The genes involved in methionine biosynthesis are scattered throughout the Escherichia coli chromosome and are controlled in a similar but not coordinated manner. The product of the metJ gene and S‐adenosylmethionine are involved in the repression of this ‘regulon’.

Engineering the Climate: The Ethics of Solar Radiation Management is a wide-ranging and expert analysis of the ethics of the intentional management of solar radiation. This book will be a useful tool for policy-makers, a provocation for ethicists, and an eye-opening analysis for both the scientist and the general reader with interest in climate change.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...) along with a specific use case in IDO. Description logic restrictions are used to formalize statements relating to these combinations. (shrink)

Representing the kinetic state of a patient (posture, motion, and activity) during vital sign measurement is an important part of continuous monitoring applications, especially remote monitoring applications. In contextualized vital sign representation, the measurement result is presented in conjunction with salient measurement context metadata. We present an automated annotation system for vital sign measurements that uses ontologies from the Open Biomedical Ontology Foundry (OBO Foundry) to represent the patient’s kinetic state at the time of measurement. The annotation system is applied (...) to data generated by a wearable personal status monitoring (PSM) device. We demonstrate how annotated PSM data can be queried for contextualized vital signs as well as sensor algorithm configuration parameters. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Sequence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

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)

ABSTRACT:While the literature on psychedelic medicine emphasizes the importance of set and setting alongside the quality of subjective drug effects for therapeutic efficacy, few scholars have explored the therapeutic frameworks that are used alongside psychedelics in the lab or in the clinic. Based on a narrative analysis of the treatment manual and post-session experience reports from a pilot study of psilocybin-assisted treatment for tobacco smoking cessation, this article examines how therapeutic frameworks interact with the psychedelic substance in ways that can (...) rapidly reshape participants' identity and sense of self. We identified multiple domains relating to identity shift that appear to serve as smoking cessation mechanisms during psilocybin sessions, each of which had an identifiable presence in the manualized treatment. As psychedelic medicine becomes mainstream, consensual and evidence-based approaches to psychedelic-assisted identity shift that respect patient autonomy and encourage empowerment should become areas of focus in the emergent field of psychedelic bioethics. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Rembrandt and LearningRalph A. Smith (bio)IntroductionIt appears to be a defining characteristic of Rembrandt’s works—as important as the brushstrokes, the underdrawing, the types of ground and the paints used—that they move people exceedingly. [T]hey help us feel something of what the artist may have felt about youth, old age, friendship, isolation, and love.—Anthony Bailey[For] Rembrandt, imperfections are the norm of humanity, which is why he will always speak (...) across centuries to those for whom art might be something other than the quest for ideal form.—Simon SchamaArt can arouse the senses, touch the feelings, and stir the passions. In exercising these formidable powers, the artist should respect certain limits of good taste and moral propriety. Rembrandt possessed unequal skill in depicting the passions in original ways without breaking the code. Well, hardly ever.—Gary SchwartzThe National Endowment for the Humanities (NEH) Rembrandt Project was designed to apply state-of-the-art digital technology to the development of the multiple competencies needed for understanding and appreciating [End Page 101] Rembrandt and his time. As educational consultant to the project, I was given the assignment of conceptualizing a framework that would accommodate and illuminate the project’s purposes. This meant that I not only had to refamiliarize myself with seventeenth-century Dutch art and culture and with the national and state standards for the visual arts but also acquaint myself with the standards for socials studies; both sets of standards occupy a prominent place in the project and are the subject of the third section of this article. The overarching viewpoint from which I approached my assignment, however, was that of the humanities, a topic to which I turn first. Furthermore, since the project’s foremost concern is with masterpieces of the visual arts, I thought it apposite to address briefly some issues in aesthetics, especially those that relate to experiencing artworks appropriately. Having surveyed the project from the perspectives mentioned, I then ask to what extent it was successful in avoiding the pitfalls that often frustrate the implementation of novel ideas and methods.1The HumanitiesThe following interpretation of the humanities is condensed from the writings of two distinguished philosophers, Albert William Levi and Walter Kaufmann, and the historian Paul Gagnon. Levi, an early member of the National Council for the Humanities and for most of his career a distinguished professor of the humanities at Washington University, was once asked to define the essence of the humanities. He replied that the purposes of the humanities are to encourage persons to “to think critically, to communicate successfully, and to walk proudly with [their] tradition.”2 Noteworthy in this terse statement is its emphasis on the procedural aspects of the humanities, that is, their effects on human actions and attitudes. Such emphasis accorded well with the tradition of the Middle Ages, which construed the humanities as skills of organizing and understanding human experience. Levi, however, also acknowledged the Renaissance conception of the humanities as subject matters, thereby paying tribute to the endeavors of Renaissance scholars who devoted themselves to recovering and transmitting the literary texts of antiquity. A strong believer in historical continuity, Levi synthesized the Medieval and Renaissance traditions by proposing that the humanities be understood as skills of communication, continuity, and criticism. These skills have their substantive grounding in languages and literatures, history, and philosophy, the latter conceived as critical reflection.3 After pondering Levi’s interpretation, I added another “c,” the arts of creation, to his troika. Thus, the humanities can be understood as indispensable to human experience because they are the arts of creation, communication, continuity, and criticism.Another view of the purposes of the humanities and their relevance to the project can be found in the writings of the historian Paul Gagnon. He [End Page 102] stressed the importance of preparing the young for citizenship, personal cultivation, and vocation within a curriculum committed to the values of equity and competence.4 Gagnon interpreted the study of history as providing critical checks on reality, imparting insights into the various ways in which persons have used historical knowledge to find their place in the flow of events, and... (shrink)

The Industrial Ontologies Foundry (IOF) was formed to create a suite of interoperable ontologies. Ontologies that would serve as a foundation for data and information interoperability in all areas of manufacturing. To ensure that each ontology is developed in a structured and mutually coherent manner, the IOF has committed to the tiered architecture of ontology building based on the Basic Formal Ontology (BFO) as top level. One of the critical elements of a successful tiered architecture build is the domain mid-level (...) ontologies. However, thus far there has been no mid-level manufacturing ontology that is based on BFO. The IOF has recently released the IOF Core version 1 beta to fill this gap. This paper documents the development process and gives an overview of the current content of the IOF Core. Finally, the paper describes how the IOF Core can be used as the basis for a more domain-specific Supply Chain Ontology. (shrink)

Many modern discussions on Vocational education and Training (VET) only consider it’s goals in terms of the labor market or social inclusion. This article argues that vocations are an important contribution to the common good of society as whole, and not only a method of securing laborers. In order to acknowledge this contribution there needs to be a reorientation on VET from an educational perspective first and foremost. In order to do this, this article revisits a public debate John Dewey (...) had with two early educational reformers David Snedden and Charles Prosser in the early twentieth century. In this debate, the economic arguments used by Snedden and Prosser, which have found their echoes in the modern VET debates were opposed to the educational arguments of Dewey. This article wishes to show the significant educational nature of Dewey’s counter arguments and argue for the relevance of this approach in the modern VET discussion. (shrink)

This paper presents a non-reductionist framework of eight nested modes of evolution that have successively emerged to organize the reproduction of all organisms, from the blue-green algae to our societies. The processes of biological, "Darwinian," evolution are those of drift during reproduction, and of selection. The key unit of evolutionary time is the generation, and its locus is the organisms' life-cycle setup. Different life-cycle setups support different mechanisms of reproduction, and therefore different modes of evolution. By tracing the different life-cycle (...) setups attested throughout Life's History, we are able to characterize the successive modes of evolution with which they are associated. The present attempt has led to a characterization of the following eight nested modes of evolution: Basic; Reptilian; Archaic Mammalian; Progressive Mammalian; Socio-cultural; Extrasomatically Enhanced Socio-cultural; Tinkering; and finally Para-biological. These successively emerging modes govern a progressively reduced number of life-forms. The first four modes are "Darwinian" in the strict sense. The fifth, or socio-cultural mode, which governs whale and elephant societies in addition to hominoids, is already not "Darwinian" in the traditional sense. The last three modes have emerged with the genus homo, through the progressive extension of its life-cycle setups. The present framework is to be used heuristically, as a prism with which to separate the evolutionary spectrum of the constituent elements of human behavior. An example of such a behavioral evolutionary spectrum is presented in the conclusion, and is used to compare the present framework with those recently proposed by Maynard Smith and Szathmáry and by Foley. (shrink)

What does it look like when an organization tentatively steps away from an exclusively rules-based regime and begins to attend to both rules and principles? What insights and guidance can ethicists and ethical theory offer? This paper is a case study of an organization that has initiated such a transition. The American Institute of Certified Public Accountants has begun a turn toward the promotion of ethical principles and best practices by adding a “conceptual framework” to its existing Code of Professional (...) Conduct. This conceptual framework calls upon its members to intentionally increase their awareness of significant threats to their compliance with its rules of conduct and to establish safeguards to offset or eliminate those threats. To this end, each member is required to regard every questionable situation, circumstance, transaction or relationship by attempting to view it through the eyes of an imagined reasonable third party. This paper examines this protocol theoretically and practically. First, we frame this analysis within the principles and ethical concepts that inform the professional ethics of accountants. Second, we critique the AICPA’s long-standing rules-based approach to its Code. Third, we examine the new conceptual framework with a view toward its potential for the promotion of a more principles-based approach to the professional ethics of the accounting profession. Fourth, we give attention to the notion of the “reasonable and informed third party,” which has been embedded in the new conceptual framework, and consider how two schools of thought—Adam Smith’s modernist “impartial spectator” concept and Emmanuel Lévinas’ postmodern phenomenology in regard to “the Other”—may offer theoretical support and clarity for this epistemic exercise. Finally, we point out several ways in which the AICPA’s commitment to its new conceptual framework could be strengthened and enhanced. (shrink)

Albert O. Hirschman was a development economist and political theorist whose work is essential reading for anyone interested in understanding how economic life figures in the political worlds we inhabit and the ways in which we give meaning to our lives in market-based societies. Perhaps best known for the distinction between 'exit' and 'voice', Hirschman was a prolific theorist who wrote about the role individual moral virtue and individual self-interest should play in economic activity, how economic growth in the (...) developing world might best be achieved, and the reactionary rhetoric of neo-conservative politicians in the late 1980s, to list but some of the areas he covered. Hirschman's writing was elegant; further, he understood the importance of the well-chosen word. He was, as this new biography by Jeremy Adelman shows, an economist for whom the essays of Montaigne were as important as the writings of Ricardo and Smith. (shrink)

Drawing on the work of Albert Camus this paper offers a critique of certain discourses around ‘novel ecosystems’. These new species ‘assemblages’ are frequently defended, or even celebrated, as exemplifying resilience and adaptability to the environmental repercussions of a global situation inaccurately glossed as ‘The Anthropocene’. Here the increasing prevalence of economically generated changes, including the accelerating translocations of species, are set against earlier conservation values emphasizing protection of ‘natural’ and ‘native’ ecologies. The proliferation of novel ecosystems, together with (...) an instrumental emphasis on their functional, ‘pragmatic’, and economic benefits, appears to make environmentalists’ ethical concerns about the loss of endangered others seem ‘absurd’ and frames conservation as a Sisyphean task. Yet Camus early work provides arguments for ethical / political resistance in just such absurd and extreme circumstances. (shrink)

The author characterizes the model of rationality devised by critical rationalism in opposition to the classic model of rationality and as an alternative to this. He illustrates and criticizes the trichotomous theory of knowledge which, going back to Max Scheler, is received in a secularized version by Habermas and Apel, also under the influence of the hermeneutic tradition of Heidegger and Gadamer and of the so-called “critical theory” of Max Horkheimer and Theodor Adorno. The author criticizes historicism as it expects (...) to be an alternative to naturalism and not to make use of the method based on scientific laws. The author proposes as an example of technological social science the model developed in economics starting from Adam Smith. With regard to legal theories, natural law is rejected because of its sociomorphic cosmology. It is proposed that legal science as social technology has two parts. One part aims at efficient interpretations of valid law (for the space-time region concerned) and a second part aims at the construction of efficient norms for the modification of valid law by legislation. (shrink)

I take issue with two suggestions of Joel Feinberg's: first, that it is incoherent to suppose that human life as such is absurd, and, second, that a particular human life may be absurd and yet saved from being tragic by being fulfilled. I also argue that human life as such may well be absurd and I consider various responses to this.

A modern philosopher described religion as “that region in which all the enigmas of the world are solved.” Smith argues in Experience and God that religion itself has become an enigma for modern man. In the book, smith attempts to reunite philosophy with religion. He argues that in recent decades the prevailing attitude has been chiefly one of indifference. This indifference, leading to the failure of understanding can be overcome only through radical reflection and self-criticism: a re-consideration of (...) the nature of religion, its place in the total structure of human life, and its relations to the secular culture in which the faith of man must live. The task Smith lays out must be of a largely philosophical nature, not only because of the necessity to understand religion in relation to a comprehensive scheme of things, but also because the idea of religion is intimately connected with the issues of metaphysics. Smith’s purpose is to bridge the gap between the ontological approach to God as represented by Augustine, Anselm, and Bonaventure, and the cosmological approach represented by Thomas Aquinas and Albert the Great. Smith shows that, although the two approaches significantly differ, they can be interpreted as ways of leading the meditating mind to the Presence of God, through the soul and through the world. (shrink)

Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical examples that (...) have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities. Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines. Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise. (shrink)

In recent years it has become popular to model putative refutations of skepticism on Kant's answer to Hume, that is, on transcendental arguments purporting to show that the skeptical theses presupposes essential features of the very conceptual scheme they call into question. In his book, Oneself as Another, Paul Ricoeur makes the claim that transcendental considerations of the sort invalidate Edmund Husserl's foundationalist epistemological enterprise, that of uncovering the genesis of primitive concepts of oneself, world, and others in a primordial (...) solipsistic stage from which all trace of others is excluded. According to Ricoeur the concept of others must be presupposed throughout. This paper examines the experiential evidence for four of the transcendental arguments endorsed by Ricoeur, each treating one of four key concepts--the concept of oneself as subject, that of one's flesh, that of one's body, and that of other selves. It finds that in each case Ricoeur’s argument fails, and that in each case Husserl is right to claim that a rudimentary nonlinguistic concept may arise within the confines of first-person perceptual experience. The paper then briefly examines the source of Ricoeur's erroneous evaluation. (shrink)