What is 'homology thinking' and what is it for?

ABSTRACT In this paper I examine the thesis by Marc Ereshefsky that, in evolutionary biology, there is a third style of thinking, besides the well-known 'population thinking' and 'tree thinking.' Ereshefsky proposes 'homology thinking' as a third approach, focused on the transformation of organismal phenotypes. In this short commentary, I aim at identifying the underlying biological assumptions for homology thinking and how they can be put to work in a research program within evolutionary biology. I propose that homology thinking is based on three insights: 1) multicellular organisms consist of developmentally individualized parts (sub-systems); 2) that developmental individuation entails evolutionary individuation, that is, variational quasi-independence; and 3) these individuated body parts are inherited, though indirectly, and form lineages that are recognized as homologies. These facts support a research program focused on the modification and origination of individuated body parts that supplements and puts into perspective the population genetic and phylogenetic approaches to the study of evolution. J. Exp. Zool. (Mol. Dev. Evol.) 326B:3-8, 2016. © 2015 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]