Despite the promises made by molecular evolutionists since the early 1960s that phylogenies would be readily reconstructed using molecular data, the construction of molecular phylogenies has both retained many methodological problems of the past and brought up new ones of considerable epistemic relevance. The field is driven not only by changes in knowledge about the processes of molecular evolution, but also by an ever-present methodological anxiety manifested in the constant search for an increased objectivity—or in its converse, the avoidance of (...) subjectivity.This paper offers an exhaustive account of the methodological and conceptual difficulties embedded in each of the steps required to elaborate molecular phytogenies. The authors adopt a historical perspective on the field in order to follow the development of practices that seek to increase the objectivity of their methods and representations. These include the adoption and development of explicit criteria for evaluation of evidence, and of procedures associated with methods of statistical inference, quantification and automation. All these are linked to an increasing use of computers in research since the mid 1960s. We will show that the practices of objectivity described are highly dependent on the problems and tools of molecular phylogenetics. (shrink)

The formal definition of species as explanatory hypotheses presented by Fitzhugh is emended. A species is an explanatory account of the occurrences of the same character among gonochoristic or cross-fertilizing hermaphroditic individuals by way of character origin and subsequent fixation during tokogeny. In addition to species, biological systematics also employs hypotheses that are ontogenetic, tokogenetic, intraspecific, and phylogenetic, each of which provides explanatory hypotheses for distinctly different classes of causal questions. It is suggested that species hypotheses can not be applied (...) to organisms with obligate asexual, parthenogenetic, and self-fertilizing modes of reproduction. Hypotheses explaining shared characters among such organisms are, instead, strictly phylogenetic. Several implications of this emended definition are examined, especially the relations between species, intraspecific, and phylogenetic hypotheses, as well as the limitations of species names to be applied to temporally different characters within populations. (shrink)

Deduction leads to causal explanation in phylogenetic inference when the evidence, the systematic character, is conceptualized as a transformation series. Also, the deductive entailment of modus tollens is satisfied when those kinds of events are operationalized as patristic difference. Arguments to the contrary are based largely on the premise that character-states are defined intensionally as objects, in terms of similarity relations. However, such relations leave biologists without epistemological access to the causal explanation and explanatory power of historical statements. Moreover, the (...) prediction-making to which those kinds of relations are limited in practice can lead to a category error—the mental conversion of an abstraction into a thing . The latter practices and problems characterize pattern cladistics, taxa being interpreted as homeostatic property cluster natural kinds, and other instrumentalist research programs. (shrink)

Framing systematics as a field consistent with scientific inquiry entails that inferences of phylogenetic hypotheses have the goal of producing accounts of past causal events that explain differentially shared characters among organisms. Linking observations of characters to inferences occurs by way of why-questions implied by data matrices. Because of their form, why-questions require the use of common-cause theories. Such theories in phylogenetic inferences include natural selection and genetic drift. Selection or drift can explain ‘morphological’ characters but selection cannot be causally (...) applied to sequences since fitness differences cannot be directly associated with individual nucleotides or amino acids. The relation of selection to sequence data is by way of downward or top-down causation from those phenotypes upon which selection occurs. The application of phylogenetic inference to explain sequence data is thus restricted to instances where drift is the relevant theory; those nucleotides or amino acids that can be explained via downward causation are precluded from inclusion in the data matrix. The restrictions on the inclusion of sequence data in phylogenetic inferences equally apply to species hypotheses, precluding the more restrictive approach known as DNA barcoding. Not being able to discern drift and selection as relevant causal mechanisms can severely constrain the inclusion and explanations of sequence data. Implications of such exclusion are discussed in relation to the requirement of total evidence. (shrink)

Three competing ‘methods’ have been endorsed for inferring phylogenetic hypotheses: parsimony, likelihood, and Bayesianism. The latter two have been claimed superior because they take into account rates of sequence substitution. Can rates of substitution be justified on its own accord in inferences of explanatory hypotheses? Answering this question requires addressing four issues: (1) the aim of scientific inquiry, (2) the nature of why-questions, (3) explanatory hypotheses as answers to why-questions, and (4) acknowledging that neither parsimony, likelihood, nor Bayesianism are inferential (...) actions leading to explanatory hypotheses. The aim of scientific inquiry is to acquire causal understanding of effects. Observation statements of organismal characters lead to implicit or explicit why-questions. Those questions, conveyed in data matrices, assume the truth of observation statements, which is contrary to subsequently invoking substitution rates within inferences to phylogenetic hypotheses. Inferences of explanatory hypotheses are abductive in form, such that some version of an evolutionary theory(ies) is/are included or implied. If rates of sequence evolution are to be considered, it must be done prior to, rather than within abduction, which requires renaming those putatively-shared nucleotides subject to substitution rates. There are, however, no epistemic grounds for renaming characters to accommodate rates, calling into question the legitimacy of causally accounting for sequence data. (shrink)