J. Kirk Fitzhugh

The slide shows presented here represent a synthesis of my investigations during the past several years into the inferential basis of phylogenetic systematics. While the popularity of phylogenetic systematic methods surpasses that of 'evolutionary taxonomy' or 'phenetics,' the arguments
presented in its defense have often relied upon the need to associate the inference of phylogenetic hypotheses with the philosopher of science, Karl R. Popper. Popper's influence on 20th century science has principally been in the area of hypothesis testing, often incorrectly referred to as the 'hypothetico-deductive method.'

View research web shows:

I. The Inferential Basis of Phylogenetic Systematics

II. The Inferential Structure of Semaphoronts, Species and Supraspecific Taxa

III. The Philosophical Basis of Character Coding

IV. The Requirement of Total Evidence

V. Homology vs Homogeny

VI. Testing Phylogenetic Hypotheses

Regrettably, however, the adoption of hypothetico-deductivism has left many scientists with the
view that there only exists a 'logic of justification,' wherein the only component of science
worthy of consideration is the testing of theories and hypotheses by way of the deduction of
observable consequences. Such an approach has left virtually untouched any consideration of
the 'logic of discovery,' i.e., the inferential practices applied in all fields of science for the
development of theories and hypotheses.

In the field of phylogenetic systematics, the negative effect of hypothetico-deductivism has been
nothing short of profound. For instance, there are the commonly held, interrelated
misconceptions that (1) inferences of phylogenetic hypotheses are deductive, and (2) that
Popperian testing occurs on a regular basis during the act of hypothesis inference. A recurring
theme in the slide shows presented here will be to point out that such strict adherence to deduction
is not only impossible, but also counterintuitive.

Alternatively, there is another popular school of thought in which it is contended that
phylogenetic inference is in some way a matter of statistical or probable estimation. To hold
such a position assumes one has critically examined the non-deductive nature of explanatory
hypothesis inference. Such has, however, not been the case with respect to phylogenetic
systematics, which leaves most probabilistic approaches as nothing more than irrelevant
curiosities. Indeed, neither the Popperian nor the 'probabilistic' school of thought has correctly
characterized the inferential structure of phylogenetics such that either can be defended. The
principle reason being that the inferential form to which phylogenetic inference is a member has
never been formally addressed by phylogenetic systematists.

The slide shows presented here outlines the logical and inferential bases of phylogenetic
systematics, from which are then addressed such issues as the actual relations of the inference of
phylogenetic hypotheses to the testing of those hypotheses, as well as the nature of coding
observations for the purposes of inferring explanatory hypotheses which account for those
observations. Similarly, by critically examining the logic of phylogenetic inference, the correct
relationships of the concepts of 'homology' and 'homoplasy' to phylogenetic hypotheses become
clear, and the long-standing issue of whether or not to combine classes of data in the act of
inferring hypotheses is readily resolved.

In summary, the logical foundations of historical inference extend throughout all aspects of the
field of phylogenetic systematics. The implications for the myriad of methods and opinions
regarding phylogenetic inference are far more substantial than have been previously identified.
My goal in presenting these slide shows of my research into this subject is to stimulate greater
critical thought and discussion into understanding what we do as scientists, rather than blindly
accepting methods as scientifically efficacious simply because those methods are popular.

JKF, April 2004