1. What phylogeny (but not classification) is has bearing on how we should try to recover it. Descent with ancestrally constrained (but also facilitated) adaptive (and other) modifications, largely through natural and sexual selection, contains a host of post-Darwinian advances in evolutionary biology that relate to this fundamentally Darwinian view of the evolutionary process. This complex array of precepts is both the theoretical foundation of a Darwinian phylogenetic analysis and the basis for any comprehensive theory of function (in a broad sense) and structure. Meaningful functional (in a full Darwinian sense) and phylogenetically oriented biology is the study of the results of selection and other attributes, and of the process of their acquisition.
2. Fundamentally structuralist approaches consider the goals of adaptational and other evolutionary analysis to be unattainable for fossils and extant organisms. Yet adaptations or sexual-selection- related paraphernalia in extinct species are often better understood than their phylogeny. Such attributes may form the framework of an analysis. A functional and adaptational (ecologically utilitarian) assessment of traits in both extant and extinct organisms (whenever possible) is necessary in order to reliably establish polarities of homologous features. Such practice enables students of phylogeny to cull convergent attributes from a body of characteristic features. The Darwinian method, contrary to misconstrued characterizations that it permits only the use of adaptive characters in phylogenetics (e.g., Schuh 2000), informs of the incidental and phyletically relevant attributes in assessing the adaptive solutions. The homologously shared and derived, or transformationally homologous, features so obtained are the taxonomic properties against which lineage and taxon phylogeny hypotheses may be tested.
3. A Darwinian evolutionary explanation involves both the causal and historically mediated components of a particular transformation, an evolutionary becoming. Its macrotaxonomic expression is constrained by heuristics, which are not directly relevant to phylogenetics. A sharp divide between functional and evolutionary explanations, distinction are more practice-based than theory-based. These should be replaced by a less dichotomous, less hierarchic, and far more interrelated or "temporally-looped" set of theories and concepts regarding the relationship between the evolution of function and biorole of features. Functional analysis (broad, Darwinian sense) and the biostratigraphical record are the valid bases of transformational analysis of organismal attributes in phylogenetics (Bock 1981). The results of the transformational analyses of features and the subsequent understanding of the relationships of lineages, independent of parsimony taxograms, are prerequisites for a meaningfully tested taxon phylogeny. Both adaptational and phylogenetic analyses are inferential about specific events in the past. Mapping the results of the "causal role function" approach of Lauder and colleagues onto taxograms, a structuralist perspective that is now labeled by its practitioners as the "new adaptationism," does not advance the cause of phylogenetic reconstruction.
4. In spite of the obvious data-based limits of the past that were previously noted, there is no reason to reject either specific historical narrative explanations, or their rigorous tests, dealing with adaptations, or phylogenetic estimates of character transformations. These activities are the core of comparative biology and macroevolutionary science, and the testing of phylogenetic hypotheses of lineages and taxa fundamentally relies on them (Figure 1). Organisms are adapted (= "fit," in a fully Darwinian sense) and an understanding of selection-produced attributes (e.g., mechanical adaptations or dimorphisms) can have a significant influence on choosing features against which phylogenetic estimates can be tested. Thus, functional understanding is essential in any estimation of phylogeny. Model-based analysis of attributes of selected extant species is a cornerstone of this activity.
5. Taxograms, bereft of specific taxic derivation (origins), do not reflect the lineage-based reality of phylogenetics. Axiomatized attempts to reflect the history of organisms as taxograms, node-based holophyla, without paraphyla is an illusory practice. It is contradicted by the continuity of all lineages in the evolutionary process, and the necessity to make arbitrary demarcations when delineating taxa.

In closing, I note that the attempt at the expurgation of the fully Darwinian (= adaptive) context of evolutionary change from both conceptual and operational methods has been largely driven by a belief that analysis of patterns independent of tested evolutionary theory will yield a theory of evolution of such generality, and that this theory will replace an expanding Modern Synthesis (see Eldredge and Cracraft, 1980; Grande and Rieppel, 1994; Rieppel and Grande 1994). Beyond claims that Darwin has been reinvented (Eldredge 1995; and in this process, not coincidentally, omitted from phylogenetics) and the rise of a hardened taxic paradigm of parsimony-based cladistics, nothing of the sort has materialized thus far.