A biochemical pathway is a sequence of chemical reactions in a biological organism. Such pathways specify mechanisms that explain how cells carry out their major functions by means of molecules and reactions that produce regular changes. Many diseases can be explained by defects in pathways, and new treatments often involve finding drugs that correct those defects. This paper presents explanation schemas and treatment strategies that characterize how thinking about pathways contributes to biomedical discovery. It discusses the significance of pathways for understanding the nature of diseases, explanations, and theories.

I outline Gould's conception of evolutionary theory and his ways of contrasting it with contemporary Darwinism; a contemporary Darwinism that focuses on the natural selection of individual organisms. Gould argues for a hierarchical conception of the living world and of the evolutionary processes that have built that living world: organisms are built from smaller components (genes, cells) and are themselves components of groups, populations, species, lineages. Selection, drift and constraint are important to all of these levels of biological organization, not just that of individual organisms. Moreover, both drift and constraint are more important than orthodoxy supposes. While having some sympathy for both of these lines of argument, I argue that they are more problematic than Gould supposes, and that he understates the power and the heterogeneity of orthodox conceptions of life's evolution.

Ontological questions in biology have typically focused on the nature of species: what are species; how are they identified and individuated? There is an analogous, but much neglected concern: what are characters; how are they identified and individuated? Character individuation is significant because biological systematics relies on a parsimony principle to determine phylogeny and classify taxa, and the parsimony principle is usually interpreted to favor the phylogenetic hypothesis that requires the fewest changes in characters. But no character individuation principle identified so far is adequate. For biological systematics we need a better way of conceiving characters.

According to a prominent view of evolutionary theory, natural selection and the processes of development compete for explanatory relevance. Natural selection theory explains the evolution of biological form insofar as it is adaptive. Development is relevant to the explanation of form only insofar as it constrains the adaptation-promoting effects of selection. I argue that this view of evolutionary theory is erroneous. I outline an alternative, according to which natural selection explains adaptive evolution by appeal to the statistical structure of populations, and development explains the causes of adaptive evolution at the level of individuals. Only together can a statistical theory of selection and a mechanical theory of development explain why populations of organisms comprise individuals that are adapted to their conditions of existence.

Murray Gell-Mann has proposed the concept of effective complexity as a measure of information content. The effective complexity of a string of digits is defined as the algorithmic complexity of the regular component of the string. This paper argues that the effective complexity of a given string is not uniquely determined. The effective complexity of a string admitting a physical interpretation, such as an empirical data set, depends on the cognitive and practical interests of investigators. The effective complexity of a string as a purely formal construct, lacking a physical interpretation, is either close to zero, or equal to the string's algorithmic complexity, or arbitrary, depending on the auxiliary criterion chosen to pick out the regular component of the string. Because of this flaw, the concept of effective complexity is unsuitable as a measure of information content.

In the social sciences we hardly can create laboratory conditions, we only can try to find out which kinds of experiments Nature has carried out. Knowledge about Nature's designs can be used to infer conditions for reliable predictions. This problem was explicitly dealt with in Haavelmo's (1944) discussion of autonomous relationships, Friedman's (1953) as-if methodology, and Simon's (1961) discussions of nearly-decomposable systems. All three accounts take Marshallian partitioning as starting point, however not with a sharp ceteris paribus razor but with the blunt knife of negligibility assumptions. As will be shown, in each account reflection on which influences are negligible, for what phenomena and for how long, played a central role.

We discuss a recent proposal by Albert (1994a; 1994b; 2000, ch. 7) to recover thermodynamics on a purely dynamical basis, using the quantum theory of the collapse of the wave function by Ghirardi, Rimini, and Weber (1986). We propose an alternative way to explain thermodynamics within no-collapse interpretations of quantum mechanics. Our approach relies on the standard quantum mechanical models of environmental decoherence of open systems (e.g., Joos and Zeh 1985; Zurek and Paz 1994). This paper presents the two approaches and discusses their advantages. The problems faced by both approaches will be discussed in a sequel (Hemmo and Shenker 2003).

Some have suggested that certain classical physical systems have undecidable long-term behavior, without specifying an appropriate notion of decidability over the reals. We introduce such a notion, decidability in μ (or d-μ) for any measure μ, which is particularly appropriate for physics and in some ways more intuitive than Ko's (1991) recursive approximability (r.a.). For Lebesgue measure λ, d-λ implies r.a. Sets with positive λ-measure that are sufficiently “riddled” with holes are never d-λ but are often r.a. This explicates Sommerer and Ott's (1996) claim of uncomputable behavior in a system with riddled basins of attraction. Furthermore, it clarifies speculations that the stability of the solar system (and similar systems) may be undecidable, for the invariant tori established by KAM theory form sets that are not d-λ.

Philosophers of chemistry, following the lead of physicists, have been slow to realize that molecular descriptions issuing from quantum mechanics in the absence of chemical theory are fatally flawed. In the wake of this realization, new topics have begun to unfold—including new metaphysical issues, new concerns about the philosophy of chemistry's place in the philosophy of science, and new accounts of how properties are observed, inferred, and presented. A recent collection of essays, Of Minds and Molecules: New Philosophical Perspectives on Chemistry edited by Nalini Bhushan and Stuart Rosenfeld, reveals what some of these new issues are and suggests new directions for the philosophy of chemistry.

I present a response to Vollmer's review of the book Of Minds and Molecules, and especially her comments on my own article therein. This provides an opportunity to discuss two central ideas in the philosophy of chemistry. These are the distinction between elements as simple substances (element-1) and elements as basic substances (element-2) and Paneth's proposed intermediate position for philosophy of chemistry. The response also discusses the question of isotopes in relationship to the nature of the elements and their classification as well as the philosophical status of atomic orbitals.

A Bayesian account of the virtue of unification is given. On this account, the ability of a theory to unify disparate phenomena consists in the ability of the theory to render such phenomena informationally relevant to each other. It is shown that such ability contributes to the evidential support of the theory, and hence that preference for theories that unify the phenomena need not, on a Bayesian account, be built into the prior probabilities of theories.

It has been argued, most trenchantly by Nancy Cartwright, that the diversity of the concepts and regularities we actually use to describe nature and predict and explain its behavior leaves us with no reason to believe that our foundational physical theories actually “apply” outside of delicately contrived systems within the laboratory. This paper argues that, diversity of method notwithstanding, there is indeed good reason to think that the foundational laws of physics are universal in their scope.