The recent explosion of interest in epigenetics is often portrayed as the dawning of a scientific revolution that promises to transform biomedical science along with developmental and evolutionary biology. Much of this enthusiasm surrounds what we call the epigenetic switch hypothesis, which regards certain examples of epigenetic inheritance as an adaptive organismal response to environmental change. This interpretation overlooks an alternative explanation in terms of coevolutionary dynamics between parasitic transposons and the host genome. This raises a question about whether epigenetics (...) researchers tend to overlook transposon dynamics more generally. To address this question, we surveyed a large sample of scientific publications on the topics of epigenetics and transposons over the past fifty years. We found that enthusiasm for epigenetics is often inversely related to interest in transposon dynamics across the four disciplines we examined. Most surprising was a declining interest in transposons within biomedical science and cellular and molecular biology over the past two decades. Also notable was a delayed and relatively muted enthusiasm for epigenetics within evolutionary biology. An analysis of scientific abstracts from the past twenty-five years further reveals systematic differences among disciplines in their uses of the term epigenetic, especially with respect to heritability commitments and functional interpretations. Taken together, these results paint a nuanced picture of the rise of epigenetics and the possible neglect of transposon dynamics, especially among biomedical scientists. (shrink)

The word “gene” means different things to different people, and can even be used in multiple ways by the same individual. In this review, I follow a particular thread running through Griffith and Stotz’s “Genetics and Philosophy: an introduction”, which is the way that methods of investigation influence the way we define the concept of “gene”, from nineteen century breeding experiments to twenty-first century big data bioinformatics. These different views lead to a set of gene concepts, which only partially overlap (...) each other, each of which picks up on a different part of gene behaviour, function or scientific utility. This plurality of concepts carries over to the use of the concept of “information” in biology, where the non-overlapping concepts can be connected to whether you view the genome as a blueprint for development, a response to environmental triggers, an engine of heritability, or a document of history. (shrink)

This paper defends an internalist perspective of selection based on the hypothesis that considers living evolutionary units as Maxwell's demons (MD) or Zurek's Information Gathering and Using Systems (IGUS). Individuals are considered as IGUS that extract work by means of measuring and recording processes. Interactions or measurements convert uncertainty about the environment (Shannon's information, H) into internalized information in the form of a compressed record (Chaitin's algorithmic complexity, K). The requirements of the model and the limitations inherent to its formalization (...) are discussed. This approach offers an alternative view to the causes of evolutionary variations which goes beyond the classical Lamarckian-Darwinian controversy. I argue that random variations only apply near-to-equilibrium at the time organisms have attained structural closure, and that a speed up of mutation rates that facilitates the production of directed variations occurs far-from-equilibrium due to organisms' openness to the surrounding conditions. However, real organisms are located somewhere between the above two cases and thus, operate at an intermediate stage where there is a maximum efficiency of H/K conversion. In consequence, IGUS keep their autonomy and evolving capacity by compromising between external circumstances and inner constraints. This compromise is made possible by closure regulation. Likewise, this model explains why nature has favored the selection of agents capable of selectively recording a partial description of their environment. (shrink)