Immunology researchers are beginning to explore the possibilities of reproducibility, reuse and secondary analyses of immunology data. Open-access datasets are being applied in the validation of the methods used in the original studies, leveraging studies for meta-analysis, or generating new hypotheses. To promote these goals, the ImmPort data repository was created for the broader research community to explore the wide spectrum of clinical and basic research data and associated findings. The ImmPort ecosystem consists of four components–Private Data, Shared Data, Data (...) Analysis, and Resources—for data archiving, dissemination, analyses, and reuse. To date, more than 300 studies have been made freely available through the ImmPort Shared Data portal , which allows research data to be repurposed to accelerate the translation of new insights into discoveries. (shrink)

On March 14-15, 2006, at the US National Institute of Standards and Technology (NIST) in Gaithersburg, MD there took place the first Upper Ontology Summit (UOS). This was a convening of custodians of several prominent upper ontologies, key technology participants, and interested other parties, with the purpose of finding a means to relate the different ontologies to each other. The result is reflected in a joint communiqué, directed to the larger ontology community and the general public, and expressing a joint (...) intent to build bridges among the existing upper ontologies in ways designed to increase and rationalize their utilization and to enhance their semantic interoperability. (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)

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)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (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)

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 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)

While several tests and strategies are recommended for colorectal cancer (CRC) screening, studies suggest that primary care providers often recommend colonoscopy without providing information about its risks or alternatives. These observations raise concerns about the quality of informed consent for screening colonoscopy.

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)

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)

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)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (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.

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)

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)

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)

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.

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)

According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (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)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

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 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)

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)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Aworkshop was held August 26–28, 2015, by the Earth- Life Science Institute (ELSI) Origins Network (EON, see Appendix I) at the Tokyo Institute of Technology. This meeting gathered a diverse group of around 40 scholars researching the origins of life (OoL) from various perspectives with the intent to find common ground, identify key questions and investigations for progress, and guide EON by suggesting a roadmap of activities. Specific challenges that the attendees were encouraged to address included the following: What key (...) questions, ideas, and investigations should the OoL research community address in the near and long term? How can this community better organize itself and prioritize its efforts? What roles can particular subfields play, and what can ELSI and EON do to facilitate research progress? (See also Appendix II.) The present document is a product of that workshop; a white paper that serves as a record of the discussion that took place and a guide and stimulus to the solution of the most urgent and important issues in the study of the OoL. This paper is not intended to be comprehensive or a balanced representation of the opinions of the entire OoL research community. It is intended to present a number of important position statements that contain many aspirational goals and suggestions as to how progress can be made in understanding the OoL. The key role played in the field by current societies and recurring meetings over the past many decades is fully acknowledged, including the International Society for the Study of the Origin of Life (ISSOL) and its official journal Origins of Life and Evolution of Biospheres, as well as the International Society for Artificial Life (ISAL). (shrink)

Smith has argued that moral realism need not be threatened by apparent moral disagreement. One reason he gives is that moral debate has tended to elicit convergence in moral views. From here, he argues inductively that current disagreements will likely be resolved on the condition that each party is rational and fully informed. The best explanation for this phenomenon, Smith argues, is that there are mind-independent moral facts that humans are capable of knowing. In this paper, I seek (...) to challenge this argument—and more recent versions of it—by arguing that historical convergence in moral views may occur for various arational reasons. If such reasons possibly result in convergence—which Smith effectively concedes—then the moral realist would require an additional a posteriori argument to establish that convergence in moral views occurred for the right reasons. Hence, Smith-style arguments, as they stand, cannot be mobilised in support of moral realism. Rather, this investigation demonstrates the necessity of a genuine history of morality for any convergence claim in support of a meta-ethical view. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

In this dissertation, I consider a hitherto underexplored concept of ‘human minimum’ as proposed by H. Odera Oruka to obligate responsibility as an approach to tackling extreme poverty in Africa and beyond. I aim to establish, among other things, why it is morally problematic and economically counterproductive to demand equal moral responsibility from all moral agents irrespective of their economic differences to ensure the implementation of the human minimum or the elimination of extreme poverty. To achieve the aforementioned, I attempt (...) to answer two significant questions, to wit: What are some of the moral implications of ensuring that a society attains the human minimum as an approach to fighting extreme poverty? Who has a greater moral responsibility for ensuring the attainment of the human minimum between the government, non-governmental/nonprofit organisations, and individual members of society? In Oruka’s philosophy, enforcement of a global human minimum is the equal moral obligation of all moral agents—all those situated above the poverty line. I will demonstrate why ignoring the economic differences – and inequalities – of those who qualify as moral agents in Oruka’s conceptualisation of extreme poverty, particularly in continental Africa, risks plunging more of those who live a little above the human minimum threshold into poverty. I then argue that a disproportionate distribution of responsibility that is sensitive to the economic disparities that exist among the non-poor population holds a better promise for success in the fight against extreme poverty in Africa. (shrink)

»Keine Bewusstseinstheorie ohne Wissenstheorie«, d.h. die Reflexion auf die grundbegrifflichen Voraussetzungen ist notwendig, um gültige Aussagen über das Bewusstsein treffen zu können. Im Gegensatz zum Realmonismus handelt es sich bei dieser kritischen Position um einen transzendentalen Dualismus, der die Form des Bewusstseins eigens reflektiert, um damit die Voraussetzungen zu klären, unter denen das Bewusstsein überhaupt thematisiert werden muss. Der wissenstheoretische Anteil umfasst diese transzendentale Reflexion als eine reflexive Epistemologie mit einem eige- nem, d.h. hier insbesondere nicht-empirischem Geltungsanspruch: Wissen basiert nicht (...) ausschließlich auf der biologischen Wirklichkeit, sondern beruht auch auf einer gegenüber der Natur eigenständigen epistemischen »Sphäre«. Diese Sphäre wird in der folgenden Untersuchung herausgearbeitet und in ihrer Irreduzibilität erwiesen. Es wird sich zeigen, dass eine gültige Bewusstseinstheorie nur durch formale Selbstbezüglichkeit möglich ist. (shrink)

I shall attempt in what follows to show how mereology, taken together with certain topological notions, can yield the basis for future investigations in formal ontology. I shall attempt to show also how the mereological framework here advanced can allow the direct and natural formulation of a series of theses – for example pertaining to the concept of boundary – which can be formulated only indirectly (if at all) in set-theoretic terms.

This paper seeks to clarify and defend the proposition that moral realism is best elaborated as a moral doctrine. I begin by upholding Ronald Dworkin’s anti-Archimedean critique of the error theory against some strictures by Michael Smith, and I then briefly suggest how a proponent of moral realism as a moral doctrine would respond to Smith’s defense of the Archimedeanism of expressivism. Thereafter, this paper moves to its chief endeavor. By differentiating clearly between expressivism and quasi-realism, the paper (...) highlights both their distinctness and their compatibility. In so doing, it underscores the affinities between Blackburnian quasi-realism and moral realism as a moral doctrine. Finally, this paper contends—in line with my earlier work on these matters—that moral realism as a moral doctrine points to the need for some reorienting of meta-ethical enquiries rather than for the abandoning of them. (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.

"Modern History" versions of the etiological theory claim that in order for a trait X to have the proper function F, individuals with X must have been recently favored by natural selection for doing F (Godfrey-Smith 1994; Griffiths 1992, 1993). For many traits with prototypical proper functions, however, such recent selection may not have occurred: traits may have been maintained due to lack of variation or due to selection for other effects. I examine this flaw in Modern History accounts (...) and offer an alternative etiological theory, the Continuing Usefulness account, which appears to avoid such problems. (shrink)

A sketch of the history of the opposition between propositional and practical knowledge is followed by a brief account of the relevant ideas of Merleau-Ponty, Polanyi, and H. and S. Dreyfus (on expertise and artificial intelligence). The paper concludes with a discussion of the work of Ryle on the notion of a ‘discipline’, drawing implications for a theory of traditions.

The paper seeks to show how the world of everyday human cognition might be treated as an object of ontological investigation in its own right. The paper is influenced by work on affordances and prototypicality of psychologists such as Gibson and Rosch, by work on cognitive universals of the anthropologist Robin Horton, and by work of Patrick Hayes and others on ‘naive’ or ‘qualitative physics’. It defends a thesis to the effect that there is, at the heart of common (...) sense, a theoretical core of true propositions pertaining to mesoscopic objects, and that the latter are to be understood as relating mereologically to the objects studied by physical science. (shrink)

in Abortion and the Status of the Fetus, Volume XIII of the series, “Philosophy of Medicine,” eds. William B. Bondeson, H. Tristram Englehardt, Stuart Spicker, and Daniel H. Winship (Dordrecht, Holland/Boston, Massachusetts: D. Reidel, 1983), pp. 229-245.