Homology – or the similarity of the structure, physiology, or development betweendifferent species owing to common descent – is a fundamental concept in all biological research. That the model organisms we use are an appropriate model for human biology – and that studying the basic biology of these organisms has something to teach us about ourselves – underlies the way in which biological and medical research is conducted. But homology is multi-faceted, and at best, tricky to define. Often defined as similarity stemming from common ancestry, in truth it can be defined at multiple levels of biological hierarchy. Traits that are homologous at one level–such as anatomical–may not be homologous at another level–such as developmental. The framework of observation can therefore affect whether or not a system is defined as “homologous”. The research presented in this thesis aims to investigate the effectiveness of various techniques of assessing homology of non-structural features; with a specific focus on traits shared across animals, such as the origin of novel cell types and “conserved” genetic responses. In this chapter I will lay out the specific research questions and aims of this dissertation, its significance and its limitations. I conclude by arguing for the value of using character identity over character state (following McKenna et al. 2021) in assessing homology of non-structural characters, as well as potential ways of contextualizing these features.