Much has been written about the theoretical issues of functional biology, in a broad sense, as these pertain to the study of living organisms, but far less regarding the relevance and significance of function and adaptation for the historical understanding of fossil and living animals. Furthermore, although most ideas of function have always been tied to adaptations (e.g., Pranger 1990), there has also been a tacit general belief that adaptations (or the adaptedness) of fossils cannot really be ascertained. Little attention has been paid to different historical and systemic levels of adaptations within lineages and taxonomic species of these lineages beyond the taxic (and fundamentally punctuationist) conceptualization (e.g., Gould and Vrba 1982). As a result, the usefulness of adaptational analysis and the applicability of ecological inferences for phylogenetic analysis of both fossil and extant taxa has been all but ignored, if not explicitly berated.

The philosopher Amundson (1996, p. 29), in his scholarly account of the history of ideas regarding adaptation, has stated that "Darwin sided with function." To attribute "siding" to Darwin, however, given his elaborate presentation of the theory of descent based on homology and the paleontological record, is rather problematic. Such an opinion expresses a lack of familiarity with the corpus of Darwin's work, and misconstrues Darwin, the modern phylogenist. For Darwin to reformulate the structuralist notions of his day into the theory of descent (evolutionary process) required something entirely different from "siding." Darwin sublimated both "structuralist" and "adaptationist (functionalist)" views of character equivalence into the cornerstone of the phylogenetic method, practiced in a variety of different forms since 1859.

As a consequence of the modern sidelining of the relevance of function to phylogenetic analysis (and, even worse, a studied misunderstanding of its role in phylogenetics), there has been relatively little attention given to the connection between functional biology and transformational analysis to phylogeny estimation in the past three decades of phylogenetics-related literature. Furthermore, judging from the masses of phylogenetic studies published, most of what has been written in the theoretical literature about function is either ignored or misunderstood by most practitioners of numerical cladistics, including stratocladistics. But the functional literature itself is often both equivocal and confused regarding the role of functional biology and its relationship to the estimation of phylogeny. This is peculiar because what phylogeny is (as we understand it within well-tested Darwinian theory) should have a bearing on the methods we use to reconstruct it. It is for this reason that I undertake the task of briefly drawing attention to some theoretical and methodological relationships (both ontological and epistemological) between functional analysis (sensu lato) and phylogenetics (but not the construction of taxograms or classifications). First, I look at the general theoretical issues that relate to the estimation of adaptations in fossils and their phylogenetics. Second, I examine some of the competing views of what functional biology is supposed to be in relation to functional and evolutionary analyses that include fossils. Third, I specifically make connections between a broad concept of functional biology and Darwinian phylogenetic analysis (but not the taxonomic expression of well-tested phylogenies). Finally, I take a closer look at issues surrounding transformational analysis and attempt to refute arguments leveled against the concept of mosaic evolution based on the taxic conceptualization of phylogeny.