Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold.

The partial cooperation displayed by subjects in the Centipede Game deviates radically from the predictions of traditional game theory. Even standard, infinite population, evolutionary settings have failed to provide an explanation for this behavior. However, recent work in finite population evolutionary models has shown that such settings can produce radically different results from the standard models. This paper examines the evolution of partial cooperation in finite populations. The results reveal a new possible explanation that is not open to the standard models and gives us reason to be cautious when employing these otherwise helpful idealizations.

The structure-mapping theory has become the de facto standard account of analogies in cognitive science and philosophy of science. In this paper I propose a distinction between two kinds of domains and I show how the account of analogies based on structure-preserving mappings fails in certain (object-rich) domains, which are very common in mathematics, and how the axiomatic approach to analogies, which is based on a common linguistic description of the analogs in terms of laws or axioms, can be used successfully to explicate analogies of this kind. Thus, the two accounts of analogies should be regarded as complementary, since each of them is adequate for explicating analogies that are drawn between different kinds of domains. In addition, I illustrate how the account of analogies based on axioms has also considerable practical advantages, for example, for the discovery of new analogies.

In a recent paper, Malament (2004) employs a time reversal transformation that differs from the standard one, without explicitly arguing for it. This is a new and important understanding of time reversal that deserves arguing for in its own right. I argue that it improves upon the standard one. Recent discussion has focused on whether velocities should undergo a time reversal operation. I address a prior question: What is the proper notion of time reversal? This is important, for it will affect our conclusion as to whether our best theories are time-reversal symmetric, and hence whether our spacetime is temporally oriented.

In biology, the ‘ecological orientation’ rests on a commitment to examining systems, and the conceptual challenge of defining that system now employs techniques and concepts adapted from diverse disciplines (i.e., systems philosophy, cybernetics, information theory, computer science) that are applied to biological simulations and model building. Immunology has joined these efforts, and the question posed here is whether the discipline will remain committed to its theoretical concerns framed by the notions of protecting an insular self, an entity demarcated from its environment, or will shift its focus of interest to a wider context. An ecological perspective emphasizes the interchange between the organism and its environment, the processing of information, and the regulation arising from responses to this larger context. Moving from the first attempts at modeling the immune system as a closed network, immunologists have joined the general interest in systems analysis, and that move might portend a significant shift to an open, more holistic consideration of immune regulation.