Since the late 1990s, the characterization of complete DNA sequences for a large and taxonomically diverse set of species has continued to gain in speed and accuracy. Sequence analyses have indicated a strikingly baroque structure for most eukaryotic genomes, with multiple repeats of DNA sequences and with very little of the DNA specifying proteins. Much of the DNA in these genomes has no known function. These results have generated strong interest in the factors that govern the evolution of genome architecture. (...) While adaptationist ‘just so’ stories have been offered, recent theoretical analyses based on mathematical population genetics strongly suggest that non-adaptive processes dominate genome architecture evolution. This article critically synthesizes and develops these arguments, explicating a core argument along with several variants. It provides a critical assessment of the evidence that supports these arguments’ premises. It also analyses adaptationist responses to these arguments and notes potential problems with the core argument. These theoretical analyses continue the molecular reinterpretation of evolution initiated by the neutral theory in 1968. The article ends by noting that some of these arguments can also be extended to evolution at higher levels of organization which raises questions about adaptationism in general. This remains a puzzle because there is probably little reason to doubt that many organismic features are genuine adaptations. 1 Introduction2 Preliminaries: Senses of Adaptationism3 Genome Architecture3.1 Surprises of early eukaryotic genetics3.2 Genome structure, post-20014 The Case against Adaptationism4.1 Just so stories versus population genetics4.2 The core argument4.3 Three variants of the core argument4.4 Examples: Non-adaptive features of the genome5 Adaptationist Responses6 Concluding Remarks. (shrink)

The discussion with Rao and Nanjundiah about the history of interactions between J. B. S. Haldane and Ernst Mayr is further extended in this note. The nature of the dispute about beanbag genetics is explicated as consisting of two separate issues, one about the role of mathematical analysis in evolutionary biology, and the other about the value of single-locus genic models.

Frank has recently argued for an information-theoretic interpretation of natural selection. This interpretation is based on the identification of a measure related to the Malthusian parameter (for population change) with the Jeffreys divergence between the present allelic distribution of the population and that distribution in the next generation. It is pointed out in this analysis that this identification only holds if the mean fitness of the population is a constant, that is, there is no selection. This problem is used to (...) argue for the superiority of the standard dynamical interpretation of natural selection over its information-theoretic counterpart. (shrink)

Speciation—the origin of new species—has been one of the most active areas of research in evolutionary biology, both during, and since the Modern Synthesis. While the Modern Synthesis certainly shaped research on speciation in significant ways, providing a core framework, and set of categories and methods to work with, the history of work on speciation since the mid-twentieth century is a history of divergence and diversification. This piece traces this divergence, through both theoretical advances, and empirical insights into how different (...) lineages, with different genetics and ecological conditions, are shaped by very different modes of diversification. (shrink)

A framework is presented in which the role ofdevelopmental rules in phenotypic evolution canbe studied for some simple situations. Usingtwo different implicit models of development,characterized by different developmental mapsfrom genotypes to phenotypes, it is shown bysimulation that developmental rules and driftcan result in directional phenotypic evolutionwithout selection. For both models thesimulations show that the critical parameterthat drives the final phenotypic distributionis the cardinality of the set of genotypes thatmap to each phenotype. Details of thedevelopmental map do not matter. If phenotypesare (...) randomly assigned to genotypes, the lastresult can also be proved analytically. (shrink)

Since its appearance, Evolutionary Developmental Biology (EvoDevo) has been called an emerging research program, a new paradigm, a new interdisciplinary field, or even a revolution. Behind these formulas, there is the awareness that something is changing in biology. EvoDevo is characterized by a variety of accounts and by an expanding theoretical framework. From an epistemological point of view, what is the relationship between EvoDevo and previous biological tradition? Is EvoDevo the carrier of a new message about how to conceive evolution (...) and development? Furthermore, is it necessary to rethink the way we look at both of these processes? EvoDevo represents the attempt to synthesize two logics, that of evolution and that of development, and the way we conceive one affects the other. This synthesis is far from being fulfilled, but an adequate theory of development may represent a further step towards this achievement. In this article, an epistemological analysis of EvoDevo is presented, with particular attention paid to the relations to the Extended Evolutionary Synthesis (EES) and the Standard Evolutionary Synthesis (SET). (shrink)

In this paper I take evolutionary biology as an example to reflect on the role of philosophy and on the transformations that philosophy is constantly stimulated to do in its own approach when dealing with science. I consider that some intellectual movements within evolutionary biology (more specifically, the various calls for 'synthesis') express metascientific views, i.e., claims about 'what it is to do research' in evolutionary biology at different times. In the construction of metascientific views I see a fundamental role (...) to be played by philosophy, and, at the same time, a need to complement the philosophical methods with many more methods coming from other sciences. What leads philosophy out of itself is its own attention to scientific practice. My humble methodological suggestions are, at this stage, only meant to help us imagine metascientific views that are built with a more scientific, interdisciplinary approach, in order to attenuate partiality, subjectivity and impressionism in describing the scientific community. And yet, we should not be naïve and imbued with the myth of 'datadriven' research, especially in this field: other complex issues about metascientific views call for a serious, constant philosophical reflection on scientific practice. (shrink)

The chapter explains why evolutionary genetics – a mathematical body of theory developed since the 1910s – eventually got to deal with culture: the frequency dynamics of genes like “the lactase gene” in populations cannot be correctly modeled without including social transmission. While the body of theory requires specific justifications, for example meticulous legitimations of describing culture in terms of traits, the body of theory is an immensely valuable scientific instrument, not only for its modeling power but also for the (...) amount of work that has been necessary to build, maintain, and expand it. A brief history of evolutionary genetics is told to demonstrate such patrimony, and to emphasize the importance and accumulation of statistical knowledge therein. The probabilistic nature of genotypes, phenogenotypes and population phenomena is also touched upon. Although evolutionary genetics is actually composed by distinct and partially independent traditions, the most important mathematical object of evolutionary genetics is the Mendelian space, and evolutionary genetics is mostly the daring study of trajectories of alleles in a population that explores that space. The ‘body’ is scientific wealth that can be invested in studying every situation that happens to turn out suitable to be modeled as a Mendelian population, or as a modified Mendelian population, or as a population of continuously varying individuals with an underlying Mendelian basis. Mathematical tinkering and justification are two halves of the mutual adjustment between the body of theory and the new domain of culture. Some works in current literature overstate justification, misrepresenting the relationship between body of theory and domain, and hindering interdisciplinary dialogue. (shrink)