In classically based modal logic, there are three common conceptions of necessity, the universal conception, the equivalence relation conception, and the axiomatic conception. They provide distinct presentations of the modal logic S5, all of which coincide in the basic modal language. We explore these different conceptions in the context of the relevant logic R, demonstrating where they come apart. This reveals that there are many options for being an S5-ish extension of R. It further reveals a divide between the universal (...) conception of necessity on the one hand, and the axiomatic conception on the other: The latter is consistent with motivations for relevant logics while the former is not. For the committed relevant logician, necessity cannot be the truth in all possible worlds. (shrink)

There appears to be few, if any, limits on what sorts of logical connectives can be added to a given logic. One source of potential limitations is the motivating ideology associated with a logic. While extraneous to the logic, the motivating ideology is often important for the development of formal and philosophical work on that logic, as is the case with intuitionistic logic. One family of logics for which the philosophical ideology is important is the family of relevant logics. In (...) this paper, I explore the limits of what a relevant connective is, showing how some basic criteria motivated by the ideology of relevant logicians provide robust limits on potential connectives. These criteria provide some plausible necessary conditions on being a relevant connective. (shrink)

In this article, we present a definition of a hyperintensionality appropriate to relevant logics. We then show that relevant logics are hyperintensional in this sense, drawing consequences for other non-classical logics, including HYPE and some substructural logics. We further prove results concerning extensionality in relevant logics. We close by discussing related concepts for classifying formula contexts and potential applications of these results.

The operational semantics of Urquhart is a deep and important part of the development of relevant logics. In this paper, I present an overview of work on Urquhart’s operational semantics. I then present the basics of collection frames. Finally, I show how one kind of collection frame, namely, functional set frames, is equivalent to Urquhart’s semilattice semantics.

In this paper, I motivate the addition of an actuality operator to relevant logics. Straightforward ways of doing this are in tension with standard motivations for relevant logics, but I show how to add the operator in a way that permits one to maintain the intuitions behind relevant logics. I close by exploring some of the philosophical consequences of the addition.

Various theorists have endorsed the “communication argument”: communicative capacities are necessary for morally responsible agency because blame aims at a distinctive kind of moral communication. I contend that existing versions of the argument, including those defended by Gary Watson and Coleen Macnamara, face a pluralist challenge: they do not seem to sit well with the plausible view that blame has multiple aims. I then examine three possible rejoinders to the challenge, suggesting that a context-specific, function-based approach constitutes the most promising (...) modification of the communication argument. (shrink)

Relevant logics are a family of non-classical logics characterized by the behavior of their implication connectives. Unlike some other non-classical logics, such as intuitionistic logic, there are multiple philosophical views motivating relevant logics. Further, different views seem to motivate different logics. In this article, we survey five major views motivating the adoption of relevant logics: Use Criterion, sufficiency, meaning containment, theory construction, and truthmaking. We highlight the philosophical differences as well as the different logics they support. We end with some (...) questions for future research. (shrink)

An important question for proponents of non-contractive approaches to paradox is why contraction fails. Zardini offers an answer, namely that paradoxical sentences exhibit a kind of instability. I elaborate this idea using revision theory, and I argue that while instability does motivate failures of contraction, it equally motivates failure of many principles that non-contractive theorists want to maintain.

Few debates in environmental philosophy have been more heated than the one over the nature of wilderness. And yet, when one surveys the present scene, one finds that a variety of different conceptions of wilderness are still quite popular – some more so in certain professions than others. In this paper, I look at three popular conceptions of wilderness with an eye toward sussing out the good and the bad them. I look at what I call (1) the folk view (...) of wilderness, (2) Leopold’s conception of wilderness, and (3) the legal conception of wilderness (as found in the Wilderness Act of 1964). In the final part of the paper, I sketch out a sort of spectrum account of wilderness, one that I argue allows us to capture more cases of wilderness and might serve as a useful tool in future conservation efforts. (shrink)

It is widely agreed that reactive attitudes play a central role in our practices concerned with holding people responsible. However, it remains controversial which emotional attitudes count as reactive attitudes such that they are eligible for this central role. Specifically, though theorists near universally agree that guilt is a reactive attitude, they are much more hesitant on whether to also include shame. This paper presents novel arguments for the view that shame is a reactive attitude. The arguments also support the (...) view that shame is a reactive attitude in the sense that concerns moral accountability. The discussion thereby challenges both the view that shame is not a reactive attitude at all, suggested by philosophers such as R. Jay Wallace and Stephen Darwall, and the view that shame is a reactive attitude but does not concern moral accountability, recently defended by Andreas Carlsson and Douglas Portmore. (shrink)

Environmental philosophy plays an important role, directly and indirectly, in many parts of society, including land and wildlife management (Leopold, 1949; Minteer, 2015), political activism (Abbey, 1968; Malm, 2020),and technological research and development (Baum & Owe, 2022; Donhauser et al., 2021). Environmental philosophy uncovers the ethical relationships existing between humans and the living and non-living world. It reveals the nuances of our scientific ecological concepts. And it tries to tell us how we might act – individually or collectively – to (...) better achieve our environmental goals. The aim of this special issue is to explore the limits and ever-expanding outer edges of this increasingly important area of philosophical thought. (shrink)

In Saving Truth from Paradox, Hartry Field presents and defends a theory of truth with a new conditional. In this paper, I present two criticisms of this theory, one concerning its assessments of validity and one concerning its treatment of truth-preservation claims. One way of adjusting the theory adequately responds to the truth-preservation criticism, at the cost of making the validity criticism worse. I show that in a restricted setting, Field has a way to respond to the validity criticism. I (...) close with some general considerations on the use of revision-theoretic methods in theories of truth. (shrink)

In this paper, I examine the ethics of nonviolent protest when a violent response is either foreseen or intended. One central concern is whether protesters, who foresee a violent response but persist, are provoking the violence and whether they are culpable for any eventual harms. A second concern is whether it is permissible to publicize the violent response for political advantage. I begin by distinguishing between two senses of the term provoke: a normative sense where a provocateur knowingly imposes an (...) unjustified risk of a violent response, and a descriptive sense where the respondent feels provoked. I argue that, when the risk of a violent response is justified, the protesters are not provocateurs but akin to nonculpable, entrapping agents who create an opportunity for the regime to respond with disproportionate violence. The regime’s response can disclose its brutality or criminality and this can be fairly publicized for political advantage. When nonviolent protesters create an unjustified risk of violence either because the injustice they oppose is insufficient to justify the risk of a violent response or because the risked harms are disproportionate with the likely political advantages derived from the protest, they are partially culpable provocateurs. However, I argue these partially culpable provocateurs can still permissibly publicize the disproportionate violence of the regime so as to shape public opinion. (shrink)

This article examines how facial recognition technology reshapes the philosophical debate over the ethics of video surveillance. When video surveillance is augmented with facial recognition, the data collected is no longer anonymous, and the data can be aggregated to produce detailed psychological profiles. I argue that – as this non-anonymous data of people’s mundane activities is collected – unjust risks of harm are imposed upon individuals. In addition, this technology can be used to catalogue all who publicly participate in political, (...) religious, and socially stigmatised activities, and I argue that this would undermine central interests of liberal democracies. I examine the degree to which the interests of individuals and the societal interests of liberal democracies to maintain people’s obscurity while in public coincide with privacy interests, as popularly understood, and conclude that there is a practical need to articulate a novel right to obscurity to protect the interests of liberal democratic societies. (shrink)

A common refrain in and outside academia is that prominent sports figures ought to engage more in the public discourse about political issues. This idea parallels the idea that athletes ought to be role models in general. This paper first examines and critiques the “athlete as role model” argument and then applies this critique to the “athlete as political activist” argument. Appealing to the empirical political psychological literature, the paper sketches an argument that athlete activism might actually do more harm (...) than good. (shrink)

When asked which of our concepts are normative concepts, metaethicists would be quick to list such concepts as GOOD, OUGHT, and REASON. When asked why such concepts belong on the list, metaethicists would be much slower to respond. Matti Eklund is a notable exception. In his recent book, Choosing Normative Concepts, Eklund argues by elimination for “the Normative Role view” that normative concepts are normative in virtue of having a “normative role” or being “used normatively”. One view that Eklund aims (...) to eliminate is “the Metaphysical view” that normative concepts are normative in virtue of referring to normative properties. In addition to arguing that Eklund’s objection looks doubtful by its own lights, we argue that there are several plausible versions of the Metaphysical view that Eklund doesn’t eliminate, defending various claims about normative concepts and their relationships to deliberation, competence, reference, and possession along the way. (shrink)

In this article, I analyze how the Harry Potter novels bring to awareness two fundamental aspects of the human condition: the importance of one’s choices and the inevitability of one’s mortality. These are highlighted through the contrast of the characters of Harry Potter and Lord Voldemort.

Can reasoning improve moral judgments and lead to moral progress? Pessimistic answers to this question are often based on caricatures of reasoning, weak scientific evidence, and flawed interpretations of solid evidence. In support of optimism, we discuss three forms of moral reasoning (principle reasoning, consistency reasoning, and social proof) that can spur progressive changes in attitudes and behavior on a variety of issues, such as charitable giving, gay rights, and meat consumption. We conclude that moral reasoning, particularly when embedded in (...) social networks with mutual trust and respect, is integral to moral progress. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

Arguments attempting to debunk moral beliefs, by showing they are unjustified, have tended to be global, targeting all moral beliefs or a large set of them. Popular debunking arguments point to various factors purportedly influencing moral beliefs, from evolutionary pressures, to automatic and emotionally-driven processes, to framing effects. We show that these sweeping arguments face a debunker’s dilemma: either the relevant factor is not a main basis for belief or it does not render the relevant beliefs unjustified. Empirical debunking arguments (...) in ethics can avoid this predicament, but only if they are refocused on highly selective classes of moral belief. Experimental data can combine with familiar consistency reasoning to reveal that like cases are not being treated alike. Selective debunking arguments are unlikely to yield sweeping sceptical conclusions, but they can lead to rational moral change. (shrink)

The Unified Medical Language System and the Gene Ontology are among the most widely used terminology resources in the biomedical domain. However, when we evaluate them in the light of simple principles for wellconstructed ontologies we find a number of characteristic inadequacies. Employing the theory of granular partitions, a new approach to the understanding of ontologies and of the relationships ontologies bear to instances in reality, we provide an application of this theory in relation to an example drawn from the (...) context of the pathophysiology of hypertension. This exercise is designed to demonstrate how, by taking ontological principles into account we can create more realistic biomedical ontologies which will also bring advantages in terms of efficiency and robustness of associated software applications. (shrink)

We present a new frame semantics for positive relevant and substructural propositional logics. This frame semantics is both a generalisation of Routley–Meyer ternary frames and a simplification of them. The key innovation of this semantics is the use of a single accessibility relation to relate collections of points to points. Different logics are modeled by varying the kinds of collections used: they can be sets, multisets, lists or trees. We show that collection frames on trees are sound and complete for (...) the basic positive distributive substructural logic $\mathsf {B}^+$, that collection frames on multisets are sound and complete for $\mathsf {RW}^+$ (the relevant logic $\mathsf {R}^+$, without contraction, or equivalently, positive multiplicative and additive linear logic with distribution for the additive connectives), and that collection frames on sets are sound for the positive relevant logic $\mathsf {R}^+$. The completeness of set frames for $\mathsf {R}^+$ is, currently, an open question. (shrink)

The International Classification of Functioning, Disability and Health provides a classification of human bodily functions, which, while exhibiting non-conformance to many formal ontological principles, provides an insight into which basic functions such a classification should include. Its evaluation is an important first step towards such an adequate ontology of this domain. Presented at the 13th Annual North American WHO Collaborating Center Conference on the ICF, 2007.

We argue that distinct conditionals—conditionals that are governed by different logics—are needed to formalize the rules of Truth Introduction and Truth Elimination. We show that revision theory, when enriched with the new conditionals, yields an attractive theory of truth. We go on to compare this theory with one recently proposed by Hartry Field.

1. Over the last 50 years or so, and especially over the last few decades, the U.S. and many other societies have undergone a large, rapid, and broad decline in anti-gay attitudes. The magnitude, s...

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

We provide a methodology for the creation of ontological partitions in biomedicine and we test the methodology via an application to the phenomenon of blood pressure. An ontology of blood pressure must do justice to the complex networks of intersecting pathways in the organism by which blood pressure is regulated. To this end it must deal not only with the anatomical structures and physiological processes involved in such regulation but also with the relations between these at different levels of granularity. (...) For this purpose our ontology offers a variety of distinct partitions � of substances, processes and functions � and integrates these together within a single framework via transitive networks of part-whole and dependence relations among the entities in each of these categories. The paper concludes with a comparison of this methodology with the approaches of GOTM, KEGG, DIP and BIND and provides an outline of how the methodology is currently being applied in the field of biomedical database integration. (shrink)

that can serve as a foundation for more refined ontologies in the field of proteomics. Standard data sources classify proteins in terms of just one or two specific aspects. Thus SCOP (Structural Classification of Proteins) is described as classifying proteins on the basis of structural features; SWISSPROT annotates proteins on the basis of their structure and of parameters like post-translational modifications. Such data sources are connected to each other by pairwise term-to-term mappings. However, there are obstacles which stand in the (...) way of combining them together to form a robust meta-classification of the needed sort. We discuss some formal ontological principles which should be taken into account within the existing datasources in order to make such a metaclassification possible, taking into account also the Gene Ontology (GO) and its application to the annotation of proteins. (shrink)

In one of his earliest dialogues, the Soliloquia, Augustine identifies the liberal arts (disciplinae) with truth (veritas), and employs this somewhat puzzling identification as a premise in his infamous proof of the immortality of the soul (Sol. 2.24). In this paper, I examine Augustine’s argument for this peculiar identification. Augustine maintains both (1) that the constituent propositions of the liberal arts are true, and (2) that the liberal art of dialectic (disciplina disputandi) is the “truth through which all disciplines are (...) true” (Sol. 2.21). I argue that Augustine identifies the liberal arts with truth because (1) the constituent propositions of the liberal arts are learned, and (2) dialectic’s structure is essential to the liberal arts. I further suggest that the subject matter of each liberal art reflects a distinct segment of intelligible reality, that is, the realm of the intelligible Forms. (shrink)

Kant interpreters are divided on the question of whether determinate cognition plays a role in the harmony of the faculties in aesthetic judgement. I provide a ‘non-cognitive’ interpretation that allows Kant’s statements regarding judgements of natural beauty to cohere such that determinate cognition need not be taken to perform any role in such judgements. I argue that, in aesthetic harmony, judgement privileges the free activity of the imagination over the cognizing function of the understanding for the purpose of unifying the (...) object, although the free imagination cannot violate the obscure concepts and principles of ordinary common sense. (shrink)

Quality assurance in large terminologies is a difficult issue. We present two algorithms that can help terminology developers and users to identify potential mistakes. We demon­strate the methodology by outlining the different types of mistakes that are found when the algorithms are applied to SNOMED-CT. On the basis of the results, we argue that both formal logical and linguistic tools should be used in the development and quality-assurance process of large terminologies.

The theory of granular partitions (TGP) is a new approach to the understanding of ontologies and other classificatory systems. The paper explores the use of this new theory in the treatment of task-based clinical guidelines as a means for better understanding the relations between different clinical tasks, both within the framework of a single guideline and between related guidelines. We used as our starting point a DAML+OIL-based ontology for the WHO guideline for hypertension management, comparing this with related guidelines and (...) attempting to show that TGP provides a flexible and highly expressive basis for the manipulation of ontologies of a sort which might be useful in providing more adequate Computer Interpretable Guideline Models (CIGMs) in the future. (shrink)

Kant claims that the transcendental self can be represented as a “feeling of existence” (Gefühl eines Daseins). Some interpreters take this claim to be inconsistent with Kant’s larger theory of self-consciousness. I consider the extent to which two eighteenth-century philosophy texts that Kant knew well - Tetens’ Philosophische Versuche über die menschliche Natur und ihre Entwickelung and Feder’s Logik und Metaphysik - can contribute to our understanding of Gefühl eines Daseins. I point to some continuities between Kant’s characterization of “Gefühl” (...) in Gefühl eines Daseins, and Tetens’ and Feder’s conceptualizations of Selbstgefühl. I show that Gefühl eines Daseins is prima facie consistent with Feder’s clear “I” (or Selbstgefühl) and Tetens’ clear Selbstgefühl; and both Gefühl eines Daseins and clear Selbstgefühl relate to higher cognition. Finally, I discuss whether the notion of Selbstgefühl is compatible with key aspects of Kant’s conceptualization of the self - the transcendental-empirical distinction, and the atemporality of the self. (shrink)

A Better Ape covers the evolution of morality from the birth of our ape family through the evolution of human species and all the way up to the development of modern societies. In this summary, we highlight several main elements of this account: the co-evolution of morality with intelligence and complex sociality; the role of social institutions and religious morality in the cultural evolution of behaviorally modern humans in prehistory; the increasing complexity of the moral mind through biological evolution in (...) apes, gene-culture co-evolution in various human species, cultural evolution in Homo sapiens, and rational-cultural evolution in recent centuries; and, finally, a cultural evolutionary model of progressive and regressive moral change on which a key factor driving moral progress is social and democratic integration. (shrink)

Samuel Scheffler has argued that people value tradition for its own sake because they view it as accumulated experience, and as playing an important role in forming their personal integrity, structuring their lives, and providing them with a sense of belonging. These reasons, according to Scheffler, are de facto justifications that people offer for choosing to act on purely traditional grounds. In this essay, I argue that these de facto reasons must be supplemented if they are to be seen as (...) de jure rational grounds for valuing tradition for its own sake. Such a supplementation would open up the possibility of articulating a coherent theory of moderate cosmopolitanism. (shrink)

This paper has two aims. First, it sets out an interpretation of the relevant logic E of relevant entailment based on the theory of situated inference. Second, it uses this interpretation, together with Anderson and Belnap’s natural deduc- tion system for E, to generalise E to a range of other systems of strict relevant implication. Routley–Meyer ternary relation semantics for these systems are produced and completeness theorems are proven. -/- .

The present investigation was undertaken to investigate the acute toxicity of cadmium, a heavy metal widely detected in the aquatic environment due to natural effects and anthropogenic activities, in freshwater teleost, Channa punctata (Bloch). The experiments for the bioassay were performed in semi-static test condition according to the standard guidelines. The behavioural changes in the fish were observed for all tested concentrations of the metal. The data obtained for bioassay were analyzed for median lethal concentrations (LC ) of the metal (...) by SPSS computer software. The LC 50 50 values, estimated by SPSS, with 95% confidence level were found to be:20.589 (18.326-23.221), 17.133 (14.840- 19.734), 11.815 (9.696 – 13.850) mg/L and 9.908 (7.635-12381) mg/L for cadmium chloride at 24, 48, 72 and 96 h exposure, respectively. (shrink)

Andrea Kern contends that perceptual experience is perceptual knowledge if our self-consciously held capacity for perceptual knowledge is “perfectly” actualized. I argue that this view requires further justification. First, Kern is unable to support her claim that an awareness of our self-conscious capacity for perceptual knowledge is “contained” in all our perceptions. Second, Kern’s claim that perception includes the idea of the conditions of perception is potentially inconsistent with her denial that perceptual experience enables perceptual knowledge.

Create a novel network model for mobile ad hoc network (MANET) nodes and actors in wireless sensor networks to collaborate on event processing. There are two stages in the development of distributed algorithms: setup and negotiation. The first uses weighted proportional max-min fairness to initially allocate MANET nodes across event zones, whereas the latter uses a market-based method to re-distribute the number of MANET nodes based on existing and new events. A detection technique for malicious packet dropping attacks in MANETs. (...) The mechanism of the suggested approach is Collaborative Convolutional Neural Network (CCNN), which is based on the reputation value computed for that node by its neighbours. A node's reputation value is determined by its network packet forwarding behaviour. The reputation information is collected, saved, and transferred between nodes before being calculated under various scenarios. A network simulator was used to test the proposed protocol. The simulation results demonstrate the effectiveness of its performance. Even in the presence of cryptographic procedures, our method incurs negligible network bandwidth and latency costs. Moreover, we demonstrate that the protection is still effective in the presence of misbehaving nodes and routing changes caused by mobility. While further research is needed to thoroughly evaluate our method, we feel that the concept of collaborative security in MANETs is a potential future area. (shrink)

Evidence-based medicine relies on the execution of clinical practice guidelines and protocols. A great deal of of effort has been invested in the development of various tools which automate the representation and execution of the recommendations contained within such guidelines and protocols by creating Computer Interpretable Guideline Models (CIGMs). Context-based task ontologies (CTOs), based on standard terminology systems like UMLS, form one of the core components of such a model. We have created DAML+OIL-based CTOs for the tasks mentioned in the (...) WHO guideline for hypertension management, drawing comparisons also with other related guidelines. The advantages of CTOs include: contextualization of ontologies, providing ontologies tailored to specific aspects of the phenomena of interest, dividing the complexity involved in creating ontologies into different levels, providing a methodology by means of which the task recommendations contained within guidelines can be integrated into the clinical practices of a health care set-up. (shrink)

The Gene Ontology is an important tool for the representation and processing of information about gene products and functions. It provides controlled vocabularies for the designations of cellular components, molecular functions, and biological processes used in the annotation of genes and gene products. These constitute three separate ontologies, of cellular components), molecular functions and biological processes, respectively. The question we address here is: how are the terms in these three separate ontologies related to each other? We use statistical methods and (...) formal ontological principles as a first step towards finding answers to this question. (shrink)

Recent work on the quality assurance of the Gene Ontology (GO, Gene Ontology Consortium 2004) from the perspective of both linguistic and ontological organization has made it clear that GO lacks the kind of formalism needed to support logic-based reasoning. At the same time it is no less clear that GO has proven itself to be an excellent terminological resource that can serve to combine together a variety of biomedical database and information systems. Given the strengths of GO, it is (...) worth investigating whether, by overcoming some of its weaknesses from the point of view of formal-ontological principles, we might not be able to enhance a version of GO which can come even closer to serving the needs of the various communities of biomedical researchers and practitioners. It is accepted that clinical and bioinformatics need to find common ground if the results of data-intensive biomedical research are to be harvested to the full. It is also widely accepted that no single method will be sufficient to create the needed common framework. We believe that the principles-based approach to life-science data integration and knowledge representation must be one of the methods applied. Indeed in dealing with the ontological representation of carcinomas, and specifically of colon carcinomas, we have established that, had GO (and related biomedical ontologies) followed some of the basic formal-ontological principles we have identified (Smith et al. 2004, Ceusters et al. 2004), then the effort required to navigate successfully between clinical and bioinformatics systems would have been reduced. We point here to the sources of ontologically-related errors in GO, and also provide arguments as to why and how such errors need to be resolved. (shrink)

This paper defends “Animal Universalism,” the thesis that all sentient non-human animals will be brought into Heaven and remain there for eternity. It assumes that God exists and is all-powerful, perfectly loving, and perfectly just. From these background theses, the authors argue that Animal Universalism follows. If God is perfectly loving, then God is concerned about the well-being of non-human animals, and God chooses to maximize the well-being of each individual animal when doing so does not harm other individual creatures (...) or violate creaturely freedom. If God is perfectly just, then God does not arbitrarily discriminate against non-human animals by offering humans an opportunity to enter Heaven but not offering the same to each animal. Each of these conclusions implies Animal Universalism. (shrink)

Causal models of agents have been used to analyse the safety aspects of machine learning systems. But identifying agents is non-trivial -- often the causal model is just assumed by the modeler without much justification -- and modelling failures can lead to mistakes in the safety analysis. This paper proposes the first formal causal definition of agents -- roughly that agents are systems that would adapt their policy if their actions influenced the world in a different way. From this we (...) derive the first causal discovery algorithm for discovering agents from empirical data, and give algorithms for translating between causal models and game-theoretic influence diagrams. We demonstrate our approach by resolving some previous confusions caused by incorrect causal modelling of agents. (shrink)

It is widely understood that protein functions can be exhaustively described in terms of no single parameter, whether this be amino acid sequence or the three-dimensional structure of the underlying protein molecule. This means that a number of different attributes must be used to create an ontology of protein functions. Certainly much of the required information is already stored in databases such as Swiss-Prot, Protein Data Bank, SCOP and MIPS. But the latter have been developed for different purposes and the (...) separate data-structures which they employ are not conducive to the needed data integration. When we attempt to classify the entities in the domain of proteins, we find ourselves faced with a number of cross-cutting principles of classification. Our question here is: how can we bring together these separate taxonomies in order to describe protein functions? Our proposed answer is: via a careful top-level ontological analysis of the relevant principles of classification, combined with a new framework for the simultaneous manipulation of classifications constructed for different purposes. (shrink)

This paper provisionally offers a way of addressing the predicament of a person who does not feel at home in her own concepts, because these concepts were once forced upon her by a colonial regime. If the goal for a person in such a circumstance is to overcome this alienation through intellectual means, then one way in which this might be accomplished would be to develop a hermeneutics that would enable her to ascertain the alienating aspects of her existing concepts. (...) To this end, I outline a hermeneutical strategy which requires that, in reading the colonizer’s textual tradition, the colonized/ex–colonized person must heuristically presuppose that her current concepts are entirely determined by this tradition unless these concepts can be shown to resist such determination on reflective–systematic grounds. (shrink)

Kant interpreters have contrasting views on what Kant takes to be the basis for human dignity. Several commentators have argued that human dignity can be traced back to some feature of human beings. Others contend that humans in themselves lack dignity, but dignity can be attributed to them because the moral law demands respect for humanity. I argue, alternatively, that human dignity in Kant’s system can be seen to be grounded in the reciprocal relationship between the dignity of the moral (...) law and the dignity inherent in the human constitution. The latter includes the dignity of personhood, construed as rational inner purposiveness, and the dignity of giving oneself the law and striving to follow it. (shrink)

Ontological principles are needed in order to bridge the gap between medical and biological information in a robust and computable fashion. This is essential in order to draw inferences across the levels of granularity which span medicine and biology, an example of which include the understanding of the roles of tumor markers in the development and progress of carcinoma. Such information integration is also important for the integration of genomics information with the information contained in the electronic patient records in (...) such a way that real time conclusions can be drawn. In this paper we describe a large multi-granular datasource built by using ontological principles and focusing on the case of colon carcinoma. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)