According to Kuhn, theory choice is not governed by algorithms, but by values, which influence yet do not determine theory choice. Cladistic hypotheses, however, seem to be evaluated relative to a parsimony algorithm, which asserts that the best phylogenetic hypothesis is the one that requires the fewest character changes. While this seems to be an unequivocal evaluative rule, it is not. The application of the parsimony principle is ultimately indeterminate because the choice and individuation of characters that figure in parsimony computations are indeterminate. The cladistic approach is Kuhnian because the application of parsimony depends on persuasion, background, training and tradition.

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