the phylogeographic challenge to creationism

It isn't.TTFN,WK

There are some heritable states of epigenetic modification such as DNA methylation or changes in histone acetylation/methylation.I'm assuming that by 'mutation' you mean a change in the primary sequence of DNA.TTFN,WK

Are you defining 'copy' errors as changes in copy number for a stretch of DNA rather than errors during the process of copying a DNA strand? Almost all point mutations, of whatever type, are due to errors in the copying of the DNA strand.I think that part of the problem is that your concept of 'copy' errors is unorthodox. Not really, methylation of DNA is usually associated with the compacting of the chromatin to heterochromatin which is usually transcriptionally non-active. Methylation is usually a factor
in the repression of expression of a gene. This may act to maintain genetic integrity to some extent since more transcriptionally active genes are often more prone to mutation, but that doesn't seem to be its primary function.TTFN,WK

Do you have a reference? I know that there have been a couple of alternative hypotheses put forward (Comai and Cartwright, 2005; Chaudhury, 2005), but I was unaware that there was definitive research on the subject.TTFN,WK

To be honest this doesn't really clarify things. This definition would also include the vast majority of single site mutations which you were defining as distinct from 'copy errors'.By 'reproduction process' do you mean DNA synthesis in general, as in the S phase of the cell cycle, or specifically DNA synthesis ocurring in the gametes?You seem to be making a fairly arbitrary distinction here.TTFN,WK

Because these aren't 2 different cases. Virtually every single instance of a mutation of any kind, point, inversion, duplication, deletion is the result of the process of DNA replication. When mutagenic factors alter DNA they frequently only affect 1 strand and the alteration they produce is frequently not a chemical conversion of a nucleotide to a totally different valid nucleotide but to a particularly chemically altered form of the original nucleotide or an aberant form of a different nucleotide (Alberts, et al, 2002).It is only when the DNA is copied and a new strand syntesised using the altered nucleotide as a template that a proper complementary nucleotide is introduced into the base pair, and only after a subsequent round of reproduction that a double strand will be produced with 2 properly complementary normal nucleotides.Arguably retroviral insertions don't require DNA synthesis, at least on the part of the host cell, but in the almost all classes of mutation rely on DNA synthesis, or replication, to effect a valid change in the coding sequence.That is why your distinction is arbitrary, because the processes you categorise in 1, 'radiation whatever', are also the result of your category 2 'mistakes made in the replication of DNA'.TTFN,WK