Indeed. So you can’t rule out Muller’s explanation. Behe is saying that you can’t remove one component of a structure without the whole structure failing. He is then saying that the only explanation is design. What he is actually saying is that he personally can’t think of any other reason.
If you point out Muller’s explanation to him and ask: ‘Is it possible that his explanation is correct?’ the only credible answer to that is ‘Yes’. As you said yourself: ‘the sheer complexity of the universe makes it impossible to rule out other factors’ and Mullers explanation is a very long way from being complex. In fact, it’s blazingly simple. He has proffered a very simple explanation entirely due to natural cuases.
Bradski:
I’ve read many of the various so called refutations of Behe’s “irreducible complexity” argument. What I find very interesting is that none of them wholly refute the argument. That is, each one leaves rather large back-door escapes from a full committal to the author’s purpose.
For example, Kenneth Miller points out that the
earlier version of the eukaryote, the one that had the first five or six amino acid structures found to be present in the final flagellum, and the TTSS, was transitional. This transitional mutation consisted of the first five (or six) amino acid structures that are parts of the complete TTSS apparatus. This, he says, disproves Behe’s contention that the flagellum did not evolve in simple steps, over a long period of time, based upon the efficacy of
each of the parts for another purpose. Now, what could possibly be wrong with that? Could it be that Miller left out of consideration
each of the first five - six steps, or rather, structures? Oh, and we didn’t even consider the last nine - ten steps (to the flagellum) yet?
Instead, Miller says, “If we are able to search and find an example of a
machine with fewer protein parts, contained within the flagellum,
that serves a purpose distinct from motility, the
claim of irreducible complexity is refuted. As we have also seen, the flagellum does indeed contain such a machine, a protein-secreting apparatus that carries out an important function even in species that lack the flagellum altogether. A scientific idea rises or falls on the weight of the evidence -
The Flagellum Unspun - Kenneth Miller”
But that is wrong. Either the evolutionary pathway for the TTSS is itself a product of evolution as well, or the TTSS was formed almost entirely simultaneously as a sort of “
bulk mutational evolution event;” otherwise it too underwent evolution and each of its proteins had a functional purpose that enhanced the organism in some way, and thus
each mutation survived being cast off. I am not saying that this latter postulation is incorrect, but I am saying that since it isn’t shown to be a product of an evolutionary process, necessary to the organism, why should each mutant part (and its mutational event) survive? Further, where are the transitional organisms
that show each step of the development of the pre-TTSS mechanism all the way up to the final TTSS apparatus?
What we are to believe is that the first amino acid structure was probably the result of a mutation. And then, we are to believe that that mutant structure gave rise to another mutant structure. And, that second mutant structure gave rise to a third mutant structure, etc., etc., until voilà, a TTSS apparatus appears that finally has an intrinsic value (as a complete 5 - 6 part apparatus) to the organism. However, until that fifth or sixth mutation of a mutation, none of the prior mutations’ mutations added any known intrinsic value to its immediately prior mutation (and the eukaryote), and, for all intents and purposes, should have been a relatively singular event that is discarded, like a dead weight, in the course of time.
Now, I will admit to not reading all of the literature that has ever come out on this subject, as I simply don’t have that much time. nor do I have the burning inclination. So, if there is an article answering the above questions, somebody please point me to it.
God bless,
jd
The designer cannot itself be studied – it is supernatural, outside of nature.
Really - that betrays an a priori bias. I am disappointed in you.
I have still to write up my prayer experience. 
