Most approaches to functional analysis of fossils rely on comparisons between extinct and living organisms (e.g. Raup and Stanley, 1978). Many ultimately rely on a hypothesis of homology at some level, and the link between homology and function may be direct. For example, methods based explicitly on hypotheses of homology and phylogenetic relationship with living relatives can be used to infer unpreserved attributes of fossils, including function (Bryant and Russel ,1992; Witmer, 1995). Even where functional inferences are derived from physical or mathematical models of biomechanics, the sometimes subtle influence of homology is evident. Weishampel's (1984) kinematic analysis of the details of jaw mechanics in ornithopod dinosaurs is not directly based on homology with living structures, but would probably not be possible if skulls, jaws and teeth had no homologues in living animals. In cases where relationships and homology are unknown or so poorly constrained that assessments of function have to rely entirely on analogy, analysis of functional morphology can be reduced to mere speculation.

This problem is not unique to any particular group of fossil organisms and arises, for example, in analysis of any of the more enigmatic fossil metazoans, especially those known only from Palaeozoic lagerstätten, such asTyphloesus, Anomalocaris, or Tullimonstrum. Indeed it is the novelty of enigmatic organisms and their structures, and their lack of obvious counterparts or homologues among extant taxa that makes them attractive subjects for functional investigation. Perhaps better than any other group, however, the difficulties caused by lack of homology and absence of constraint are exemplified by analyses of the nature and biological role of conodont elements. Investigations into functional morphology of the conodont skeleton illustrate a range of different techniques that can be applied to skeletal structures which are generally found as disarticulated remains and for which homologues among living taxa are unknown or questionable. Analyses of conodonts also illustrate the pitfalls which beset such investigations.