The philosophical basis of character coding for the inference of phylogenetic hypotheses

The coding of observtions of organisms into a data matrix for the inference of phylogenetic hypotheses has suffered from a variety of problems that have precluded development of a uniform approach to the issue. Probably the most notable consequence is that the philosophical basis for coding has been prominently ignored in lieu of emphasis placed on specific coding strategies. From an epistemic standpoint, part of the problem lies with the distinction of 'characters' and 'character states', which does not accurately convey perceptual beliefs or observation statements. The ability to perceive objects is by the nature of the properties of those objects. One's sense perceptions are of characters, not states; or more appropriately, one observes objects by way of the properties perceived of those objects. The proper distinction is therefore not one of character/state, but one of object/character, as communicated by subject-predicate relations. With observation statements referring to shared similarities among organisms distributed among two or more species, and phylogenetic hypotheses in the form of cladograms serving as at least tentative explanations for those effects, then what dictates the coding of observations is not adherence to a particular coding strategy, but the need to accurately convey the causal questions that address those observations. A phylogenetic data matrix is therefore not composed of columns as 'characters' and cells as 'states'. Rather, column headings indicate the observed subjects that instantiate various characters; columns represent specifiable causal questions based on observations, and cells present the subject-predicate relations of observation statements. Since data matrices must represent one's causal questions, the inclusion of outgroup taxa is justified as components of those questions. With these criteria, the coding strategies summarized by Pleijel (1995) are critiqued. It is shown that advocacy of any one of those approaches is not possible, and that strategies that incorrectly apply the notion of 'absence' are especially prone to misrepresent observations.