Evolution is frequently concentrated in bursts of rapid morphological change and speciation followed by long‐term stasis. We propose that this pattern of punctuated equilibria results from an evolutionary tug‐of‐war between host genomes and transposable elements (TEs) mediated through the epigenome. According to this hypothesis, epigenetic regulatory mechanisms (RNA interference, DNA methylation and histone modifications) maintain stasis by suppressing TE mobilization. However, physiological stress, induced by climate change or invasion of new habitats, disrupts epigenetic regulation and unleashes TEs. With their capacity (...) to drive non‐adaptive host evolution, mobilized TEs can restructure the genome and displace populations from adaptive peaks, thus providing an escape from stasis and generating genetic innovations required for rapid diversification. This “epi‐transposon hypothesis” can not only explain macroevolutionary tempo and mode, but may also resolve other long‐standing controversies, such as Wright's shifting balance theory, Mayr's peripheral isolates model, and McClintock's view of genome restructuring as an adaptive response to challenge. (shrink)

Sewall Wright and Gustave Malécot developed important theories of isolation by distance. Wright’s theory was statistical and Malécot’s probabilistic. Because of this mathematical difference, they were not clear about the relationship between their theories. In this paper, I make two points to clarify this relationship. First, I argue that Wright’s theory concerns what I call ecological isolation by distance , whereas Malécot’s concerns what I call genetic isolation by distance . Second, I suggest that if Wright’s theory is interpreted appropriately, (...) a previously unnoticed connection between the two theories emerges. †To contact the author, please write to: Yoichi Ishida, Department of History and Philosophy of Science, University of Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e‐mail: [email protected]. (shrink)

Stein has raised a fundamental problem for any attempt to characterize instrumentalism and realism as substantive alternatives. This is the distinguishability problem, which consists in the problem of developing a form of instrumentalism that is substantially different from a plausible realist alternative and the problem of showing that this form of instrumentalism does justice to actual scientific practice. Using Stein’s own discussion of Maxwell, I formulate instrumentalism and realism as a scientist’s attitudes toward models, where an attitude is understood to (...) be a complex of the scientist’s belief and intention regarding models. Developing a case study of Benzer’s modeling practice, I show that each attitude can structure inquiry differently and argue that to understand certain aspects of scientific practice, such as the practice of genetic mapping in Benzer’s work, we sometimes need to appeal to the coexistence of these attitudes. (shrink)

Robert MacArthur's mathematical ecology is often regarded as ahistorical and has been criticized by historically oriented ecologists and philosophers for ignoring the importance of history. I clarify and defend his approach, especially his use of simple mathematical models to explain patterns in data and to generate predictions that stimulate empirical research. First I argue that it is misleading to call his approach ahistorical because it is not against historical explanation. Next I distinguish three kinds of criticism of his approach and (...) argue that his approach is compatible with the first two of them. Finally, I argue that the third kind of criticism, advanced by Kim Sterelny and Paul Griffiths, is largely irrelevant to MacArthur's approach. ‡I am especially grateful to Thomas Nickles for encouragement and helpful comments on earlier versions of this paper. Thanks also to Guy Hoelzer, Stephen Jenkins, and Jay Odenbaugh for comments on an earlier draft, Kim Sterelny for clarifications of the Tasmania example, Gregory Mikkelson for references, and the audience at PSA 2006 for discussions. †To contact the author, please write to: Department of History and Philosophy of Science, University of Pittsburgh, 1017 Cathedral of Learning, Pittsburgh, PA 15260; e-mail: [email protected]. (shrink)