Part 2 - method
Functional morphology studies the way in which organisms, or their parts, function (the term functional morphology is used also in linguistics, but with a completely unrelated meaning). Often, it is possible to study a part of an organism separately from the whole organism. For instance, often it is possible to analyse the functioning of a leg in terms of its part. This provides an understanding of the biomechanical principles involved, and of the properties and performance of the structure being examined. This procedure reduces the complexity of the subject being studied, and allows one to tackle a problem of reasonable size. Once a structure has been studied piecewise, one should integrate the results into a broader picture of structures that are supposed to work together, like the skeleton and muscles of legs. However, this still does not yield a complete understanding of the structure.
The next step in a functional analysis involves an evaluation of the significance of the studied structure in the context of the whole organism. For instance, the shape and musculature of legs in a terrestrial organism may provide information on the behaviour and mode of life of the organism. This information can be expected to agree with information derived from the study of other organs or body parts, as well as from other evidence (e.g., the environment as indicated by other organisms and/or by the type of sediment). For instance, in a hypothetical example, several pieces of information derived from the study of individual characters of an organism may indicate a swimming habit, but the organism turns out to have also wings apparently suitable for flying. In such a case, something could be wrong in the initial investigation and/or interpretation. A detailed re-evaluation may show other characters related to flying, or a further analysis of the "wings" may reveal them to have a different function. Alternatively, the organism may have been a swimmer and a flyer at different times (like some water bugs do), with certain organs being used only part of the time. A self-critical attitude and a willingness to retrace and re-evaluate one's steps are prerequisites for this type of investigation.
The final step of a functional analysis is an assessment of how the studied character, or set of characters, contribute to the survival and reproductive success of the organism. The latter is the basis for selection (in Darwin's meaning, which is still regarded as a largely valid concept) and, ultimately, a major factor in influencing the results of evolution. Thus, functional morphology makes little or no sense outside an evolutionary framework. It is often profitable to perform a functional analysis of a whole group of species, rather than a single species, in order to understand how a character and its function have evolved and diversified within the group. Studies of the functional morphology of a single species may be interesting, but often their conclusions are of much lesser importance than those gained from a comparative study of a larger group.
In the context of functional morphology, similarity in shape and function may reflect a common evolutionary ancestry, or alternatively, they may be the result of evolution producing similar shapes as the result of selection proceeding in similar directions. The similarity in shape of groups that are evolutionarily unrelated is called convergence. When the convergence in shape of an organ, or organism, can be shown to have a functional and adaptive basis, one may call this phenomenon a functional convergence. The similarity in general body shape and location of the fins in porpoises (i.e., mammals), ichtyosaurs (reptiles) and sharks (fishes) is an example of functional convergence in unrelated groups.
Methods in functional morphology
There are several practical approaches to studies of functional morphology. In living organisms, function can be observed at work. In fossils, instead, our information about the organism is always incomplete. Even in the lucky instance in which we have, or can reconstruct, the complete anatomy and structure of the organism, vital portions of information are still missing. For instance, we cannot observe directly the behaviour of a fossil organisms, and therefore we must reconstruct, or infer, the missing information on the basis of indirect evidence. Diet, for instance can be inferred from the morphology of the mouthparts and masticatory organs, and from the occurrence of other fossilised organisms that may have constituted the food of our subject. In lucky instances, the gut contents of an organism may be preserved, thus providing first-hand evidence of its diet. Comparisons with living organisms similar to the fossil (either related to it, or convergent with it) are also used to confirm or disprove our reconstruction. In general, life habits and function inferred by using a variety of indirect evidence and a range of conceptual tools is more reliable than evidence derived from a single piece of evidence or a single method. Like Sherlock Holmes piecing together tiny bits of evidence, a palaeobiologist pursues several conceptual approaches and lines of thought in order to arrive to a general conclusion. However, in palaeobiology the culprit is not always apprehended, and in some cases the evidence is so scanty that there is a large margin for error. Nonetheless, a careful application of all available concepts and tools rather infrequently results in an interpretation that is proved completely wrong by subsequent study, especially if one remains self-critical and does not stretch interpretation beyond the limits of reasonability and likelihood. Even those interpretations that do prove wrong are useful to science, because they provide a test-bed to assess the validity of the methods and concepts used in research.
A more detailed discussion on the concepts and methods in functional morphology is available in:
These papers contain further references.