Philosophical debates about the concept of disease, particularly of mental disease, might benefit from reconsideration and a closer look at the established terminology and conceptual structure of contemporary medical pathology and clinical nosology. The concepts and principles of medicine differ, to a considerable extent, from the ideas and notions of philosophical theories of disease. In medical theory, the concepts of disease entity and pathologicity are, besides the concept of disease itself, of fundamental importance, and they are essentially connected to the (...) concepts cause of disease or etiological factor, natural course or natural history of disease, and pathological disposition. It is the concept of disease entity that is of key importance for understanding medical pathology and theory of disease. Its central role is shown by a short reconstruction of its main features and its intrinsic connection to the concept of pathologicity. The meaning of pathologicity is elucidated by explicating the underlying criteria. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

The paper presents a new method for generating typologies of formal-ontological relations. The guiding idea is that formal relations are those sorts of relations which hold between entities which are constituents of distinct ontologies. We provide examples of ontologies (in the spirit of Zemach’s classic “Four Ontologies” of 1970), and show how these can be used to give a rich typology of formal relations in a way which also throws light on the opposition between threeand four-dimensionalism.

We propose that all actual causes are simultaneous with their direct effects, as illustrated by both everyday examples and the laws of physics. We contrast this view with the sequential conception of causation, according to which causes must occur prior to their effects. The key difference between the two views of causation lies in differing assumptions about the mathematical structure of time.

yamato sharply distinguishes itself from other existing upper ontologies in the following respects. (1) Most importantly, yamato is designed with both engineering and philosophical minds. (2) yamato is based on a sophisticated theory of roles, given that the world is full of roles. (3) yamato has a tenable theory of functions which helps to deal with artifacts effectively. (4) Information is a ‘content-bearing’ entity and it differs significantly from the entities that philosophers have traditionally discussed. Taking into account the modern (...) society in which a flood of information occurs, yamato has a sophisticated theory of informational objects (representations). (5) Quality and quantity are carefully organized for the sake of greater interoperability of real-world data. (6) The philosophical contribution of yamato includes a theory of objects, processes, and events. Those features are illustrated with several case studies. These features lead to the intensive application of yamato in some domains such as biomedicine and learning engineering. (shrink)

Empiricists have sought to follow Hume in claiming that causality is a relation between events reducible to something more basic, e.g., regularities or counterfactuals. But all such attempts fail through their inability to distinguish cause from effect. The alternative is that causation is irreducible. Regularities are evidence of causation but do not constitute it. We understand what causation is through performing intentional actions which necessarily involve trying, which in turn just is exercising causal power.

It would appear that among scientific men discussion of the general principles of natural science has, on the whole, proved more congenial to mathematicians and physicists than to biologists. Just why this should be so might be difficult to explain or justify. But one reason seems to lie in the comparative ambiguity of the concept of causation in biology. In general, the term causation has been used in science to designate the special rôle of active factors, rather than of passive (...) or stable factors, in the determination of single events. By active factors we mean those which involve physical change, typically associated with transfer of energy; these are distinguished from stable factors or invariants which persist unchanged throughout the process under consideration. Thus in the classical isolated system, the total energy represents a stable factor which remains the same through all transformations of the system. The energy changes its form, potential or distribution, but not its total quantity. This rule of conservation defines a static condition persisting as a limiting factor through any case of change. Similarly, the permanent or unchanging factor in a machine consists in the stable properties and structural interconnections of its parts; together those constitute an invariant which fixes definitely the possible range of activity. Activity itself requires flow of energy; strictly speaking, a causal factor is not a static factor but is a change of some kind; releasing events are included under causal events since they introduce factors without which change does not occur. (shrink)

This paper examines the way in which causal relations are understood in the dominant model in contemporary medicine. It argues that the causal relation is not definable in terms of the condition relation, but that in general for conditions of an occurrence to be among its causes they must answer instrumental interests in a certain way, and there are further criteria for distinguishing 'the' cause of a disease (i.e., its etiological agent) from other causal factors, which are based upon instrumental (...) interests peculiar to medicine. It also argues that diseases are complex processes of which both clinical and underlying patho-physiological manifestations are proper parts (as contrasted with effects). (shrink)

This textbook introduces the reader to basic problems in the philosophy of science and ethics, mainly by means of examples from medicine. It is based on the conviction that philosophy, medical science, medical informatics, and medical ethics are overlapping disciplines. It claims that the philosophical lessons to learn from the twentieth century are not that nature is a 'social construction' and that 'anything goes' with respect to methodological and moral rules. Instead, it claims that there is scientific knowledge, but that (...) it is never completely secure; that there are norms, but that they are situation-bound; and that, therefore, it makes good sense to search for scientific truths and try to act in a morally decent way. Using philosophical catchwords, the authors advocate 'fallibilism' and 'particularism'; a combination that might be called 'pragmatic realism'. (shrink)

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The prevention, treatment and management of disease are closely linked to how the causes of a particular disease are explained. For multi-factorial conditions, the causal explanations are inevitably complex and competing models may exist to explain the same condition. Selecting one particular causal explanation over another will carry practical and ethical consequences that are acutely relevant for health policy. In this paper our focus is two-fold; the different models of causal explanation that are put forward within current scientific literature for (...) the high and rising prevalence of the common complex conditions of coronary artery disease and type 2 diabetes mellitus ; and how these explanations are taken up within national health policy guidelines. We examine the causal explanations for these two conditions through a systematic database search of current scientific literature. By identifying different causal explanations we propose a three-tier taxonomy of the most prominent models of explanations: evolutionary, lifecourse, and lifestyle and environment. We elaborate this taxonomy with a micro-level thematic analysis to illustrate how some explanations are semantically and rhetorically foregrounded over others. We then investigate the uptake of the scientific causal explanations in health policy documents with regard to the prevention and management recommendations of current National Service Frameworks for CAD and T2D. Our findings indicate a lack of congruence between the complexity and frequent overlap of causal explanations evident in the scientific literature and the predominant focus on lifestyle recommendations found in the mainstream health policy documents. (shrink)