How microbes "jeopardize" the modern synthesis

Thomas S. Kuhn: key to a better understanding of the extended evolutionary synthesis

In recent years, some scholars have explicitly questioned the desirability or utility of applying the classical and "old-fashioned" theories of scientific change by the likes of Karl Popper and Thomas S. Kuhn to the question of the precise nature and significance of the extended evolutionary synthesis (EES). Supposedly, these twentieth-century philosophers are completely irrelevant for a better understanding of this new theoretical framework for the study of evolution. Here, it will be argued that the EES can be fruitfully interpreted in terms of, as yet, insufficiently considered or even overlooked elements from Kuhn's theory. First, in his original, historical philosophy of science, Kuhn not only distinguished between small and big scientific revolutions, he also pointed out that paradigms can be extended and reformulated. In contrast with what its name suggests, the mainstream EES can be interpreted as a Kuhnian reformulation of modern evolutionary theory. Second, it has, as yet, also been overlooked that the EES can be interpreted in terms of Kuhn's later, tentative evolutionary philosophy of science. With the EES, an old dichotomy in evolutionary biology is maybe being formalized and institutionalized.

The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis

John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.