While the notion of chance has been central in discussions over the probabilistic nature of natural selection and genetic drift, its role in the production of variants on which populational sampling takes place has received much less philosophical attention. This article discusses the concept of chance in evolution in the light of contemporary work in evo-devo. We distinguish different levels at which randomness and chance can be defined in this context, and argue that recent research on variability and evolvability demands (...) a causal understanding of variational probabilities under which development acquires a creative, rather than a constraining role in evolution. We then provide a propensity interpretation of variational probabilities that solves a conceptual confusion between causal properties, variational probabilities and extant variation present in the literature, and explore some metaphysical consequences that follow from our interpretation, specifically with regards to the nature of developmental types. (shrink)

Expression of most genes is regulated by the interaction of multiple transcription factors with cis‐regulatory sequences. Many studies have focused on how changes in promoters and enhancers alter gene expression and phenotype. Recently, Hare et al., using elegant wet and computational approaches uncovered a series of enhancers driving the expression of the even‐skipped gene in scavenger flies (Sepsidae).1 Despite the strong sequence divergence between the enhancers in sepsids and drosophilids, they lead to remarkably similar patterns of gene expression in transgenic (...) Drosophila embryos. This can be explained by the existence of intra‐enhancer compensatory mutations and the presence of overlapping/near binding sites for activators and repressors. BioEssays 30:1052–1057, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

While Darwin pictured organismal evolution as “descent with modification” more than 150 years ago, a detailed reconstruction of the basic evolutionary transitions at the molecular level is only emerging now. In particular, the evolution of today's protein structures and their concurrent functions has remained largely mysterious, as the destruction of these structures by mutation seems far easier than their construction. While the accumulation of genomic and structural data has indicated that proteins are related via common ancestors, naturally occurring protein structures (...) are often considered to be evolutionarily robust, thus leaving open the question of how protein structures can be remodelled while selective pressure forces them to function. New information on the proteome, however, increasingly explains the nature of local and global conformational diversity in protein evolution, which allows the acquisition of novel functions via molecular transition forms containing ancestral and novel structures in dynamic equilibrium. Such structural plasticity may permit the evolution of new protein folds and help account for both the origins of new biological functions and the nature of molecular defects. BioEssays 29:1095–1104, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent work on model-based science. (...) Second, I show that the implications of this revolution need to carefully assessed depending on question being asked, for peak-shifting is not central to all evolutionary questions that fitness landscapes have been used to explore. (shrink)

A new split β‐lactamase assay promises experimental testing of the interplay of protein stability and function. Proteins are sufficiently stable to act effectively within cells. However, mutations generally destabilize structure, with effects on free energy that are comparable to the free energy of folding. Assays of protein functionality and stability in vivo enable a quick study of factors that influence these properties in response to targeted mutations. These assays can help molecular engineering but can also be used to target important (...) questions, including why most proteins are marginally stable, how mutations alter structural makeup, and how thermodynamics, function, and environment shape molecular change. Processes of self‐organization and natural selection are determinants of stability and function. Non‐equilibrium thermodynamics provides crucial concepts, e.g., cells as emergent energy‐dissipating entities that do work and build their own parts, and a framework to study the sculpting role of evolution at different scales. (shrink)

A foundational idea of evo‐devo is that morphological variation is not isotropic, that is, it does not occur in all directions. Instead, some directions of morphological variation are more likely than others from DNA‐level variation and these largely depend on development. We argue that this evo‐devo perspective should apply not only to morphology but to evolution at all phenotypic levels. At other phenotypic levels there is no development, but there are processes that can be seen, in analogy to development, as (...) constructing the phenotype (e.g., protein folding, learning for behavior, etc.). We argue that to explain the direction of evolution two types of arguments need to be combined: generative arguments about which phenotypic variation arises in each generation and selective arguments about which of it passes to the next generation. We explain how a full consideration of the two types of arguments improves the explanatory power of evolutionary theory. Also see the video abstract here: https://youtu.be/Egbvma_uaKc. (shrink)

A new split β‐lactamase assay promises experimental testing of the interplay of protein stability and function. Proteins are sufficiently stable to act effectively within cells. However, mutations generally destabilize structure, with effects on free energy that are comparable to the free energy of folding. Assays of protein functionality and stability in vivo enable a quick study of factors that influence these properties in response to targeted mutations. These assays can help molecular engineering but can also be used to target important (...) questions, including why most proteins are marginally stable, how mutations alter structural makeup, and how thermodynamics, function, and environment shape molecular change. Processes of self‐organization and natural selection are determinants of stability and function. Non‐equilibrium thermodynamics provides crucial concepts, e.g., cells as emergent energy‐dissipating entities that do work and build their own parts, and a framework to study the sculpting role of evolution at different scales. (shrink)