I think we're coming to the crux of the issue. Most people have a different understanding of what Darwinian theory is than you do. His theory is based on natural selection. That phrase was coined specifically to distinguish it from the type of selection that gets used in, say, breeding dogs.
In one million years, will whatever is doing paleontology think that dogs are not the result of natural selection? Do you think aphids don't evolve by natural selection because they are kept as slaves by ants? I guess I don't much care how civilians divide up the world into natural and unnatural selection. By this classification scheme, I guess I'm supposed to conclude that when asian flu evolves a new strain in the pigs and chickens and peasants of China, that it wasn't natural selection because humans built the henhouses and pigstys.
Insofar as scientifically meaningful distinctions go, if something happens to a genome due to variation and selection, that pretty much makes it a case of Darwinian Evolutionary theory in action. that pretty much