who were inspired by his writings, e.g., life scientists such as Haldane and Bernal. Considering the criticism raised against Engels’ dialectics by 20th-century Marxists, a dialectical diagnostic of contemporary technoscience can be achieved, which shifts the focus from artificial albumin as “living matter” to contemporary research on synthetic cells. (shrink)

This paper analyses the technoscientific objective of building a synthetic cell from a Jungian perspective. After decades of fragmentation and specialisation, the synthetic cell symbolises a turn towards restored wholeness, both at the object pole and at the subject pole. From a Jungian perspective, it is no coincidence that visual representations of synthetic cells often reflect an archetypal, mandala-like structure. As a symbol of restored unity, the synthetic cell mandala compensates for technoscientific fragmentation via active imagination, providing a visual aid (...) for the technoscientific turn towards reintegration. Although the biotechnological desire to reconstruct life in vitro has been compared to alchemy before, a Jungian analysis allows us to make this comparison more specific and precise. The problem of archetypal images, however, is that alluring prospects of reintegration may underestimate and obfuscate the deficiencies and tensions at work in the current situation. As a projection of a future wholeness, it fosters optimism, but may also function as a misleading façade, covering up collisions and complexities. This can be averted by the conscious employment of the mandala as a symbolic scaffold fostering processes of individuation and working through. (shrink)

The aim of this article is to situate Arendt’s account of labour as a critical response to humanisms of labour, or put otherwise, to situate it as an anti-humanism of labour. It compares Arendt’s account of labour with that of the most prominent humanist theorist of labour at the time of the composition of The Human Condition: Georges Friedmann. Arendt’s and Friedmann’s accounts of labour are compared specifically with respect to the range of capacities, social relations, and possibilities of fulfilment (...) at stake in the activity of labour. The comparison provides a previously unexplored context for understanding Arendt’s account of labour and her distinction between labour and work. The relevance of Arendt’s and Friedmann’s theories of labour for the contemporary debate about the meaning of work in an age of automation is also briefly discussed. (shrink)

An analysis of how the sphere of work can be considered to instantiate norms of recognition, even when those norms give rise to paradoxes and ideologies surrounding how work ought to be done and the goods at stake in it.

This chapter takes a critical look at universities from the perspective of the neopragmatist philosophy of education outlined by Richard Rorty. The chapter begins with a discussion of Rorty’s view of the ends that educational institutions properly serve in a liberal democracy. It then considers the kind of culture that Rorty takes to be conducive to those ends and the kind that is antithetical to them. Rorty sometimes characterizes the latter as a culture of ‘egotism’. After describing the main aspects (...) of such a culture, the chapter uses it as an interpretive key for understanding the ‘dark side’ of the contemporary university. Our thesis is that within a Rortyan, neo-pragmatist philosophy of higher education, the ends that universities are meant to serve in a liberal democracy are vulnerable to frustration and corruption by a culture of egotism. (shrink)

What is the fundamental purpose that justifies the existence of the modern university? The answer proposed in this essay is the promotion of social freedom. The essay begins by distinguishing social freedom from negative freedom and reflective freedom along the lines proposed by other theorists of social freedom, such as Frederick Neuhouser and Axel Honneth. After noting the need for a more developed account of the university than has so far been provided by these other theorists, the essay analyses the (...) various dimensions in which universities have, at their best, promoted social freedom. The essay then explains why it is through the promotion of social, as distinct from negative or reflective freedom, that universities fulfil their purpose. It concludes with some reflections on how this understanding of the purpose of the university fits an “immanent” model of social criticism. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Background: A bean is the seed of one of several genera of the flowering plant family Fabaceae, which are used as vegetables for human or animal food. They can be cooked in many different ways, including boiling, frying, and baking, and are used in many traditional dishes throughout the world. Beans are one of the longest-cultivated plants. Broad beans, also called fava beans, in their wild state the size of a small fingernail, were gathered in Afghanistan and the Himalayan foothills. (...) In a form improved from naturally occurring types, Beans were an important source of protein throughout old and new world history, and still are today. Objectives: The main goal of this expert system is to get the appropriate diagnosis of disease and the correct treatment. Methods: In this paper, the design of the proposed Expert System was produced to help farmers and those interested in agriculture in diagnosing many of the Bean diseases such as Fusarium wilt, Charcoal rot or ashy stem blight, Bacterial leaf spot and blight, Mung bean yellow mosaic virus, Cercospora leaf spot. The proposed expert system presents an overview of Bean diseases are given, the cause of diseases outlined and the treatment of disease whenever possible is given out. CLIPS Expert System language was used for designing and implementing the proposed expert system. Results: The proposed Bean diseases diagnosis expert system was evaluated by Agricultural experts and some friends interested in agriculture and they were satisfied with its performance. Conclusions: The proposed expert system is very useful for Farmers and those interested in agriculture. (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)

A summary of the main features of a 'recognition-theoretic' research program in the social sciences and a brief account of how it promises to advance on rival research programs in the social sciences.

This chapter offers a new criticism of the Mind argument that is both decisive and instructive. It introduces a plausible principle (γ) that places a requirement on one’s having a choice about an event whose causal history includes only other events. Depending on γ’s truth-value, the Mind argument fails in such a way that one or the other of the two main species of libertarianism is the best approach to the metaphysics of freedom. Libertarians argue the compatibility of freedom and (...) indeterminism, and their biggest obstacle is the Mind argument that argues an incompatibility between the two. The chapter aims to build a case for the truth of γ, and so for nonreductive libertarianism. This is achieved by defending it from the best objections that have been brought to light, thereby emphasizing γ’s prima facie plausibility. (shrink)

Although the contrast between ‘economy’ and culture’ that structures the Fraser-Honneth debate derives ultimately from Weber, it has a more proximate ancestry in Habermas’ work. I begin by glancing back at Habermas’ formulation, not just because its background role in shaping the current debate has not been properly acknowledged (though I believe that is the case), but because Fraser and Honneth’s original responses to it provide a nice segue into their current positions. After briefly reviewing what those responses were, I (...) then offer a critical analysis of the conceptions of economy and culture they now propose. (shrink)

In this paper, I will reread the history of molecular genetics from a psychoanalytical angle, analysing it as a case history. Building on the developmental theories of Freud and his followers, I will distinguish four stages, namely: (1) oedipal childhood, notably the epoch of model building (1943–1953); (2) the latency period, with a focus on the development of basic skills (1953–1989); (3) adolescence, exemplified by the Human Genome Project, with its fierce conflicts, great expectations and grandiose claims (1989–2003) and (4) (...) adulthood (2003–present) during which revolutionary research areas such as molecular biology and genomics have achieved a certain level of normalcy—have evolved into a normal science. I will indicate how a psychoanalytical assessment conducted in this manner may help us to interpret and address some of the key normative issues that have been raised with regard to molecular genetics over the years, such as ‘relevance’, ‘responsible innovation’ and ‘promise management’. (shrink)

This paper addresses the cultural impact of genomics and the Human Genome Project on human self-understanding. Notably, it addresses the claim made by Francis Collins that the genome is the language of God and the claim made by Max Delbrück that Aristotle must be credited with having predicted DNA as the soul that organises bio-matter. From a continental philosophical perspective I will argue that human existence results from a dialectical interaction between two types of texts: the language of molecular biology (...) and the language of civilisation; the language of the genome and the language of our socio-cultural, symbolic ambiance. Whereas the former ultimately builds on the alphabets of genes and nucleotides, the latter is informed by primordial texts such as the Bible and the Quran. In applied bioethics deliberations on genomics, science is easily framed as liberating and progressive, religious world-views as conservative an... (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements in the efficiency, (...) effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

The essay reflects on Gadamer’s ambiguous legacy for the philosophy of work. On the one hand, there are times when Gadamer reproduces the problematic distinction between language and labor which short-circuits the very idea of a hermeneutics of work. This is particularly evident in Gadamer’s reflections on technique and craftsmanship in the central sections of Truth and Method, as well as in his descriptions of the “art” of dialogue and the tasks of hermeneutics that separate them emphatically them from the (...) sphere of “making.” I raise some questions about the adequacy of the distinction Gadamer draws between techne and phronesis that structures this account. I argue here that Gadamer’s characterization of the learning process involved in the mastery of a technique, as well as his conception of the instrumentality and monologicality of technical knowledge, is difficult to sustain, especially in view of recent research in the psychology and anthropology of work. I then go on to point out that elsewhere in his oeuvre Gadamer himself is critical of the conception of work that emerges through the lens of the techne / phronesis distinction. Indeed, on these occasions he hints at a conception of work that points beyond the Arendt / Habermas conception towards a critical hermeneutics of working life. This alternative approach to work is particularly apparent in Gadamer’s appropriation of Hegel’s dialectic, in his understanding of play, and in some of his later diagnostic reflections on the spirit of the age. In section four, I offer some suggestions for explaining how the tensions evident in Gadamer’s approach to work came about. Here I am interested in what prevented Gadamer from embracing whole-heartedly the project of a hermeneutics of work that he himself helped to lay the foundations for. I conclude with some brief remarks on why we should seek to build upon these foundations and renew the project of a critical hermeneutics of work today. (shrink)