the phylogeographic challenge to creationism

Strictly speaking, a "mutation" is any genetic sequence (or lack thereof) in an offspring that does not match the portion of genome inherited from its parent(s). A "copy error" simply means that the polymerase made a mistake during replication - what you are describing (a mutation that results in two copies of some DNA sequence) is a duplication mutation.Subclassifying is definitely useful, but it is all still mutation. Even whole chromosome rearrangments/translocations are mutations.

Right. Of course, if the host reproduces and passes along the retroviral insertion to its progeny, that is heredity.It is my understanding that even movement of a transpositional element already present in the genome is considered mutation.

Oh. My. God.(welcome, by the way.)

It does include most somatic mutations when you consider a daughter cell to be "offspring" of a parent cell (within the same organism); but to be clear I was specifically referring to mutation in the sense of heredity.In any case, you seemed to be using "mutation" to specifically refer to single nucleotide changes/indels, which is incorrect terminology. You seemed to originally be using "copy errors" (incorrectly) to designate "duplications" - These seemingly incorrect terms were the ones I wanted to clarify in my post; if this isn't how you were intending to use them, then it was a matter of miscommunication.Really, a mutation is any change in the genome, no? From a single nucleotide change to whole genome duplication, it's all mutation.

Now that is you overstating the case quite a bit. The only mutations that the offspring of sexual reproduction will receive are those that end up in the haploid genome of the sperm/egg cell that intiates that offspring (for example mutations in the development/maintenance of the germ line). Definitely not all of the mutations that the parent itself accumulates from inception - quite the opposite - an extremely small number of the parent's total mutations will be passed on to its offspring. But it is all mutation, and it seems that your arbitrary use of terms and distinctions is what is muddying the waters.After all, both "source changes" and "copy changes" are the result of "copy errors" using your definitions. (Talk about confusing things unnecessarily...)Is your own invented terminology or are you getting it from some other source? I sure as hell have never heard these terms before.

I don't know if arbitrary, but it seems incorrect?Both radiation and replication error are sources of mutation in both somatic and germ cells, so your splitting sources of mutation by "independency of reproduction" does not seem valid.Or do you mean single cell "reproduction" exclusively?

An excellent post, nwr, covering many important ideas concisely and understandably. I'll try to add some detail that hopefully you'll find interesting: Dobzhansky demonstrated this in the 1950's with fruit fly experiments. He took several pairs of fruit flies from a large colony and used them to seed new colonies - creating a series of severe bottlenecked populations. These bottlenecked populations consistently and rapidly became more phenotypically variable than the founder population, which stayed relatively stable. (This is one of those classic papers I wish I could find on-line...) Yes - this is called "normalizing" or "neutralizing" selection; that is, selection that maintains the status quo. Most species can be thought of as "optimized" given their long evolutionary histories - which is why we rarely directly observe beneficial mutations. That's when normalizing selection ceases - with a change to the environment. This is why our examples of recent beneficial mutations often are the result of new environments being created by man - mutations to resist pesticides or antibiotics, or to use a synthetic like nylon as a food source.