The concept of mechanism is analyzed in terms of entities and activities, organized such that they are productive of regular changes. Examples show how mechanisms work in neurobiology and molecular biology. Thinking in terms of mechanisms provides a new framework for addressing many traditional philosophical issues: causality, laws, explanation, reduction, and scientific change.

We argue that intelligible appeals to interlevel causes (top-down and bottom-up) can be understood, without remainder, as appeals to mechanistically mediated effects. Mechanistically mediated effects are hybrids of causal and constitutive relations, where the causal relations are exclusively intralevel. The idea of causation would have to stretch to the breaking point to accommodate interlevel causes. The notion of a mechanistically mediated effect is preferable because it can do all of the required work without appealing to mysterious interlevel causes. When interlevel (...) causes can be translated into mechanistically mediated effects, the posited relationship is intelligible and should raise no special philosophical objections. When they cannot, they are suspect. (shrink)

In the context of scientists' reflections on genomics, we examine some fundamental issues in the emerging postgenomic discipline of systems biology. Systems biology is best understood as consisting of two streams. One, which we shall call ‘pragmatic systems biology’, emphasises large‐scale molecular interactions; the other, which we shall refer to as ‘systems‐theoretic biology’, emphasises system principles. Both are committed to mathematical modelling, and both lack a clear account of what biological systems are. We discuss the underlying issues in identifying systems (...) and how causality operates at different levels of organisation. We suggest that resolving such basic problems is a key task for successful systems biology, and that philosophers could contribute to its realisation. We conclude with an argument for more sociologically informed collaboration between scientists and philosophers. BioEssays 27:1270–1276, 2005. © 2005 Wiley Periodicals, Inc. (shrink)

Philosophers of neuroscience have traditionally described interfield integration using reduction models. Such models describe formal inferential relations between theories at different levels. I argue against reduction and for a mechanistic model of interfield integration. According to the mechanistic model, different fields integrate their research by adding constraints on a multilevel description of a mechanism. Mechanistic integration may occur at a given level or in the effort to build a theory that oscillates among several levels. I develop this alternative model using (...) a putative exemplar of reduction in contemporary neuroscience: the relationship between the psychological phenomena of learning and memory and the electrophysiological phenomenon known as Long-Term Potentiation. A new look at this historical episode reveals the relative virtues of the mechanistic model over reduction as an account of interfield integration. (shrink)

Robustness is a fundamental property of biological systems, observed ubiquitously across species and at different levels of organization from gene regulation to ecosystem. The theory of biological robustness argues that robustness fosters evolv-ability and that together they entail various tradeoffs as well as characteristic architectures and mechanisms. We argue that classes of biological systems have evolved to enhance their robustness by extending their system boundary through a series of symbioses with foreign biological entities . A series of major biological innovations (...) has been achieved by events consistent with this framework: horizontal gene transfer, serial endosymbiosis, oocytes-mediated vertical infection, and host-symbiont mutualism for bacterial flora. Self-extending symbiosis contributes to robustness because symbiotic foreign biological entities can enhance the adaptative capacity of the system against environmental perturbations as well as contribute novel functions. In addition, evolutionary history indicates that the degree of symbiosis achieved has substantially changed from tight integration into the genome to loose integration as bacterial flora . The most dramatic example can be seen in the symbiosis of host immune system and bacterial flora in which substantial function of host defense depends on the proper maintenance of bacterial flora and its adaptive capability. Biological systems following this type of evolutionary path might have attained high levels of functionality, robustness, and evolvability. Thus, robustness, evolution, and self-extending symbiosis may form essential system principles for biology. (shrink)