"Second of all, this doesn't change the fact that random errors are introduced by all polymerases; regulating the activity of an error-prone polymerase does not change the random nature of the mutagenesis."
It points mutation to certain times and places. That is non-Darwinian, and is more inline with designed mechanisms than atelic processes.
"I noticed you also ignored the point that chromosome segregation is random. Convenient."
It's irrelevant.
"No, I'm saying that what we've observed is consistent with evolutionary theory."
It's more consistent with creationism. We keep on running into teleology in biochemistry.
"First of all, it's DNA Poly III, not IV or V, that performs large-scale replications in E.Coli."
That's precisely the point. Poly IV comes in when and (and possibly where) the organism needs modification. This is a purposeful, planned process.
"Finally, I notice you didn't answer my question about complexity, which is at the heart of the issue here. You want to see a complex adaptation, but you refuse to precisely define it."
Well-matched parts, multiple amino acid changes across multiple genes.
"How many base pairs are required to make an adapatation complex?"
If you are in the hundreds, I would count that as complex.
"Can a prokaryote even show a complex adapatation that would satisfy your criteria?"
There are many complex adaptations. The point is that none of them occur by Darwinian mechanisms. Take for instance Pseudomonas. It can adapt to new food sources within 9 days, by putting together pairs of entirely new genes. Now, if the mutational rate which produced the genes were present throughout the entire genome, error catastrophe would quickly occur. This indicates that the mutation was directed onto a single gene. In fact, the cell even knows to put the new gene on a plasmid to ship it to the rest of the colony that hasn't discovered it yet. I discuss it here:
http://crevo.blogspot.com/2005/06/evolution-chance-and-design-to-cb940.html
Likewise, Behe shows just how slow the Darwinian mechanism is in doing a change of only a few amino acids, if it is even possible at all:
http://www.proteinscience.org/cgi/content/abstract/ps.04802904v1
Our observations of beneficial change in organisms is almost entirely driven by mechanisms of purpose, not happenstance. The idea of Darwinism is almost completely foreign to everything that happens in biochemistry. Are there completely random mutations? Sure, they exist. But they aren't playing a major role in adaptation.
So in other words, your argument against evolution is based on some arbitrary criteria and has nothing to do with evolutionary theory. Thanks, that's what I thought.
Pseudomonas / DNA Poly IV,V
Restricting mutagenesis (by whatever mechanism) to a specific part of the genome would give the organism a selective advantage and is consistent with natural selection. Hint: This is why sexual recombination is favorable. Even flu viruses show this pattern of having some parts of the genome more mutagenic than others, because natural selection favours it.
Also, note that it's very intellectually dishonest to use phrases like, "the cell even knows that" since you're implying higher order intellegence where none has been shown to exist, i.e. at the cellular level.
Our observations of beneficial change in organisms is almost entirely driven by mechanisms of purpose, not happenstance.
And yet every example of genetic change we've covered is effectively random. Even if an organism restricts mutation to a single gene, the mutated sequence will be randomly determined because of the fundamental biochemical mechanisms. Natural selection acts on those random mutations.