As a terminal lurker, I wish this discussion had taken a different direction. It's an interesting discussion and everyone has brought up (mostly) good points, but for someone coming to the site for the first time and seeing "Introduction to Genetics", this ain't it. The actual frustration stems from, well, go back and reread the first post. This thread was created in response to Faith's questions about genetics and how we can determine ancestry, taxonomy, how morphology relates to genetics, etc. Anyone with an understanding of genetics and experience in education can see from how the questions are formed that what is really needed is exactly, an Introduction to Genetics. What DNA is, how it's replicated, what can go wrong in replication, that mutations aren't 'something breaking', that it is all just chemistry. Everything from replication to translation to a cute little six-toed kitten, it's all just chemistry.
Implicit in the original post's questions are many basic misunderstandings, and they are not and will not be addressed in the direction this thread has progressed. The original questions evoke a world where one creature has a genetic environment that is qualitatively different from that of another, that genes are quantized entities that are fractured by mutations...these are easily addressed once someone has a basic understanding of the structure of DNA. Questions like, where does "Junk DNA" come from, how do you determine relatedness of close family members, are all well-understood once you can grasp basic genetics. Now, once that evidence is presented, it doesn't mean that it won't be rejected out of hand, but at least statements like Taq's regarding mutations will have context, rather than being treated like non-sequiturs.
Again, this has turned out to be an interesting discussion, but I think Dr A's proposed series (Message 3) on introductory genetics will do a lot to raise the level of question and debate in the area of ancestry, mutations, and how things actually work. Carry on.