[Annelida] re: eunicid phylogeny

Struck, Torsten Torsten.Struck at Biologie.Uni-Osnabrueck.DE
Thu Mar 23 08:34:44 EST 2006

Dear Wormers,
First of all, I want to point out that we are open for discussion and see this as an important step to progress research. However, Kirk's comment was not an invitation to discussion, but to be blunt an insult to the authors, the reviewers and the editors of a highly valued journal. A discussion means that I present my arguments in a non-dogmatic view, open-minded to the other sides and with good manners. To stand up for a point is good, but no excuse to be rude and insulting. Calling some one else's work scientifically unacceptable, meaningless and irrational is just that and does also not show open-mindedness, especially when the issue at hand is unresolved at all and more a matter of opinions than facts.
Second, we did defend partitioned analyses, so not by word but by cite. This shows, that there are others how have a different viewpoint to this matter than Kirk (and they are not that few by the way). For example, Lecointre and Deleporte (2005 Zoo. Scri. 101-117) following Rieppel's (2003 Syst. Biol. 259-271) line of abductive argumentation clearly showed  the necessity to perform partitioned analyses to detect processes, that can distort phylogenetic inference like paralogy or horizontal gene transfer. And these processes are true evolutionary events. Our newly developed PABA approach is just such a procedure.
Third, an opinion is not a fact. I can have the opinion that the sun is green. However, that does not make a fact. A scientific fact is substantiated by empirical data and testability in some way or the other. Because Kirk's line of argumentation is purely in the realm of logic and not connected to empirical data his opinion is just that an opinion.
Coming to the point of the logical foundation of phylogenetics or science in general. Every discipline and its foundation, which wants to call itself scientific, has to be connected to empirical data and testability of the hypotheses. If you wish to seek a foundation for phylogenetics purely in the logical realm as Kirk does, you will have no foundation, because you are purely in the metaphysical realm like religion is (most of them are logical in themselves). It is like building a house on water. Pure ratio brings you just this far. Anyway, essentials in pure rational/logical argumentation are that the line of argumentation is not contradictory or circular.
In the abstract of Kirk's Zootaxa article we find the following statements:
"...phylogenetic hypotheses are derived from a form of non-deductive inference commonly known as abduction. ... The proper testing of a phylogenetic hypothesis requires the deduction of specific consequences...". Furthermore, Kirk has pointed out in his contributions that phylogenetics is non-deductive. However, for proper testing he introduces deduction in phylogenetics. Thus, there is a deductive part in phylogenetics.
Regarding proper testing of phylogenetic hypotheses Kirk rejects all tests used today (Bootstrap, Jackknifing, Bremer support and so on). Furthermore,"In recognizing phylogenetic hypotheses as answers to causal questions, the popular conception of testing such hypotheses by the introduction of new characters is incorrect. New character distributions cannot be deduced from a cladogram since such a structure only has causal relevance to the characters for which the hypothesis was inferred." Thus, newly obtained data cannot be used to either corroborate or reject a previous hypothesis. Each hypothesis stands for it's own and nothing else, so much to the point of progress in science. He goes on suggesting a proper testing strategy: "The
proper testing of a phylogenetic hypothesis requires the deduction of specific consequences as closely related as possible to the specified causal events of character origins and fixation, and subsequent speciation events. Such consequences must be effects that are independent of the class of effects the hypothesis was intended to explain, i.e., character data." The
question is how the effects can be independent from the character data, if the introduction of new data is incorrect and thus not allowed. Either this statement is contradictory to the statements just two sentences before or the testing is circular and thus not valid. In next sentence Kirk provides the following as legitimate potential test evidence: "As a result, effects that stand as legitimate potential test evidence are those effects that best support the different sets of causal events presented in the hypothesis." This sentence is already circular in itself: the effects, which in the end best support our hypothesis, are the effects, which are legitimate as test evidence. In a nutshell, only what fits the hypothesis is appropriate. One could say that this is a kind of self-fulfilling prophecy. At least, you do not have to worry that the test might contradict your hypothesis.
As we can see that arguing purely in the realm of logic is full of pitfalls. Anyway, if phylogenetics wants to be more than metaphysics it has to be connected with empirical data and testability even with its foundations. Tons of studies of empirical data as well as simulated data have shown that likelihood is superior to parsimony, that bootstrapping and other tools
are valuable tests providing deeper insights into phylogenies and that using partitioning strategies is most powerful to detect processes like paralogy or horizontal gene transfer, actually it is the only possible way. At last regarding partitioning, we always partition our data. We never use all the data at hand due to good reason, because some are irrelevant for the
question at hand.
Sincerely yours,
Torsten Struck

Dr. Torsten H. Struck
University of Osnabrück
Department of Biology/Chemistry
Barbarastrasse 11
D-49069 Osnabrück

Phone: +49-541-9692859
Fax: +49-541-9692587
e-mail: struck at biologie.uni-osnabrueck.de

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