A wide range of gene knockout experiments shows that functional stability is an important feature of biological systems. On this backdrop, we present an argument for higher-level causation based on counterfactual dependence. Furthermore, we sketch a metaphysical picture providing resources to explain the metaphysical nature of functional stability, higher-level causation, and the relevant notion of levels. Our account aims to clarify the role empirical results and philosophical assumptions should play in debates about reductionism and higher-level causation. It thereby contributes to the development of a philosophical foundation for systems biology.

James Woodward offers a conception of explanation and mechanism in terms of interventionist counterfactuals. Based on a case from ecology, I show that ecologists’ approach to that case satisfies Woodward's conditions for explanation and mechanism, but his conception does not fully capture what ecologists view as explanatory. The new mechanistic philosophy likewise aims to describe central aspects of mechanisms, but I show that it is not sufficient to account for ecological mechanisms. I argue that in ecology explanation involves identification of invariant and insensitive causal relationships and descriptions of the mechanistic characteristics that make these relations possible.

Comparative genomicists seem to be convinced that the unit of measurement employed in their studies is a gene that drives the function of cells and ultimately organisms. As a result, they have come to some substantive conclusions about how similar humans are to other organisms based on the percentage of genetic makeup they share. I argue that the actual unit of measurement employed in the studies corresponds to a structural rather than a functional gene concept, thus rendering many of the implications drawn from comparative genomic studies largely unwarranted, if not completely mistaken.

Different chemical species are often cited as paradigm examples of structurally delimited natural kinds. While classificatory monism may thus seem plausible for simple molecules, it looks less attractive for complex biological macromolecules. I focus on the case of proteins that are most plausibly individuated by their functions. Is there a single, objective count of proteins? I argue that the vagaries of function individuation infect protein classification. We should be pluralists about macromolecular classification.

Ethological theory standardly attributes representational content to animal signals. In this article I first assess whether Ruth Millikan's teleosemantic theory accounts for the content of animal signals. I conclude that it does not, because many signals do not exhibit the required sort of cooperation between signal-producing and signal-consuming devices. It is then argued that Kim Sterelny's proposal, while not requiring cooperation, sometimes yields the wrong content. Finally, I outline an alternative view, according to which consumers alone are responsible for conferring representational status and determining content. I suggest that consumer-based teleosemantics reconstruct the content of both cooperative and noncooperative signals and explain how a given trait can mean different things to different consumers.

Many cases of gene-environment interaction, or $\mathrm{G}\,\times \mathrm{E}\,$, are misconstrued as evincing a genetic predisposition. I diagnose this misconstrual and then introduce a new concept—interactive predisposition—to correct for the mistake. I conclude by examining how recent debates over screening for individual predispositions are related to older debates about group differences between populations, drawing on the lessons of the latter to inform the former.

Selectionist evolutionary theory has often been faulted for not making novel predictions that are surprising, risky, and correct. I argue that it in fact exhibits the theoretical virtue of predictive capacity in addition to two other virtues: explanatory unification and model fitting. Two case studies show the predictive capacity of selectionist evolutionary theory: parallel evolutionary change in E. coli and the origin of eukaryotic cells through endosymbiosis.

Paul Churchland has recently offered a novel argument for the “objective reality” of color. The strategy he employs to make this argument is an instance of a more general research program for interpreting perceptual content, “domain-portrayal semantics.” In the first half of the article, I point out some features of color vision that complicate Churchland's conclusion, in particular, the context-sensitive and inferential nature of color perception. In the second half, I examine and defend the general research program, concluding it is naturalistic in a minimal sense and should be of interest to naturalists and nonnaturalists alike.

While many philosophers agree that evolutionary theory has important implications for the study of ethics, there has been no consensus on what these implications are. I argue that we can better understand these implications by examining two related yet distinct issues in evolutionary theory: the evolution of our moral beliefs and the evolution of cooperative behavior. While the prevailing evolutionary account of morality poses a threat to moral realism, a plausible model of how altruism evolved in human beings provides the grounding for a research program that focuses on achieving some of the more practical goals shared by ethicists.

In some recent papers, Max Coltheart has questioned the ability of neuroimaging techniques to tell us anything interesting about the mind and has thrown down the gauntlet before neuroimagers, challenging them to prove he is mistaken. Here I analyze Coltheart's challenge, show that as posed its terms are unfair, and reconstruct it so that it is addressable. I argue that, so modified, Coltheart's challenge is able to be met and indeed has been met. In an effort to delineate the extent of neuroimaging's ability to address Coltheart's concerns, I explore how different brain structure-function relationships would constrain the ability of neuroimaging to provide insight about psychological questions.

It is commonly assumed that the scientific study of emotions should focus on discrete categories such as fear, anger, sadness, joy, disgust, shame, guilt, and so on. This view has recently been questioned by the emergence of the “core affect movement,” according to which discrete emotions are not natural kinds. Affective science, it is argued, should focus on core affect, a blend of hedonic and arousal values. Here, I argue that the empirical evidence does not support the thesis that core affect is a more “natural” category than discrete emotions. I conclude by recommending a splitting strategy in our search for natural affective kinds.

Is phenomenal consciousness a problem for the brain sciences? An increasing number of researchers hold not only that it is but that its very existence is a deep mystery. That this problematic phenomenon exists is generally taken for granted: It is asserted that phenomenal consciousness is just phenomenologically obvious. In contrast, I hold that there is no such phenomenon and, thus, that it does not pose a problem for the brain sciences. For this denial to be plausible, however, I need to show that phenomenal consciousness is not phenomenologically obvious. That is the goal of this article.

Although the canonical distribution is one of the central tools of statistical mechanics, the reason for its effectiveness is poorly understood. This is due in part to the fact that there is no clear consensus on what it means to use the canonical distribution to describe a system in equilibrium with a heat bath. I examine some traditional views as to what sort of thing we should take the canonical distribution to represent. I argue that a less explored alternative, according to which the canonical distribution represents a time ensemble of sorts, has a number of advantages that rival interpretations lack.

The current status of string theory is assessed quite differently by most of the theory's exponents than by the majority of physicists in other fields. While the former tend to have a high degree of trust in string theory's viability, the latter largely share a substantially more skeptical point of view. This article argues that the controversy can be best understood in terms of a paradigmatic rift between the two sides over their understandings of theory assessment. An attempt is made to evaluate the two conflicting paradigms on their own terms.

An important contemporary version of Boltzmannian statistical mechanics explains the approach to equilibrium in terms of typicality. The problem with this approach is that it comes in different versions, which are, however, not recognized as such and not clearly distinguished. This article identifies three different versions of typicality-based explanations of thermodynamic-like behavior and evaluates their respective successes. The conclusion is that the first two are unsuccessful because they fail to take the system's dynamics into account. The third, however, is promising. I give a precise formulation of the proposal and present an argument in support of its central contention.

The main problem with the many-worlds theory is that it is not clear how the notion of probability should be understood in a theory in which every possible outcome of a measurement actually occurs. In this paper, I argue for the following theses concerning the many-worlds theory: (1) If probability can be applied at all to measurement outcomes, it must function as a measure of an agent's self-location uncertainty. (2) Such probabilities typically violate reflection. (3) Many-worlds branching does not have sufficient structure to admit self-location probabilities. (4) Decision-theoretic arguments do not solve this problem.

Within the context of general relativity, we consider one definition of a “time machine” proposed by Earman, Smeenk, and Wüthrich. They conjecture that, under their definition, the class of time machine spacetimes is not empty. Here, we prove this conjecture.

Teller argued that violations of Bell's inequalities are to be explained by interpreting quantum entangled systems according to ‘relational holism’, that is, by postulating that they exhibit irreducible (‘inherent’) relations. Teller also suggested a possible application of this idea to quantum statistics. However, the basic proposal was not explained in detail nor has the additional idea about statistics been articulated in further work. In this article, I reconsider relational holism, amending it and spelling it out as appears necessary for a proper assessment, and application, of the position.

Structural realist interpretations of generally relativistic spacetimes have recently come to enjoy a remarkable degree of popularity among philosophers. I present a challenge to these structuralist interpretations that arises from considering cosmological models in general relativity. As a consequence of their high degree of spacetime symmetry, these models resist a structuralist interpretation. I then evaluate the various strategies available to the structuralist to react to this challenge.

Newton's argument for universal gravitation in the Principia eventually rested on the third “Rule of Philosophizing,” which warrants the generalization of “qualities of bodies.” An analysis of the rule and the history of its development indicate that the term ‘quality’ should be taken to include both inherent properties of bodies and relations among systems of bodies, generalized into ‘laws'. By incorporating law-induction into the rule, Newton could legitimately rebuff objections to his theory by claiming that universal gravitation was justified by his method even if he could not specify the cause of gravity.