In this paper I discuss a recent theory on functions called Organizational Account. This theory seeks to provide a new definition of function that overcomes the distinction between etiological and dispositional accounts and that could be used in biology as well as in technology. I present a definition of function that I think captures the intuitions of Organizational Accounts and consider several objections.

Numerous research groups are now utilizing Basic Formal Ontology as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three existing BFO subcategories of realizable entity, namely function, role, and disposition. It proposes one further sub-category of tendency, and considers the merits of recognizing two sub-categories of function for domain ontologies, namely, artifactual and biological function. The motivation is to help advance the coherent ontological treatment of functions, roles, and dispositions, (...) to help provide the potential for more detailed classification, and to shed light on BFO’s general make-up and use. (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)

This paper reviews the debate on the notion of biological function and on functional explanation as this takes place in philosophy. It describes the different perspectives, issues, intuitions, theories and arguments that have emerged. The author shows that the debate has been too heavily influenced by the concerns of a naturalistic philosophy of mind and argues that in order to improve our understanding of biology the attention should be shifted from the study of intuitions to the study of the actual (...) practice of biological inquiry. (shrink)

Time is a pervasive notion of high impact in information systems and computer science altogether. Respective understandings of the domain of time are fundamental for numerous areas, frequently in combination with closely related entities such as events, changes and processes. The conception and representation of time entities and reasoning about temporal data and knowledge are thus significant research areas. Each representation of temporal knowledge bears ontological commitments concerning time. Thus it is important to base temporal representations on a foundational ontology (...) that covers general categories of time entities. In this article we introduce and discuss two consecutive ontologies of time that have been developed for the top-level ontology General Formal Ontology. The first covers intervals, named chronoids, and time boundaries of chronoids, as a kind of time points. One important specialty of time boundaries is their ability to coincide with other time boundaries. The second theory extends the first one by additionally addressing time regions, i.e., mereological sums of chronoids. Both ontologies are partially inspired by ideas of Franz Brentano, especially from his writings about the continuum. In particular, we view continuous time intervals as a genuine phenomenon which should not be identified with intervals of real numbers. On these grounds the resulting ontologies allow for proposing novel contributions to several problematic issues in temporal representation and reasoning, among others, the Dividing Instant Problem and the problem of persistence and change. Following our general approach to ontology development, both ontologies are axiomatized as formal theories in first-order logic and are analyzed metalogically. We prove the consistency of both ontologies, and completeness and decidability for one. Moreover, standard time theories with points and intervals are covered by both theories. (shrink)

Many objects in the world have functions. Typewriters are for typing. Can-openers are for opening cans. Lawnmowers are for cutting grass. That is what these things are for. Every day around the world people attribute functions to objects. Some of the objects with functions are organs or parts of living organisms. Hearts are for pumping blood. Eyes are for seeing. Countless works in biology explain the “Form, Function, and Evolution of... ” everything from bee dances to elephant tusks to pandas’ (...) ‘thumbs’. Many scientific explanations, in areas as diverse as psychology, sociology, economics, medical research, and neuroscience, rest on appeals to the function and/or malfunction of things or systems. They talk of how humans and other organisms or their parts work, what their functions are, why they are present, and how different situations will affect them and how they will react. Philosophers, going back to Aristotle, used to make generous use of functions in describing objects, organisms, their interactions, and even as the basis of ethics and metaphysics. And yet, since the Enlightenment, talk of the function of natural objects, teleological function, began to be viewed with suspicion, as the mechanical model of the world replaced the old Aristotelian model. From a religious standpoint, it used to be easy to see how objects in the natural world could have natural functions, for God was said to instill functions by design throughout Creation. But philosophers became increasingly reluctant to invoke God to solve every difficult philosophical problem, and became unwilling to indulge in such religious explanations of teleology. (shrink)