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)

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)

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.

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.

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)

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)

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

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)

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)

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)

Reid's Inquiry into the Human Mind on the Principles of Common Sense devotes more space to double vision than to any other topic. In what follows, I examine why this subject was so important to Reid and why he dealt with it as he did. I also consider whether his argument for his position begs the question against his main opponents, Berkeley and Robert Smith. I show that, as Reid presented it, it does, but that he could have said (...) more than he did in reply to Smith. My discussion of why double vision was important for Reid begins with an exposition of the relevance of the theory of vision for one of Reid's principal concerns in the Inquiry: the concern to respond to scepticism concerning our knowledge of an external world. I then turn to consider how Reid's account of double vision contributes to his epistemological realism and why the alternative account offered by Berkeley and Smith challenges it. (shrink)

(This paper has since been republished in _Kant's Critique of Pure Reason: Critical Essays_, edited by Patricia Kitcher [Lanham: Rowman and Littlefield, 1998], 21-44.) Kant's claim that space and time are "forms of intuition" is contrasted with the nativist claim that space is an innate idea or construct of the mind and with the empiricist claim that space is given in or learned from experience. It is argued that the nativism/empiricism debate masks a more fundamental disagreement between sensationism and constructivism. (...) Kant's account of space- and time-cognition is shown to be neither sensationist nor constructivist and as a consequence to be "nativistic" in a sense which commentators from Vaihinger and Kemp Smith to Patricia Kitcher have failed to capture. (shrink)

Reid's Inquiry into the Human Mind on the Principles of Common Sense devotes more space to double vision than to any other topic. In what follows, I examine why this subject was so important to Reid and why he dealt with it as he did. I also consider whether his argument for his position begs the question against his main opponents, Berkeley and Robert Smith. I show that, as Reid presented it, it does, but that he could have said (...) more than he did in reply to Smith. My discussion of why double vision was important for Reid begins with an exposition of the relevance of the theory of vision for one of Reid's principal concerns in the Inquiry: the concern to respond to scepticism concerning our knowledge of an external world. I then turn to consider how Reid's account of double vision contributes to his epistemological realism and why the alternative account offered by Berkeley and Smith challenges it. (shrink)

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’.

Against the claims of Russell, Goodman, and Albert Casullo, this paper argues that the location of phenomena in visual space cannot be determined through reference to monadic local properties of the visual field.

This paper was originally published in _Journal of the History of Ideas_ 51 (1990): 573-597. Kant's claim that space and time are "forms of intuition" is contrasted with the nativist claim that space is an innate idea or construct of the mind and with the empiricist claim that space is given in or learned from experience. It is argued that the nativism/empiricism debate masks a more fundamental disagreement between sensationism and constructivism. Kant's account of space- and time-cognition is shown to (...) be neither sensationist nor constructivist and as a consequence to be "nativistic" in a sense which commentators from Vaihinger and Kemp Smith to Patricia Kitcher have failed to capture. (shrink)

A survey of work on perception, mind, and mental representation by 18th century philosophers after Berkeley, notably Robert Smith, William Porterfield, David Hume, Etienne de Condillac, and Thomas Reid.

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)

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)

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)

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)

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.