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.

The role played by the concept of genetic coding in biology is discussed. I argue that this concept makes a real contribution to solving a specific problem in cell biology. But attempts to make the idea of genetic coding do theoretical work elsewhere in biology, and in philosophy of biology, are probably mistaken. In particular, the concept of genetic coding should not be used (as it often is) to express a distinction between the traits of whole organisms that are coded for in the genes and the traits that are not.

The representation theorems of expected utility theory show that having certain types of preferences is both necessary and sufficient for being representable as having subjective probabilities. However, unless the expected utility framework is simply assumed, such preferences are also consistent with being representable as having degrees of belief that do not obey the laws of probability. This fact shows that being representable as having subjective probabilities is not necessarily the same as having subjective probabilities. Probabilism can be defended on the basis of the representation theorems only if attributions of degrees of belief are understood either antirealistically or purely qualitatively, or if the representation theorems are supplemented by arguments based on other considerations (simplicity, consilience, and so on) that single out the representation of a person as having subjective probabilities as the only true representation of the mental state of any person whose preferences conform to the axioms of expected utility theory.

One of the issues dividing “absolutists” and “relationists” is the question whether all motion is relative motion or, in the words of Earman, spacetime has “structures that support absolute quantities of motion.” This paper argues that, despite the enormous literature bearing on the topic, it is problematic to formulate a general criterion for when a quantity counts as absolute in contrast to merely relative in a way that is not hopelessly parasitic on other, presumably distinct, senses of “absolute.” Furthermore, I suggest that the vicissitudes of the evolution of the concept of absolute motion have contributed to this difficulty.

The explanatory significance of equilibrium depends on the underlying dynamics. A number of questions of stability and robustness are relevant. Here I investigate these questions with respect to some simple evolutionary models from my book, Evolution of the Social Contract. These models use the replicator dynamics. In each of these models I identify the equilibria and characterize their local dynamic stability properties. In two of the models, I show that one equilibrium is globally asymptotically stable. I then show that the foregoing results are robust over a large class of adaptive dynamics that might be considered as alternatives to the replicator dynamics. I investigate the structural stability properties of the three models. The question of the structural stability of a model of bargaining with correlated encounters raised by D'Arms, Batterman, and Górny (1998) is answered in the affirmative. The other two models are not structurally stable. Modification of a structurally unstable signaling system to allow for correlated encounters results in a structurally stable model.

Arthur Fine's Natural Ontological Attitude (NOA) is intended to provide an alternative to both realism and antirealism. I argue that the most plausible meaning of “natural” in NOA is “nonphilosophical,” but that Fine comes to NOA through a particular conception of philosophy. I suggest that instead of a natural attitude we should adopt a philosophical attitude. This is one that is self-conscious, pragmatic, pluralistic, and sensitive to context. I conclude that when scientific realism and antirealism are viewed with a philosophical attitude there are still legitimate philosophical questions to address.

Evolutionary psychology and social constructionism are widely regarded as fundamentally irreconcilable approaches to the social sciences. Focusing on the study of the emotions, we argue that this appearance is mistaken. Much of what appears to be an empirical disagreement between evolutionary psychologists and social constructionists over the universality or locality of emotional phenomena is actually generated by an implicit philosophical dispute resulting from the adoption of different theories of meaning and reference. We argue that once this philosophical dispute is recognized, it can be set aside. When this is done, it becomes clear that the two approaches to the emotions complement, rather than compete with, one another.

Some biochemical systems require multiple, well-matched parts in order to function, and the removal of any of the parts eliminates the function. I have previously labeled such systems “irreducibly complex,” and argued that they are stumbling blocks for Darwinian theory. Instead I proposed that they are best explained as the result of deliberate intelligent design. In a recent article Shanks and Joplin analyze and find wanting the use of irreducible complexity as a marker for intelligent design. Their primary counterexample is the Belousov-Zhabotinsky reaction, a self-organizing system in which competing reaction pathways result in a chemical oscillator. In place of irreducible complexity they offer the idea of “redundant complexity,” meaning that biochemical pathways overlap so that a loss of one or even several components can be accommodated without complete loss of function. Here I note that complexity is a quantitative property, so that conclusions we draw will be affected by how well-matched the components of a system are. I also show that not all biochemical systems are redundant. The origin of non-redundant systems requires a different explanation than redundant ones.

David Hull accounts for the success of science in terms of an invisible hand mechanism, arguing that it is difficult to reconcile scientists' self-interestedness or their desire for recognition with traditional philosophical explanations for the success of science. I argue that we have less reason to invoke an invisible hand mechanism to explain the success of science than Hull implies, and that many of the practices and institutions constitutive of science are intentionally designed by scientists with an eye to realizing the very goals that Hull believes need to be explained by reference to an invisible hand mechanism. Thus, I reduce the scope of Hull's invisible hand explanation and supplement it by appealing to a hidden hand explanation.