Amazing. So Ken Miller has thoroughly refuted the idea of irreducible complexity, which makes the other essays not even worth reading? Isn’t that kind of like saying that the prosecution has so thoroughly proven the guilt of the defendant that the defense isn’t even worth hearing~ that the defense shouldn’t be given the opportunity to cross-examine witnesses and present evidence?
If a judge were to instruct a jury that they don’t need to listen to the defense because the prosecution has already proven itself to be right, it would be grounds for a mistrial.
Anyway, you can find a well-written Bill Dembski article here which addresses Ken Miller's critique. Lots of theocratic, bible thumping, scientifically illiterate goodness. Not.
BTW, many folks don't seem to understand the difference between the terms rebut and refute. Rebut is when you take a swing, refute is when you hit it out of the park. I can't count the number of times someone has said in an internet discussion, "this was all refuted here". When I follow the link, I find, not a refutation, but merely a rebuttal. And usually a weak one. The mere fact that an argument has been attacked is not indicative of whether the argument has been defeated. At least for reasonable folks.
I don't claim that Dembski has refuted anything in his paper. I only claim that he makes a reasonable argument.
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Dembski's first counterargument has a false basis in that he claims scientists have no models for the evolution of the flagellum. Dembski admits this when he says that Miller attributes that evolution to a type III secretory system, but Dembski jumps from his personal disagreement with that model to saying that scientists have no models.
Likewise for Irreducible Complexity: His argument to defend IC is that biological systems have IC, that (false again) evolutionary scientists do not know how to explain IC, and that human design can produce IC, therefore biological systems must be designed. This is a fundamental logical error: He has made no attempt to exclude other explanations for IC in the system. This is why scientists point out that ID has no positive evidence for design.
His claims on TTSS-to-flagellum evolutionary models are misplaced and some years out of date. The models usually do not say that a flagellum evolved from TTSS, but from a TTSS precursor. Gophna et al. (2003), Matzke (2003) and Musgrave (2004) go into more detail and are both more current and include better information than what Dembski cites as the "best current" information (Nguyen (2000)). The claim that the flagellum's additional proteins are unique is unsupported and either false or misleading in that those proteins have homologues, if not exact copies, in other parts of the cell.
Later, it is easy for Dembski to dismiss Darwin's theory of evolution as explaining beneficial mutations in DNA, and to quote Darwin as noting that gap. Has he forgetten that Darwin wrote "The Origin of Species" almost a century before DNA's genetic content and helical structure were discovered? This is why evolutionary scientists tend to talk about the modern synthesis (including both Darwinian evolution and DNA mutations, including selection-neutral changes) rather than strict Darwinian evolution.
The rest of his essay seems likely to hold similar flaws, but this is getting boring.
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