Your rather dogmatic affirmations deserve very long answers, but for the moment I would like only to clarify a fundamental misunderstanding about the flagellum and Behe’s IC, becuse you, like others, go on repeating, after Miller, the false concept that IC of the flagellum has been refuted. I’ll try to keep it simple (and yes, I have read the paper to which Miller refers).
The discussions about homologies, more or less strict, of some proteins of the flagellum to others of T3SS pump or of any other existing molecular machine are very debatable (indeed, any discussion about homologies is totally debatable) and completely irrelevant to the concept of IC. All so called answers to Behe’s formidable concept of IC seem to be completely unaware that IC is about the realistic credibility of a causal mechanism. So, to refute the IC of the flagellum, correctly affirmed by Behe, any darwinist should succeed in showing a sufficiently detailed and credible causal mechanism which can have produced the flagellum. In other words, something like that:
1) Let’s start form an organism, a bacterium, which has no flagellum, but has, for instance, the pump wich is supposed to have produced, evolutionarily speaking, the flagellum. Let’s call this bacterium A.
2) Let’s consider the final goal, that is a bacterium which has the flagellum. Let’s call that B.
3) Now, let’s calculate, even approximately, the modifications which can bring from A to B, and express them in number of necessary point mutations (or, if you don’t like mutations, in number of any given single random event you like, be it gene duplication, inversion, deletion, or any other thing). Let’s call every single random event which is necessary to go from A to B a “genetic bit”. Plese note that, even if the model is not completely detailed, it should be realistic enough to account for the transformation from the A genome to the B genome, at least as far as a fully functional flagellum is concerned.
4) Now, let’s divide the transition in any number of intermediate states.
The model will be successful in refuting the IC of the flagellum if, and only if:
a) Each intermediate state differs from the previous and the following one for a number of “genetic bits” small enough not to face unsurmountable probabilistic difficulties (in other words, no more than a few unrelated mutations are allowed, probably no more than two or three, but we can be more generous, if you need)
b) Each intermediate state is specifically selectable because of a distinct functional advantage, capable of giving a reproductiove advantage and therefore a sufficient expansion of the mutated clone (here, unfortunately, we cannot be generous, distinct functional advantage must be present at each selected step).
In my knowledge, nobody has ever even vaguely attempted to refuted the IC of the flagellum (or of any other IC structure) in this way.
Please note that I am not asking too much. I am not asking, for example, that such a model be “proven” as real. I will be satisfied with a theoric model, provided it is detailed enough, credible, and quantitavely analyzed at the molecular level.
Furthermore, I am not asking that the increased function of each intermediate state be the same as the final (or initial) function. Any form of the mythological “cooption” is allowed, provided that the coopted functions are demonstrated and that their molecular derivation from other functions in terms of a very small number of “genetic bits” be verified.
I am, anyway, asking that the model eaxplain all the necessary molecular changes in as much detail as reasonalbly possible, and that it include not only the changes in the effector genes (the proteins), but also all the new regulatory and assembling functions, at least as far as we can understand a minimum of them (for instance, the necessay regulations of transcription, the correct rate, the temporal sequence, and so on). I understand that almost nothing is known of these matters, and therefore I would be happy, in a first moment, with the explanation of the modifications in the final proteins, but let’s remember that, probably, the greatest impossibilities are to be found in the “evolution” of the new regulatory network.
In the light of what above said, I can confidently affirm: nobody, and I mean nobody, has in any way refuted the irreducible complexity of the flagellum, as shown by Behe.
Darwinists claim to have such an explanation for everything, but when you actually ask for it, all you get are excuses and cries of "foul!" And yet still they believe.