According to the semantic view of scientific theories, theories are classes of models. I show that this view—if taken literally—leads to absurdities. In particular, this view equates theories that are distinct, and it distinguishes theories that are equivalent. Furthermore, the semantic view lacks the resources to explicate interesting theoretical relations, such as embeddability of one theory into another. The untenability of the semantic view—as currently formulated—threatens to undermine scientific structuralism.

It is proposed that we use the term “approximation” for inexact description of a target system and “idealization” for another system whose properties also provide an inexact description of the target system. Since systems generated by a limiting process can often have quite unexpected—even inconsistent—properties, familiar limit processes used in statistical physics can fail to provide idealizations but merely provide approximations.

Reductionists in biology claim that all biological events can be explained in terms of genes and macromolecules alone, while antireductionists argue that some biological events must be explained at a higher level. The literature, however, does not distinguish between different kinds of molecular explanation. The goal of this article is to identify and analyze three such kinds. The analysis of molecular explanations herein carries an important philosophical implication; in shunning crude reductionism and extreme versions of holism, we can combine the insights of thoughtful reductionists with sophisticated antireductionism. When this is done, the question of explanatory reductionism becomes less substantial than often supposed.

Homology is a biological sameness relation that is purported to hold in the face of changes in form, composition, and function. In spite of the centrality and importance of homology, there is no consensus on how we should understand this concept. The two leading views of homology, the genealogical and developmental accounts, have significant shortcomings. We propose a new account, the hierarchical-dependency account of homology, which avoids these shortcomings. Furthermore, our account provides for continuity between special, general, and serial homology.

Understanding the role mechanistic constraints play in shaping evolution can relieve the tension between the generally accepted intuition that there are no strict laws in biology and empirical findings showing that evolutionary processes are biased toward preferred outcomes. Mechanistic constraints explain why some evolutionary outcomes are more probable than others and allow for predictions in specific lineages. At the same time, mechanistic constraints are neither necessary nor universal in the way laws are traditionally characterized: they remain contingent on the past evolution of the biological mechanisms underpinning them and only constrain the future evolution of the organisms possessing them.

We offer an account of empathetic pain that preserves the distinctions among standard pain, contagious pain, empathetic pain, sympathy for pain, and standard pain ascription. Vicarious experiences of both contagious and empathetic pain resemble to some extent experiences of standard pain. But there are also crucial dissimilarities. As neuroscientific results show, standard pain involves a sensorimotor and an affective component. According to our account, contagious pain consists in imagining the former, whereas empathetic pain consists in imagining the latter. We further argue that awareness of another's standard pain is part of empathetic pain, but empathetic awareness of another's standard pain differs from believing that another is in standard pain.

The basic education of philosophers of science during the second half of the twentieth century was founded on the seven Rs: the three basic Rs and the topics of Rationality, Realism, Reductionism, and Relativism. The topic and ideas in this volume are foundational and challenging. They challenge and replace the ancient notion of philosophy as unified knowledge and the corresponding images of the tree of knowledge and encyclopedia forests.

Philosophy of Science owes a considerable debt of gratitude to its referees—the Associate Editors, the members of the Editorial Board, and the many other individuals who help to review submissions. In acknowledgement of their essential service, we list here the names of those individuals who have refereed papers during the years 2010 and 2011.