Homology is 'a word ripe for burning'. But how should it be defined? Superficially, it's often identified as similarity in morphology reflecting a common evolutionary origin; but can we give a more rigorous approach? Like 'species', the many definitions of homology fall into two basic forms: developmental and taxic. The developmental approach is based on ontogeny, and two characters are homologous if they have an identical set of developmental constraints. The taxic definition is based on cladistics and identifies a homologues as a synapomorphy (a trait that characterises a monophyly). Some complications arise with structural homology, for instance, the wings or bats and birds can be considered convergent as they are differently arranged (and lack common ancestry); but they can be considered homologous at the level or the organism (because they evolved from the same pattern or vertebrate forelimb traceable to a common ancestor). Circular reasoning also arises with structural homology in that it is used to build a phylogeny and that phylogeny is subsequently used to infer homology (notice the circularity); a phylogeny must be initially constructed based on evidence before homology is proposed. What about evo-devo? This is also unhelpful for a working definition of homology, different pathways of development can converge on the same adult form, such as the methods of gastrulation and the many routes of developmental regeneration in the hydroid Tubularia. Even the embryonic developmental origin is unuseful as it relies on the subsequent interactions between cells and fails to give a conserved adult morphology. Molecular markers such as genes succumb to hierarchical disconnect (whereby homologous characters produce non-homologous traits). A classic example is the gene PAX6 in eye development which is found and transcribed in species as diverse as insects, humans, squids and even primitive eyed nemertines and platyhelminths.
Experiments involving grafting of Drosophila PAX6 into Drosophila limbs or wings can place eyes in incorrect positions; when mice PAX6 is inserted into Drosophila, it is expressed as mouse-like. These grafting tests indicate that the adjustability for change does not lie in the genes as in the regulatory network of genes that code for expression. The need by to redefine homology at different hierarchical levels is also indicated in other characters. For a long time, arthropod compound eyes had been thought to have evolved rather independently of the vertebrate simple eye; now this seems improbable given the immense similarity between cephalopod and vertebrate eyes (commonly attributed to convergence). In essence, the gene starting eye formation is homologous but it's expression is not necessarily homologous. Hierarchical disconnect in the form of nonhomologous traits causing homologous characters is also noted. With the exception of urodele amphibians, all tetrapods develop tissue between their primordial digits and later undergo apoptosis. But in newts and salamanders, there is no need for apoptosis and digits take a separate developmental pathway. The evolutionary hypothesis is that salamanders and newts (or one of their ancestral species) lost the ability of apoptosis between digits and differential growth is a derived process. Novel genes exchanged for older ones can also cause the same homologous morphology (co-option of genes during evolution for very distinct functions).