This paper explores varieties of scientific structuralism. Central to our investigation is the notion of ‘shared structure’. We begin with a description of mathematical structuralism and use this to point out analogies and disanalogies with scientific structuralism. Our particular focus is the semantic structuralist's attempt to use the notion of shared structure to account for the theory-world connection, this use being crucially important to both the contemporary structural empiricist and realist. We show why minimal scientific structuralism is, at the very least, a powerful methodological standpoint. Our investigation also makes explicit what more must be added to this minimal structuralist position in order to address the theory-world connection, namely, an account of representation.

Should philosophers of science be paying attention to developments in “nanoscience”? Undoubtedly, it is too early to tell for sure. The goal of this paper is to take a preliminary look. In particular, I look at the use of computational models in the study of nano-sized solid-state materials. What I find is that there are features of these models that appear on their face to be at odds with some basic philosophical intuitions about the relationships between different theories and between theories and their models. My conclusion is that developments in nanoscience are not an unlikely place for novel insights in the philosophy of science to emerge.

Starting with the view that methodological constraints depend upon the nature of the system investigated, a tripartite division between theoretical, semitheoretical, and empirical discoveries is made. Many nanosystems can only be investigated semitheoretically or empirically, and this aspect leads to some nanophenomena being weakly emergent. Self-assembling systems are used as an example, their existence suggesting that the class of systems that is not Kim-reducible may be quite large.

This paper starts by looking at the coincidence of surprising behavior on the nanolevel in both matter and simulation. It uses this coincidence to argue that the simulation approach opens up a pragmatic mode of understanding oriented toward design rules and based on a new instrumental access to complex models. Calculations, and their variation by means of explorative numerical experimentation and visualization, can give a feeling for a model's behavior and the ability to control phenomena, even if the model itself remains epistemically opaque. Thus, the investigation of simulation in nanoscience provides a good example of how science is adapting to a new instrument: computer simulation.

In this paper, I provide an account of scientific representation that makes sense of the notion both at the nanoscale and at the quantum level: the partial mappings account. The account offers an extension of a proposal developed by R. I. G. Hughes in terms of denotation, demonstration, and interpretation (DDI). I first argue that the DDI account needs some amendments to accommodate representation of nano and quantum phenomena. I then introduce a generalized framework with the notions of unsharp denotation, unsharp interpretation, and partial mappings. I conclude by arguing that the resulting view not only accommodates nano and quantum representations but also makes sense of representation by imaging in (scanning tunneling) microscopy.

How, according to Darwin, does chance variation affect evolutionary outcomes? In his 1866 book, On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects, Darwin developed an argument that played an important role in his overall case for evolution by natural selection, as articulated in later editions of the Origin. This argument also figured significantly in Darwin's reflections on the theological dimensions of evolution by natural selection.

Evolutionary models can explain the dynamics of populations, how genetic, genotypic, or phenotypic frequencies change with time. Models incorporating chance, or drift, predict specific patterns of change. These are illustrated using classic work on blood types by Cavalli-Sforza and his collaborators in the Parma Valley of Italy, in which the theoretically predicted patterns are exhibited in human populations. These data and the models display properties of ensembles of populations. The explanatory problem needs to be understood in terms of how likely an observed change, in either a population or an ensemble, would be under drift alone; this is fundamentally a matter of chance. Understood in this way, issues of drift and chance undercut most recent philosophical, but not biological, discussions of the role of “genetic drift.”

In a small handful of papers in theoretical population genetics, John Gillespie (2000a, 2000b, 2001) argues that a new stochastic process he calls “genetic draft” is evolutionarily more significant than genetic drift. This case study of chance in evolution explores Gillespie's proposed stochastic evolutionary force and sketches the implications of Gillespie's argument for philosophers’ explorations of genetic drift.

This article offers three contrasting cases of the use of neutrality and drift in molecular evolution. In the first, neutrality is assumed as a simplest case for modeling. In the second and third, concepts of drift and neutrality are developed within the context of population genetics testing and the development and application of the molecular clock.

The four case studies on chance in evolution provide a rich source for further philosophical analysis. Among the issues raised are the following: Are there different conceptions of chance at work, or is there a common underlying conception? How can a given concept of chance be distinguished from other chance concepts and from nonchance concepts? How can the occurrence of a given chance process be distinguished empirically from nonchance processes or other chance processes? What role does chance play in evolutionary theory? I argue that in order to answer these questions, a careful distinction between process and outcome must be made; however, the purpose of this essay is not to answer these questions definitively, but rather to elaborate on them and to provide a starting point for further discussion.

Case studies of diverse scientific fields show how scientists use a range of resources to generate new interpretative models and to establish their plausibility as explanations of a domain. They accomplish this by manipulating imagistic representations in particular ways. I show that scientists in different domains use the same basic transformations. Common features of these transformations indicate that general cognitive strategies of interpretation, simplification, elaboration, and argumentation are at work. Social and historical studies of science emphasize the diversity of local contexts of practice. However, the existence of common strategies shows that this diversity masks an important repertoire of cognitive strategies. Scientists use this repertoire to adapt their representations to meet the cognitive demands of different contexts of practice. This paper considers the implications of this finding for the notion of scientists as cognitive agents in distributed knowledge-producing systems.

This paper examines the nature of model-based reasoning in the interplay between theory and experiment in the context of biomedical engineering research laboratories, where problem solving involves using physical models. These “model systems” are sites of experimentation where in vitro models are used to screen, control, and simulate specific aspects of in vivo phenomena. As with all models, simulation devices are idealized representations, but they are also systems themselves, possessing engineering constraints. Drawing on research in contemporary cognitive science that construes cognition as occurring in a complex distributed system comprising people and artifacts, I argue that reasoning with model systems is a constraint satisfaction process involving co-construction, manipulation, and revision of mental and physical models.

In previous publications I have argued that much scientific activity should be thought of as involving the operation of distributed cognitive systems. Since these contributions to the cognitive study of science appear in venues not necessarily frequented by philosophers of science, I begin with a brief introduction to the notion of a distributed cognitive system. I then describe what I take to be an exemplary case of a scientific distributed cognitive system, the Hubble Space Telescope (HST). I do not here reargue the case for conceiving of systems like the HST as distributed cognitive systems. Rather, I examine a question that arises once one has adopted the perspective of distributed cognitive systems, namely, the role of agency in a distributed cognitive system. Here I argue, contrary to several advocates of distributed cognitive systems, that we should regard the human components of distributed cognitive systems as the only sources of agency within such systems. In particular, we should not extend notions of agency to such systems as a whole.

Some ecologists have argued that theoretical model building in population and community ecology has gone evidentially unconstrained. In the essay, I argue that “bottle experiments” offer ecological model building evidential constraints and illustrate this by considering work on chaotic models tested by the dynamics of flour beetles. Critics reply that these experiments are importantly unlike nonmanipulated natural systems and thus do not constitute genuine tests of the models. I conclude by considering two responses to this worry and a suggestion on how to move forward on this debate.

Modelers often rely on robustness analysis, the search for predictions common to several independent models. Robustness analysis has been characterized and championed by Richard Levins and William Wimsatt, who see it as central to modern theoretical practice. The practice has also been severely criticized by Steven Orzack and Elliott Sober, who claim that it is a nonempirical form of confirmation, effective only under unusual circumstances. This paper addresses Orzack and Sober's criticisms by giving a new account of robustness analysis and showing how the practice can identify robust theorems. Once the structure of robust theorems is clearly articulated, it can be shown that such theorems have a degree of confirmation, despite the lack of direct empirical evidence for their truth.

Initially, models of chemical systems displaying oscillatory behavior were judged successful if they could show how such behavior was even possible. Recently, however, reaction mechanisms for chemical oscillators have been subjected to more stringent experimental tests. I examine strategies for model testing that flow from theoretical considerations, in particular, the types of feedback relations between chemical species required to produce oscillatory behavior in mechanistic models. These theoretical considerations allow chemists to work around important practical considerations such as an inability to measure certain species in the experimental system. These sorts of testing strategies illuminate chemists’ desiderata for a “good model.”

In 1966, Richard Levins argued that there are different strategies in model building in population biology. In this paper, I reply to Orzack and Sober's (1993) critiques of Levins and argue that his views on modeling strategies apply also in the context of evolutionary genetics. In particular, I argue that there are different ways in which models are used to ask and answer questions about the dynamics of evolutionary change, prospectively and retrospectively, in classical versus molecular evolutionary genetics. Further, I argue that robustness analysis is a tool for, if not confirmation, then something near enough, in this discipline.