The American writer Mark Twain once said, "Whenever you find you are on the
side of the majority, it is time to pause and reflect."
I am glad to see Torsten's thoughtful comments and his willingness to
pursue this discussion. My comments will address the scientific merits of
his reply, not his or Ken Halanych's accusations against my character. To
state that a method is scientifically unacceptable is neither rude nor
insulting, given that I was speaking of methods, not individuals. If I
wanted impugn the credibility of anyone, then I would have structured my
message quite differently. What I pointed out is that certain methods are
either incorrectly applied in phylogenetics, or lead to results that are
meaningless or cannot be rationally interpreted.
On the matter of partitioned analysis, Torsten cites Lecointre and
Deleporte (2005). This is a good paper in that it discusses the
requirement of total evidence (RTE) to some extent, as well as
abduction. But, Lecointre and Deleporte neither adequately discuss
abductive inference or the RTE. As such, one cannot rely solely on the
systematics literature for a defense of partitioning. Lecointre and
Deleporte's understanding of the RTE is not entirely correct, especially
with regard to the nature of positive or negative evidential relevance,
which is a critical factor in correctly considering the merits of
partitioning. I specifically address their claim that partitioned analyses
are necessary in my forthcoming paper in Biology & Philosophy:
'The present discussion calls into question the position taken by Lecointre
and Deleporte (2005: 106, fig. 5; see also Grande 1994), that "Performing a
simultaneous analysis right from the beginning is of little methodological
value." Rather, they contend that "points of disagreement between trees
are either artifactual or due to a process of discord..." (Lecointre and
Deleporte 2005: 107), indicating that some character data must be
excluded. The matter of deciding what sets of character evidence are
abductively relevant to one another requires a three-step process according
to Lecointre and Deleporte: (1) infer phylogenetic hypotheses for
partitioned sets of data; (2) determine the extent to which character
incongruence exists among those hypotheses; (3) if, according to the
incongruence length difference test of Farris et al. (1995), hypotheses
exhibit significant character incongruence, then "misleading" data are to
be removed prior to the final objective, which is the inference of
hypotheses from the total "relevant" data. Contrary to what Lecointre and
Deleporte (2005) state, the "misleading" data that are removed must be
interpreted as "irrelevant" sensu Carnap (1950), rather than relevant. The
more significant problem with their approach is that separate explanatory
hypotheses do not have the capacity to determine what sets of observations
are irrelevant to the explanation of other observations. Recall as well
that relevance can be positive or negative, such that contradictory
hypotheses inferred from the same causal theory... indicate that
observations are negatively relevant. As was noted for the inferences
[presented earlier in the paper], and will be discussed in a later section
(see The Myth of "Cladogram" Comparisons), applying the same causal theory
to partitioned data sets for the same organisms results in hypotheses that
cannot be rationally compared, as each of these hypotheses stands as an
explanatory account that only pertains to the effects from which the
hypotheses were inferred. The fact that these hypotheses can contradict
one another cannot be interpreted as "artifact" or "discord." The best
that can be claimed for such contradictions is, as mentioned above, that
all data that are to be explained using the same theory are relevant
(positively or negatively) to one another. The matter of relevance must be
given due consideration prior to inferring an explanatory hypothesis,
rather than treating sets of hypotheses as the arbiters of rational
reasoning. Indeed, the matter of relevance is to be considered as part of
the formulation of the causal questions and selection of applicable theory,
and not within the inferential procedures that are employed after these
tasks have been accomplished.'
In order to perform partitioned analyses, one must assume that the data are
irrelevant to each other. But, if data are irrelevant, then one could not
causally account for both sets of data using the same causal theory, for
this would violate the condition of relevance. As the matter of relevance
or irrelevance is something that must be decided prior to abductive
inference, it is not possible to compare separate hypotheses from
partitioned data and decide after the fact that those data are relevant,
positively or negatively, or irrelevant. Unlike what we see in
systematics, the RTE is not a controversial issue as it is one of the
central rules for rational, non-deductive reasoning. If one wishes to
defend partitioned analyses then they will have to show that the RTE does
not hold. Lecointre and Deleporte (2005), and other systematists, have
never been able to successfully make this claim. I agree with Torsten that
one has to contend with matters such as paralogy or horizontal gene
transfer. The problem, however, is that explanatory hypotheses do not
provide the basis for deciding what effects are in need of being explained
by those hypotheses. The criterion for such a decision is relevance, and
this is considered prior to an abductive inference.
I will briefly dispel Torsten's misconception of the term 'fact,'
especially his claim that 'an opinion is not a fact.' Here is a definition
provided by Mahner & Bunge (1997: 34, Foundations of Biophilosophy): '...a
fact is either the being of a thing in a given state, or an event occurring
in a thing.' So, if I state, 'Partitioned analysis is erroneous,' this
statement conveys a fact, that part of my state of being is to hold a
certain opinion about partitioned analysis. In other words, it is a fact
that I hold that opinion. Or more specifically, it is a fact that certain
neurons in my brain are excited in a specific order such that I utter the
words, 'Partitioned analysis is irrational.' Just like stated opinions,
observation statements are reflections of mental constructs that convey
what one believes to be facts.
Torsten then claims that my 'foundation for phylogenetics [is] purely in
the logical realm.' No, incorrect. All fields of science operate under
the more general conditions of imposed by logic, epistemology, and
philosophy of science, to name just a few. What I have attempted to do is
to investigate the philosophical foundations of phylogenetic systematics
within the conditions stipulated by these broader realms. We need to fully
evaluate the nature of abductive inference as it applies to
phylogenetics. We have to evaluate the veracity of our methods against
what we claim to be our goal in phylogenetics, as well as the goal in all
sciences. Torsten's comparison of my evaluation of phylogenetics as 'like
building a house on water' only indicates to me that he does not comprehend
the importance of philosophy of science to the critical evaluation of
phylogenetic methods.
Torsten then addresses the topic of testing based only on the abstract of
my Zootaxa paper. He seems to confuse the testing of hypotheses by
evidence as opposed to the inference of hypotheses by certain effects. The
bottom line is that character data cannot be used to test any phylogenetic
hypothesis since those data cannot be deduced as potential tests. One
cannot test a hypothesis inferred to explain the very effects used to test
that hypothesis. As phylogenetic hypotheses are causal claims, what must
be tested are the statements regarding the specific events of character
origin and speciation. Character data cannot test those two classes of
events. Rather, the necessary test evidence must be of a form directly
related to the events themselves that provide evidence that those specific
events did occur. Torsten fails to make the necessary distinction between
effects used to infer a hypothesis and evidence used to test that
hypothesis. This is not a matter of 'arguing purely in the realm of
logic.' The procedures for testing are clearly outlined in the philosophy
of science literature, which again I cite in my paper.
And finally, Torsten repeats the mantra, likelihood is superior to
parsimony, etc., etc. For some reason he once again did not reply directly
to the specifics of what I said earlier about those concepts. In fact, I
do not even state that I advocate parsimony over likelihood! What I
claimed is that neither has been correctly applied to the characterization
of abductive inference in phylogenetics. If list members want to pursue
the relations between likelihood and parsimony as they apply to abduction,
that bootstrapping is applicable to statistical, not explanatory
hypotheses, and other amusing notions, then please take a look at my
paper. And, I encourage more discussion!
Kirk
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J. Kirk Fitzhugh, Ph.D.
Curator of Polychaetes
Research & Collections Branch
Los Angeles County Museum of Natural History
900 Exposition Blvd
Los Angeles CA 90007
Phone: 213-763-3233
FAX: 213-746-2999
e-mail: kfitzhug at nhm.orghttp://www.nhm.org/research/annelida/index.html
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