When modelling complex systems one can not include all the causal factors, but one has to settle for partial models. This is alright if the factors left out are either so constant that they can be ignored or one is able to recognise the circumstances when they will be such that the partial model applies. The transference of knowledge from the point of application to the point of learning utilises a combination of recognition and inference ­ a simple model of (...) the important features is learnt and later situations where inferences can be drawn from the model are recognised. Context is an abstraction of the collection of background features that are later recognised. Different heuristics for recognition and model formulation will be effective for different learning tasks. Each of these will lead to a different type of context. Given this, there are (at least) two ways of modelling context: one can either attempt to investigate the contexts that arise out of the heuristics that a particular agent actually applies (the `internal' approach); or (if this is feasible) one can attempt to model context using the external source of regularity that the heuristics exploit. There are also two basic methodologies for the investigation of context: a top-down (or `foundationalist') approach where one tries to lay down general, a priori principles and a bottom-up (or `scientific') approach where one can try and find what sorts of context arise by experiment and simulation. A simulation is exhibited which is designed to illustrate the practicality of the bottom-up approach in elucidating the sorts of internal context that arise in an artificial agent which is attempting to learn simple models of a complex environment. It ends with a plea for the cooperation of the AI and Machine Learning communities as both learning and inference is needed if context is to make complete sense. (shrink)

If all the participants in the color ontology debate are naturalists with good sciences on their side, how could color subjectivism win? The apparent reason is that subjectivism is supported by the opponent process theory that is a successful neurophysiological reduction of colors. We will argue that the real reason is the unique reductive methodology of the opponent paradigm. We will undermine subjectivism by arguing against the methodology.

The theory of concepts advanced in the dissertation aims at accounting for a) how a concept makes successful practice possible, and b) how a scientific concept can be subject to rational change in the course of history. Traditional accounts in the philosophy of science have usually studied concepts in terms only of their reference; their concern is to establish a stability of reference in order to address the incommensurability problem. My discussion, in contrast, suggests that each scientific concept consists of (...) three components of content: 1) reference, 2) inferential role, and 3) the epistemic goal pursued with the concept's use. I argue that in the course of history a concept can change in any of these three components, and that change in one component—including change of reference—can be accounted for as being rational relative to other components, in particular a concept's epistemic goal.This semantic framework is applied to two cases from the history of biology: the homology concept as used in 19th and 20th century biology, and the gene concept as used in different parts of the 20th century. The homology case study argues that the advent of Darwinian evolutionary theory, despite introducing a new definition of homology, did not bring about a new homology concept (distinct from the pre-Darwinian concept) in the 19th century. Nowadays, however, distinct homology concepts are used in systematics/evolutionary biology, in evolutionary developmental biology, and in molecular biology. The emergence of these different homology concepts is explained as occurring in a rational fashion. The gene case study argues that conceptual progress occurred with the transition from the classical to the molecular gene concept, despite a change in reference. In the last two decades, change occurred internal to the molecular gene concept, so that nowadays this concept's usage and reference varies from context to context. I argue that this situation emerged rationally and that the current variation in usage and reference is conducive to biological practice.The dissertation uses ideas and methodological tools from the philosophy of mind and language, the philosophy of science, the history of science, and the psychology of concepts. (shrink)

Watson and Crick’s discovery of the structure of DNA led to developments that transformed many biological sciences. But what were the relevant developments and how did they transform biology? Much of the philosophical discussion concerning this question can be organized around two opposing views: theoretical reductionism and layer-cake antireductionism. Theoretical reductionist and their anti-reductionist foes hold two assumptions in common. First, both hold that biological knowledge is structured like a layer cake, with some biological sciences, such as molecular biology cast (...) at lower levels of organization, and others, such as classical genetics, cast at higher levels. Second, both assume that scientific knowledge is structured by theory and that the productivity of scientific research depends on whether the underlying theory identifies the fundamentals upon which the phenomena to be explained and investigated depend. In the first part of this paper, I challenge these assumptions. In the second part, I show how recasting the basic theory of classical genetics made it possible to retool the methodologies of genetics. It was the investigative power of these retooled methodologies, and not the explanatory power of a gene-based theory, that transformed biology. (shrink)

In the contemporary life sciences more and more researchers emphasize the “limits of reductionism” (e.g. Ahn et al. 2006a, 709; Mazzocchi 2008, 10) or they call for a move “beyond reductionism” (Gallagher/Appenzeller 1999, 79). However, it is far from clear what exactly they argue for and what the envisioned limits of reductionism are. In this paper I claim that the current discussions about reductionism in the life sciences, which focus on methodological and explanatory issues, leave the concepts of a reductive (...) method and a reductive explanation too unspecified. In order to fill this gap and to clarify what the limits of reductionism are I identify three reductive methods that are crucial in the current practice of the life sciences: decomposition, focusing on internal factors, and studying parts in isolation. Furthermore, I argue that reductive explanations in the life sciences exhibit three characteristics: first, they refer only to factors at a lower level than the phenomenon at issue, second, they focus on internal factors and thus ignore or simplify the environment of a system, and, third, they cite only the parts of a system in isolation. (shrink)