To understand the behavior of a complex system, one must understand the interactions among its parts. Doing so is difficult for nondecomposable systems, in which the interactions strongly influence the short term behavior of the parts. Science's principal tool for dealing with nondecomposable systems is a variety of probabilistic analysis that I call EPA. I show that EPA's power derives from an assumption that appears to be false of nondecomposable complex systems, in virtue of their very nondecomposability. Yet EPA is extremely successful. I aim to find an interpretation of EPA's assumption that is consistent with, indeed that explains, its success.

Homeostatic Property Cluster (HPC) theory suggests that species and other biological taxa consist of organisms that share certain similarities. HPC theory acknowledges the existence of Darwinian variation within biological taxa. The claim is that “homeostatic mechanisms” acting on the members of such taxa nonetheless ensure a significant cluster of similarities. The HPC theorist's focus on individual similarities is inadequate to account for stable polymorphism within taxa, and fails properly to capture their historical nature. A better approach is to treat distributions of traits in species populations as irreducible facts, explained in terms of selection pressures, genealogy, and other evolutionary factors. We call this view Population Structure Theory (PST). PST accommodates the view, implicit in biological systematics, that species are identified by reference to particular historical populations.

In this paper, we identify a new and mathematically well-defined sense in which the coherence of a set of hypotheses can be truth-conducive. Our focus is not, as usual, on the probability, but rather on the confirmation of a coherent set and its members. We show that if evidence confirms a hypothesis, confirmation is ‘transmitted’ to any hypotheses that are sufficiently coherent with the former hypothesis, according to some appropriate probabilistic coherence measure such as Olsson's or Fitelson's measure. Our findings have implications for scientific methodology, as they provide a formal rationale for the method of indirect confirmation and the method of confirming theories by confirming their parts.

I argue that four of the fundamental claims of those calling themselves ‘genic pluralists’—Philip Kitcher, Kim Sterelny, and Ken Waters—are defective. First, they claim that once genic selectionism is recognized, the units of selection problems will be dissolved. Second, Sterelny and Kitcher claim that there are no targets of selection (interactors). Third, Sterelny, Kitcher, and Waters claim that they have a concept of genic causation that allows them to give independent genic causal accounts of all selection processes. I argue that each one of these claims is either false or misleading. Moreover, the challenge that arises from the availability of genic causal accounts, namely, the inability to choose on rational grounds among genic and higher-level accounts, is unsupported.

The concept of genetic information is controversial because it attributes semantic properties to what seem to be ordinary biochemical entities. I argue that nucleic acids contain information in a semantic sense, but only about a limited range of effects. In contrast to other recent proposals, however, I analyze genetic information not in terms of a naturalized account of biological functions, but instead in terms of the way in which molecules determine their products during processes known as template-directed syntheses. I argue that determining an outcome in a certain way is constitutive for being an instruction. On this account, the content of genetic information is identified with the template's properties, which determine the product in the way constitutive for instructions.

I examine different arguments that could be used to establish indeterminism of neurological processes. Even though scenarios where single events at the molecular level make the difference in the outcome of such processes are realistic, this falls short of establishing indeterminism, because it is not clear that these molecular events are subject to quantum mechanical uncertainty. Furthermore, attempts to argue for indeterminism autonomously (i.e., independently of quantum mechanics) fail, because both deterministic and indeterministic models can account for the empirically observed behavior of ion channels.

In this paper, I consider ways of responding to critiques of natural kinds monism recently suggested from the pluralist camp. Even if monism is determined to be untenable in certain domains (say, about species), it might well be tenable in others. Chemistry is suggested to be such a monist-friendly domain. Suggestions of trouble for chemical kinds can be defused by attending to the difference between monism as a metaphysical thesis and as a claim about classification systems. Finally, I consider enantiomers as a test case for the monism/pluralism debate. The question of whether enantiomers differ in kind does not appear easily answerable. I suggest that this legislates for pluralism in chemistry.

A number of arguments have been given to show that the modal interpretation of ordinary nonrelativistic quantum mechanics cannot be consistently extended to the relativistic setting. We find these arguments inconclusive. However, there is a prima facie reason to think that a tension exists between the modal interpretation and relativistic invariance; namely, the best candidate for a modal interpretation adapted to relativistic quantum field theory, a prescription due to Rob Clifton (2000), comes out trivial when applied to a number of systems of physical interest. However, it is far from clear whether this difficulty for the modal interpretation is traceable to relativistic invariance per se or to the infinite number of degrees of freedom involved. In any case, the proponents of the modal interpretation have work to do.

In cognitive psychology, concepts are those bodies of knowledge that are stored in long-term memory and are used by default in human beings’ higher cognitive processes (categorization, inductive and deductive reasoning, etc.). Most psychologists of concepts assume that these mental representations share many scientifically important properties, and the psychology of concepts is expected to describe those properties. Psychologists assume thereby that concepts constitute a natural kind. I call this assumption the natural kind assumption. This article challenges the natural kind assumption. It is argued that a growing body of evidence suggests that concepts do not constitute a natural kind. Hence, the notion of concept is inappropriate, if one aims at formulating scientifically relevant inductive generalizations about the human mind.

I clarify the difference between pluralist and monist interpretations of levels of selection disputes. Lloyd has challenged my claim that a plurality of models correctly accounts for situations such as maintenance of the sickle-cell trait, and I revisit this example to show that competing theories don't disagree about the existence of ‘high-level’ or ‘low-level’ causes; rather, they parse these causes differently. Applying Woodward's theory of causation, I analyze Sober's distinction between ‘selection of’ versus ‘selection for’. My analysis shows that this distinction separates true causes from pseudocauses, but it also reveals that the distinction is irrelevant to the levels debate; it makes no sense to say true causes are at higher levels and not lower levels. The levels debate is not about separating real causes from pseudocauses; it's about finding useful ways to parse and disentangle causes.

There is a need to bring the work of philosophers such as Millikan who take an evolutionary approach to the study of the mind more in harmony with work in the cognitive neurosciences. Studies of the brain suggest that knowledge in the cortex may be organized by sensory modality-specific properties rather than by hierarchies of substance concepts, regardless of how adaptive Millikan argues the latter would be. Ryder's work on SINBAD networks, which purports to support Millikan's conclusions, does not decide this issue. The ability to make cross-modal identifications of individuals and kinds may be only a recent evolutionary adaptation.

Probability theory is important not least because of its relevance for decision making, which also means: its relevance for the single case. The frequency theory of probability on its own is irrelevant in the single case. However, Howson and Urbach argue that Bayesianism can solve the frequentist's problem: frequentist-probability information is relevant to Bayesians (although to nobody else). The present paper shows that Howson and Urbach's solution cannot work, and indeed that no Bayesian solution can work. There is no way to make frequentist probability relevant.

Physicalism and antireductionism are the ruling orthodoxy in the philosophy of biology. But these two theses are difficult to reconcile. Merely embracing an epistemic antireductionism will not suffice, as both reductionists and antireductionists accept that given our cognitive interests and limitations, non-molecular explanations may not be improved, corrected or grounded in molecular ones. Moreover, antireductionists themselves view their claim as a metaphysical or ontological one about the existence of facts molecular biology cannot identify, express or explain. However, this is tantamount to a rejection of physicalism and so causes the antireductionist discomfort. In this paper we argue that vindicating physicalism requires a physicalistic account of the principle of natural selection, and we provide such an account. The most important payoff to the account is that it provides for the very sort of autonomy from the physical that antireductionists need without threatening their commitment to physicalism.

The study of similarity is fundamental to biological inquiry. Many homology concepts have been formulated that function successfully to explain similarity in their native domains, but fail to provide an overarching account applicable to variably interconnected and independent areas of biological research despite the monistic standpoint from which they originate. The use of multiple, explicitly articulated homology concepts, applicable at different levels of the biological hierarchy, allows a more thorough investigation of the nature of biological similarity. Responsible epistemological pluralism as advocated herein is generative of fruitful and innovative biological research, and is appropriate given the metaphysical pluralism that underpins all of biology.

In three recent papers, Wayne Myrvold (1996, 2003) and Timothy McGrew (2003) have developed Bayesian accounts of the virtue of unification. In his account, McGrew demonstrates that, ceteris paribus, a hypothesis that unifies its evidence will have a higher posterior probability than a hypothesis that does not. Myrvold, on the other hand, offers a specific measure of unification that can be applied to individual hypotheses. He argues that one must account for this measure in order to calculate correctly the degree of confirmation that a hypothesis receives from its evidence. Using the probability calculus, I prove that the two accounts of unification require the same underlying inequality; thus, McGrew and Myrvold have accounted for unification in fundamentally identical probabilistic terms. I then evaluate five putative counterexamples to this account and show that these examples, far from disqualifying it, serve to clarify our notion of unification by disentangling it from a host of other concepts.

Huw Price (1996, 2002, 2003) argues that causal-dynamical theories that aim to explain thermodynamic asymmetry in time are misguided. He points out that in seeking a dynamical factor responsible for the general tendency of entropy to increase, these approaches fail to appreciate the true nature of the problem in the foundations of statistical mechanics (SM). I argue that it is Price who is guilty of misapprehension of the issue at stake. When properly understood, causal-dynamical approaches in the foundations of SM offer a solution for a different problem; a problem that unfortunately receives no attention in Price's celebrated work.

Since the fundamental challenge that I laid at the doorstep of the pluralists was to defend, with nonderivative models, a strong notion of genic cause, it is fatal that Waters has failed to meet that challenge. Waters agrees with me that there is only a single cause operating in these models, but he argues for a notion of causal ‘parsing’ to sustain the viability of some form of pluralism. Waters and his colleagues have some very interesting and important ideas about the sciences, involving pluralism and parsing or partitioning causes, but they are ideas in search of an example. He thinks he has found an example in the case of hierarchical and genic selection. I think he has not.

In seeking to explain the evolution of social cooperation, many scholars are using increasingly complex game-theoretic models. These complexities often model readily observable features of human and animal populations. In the case of previous games analyzed in the literature, these modifications have had radical effects on the stability and efficiency properties of the models. We will analyze the effect of adding spatial structure to two communication games: the Lewis Sender-Receiver game and a modified Stag Hunt game. For the Stag Hunt, we find that the results depart strikingly from previous models. In all cases, the departures increase the explanatory value of the models for social phenomena.