I thought my posts were directed at irreducible complexity, but go ahead.
Thanks.
The best argument I have seen for irreducible complexity was made by Dembski here:
http://www.designinference.com/documents/2004.01.Irred_Compl_Revisited.pdf
He breaks it down this way:
The problem is that for an irreducibly complex system, its basic function is attained only when all components from the irreducible core are in place simultaneously. It follows that if natural selection is going to select for the function of an irreducibly complex system, it has to produce the irreducible core all at once or not at all. That might not be a problem if the systems in question were simple. But they are not. The irreducibly complex biochemical systems that Michael Behe, for instance, considered in Darwin’s Black Box are protein machines consisting of numerous distinct proteins each of which is indispensable to the machine’s basic function. Darwinism, committed as it is to a gradual evolutionary process that incrementally builds complexity and function, now faces a dilemma. Darwinian evolution cannot produce an irreducibly complex system exhibiting a given basic function by having natural selection act on and improve simpler precursors that already display that function. The problem is that the function doesn’t exist, and therefore is not selectable by natural selection, until the irreducibly complex system is in place already. It follows that Darwinian evolution can produce an irreducibly complex system that serves a given basic function only by taking already existing systems that serve different functions and redeploying them to form the irreducibly complex system. But, as we shall see later in this essay, there is no evidence that the redeployments required to form such irreducibly complex systems could happen, much less be properly coordinated, by a gradual Darwinian evolutionary process. Instead, the evidence suggests that any such redeployment would require such massive coordination of the redeployed systems as to place the resulting irreducibly complex system beyond the reach of Darwinian evolution. Of course, such massive coordination bespeaks design.
The best response I've seen was with the first link that you provided. The diagram at the end of the paper shows step by step how flagellum could have evolved. The gauntlet is that each step needs to be selectable--it has to provide an advantage to the organism, and then has to survive long enough to be embedded. In short, it needs to be superior enough to the previous version to provide advantage over competing organisms. Then the next step has to occur, and meet the same challenge. This challenge is imposed by Natural Selection itself.
Table 6 addresses this by assigning broad terms like export, secretion, adhesion, dispersal, and taxis. Referring back to the previous text, where these advantages are explored in more detail, reveals a key weakness: the starting point is a device used for secretion that is homologous to flagellum.
To justify the availability of the components that later get folded into the ancestral type III secretion system as well as the availability of this system itself as a starting point for his model, Matzke looks to evidence from molecular homology. Perhaps the biggest stretch is getting the ancestral type III secretion system itself to start the ball rolling since, as Matzke himself admits, the best evidence points to this system arising only after metazoans have been on the scene, and thus many hundreds of millions of years after the origin of the flagellum. Thus Matzke makes an unconvincing argument for homologies between the type III system and an ATP synthetase system. As Matzke admits, "sequence similarity searches do not turn up significant hits," so the putative homology is based on some unspecified similarity metric and is therefore less than rigorous. The other components that subsequently need to get folded into this starting system are less of a stretch but still highly dubious. For a number of the proteins that make up the flagellum, there simply are no known homologues. And for others, there is no reason to think that they were available for co-option in the actual ancestral line leading from a bacterium with no flagellum (and no genes for the flagellum as well as no homologues for these genes either) to one with a modern flagellum. Matzke just helps himself to whatever biochemical products are available in whatever living forms are available subject only to a very loose conception of homology. Anything in this ballpark, and even purely hypothesized biochemical products, constitute fair game for co-option in Matzke's model.
This is part of Dembski's response, and I think it is valid.
http://www.designinference.com/documents/2003.11.Matzke_Response.htm
As to demonstrating the selective advantage of each of the transitional steps, Dembski argues it is not shown convincingly, which I agree with. The problem, I admit, with this counterargument is "convincing" isn't a convincing thresshold. That aside, even if ID stipulates to this selective advantage, Dembski continues,
Notwithstanding, let me grant Matzke all the selective advantage he needs in moving from one step to the next in his model. The biggest obstacle justifying his model still remains to be addressed, namely, showing that each step in the model is reasonably likely to follow from the previous one. Darwinism is a theory of process. It says that you can proceed from point A to point B in biological configuration space provided that you can take small enough steps where each step is fitness enhancing (or at least not fitness detracting). The steps need to be small because Darwinism is a theory of gradual incremental change where each step along the way is reasonably probable. As Darwin put it in his Origin, for his theory to succeed it must explain biological complexity in terms of "numerous, successive, slight modifications." Anything else would cause his theory to founder on the rocks of improbability.
Are the transitions from one step to the next in Matzke's model reasonably probable? Does each step in his model constitute only a "slight modification" (sensu Darwin)? There's no way to tell because the model is not sufficiently detailed. As I pointed out earlier, all we have in hand is the modern type III secretion system, the modern bacterial flagellum, and various homologous biochemical structures embedded in the flagellum present in extant organisms. We don't have the intermediates that Matzke posits nor the ancestral type III secretion system. We don't know what they look like. We don't have their precise biochemical specification. We don't know if the intermediate systems that Matzke's model hypothesizes would work. We have no way of determining how easy or hard it is for the Darwinian mechanism to bridge the steps in Matzke's model. Matzke, throughout his article, invokes gene duplications and mutations at key points where the Darwinian mechanism is supposed to effect transitions that are reasonably probable. But what gene exactly is being duplicated? And what locus on a gene is being mutated? Matzke never says. Indeed, his model is so unspecific that he cannot answer these questions. But unless we know the answer to such questions, there's no way to know whether the transitions Matzke describes are reasonably probable and therefore of the type required by Darwin's theory.
So the end result is that Matzke's argument doesn't deliver what it promises, and at best still resorts to explaining the tough questions with "evolution did it." Matzke, as Dembski points out, doesn't deliver a detailed, step-by-step, testable, hypothesis. It may be a starting point, but it doesn't make a sufficient, plausible case for the natural selection of the components of flagellum.