A framework for protein classification

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

Topological Foundations of Cognitive Science

A collection of papers presented at the First International Summer Institute in Cognitive Science, University at Buffalo, July 1994, including the following papers: ** Topological Foundations of Cognitive Science, Barry Smith ** The Bounds of Axiomatisation, Graham White ** Rethinking Boundaries, Wojciech Zelaniec ** Sheaf Mereology and Space Cognition, Jean Petitot ** A Mereotopological Definition of 'Point', Carola Eschenbach ** Discreteness, Finiteness, and the Structure of Topological Spaces, Christopher Habel ** Mass Reference and the Geometry of Solids, Almerindo E. Ojeda ** Defining a 'Doughnut' Made Difficult, N .M. Gotts ** A Theory of Spatial Regions with Indeterminate Boundaries, A.G. Cohn and N.M. Gotts ** Mereotopological Construction of Time from Events, Fabio Pianesi and Achille C. Varzi ** Computational Mereology: A Study of Part-of Relations for Multi-media Indexing, Wlodek Zadrozny and Michelle Ki

On the Argument from Physics and General Relativity

I argue that the best interpretation of the general theory of relativity has need of a causal entity, and causal structure that is not reducible to light cone structure. I suggest that this causal interpretation of GTR helps defeat a key premise in one of the most popular arguments for causal reductionism, viz., the argument from physics

Robot rights? Towards a social-relational justification of moral consideration \ud

Should we grant rights to artificially intelligent robots? Most current and near-future robots do not meet the hard criteria set by deontological and utilitarian theory. Virtue ethics can avoid this problem with its indirect approach. However, both direct and indirect arguments for moral consideration rest on ontological features of entities, an approach which incurs several problems. In response to these difficulties, this paper taps into a different conceptual resource in order to be able to grant some degree of moral consideration to some intelligent social robots: it sketches a novel argument for moral consideration based on social relations. It is shown that to further develop this argument we need to revise our existing ontological and social-political frameworks. It is suggested that we need a social ecology, which may be developed by engaging with Western ecology and Eastern worldviews. Although this relational turn raises many difficult issues and requires more work, this paper provides a rough outline of an alternative approach to moral consideration that can assist us in shaping our relations to intelligent robots and, by extension, to all artificial and biological entities that appear to us as more than instruments for our human purpose