FW: [Annelida] re: eunicid phylogeny
Torsten.Struck at Biologie.Uni-Osnabrueck.DE
Sat Mar 25 02:08:46 EST 2006
For some own reason to me, my e-mail got truncated, so just for completeness, here is the complete one. And as a final comment logic and epistemology are all metaphysical in nature, that the have not to connected to the physical world. With regard to premises this even more the case for arguments and assumptions in metaphysics, logic and epistemology.
I just want to give some last comments, because I do not see that we will come to an agreement on this point anyway. I admit that I cannot see that Kirk could put forward arguments (as long as they are purely metaphysical arguments) that could convince me. As I see it, we in an open debate, which is not resolved yet all (as I stated before). The methods we used and developed were neither scientifically unacceptable nor the results meaningless or not rational explainable. In contrast, they are well proven by empirical data.
Also, I am surprised to read that Kirk does not see the connection between methods and persons who developed and used them. I would like to see the scientist who will not be offended if her/his work or parts of it is called scientifically unacceptable, meaningless and irrational in a public forum. As any other scientist I take science seriously and do it by heart and with passion. Thus, there is always a personal bound to our work. As matter of fact in his first e-mail he did present his critical comments not as opposing viewpoints to consider, but as strong, matter-of-factly statements.
I oppose the intention from Kirk that I do not comprehend the merits of philosophy of science to the critical evaluation of phylogenetic method. However, I am opposed to pure non-empiric argumentation in epistemology. Most hottest debate in philosophy were and still are those which are purely embedded in the metaphysical realm. Among others, this due to reason that you cannot differentiate which assumptions are true. An example from theology, every time they proof the existence of god, they always show in the same time his non-existence. Thus, every foundation of science has to be connected to empirical data and studies. That way I am more in line with the empiricism advocated by Hume or Locke.
Kirk repeatedly states that I miss his points. He may see it that way, but he also misses or does not even address some of the problems we raised. For example, he recognized the problem of paralogy or horizontal gene transfer, but did not propose anyway to solve the problem if he does not want to partition the data set. These are true problems with real data and this shows the problem when the foundation is not connected to the physical world. As Kant stated in his "Kritik der reinen Vernunft": "Gedanken ohne Inhalt sind leer, Anschauungen ohne Begriffe sind blind."(Ideas without content are empty, views without terms are blind). This means, the pure thinking has to be embedded in some kind of textual material, it needs observations/physical data. Furthermore, we partition all the time, we investigate only a certain taxon, certain set of genes or features. Additionally, partition has a long hold tradition in science and philosophy of science reaching back to Sir Francis Bacon. To partition problems/data is what we do to get specific answers (it is called reductionism). Later the parts are put back together to get further insights. And it has to be pointed out that these parts are not irrelevant of each other.
Interestingly, he does not directly address the problems of circularity and contradiction except for pointing out that effects and evidence are not not the same. Something I did not state. Furthermore, he does not put forward any specifics how to perform such tests if "Character data cannot test those two classes of events [character origin and speciation]". To test my hypotheses I need some kind of physical data and this will be new or old character data in anyway. A short remark, if the abstract (the summary of the main conclusions of a paper) already shows circularity and contradiction, what can we expect from the whole paper?
Kirk often invokes misconception by others. For example, I should have misunderstood fact. He provides a definition 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." However, this matches exactly what I said about facts: "A scientific fact is substantiated by empirical data...". And I think I made myself pretty clear meant the content of an opinion and not the opinion itself. So Kirk stating "...it is a fact that I hold that opinion" is not more than an anecdote.
At last, risking to repeat our mantra again the methods we used are scientific and the best available to date (e.g., Likelihood outperforms parsimony, it is neither a mantra nor a myth). In his Zootaxa article Kirk states: "The consequence is that parsimony has logical priority over likelihood in abduction,...". Thus, he advocates parsimony over likelihood contrary to his statement in the last e-mail. A myth would be Kirk's proper testing if it is not connected to any kind of physical data. A mythical explanation invokes a new layer of explanation for an observed phenomena without any connection to physical data. For example: Were does the water from spring under a stone come from? In the stone is an unseen goblin, out whose mouth comes the water. So may persons should more careful when using phrases like myth or scientifically unacceptable.
It has been stated here that Kirk is representing the minority. However looking back in history, that the position regarding for example parsimony he helds was a long time in the majority. And it was not such that when Likelihood procedures emerged that they were that sexy, so that everybody jumped on them, because they are much more time consuming all their aspects than parsimony. So it took a long time turn the tide (more than a decade).
------ NEW CONTACT INFORMATION ------
Dr. Torsten H. Struck
University of Osnabrück
Department of Biology/Chemistry
e-mail: struck at biologie.uni-osnabrueck.de
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