This essay advocates a “functional” approach to causation and causal reasoning: these are to be understood in terms of the goals and purposes of causal thinking. This approach is distinguished from accounts based on metaphysical considerations or on reconstruction of “intuitions.”

This paper clarifies the historical nature of species by showing that species are path-dependent entities. A species’ identity is not determined by its intrinsic properties or its origin, but by its unique evolutionary path. Seeing that species are path-dependent entities has three implications: it shows that origin essentialism is mistaken, it rebuts two challenges to the species-are-historical-entities thesis, and it demonstrates that the identity of a species during speciation depends on future events.

For a population to undergo evolution by natural selection, it is assumed that the constituents of the population form parent-offspring lineages, that is, that they must reproduce. I challenge this assumption by dividing the notion of reproduction into two subprocesses, that is, multiplication and inheritance, that produce parent-offspring lineages between the parts of a population, and I show that their population-level roles, generation and memory, respectively, can be effected by processes that do not rely on such local-level lineages. I further argue that these two population-level processes, not local parent-offspring lineages, are necessary conditions for a population to undergo Darwinian evolution.

Elsewhere, I defend the “causal interactionist population concept” (CIPC). Here I further defend the CIPC by showing how it clarifies another concept that biologists grapple with, namely, environment. Should we understand selection as ranging only over homogeneous environments or, alternatively, as ranging over any habitat area we choose to study? I argue instead that the boundaries of the population dictate the range of the environment, whether homogeneous or heterogeneous, over which selection operates. Thus, understanding the concept of population helps us to understand concepts of selective environment, exemplifying the importance of the CIPC to other concepts and debates.

Experimental modeling in biology involves the use of living organisms (not necessarily so-called model organisms) in order to model or simulate biological processes. I argue here that experimental modeling is a bona fide form of scientific modeling that plays an epistemic role that is distinct from that of ordinary biological experiments. What distinguishes them from ordinary experiments is that they use what I call “in vivo representations,” where one kind of causal process is used to stand in for a physically different kind of process. I discuss the advantages of this approach in the context of evolutionary biology.

Methodological individualism has a long, successful, and controversial track record in the social sciences. Its record in ecology is much shorter but proving as successful and controversial with so-called individual-based models. Distinctions and debates about methodological individualism in social sciences clarify the commitments of this general, individualistic approach to modeling ecological phenomena and show that there is a lot recommending it. In particular, a representational priority on individual organisms yields a cogent albeit deflationary account of ecological emergence and helps reveal how quite disparate models and theories in ecology might be unified.

Proponents of individual-based modeling in ecology claim that their models explain the emergence of population-level behavior. This article argues that individual-based models have not, as yet, provided such explanations. Instead, individual-based models can and do demonstrate and explain the emergence of population-level behaviors from individual behaviors and interactions.

The aim of teleosemantics is to give a scientifically respectable or ‘naturalistic’ theory of mental content. This paper focuses on one of the key concepts of teleosemantics: biological function. It has been universally accepted in the teleosemantics literature that the account of biological function one should use to flesh out teleosemantics is that of etiological function. My claim is that if we replace this concept of function with an alternative one and if we also restrict the scope of teleosemantics, we can arrive at an account of biologizing mental content that is much less problematic than the previous attempts.

Multilevel research strategies characterize contemporary molecular inquiry into biological systems. We outline conceptual, methodological, and explanatory dimensions of these multilevel strategies in microbial ecology, systems biology, protein research, and developmental biology. This review of emerging lines of inquiry in these fields suggests that multilevel research in molecular life sciences has significant implications for philosophical understandings of explanation, modeling, and representation.

This article concerns how rule-following behavior might evolve, how an old evolved rule might come to be appropriated to a new context, and how simple concepts might coevolve with rule-following behavior. In particular, we consider how the transitive inferential rule-following behavior exhibited by pinyon and scrub jays might evolve in the context of a variety of the Skyrms-Lewis signaling game, then how such a rule might come to be appropriated to carry out inferences regarding stimuli different from those involved in the original evolution of the rule, and how this appropriation involves a step toward the evolution of basic ordinal concepts.

This article uses sim-max games to model perceptual categorization with the goal of answering the following question: To what degree should we expect the perceptual categories of biological actors to track properties of the world around them? I argue that an analysis of these games suggests that the relationship between real-world structure and evolved perceptual categories is mediated by successful action in the sense that organisms evolve to categorize together states of nature for which similar actions lead to similar results. This conclusion indicates that both strongly realist and strongly antirealist views about perceptual categories are too simple.

Recent models using simple signaling games provide a theoretical setting for investigating the evolutionary connection between signaling and behavioral plasticity. These models have shown that plasticity is typically eliminated in common-interest signaling games. In many real cases of signaling, however, interests do not align. Here, I present a model of the evolution of plasticity in signaling games and consider games of common, opposed, and partially aligned interests. I find that the setting of partial common interest is most conducive to the evolution of plasticity. Plastic individuals succeed by learning when to deceive others and when to trust others’ signals.

Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about “genetic information” can be resolved by seeing the genome as a cell-level memory with no sender.

Recent work on the evolution of signaling systems provides a novel way of thinking about genetic information, where information is passed between genes in a regulatory network. I use examples from evolutionary developmental biology to show how information can be created in these networks and how it can be reused to produce rapid phenotypic change.

What are the functional units of the brain? If the function of the brain is to process information-carrying signals, then the functional units will be the senders and receivers of those signals. Neurons have been the default candidate, with action potentials as the signals. But there are alternatives: synapses fit the action potential picture more cleanly, and glial activities (e.g., in astrocytes) might also be characterized as signaling. Are synapses or nonneuronal cells better candidates to play the role of functional units? Will informational signaling still be the best model for brain function if we move beyond the neuron doctrine?

Recent work combining cognitive neuroscience with computational modeling suggests that distributed patterns of neural firing may represent probability distributions. This article asks, what makes it the case that distributed patterns of firing, as well as carrying information about (correlating with) probability distributions over worldly parameters, represent such distributions? In examples of probabilistic population coding, it is the way information is used in downstream processing so as to lead to successful behavior. In these cases content depends on factors beyond bare information, contra Brian Skyrms’s view that representational content can be fully characterized in information-theoretic terms.

In this paper I argue that certain methodological conventions within psychophysics reflect a continued uncertainty over the reliability of subjects’ introspective judgements. Firstly, different psychophysical methods do not rely equally on the introspective capabilities of experimental subjects. I contrast “minimally introspective” tasks with “introspection-reliant” ones. It is only in the latter that introspection can be said to have a nontrivial role in the subjects’ performance. Secondly, my distinction maps onto a number of important methodological divisions in vision science. The introspection-reliant categorization captures many of the tasks typically considered less able to yield useful information regarding the processes underlying visual sensation.

While philosophical discussions of first-person methods often turn on the veridicality of first-person reports, I argue that more attention should be paid to the circumstances and aims of their experimental production in the science of perception. After pointing to the ‘constructedness’ of first-person reports, I raise questions about the criteria by which to judge whether they illuminate something about the nature of perception. I illustrate this point with a historical debate between Gestalt psychologists and atomists, both of whom used first-person methods to investigate perception, but who disagreed deeply over the epistemic value of their respective first-person data.

Some experiments in perceptual psychology measure perceivers’ phenomenal experiences of objects versus their cognitive assessments of object properties. Analyzing such experiments, this article responds to Pizlo’s claim that much work on shape constancy before 1985 confused problems of shape ambiguity with problems of shape constancy. Pizlo fails to grasp the logic of experimental designs directed toward phenomenal aspects of shape constancy. In the domain of size perception, Granrud’s studies of size constancy in children and adults distinguish phenomenal from cognitive factors.