Analogies and homologies
An ancient but still valid and modern debate in evolutionary biology, and also for understanding development, is to distinguish analogies from homologies.
Convergent, recurrent adaptations are likely to occur when a strong selective pressure exists: this will produce analogous organs or functions. For example the wing of a fly and the wing of a bird share a common function, bear the same name but have completely independent origins. The problem becomes however more complex if we compare bats and birds, two kinds flying vertebrates. In both cases, the forelimb has been transformed into a wing. In this respect, wings are homologous to the anterior legs of Amphibia and Reptilia, and can be thus considered, at the forelimb level, as homologous. But the flight function results from convergent, independent adaptations that are the transformation of an anterior leg into a wing: in this respect, the wings of birds and bats are analogous organs. The above example is easy to understand, but in other cases, the origin of an organ by evolutionary transformation may be very difficult to solve. For example, the wings of insects are considered as derivatives either of segmental gills or of lateral expansions of thoracic tergites (Brodsky 1994). It is however generally assumed that all insect wings share a common origin, i.e. are homologous.
The development of molecular biology and the search for molecular phylogenies has brought a new interest concerning the problem of homologous or analogous genes and functions. By comparing the sequences (DNA or amino-acids) of two genes, it is generally easy to decide whether they are homologous, deriving from a common ancestor or not. An identity of function, for example the same EC code for an enzyme, does not however implies homology. For example, all alcohol dehydrogenases (ADH) share the same code: EC 184.108.40.206. However, at the molecular level, the ADHs of yeast, maize and mammals are homologous while the Drosophila ADH is a much smaller, analogous molecule.
Evolutionists are also aware that, in the course of Evolution, gene duplications have been common (Ohno 1970) providing an opportunity for acquiring new functions. This has led to a classical problem in phylogenetic analyses. When comparing genes in different species, there are two kinds of homologies: orthologous genes derive directly from a single ancestor and have diverged after the last specific split; paralogous genes have different ancestries in closely related species, since they originated from a much older gene duplication. It is misleading to use and compare paralogous genes while believing they are orthologous. As we shall see it in the next sections, analogies and homologies are a permanent, difficult and recurrent problem in all studies of evolution and development.