. In this paper I present two ways in which climate modelers use general circulation models for exploratory purposes. The complexity of Earth’s climate system makes it difficult to predict precisely how lower-order climate dynamics will interact over time to drive higher-order dynamics. The same issues arise for complex models built to simulate climate behavior like the Community Earth Systems Model. I argue that as a result of system complexity, climate modelers use general circulation models to perform model dynamic exploration (...) and climate dynamic exploration. MDE and CDE help climate modelers to better understand the dynamic structure of the general circulation model system and the actual climate system, respectively. (shrink)

This essay extends Levins'' 1966 analysis of modelbuilding in ecology and evolutionary biology. Amodel, as the product of modeling, might bevalued according to its correspondence to reality. Yet Levins'' emphasis on provisionality and changeredirects attention to the processes ofmodeling, through which scientists select and generatetheir problems, define their categories, collect theirdata, compare competing models, and present theirfindings. I identify several points where decisionsare required that are not determined by nature. Thisinvites examination of the social considerationsmodelers are reacting to at the (...) sites of sociality.Modelers must weave socio-ecological webs so thatthe models can be seen to represent their subjectmatter at the same time as the modelers secure thesupport of colleagues, collaborators and institutions,and enjoin others to act upon their conclusions. Notonly do theory justification and theory generationmerge, but the joint project becomes simultaneouslyphilosophical and sociological. (shrink)

A key challenge in conceptualizing ecological complexity is to allow simultaneously for particularity, contingency, and structure, and for such structure to be internally differentiated,dynamically tied to its context, and subject torestructuring. Because all organisms live insuch dynamic ecological circumstances, philosophy of ecology could become the leading site for addressing difficult conceptual questions concerning the situatedness or positionality of organisms –humans included – in their changing and intersecting worlds.

: This paper explores the calibration of laboratory models in population genetics as an experimental strategy for justifying experimental results and claims based upon them following Franklin (1986, 1990) and Rudge (1996, 1998). The analysis provided undermines Coyne et al.'s (1997) critique of Wade and Goodnight's (1991) experimental study of Wright's (1931, 1932) Shifting Balance Theory. The essay concludes by further demonstrating how this analysis bears on Diamond's (1986) claims regarding the weakness of laboratory experiments as evidence, and further how (...) the calibration strategy fits within Lloyd's (1987, 1988) account of the confirmation of ecological and evolutionary models. (shrink)

The paper sketches an account of explanatory practice in which explanations are viewed as answers to explanation-requiring questions. To avoid difficulties in previous proposals, the paper uses the structuralist account of theory structure, arguing that theories are complex and evolving entities formed around a conceptual core and a set of intended applications. The argument is that this view does better justice to theories which involve a number of different kinds of theory-elements to give narrative explanations. Theories are, among other things, (...) devices which can be used to turn explanation-requiring questions into a form which allows assessment of potential answers. Evolutionary theory, both in Darwin's and the modern synthetic forms, are used as examples. The view advanced is that modern evolutionary theory need not have a unique core to which other theories serve as subcontractors. (shrink)

We give an overview of the practice of developing and using complex climate models, as seen from experiences in a major climate modelling center and through participation in the Coupled Model Intercomparison Project. We discuss the construction and calibration of models; their evaluation, especially through use of out-of-sample tests; and their exploitation in multi-model ensembles to identify biases and make predictions. We stress that adequacy or utility of climate models is best assessed via their skill against more naïve predictions. The (...) framework we use for making inferences about reality using simulations is naturally Bayesian, and has many points of contact with more familiar examples of scientific epistemology. While the use of complex simulations in science is a development that changes much in how science is done in practice, we argue that the concepts being applied fit very much into traditional practices of the scientific method, albeit those more often associated with laboratory work. (shrink)

Most models of generational succession in sexually reproducing populations necessarily move back and forth between genic and genotypic spaces. We show that transitions between and within these spaces are usually hidden by unstated assumptions about processes in these spaces. We also examine a widely endorsed claim regarding the mathematical equivalence of kin-, group-, individual-, and allelic-selection models made by Lee Dugatkin and Kern Reeve. We show that the claimed mathematical equivalence of the models does not hold. *Received January 2007; revised (...) April 2008. †To contact the authors, please write to: Elisabeth Lloyd, Department of History and Philosophy of Science, 130 Goodbody Hall, Indiana University, Bloomington, IN 47405; e-mail: [email protected]; Richard Lewontin, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA 02138; Marcus Feldman, Department of Biological Sciences, Stanford University, Stanford, CA 94305; e-mail: [email protected]. (shrink)

The conflation of two fundamentally distinct issues has generated serious confusion in the philosophical and biological literature concerning the units of selection. The question of how a unit of selection of defined, theoretically, is rarely distinguished from the question of how to determine the empirical accuracy of claims--either specific or general--concerning which unit(s) is undergoing selection processes. In this paper, I begin by refining a definition of the unit of selection, first presented in the philosophical literature by William Wimsatt, which (...) is grounded in the structure of natural selection models. I then explore the implications of this structural definition for empirical evaluation of claims about units of selection. I consider criticisms of this view presented by Elliott Sober--criticisms taken by some (for example, Mayo and Gilinsky 1987) to provide definitive damage to the structuralist account. I shall show that Sober has misinterpreted the structuralist views; he knocks down a straw man in order to motivate his own causal account. Furthermore, I shall argue, Sober's causal account is dependent on the structuralist account that he rejects. I conclude by indicating how the refined structural definition can clarify which sorts of empirical evidence could be brought to bear on a controversial case involving units of selection. (shrink)

In this paper I contrast two causal explanations of the outcome of a set of laboratory experiments in population ecology conducted by Thomas Park in the 1940s and 1950s. These experiments shed light on the problem of adducing evidence for the operation of competition (see Lloyd 1987 for a recent philosophical discussion) and are central to the group selection controversy because they form the empirical base for experimental studies of group selection conducted over the last 12 years (see Griesemer and (...) Wade 1988 for an analysis).The experiments investigated competition in laboratory populations of two flour beetle species, Tribolium confusum and Tribolium castaneum, but the results were more complex and interesting than expected; in addition to demonstrating competition in a laboratory system, they exhibited what Park called “competitive indeterminacy.” This phenomenon was of great interest to statisticians, who devised stochastic models to describe its demographic basis (e.g., M.S. Bartlett, P.H. Leslie, and J. Neyman; see Mertz 1972 for references). (shrink)

Paul Thompson, John Beatty, and Elisabeth Lloyd argue that attempts to resolve certain conceptual issues within evolutionary biology have failed because of a general adherence to the received view of scientific theories. They maintain that such issues can be clarified and resolved when one adopts a semantic approach to theories. In this paper, I argue that such conceptual issues are just as problematic on a semantic approach. Such issues arise from the complexity involved in providing formal accounts of theoretical laws (...) and scientific explanations. That complexity is due to empirical and pragmatic considerations, not one's adherence to a particular formal approach to theories. This analysis raises a broader question. How can any formal account properly represent the complex nature of empirical phenomena? (shrink)

: Where there are cases of underdetermination in scientific controversies, such as the case of the molecular clock, scientists may direct the course and terms of dispute by playing off the multidimensional framework of theory evaluation. This is because assessment strategies themselves are underdetermined. Within the framework of assessment, there are a variety of trade-offs between different strategies as well as shifting emphases as specific strategies are given more or less weight in assessment situations. When a strategy is underdetermined, scientists (...) can change the dynamics of a controversy by making assessments using different combinations of evaluation strategies and/or weighting whatever strategies are in play in different ways. Following an underdetermination strategy does not end or resolve a scientific dispute. Consequently, manipulating underdetermination is a feature of controversy dynamics and not controversy closure. (shrink)

Bionic technologies connecting biological nervous systems to computer or robotic devices for therapeutic purposes have been recently claimed to provide novel experimental tools for the investigation of biological mechanisms. This claim is examined here by means of a methodological analysis of bionics-supported experimental inquiries on adaptive sensory-motor behaviours. Two broad classes of bionic systems (regarded here as hybrid simulations of the target biological system) are identified, which differ from each other according to whether a component of the biological target system (...) is replaced by an artificial component, or else a component of an artificial system is replaced by a biological component. The role of these hybrid systems in the modelling of adaptive sensory-motor biological behaviours is discussed with reference to bionics-supported experiments on the mechanisms of body stabilization in lampreys. Methodological problems emerging from these case studies often arise in computer-based and biorobotic simulations of biological behaviours too. Accordingly, the present analysis contributes to identifying a more general regulative methodological framework for the machine-based modelling of biological systems. (shrink)

Robots are being extensively used for the purpose of discovering and testing empirical hypotheses about biological sensorimotor mechanisms. We examine here methodological problems that have to be addressed in order to design and perform “good” experiments with these machine models. These problems notably concern the mapping of biological mechanism descriptions into robotic mechanism descriptions; the distinction between theoretically unconstrained “implementation details” and robotic features that carry a modeling weight; the role of preliminary calibration experiments; the monitoring of experimental environments for (...) disturbing factors that affect both modeling features and theoretically unconstrained implementation details of robots. Various assumptions that are gradually introduced in the process of setting up and performing these robotic experiments become integral parts of the background hypotheses that are needed to bring experimental observations to bear on biological mechanism descriptions. (shrink)

The main goal of this book, The Structure and Confirmation of Evolutionary Theory, “is to introduce, develop, and demonstrate the usefulness of a precise analysis of the structure of evolutionary theory”, an analysis that treats evolutionary theory as built up out of complexly interrelated mathematical models. The book has a second goal as well, namely, “to offer … evidence of the appropriateness and utility of the semantic view of scientific theories”. The appropriate audience for the book is not obvious. It (...) is well suited for graduate courses in philosophy of biology, though it demands substantial knowledge of both disciplines. Lloyd has attempted to make it accessible to wider biological and philosophical audiences by minimizing the technical treatment of mathematical models, but I doubt that she has succeeded in making the book accessible to those unfamiliar with the models of population genetics or to biologists previously unversed in the philosophy of science. (shrink)