For those paleontologists (as well as neontologists) who study vertebrate skeletons, the species-specific microscopic as well as macroscopic attributes of bones are essential information. These are the material foundations of their science within the critical contexts of time and place. Bone tissues and skeletons are complexly imbued, because of descent and adaptation, with both the constraints and adaptive meanings of their past and present, at any moment in geological time. This is realized differently at the levels between the bone tissue, the intermediate trabecular structures, and the whole structure of a particular bone as part of a skeleton. Adaptive aspects of skeletal morphology are materially (albeit not conceptually) inseparable from their phylogenetic signals. Theoretical perspectives that ignore contextual, interpretive, and functional analyses of such complexes, and that are used subsequently to test phylogenetic hypotheses, axiomatically deprive themselves of a potentially enormous and relevant material database. Such abiological and ahistorical views about data also potentially deprive phylogenetics of an organism-based causal explanation. Science without causal explanations is a questionable enterprise.

Contrary to such general notions that the concept of adaptation is an onerous one (and should be invoked only with great caution), the adaptive nature of bone tissues, bones, joints, and skeletal systems have proven to be completely adapted within their phyletically constrained limits, both ontogenetically and phylogenetically. This does not mean that given this well-supported generality we can easily understand this or simply accept generalities without rigorous research into the specifics of such adaptations, but that phylogeny is the history of largely adaptive change, within the context of historical peculiarities of all lineages. Attempting to decipher phylogeny without researching the complex of attributes that can yield these historical peculiarities (the phylogenetic signals) is likely to yield only ephemeral patterns, no matter how rigorous the techniques (usually of fundamentally flawed conceptual methods) are that are used to arrive at them. It should be realized also that macroevolutionary guesswork about paleontological patterns that superimpose random walk models on data do not in any way corroborate notions that certain segments of phylogeny were non-adaptive (contra Gould, 1988; Vrba, 1980).

As a necessary preamble, it should be stated that each organism (a life history) is a complex composite intertwined genetically (i.e., historically) and developmentally (in current and real time). [Note: In sexually reproducing organisms the ovum itself also represents a critical component of the historical heritage beyond genetics.] The evolutionary fate of demes or species (not individuals, but continua in time) is a consequence of the interplay of both the physical world and the Darwinian context (the total environment), and the imperatives affecting the individuals that make up such evolutionary units. The Darwinian components of tested evolutionary theory are obviously not only adaptation or adaptedness through natural selection and modification through sexual selection, but also ancestrally constrained descent with modification. A combination of selectional "forces" (= causes) drives the process of differential survival, and what remains in terms of fitness (differential reproduction) for each organism is its contribution to the proportions of subsequent ontogenies (organisms). Modal patterns of the various frequencies of these variant ontogenies become fixed differently in populations or species, and these variably persist and change in lineages. Therefore, phylogeny is a succession of successful life histories (ontogenies in a broad sense) in the context of ecology. The general statements in this paragraph are a set of assumptions on which the issues discussed later depend.

The specific issues examined in this paper are concerned with neither evolutionary nor cladistic taxonomic expressions of phylogeny. The various caricatures of these schools of classification have been discussed in the partisan literature. As stated by Padian (1999), Darwin's concern was mainly with the expression of phylogeny in formal classifications. But it is a mistake to ignore that it was already just as obvious to Darwin (as it is today) that phylogeny is both constrained and facilitated by ancestry, which guides selectionally-mediated descent. Darwin also fully understood that all information was to be used to test phylogenies and that their taxonomic expression was fraught with the compromises that such heuristic activity must face. It is just as obvious now, as already noted, as it was to Darwin that what this phylogeny is should direct the construction of methods, our epistemology, in order to recover it.

Given that a well-tested general understanding of phylogeny (its estimation at best) is a nearly universal goal among modern systematists, the first reaction that comes to mind regarding the adaptedness of past samples of lineages (the fossils) among theoreticians (often neontologists) is that they are dead, so what, if anything, can be said about their adaptations with any degree of corroboration? It should not need repeating here that science is a probabilistic enterprise with equal doses of deductive and inductive activities, contra the Popperian views endlessly defended in the pages of Cladistics, and that its various problems can be "solved" or even "resolved" only with varying degrees of success (e.g., see, again, the Popperian and logical-positivist text on cladistics by Schuh 2000). Yet some of the least "falsifiable" or "provable," but often well-corroborated, answers to questions can be the most important for understanding causes and history (these often being the least logical in a linear sense).

Adaptations in fossil taxa cannot ever be fully understood, but it is also questionable, to a lesser degree, whether they can be completely understood for most living species as well. The reason for the latter is partly theoretical, but primarily because the operational difficulties can be enormous for complex metazoans. These issues are independent of the adaptive nature of the evolutionary process itself. We need to remind ourselves at this point that we should be equally aware of the fact that, although phylogeny also resides in the past, we nevertheless pursue it with zest. And there are very good reasons why we should, therefore, do the same with regard to functional and adaptive analysis for both fossils and living species. There is surely more to adaptational analysis of fossil entities than Novacek's (1996, p. 315) remark that "[t]his situation leaves us looking for something to salvage for the purpose of scientific inquiry." Does this mean that often the litanies of  dubious synapomorphies that overwhelm many morphological databases in cladistic analyses of fossils are the proper foundations for a cladogeny that should guide adaptational assessment?

Ontological issues surrounding adaptation as a process, because of the thorny issue of "current utility", cannot be resolved (see later). Such philosophical conundrums, however, do not make the process of adaptation and its results any less real. But it should be realized, because it is not widely appreciated, that the explanation of adaptations in fossils, as independent of phylogeny as the concept of adaptation can be of phylogeny, is often less of an epistemological problem than the attempts at valid testing (i.e., corroboration) of many phylogenetic hypotheses without independent transformational and functional understanding. The currently dominant view eschews the relevance of adaptational analysis for phylogenetics, if not for so called "scenario building", as I briefly discuss later. According to this view, cladograms, based on parsimony-driven distribution analyses of "synapomorphies" (i.e., untested homology hypotheses of uniquely shared similarities between taxa), represent the foundations (deductive and scientific) of all other historically relevant analysis (e.g., Eldredge and Cracraft 1980; Simmons 1993; Novacek 1996).