Cytachrome C and neutral drift

Hi judge,I think this is an important point - the reason Cytochrome C is commonly used to examine common descent doesn't really have anything to do with whether or not genetic change is exclusively the result of neutral drift.The reason Cytochrome C is used is because it is required for life in all prokaryotes and eukaryotes, and is simply available for comparison. That is, most other genes would simply not exist in a portion of the "Tree of Life", and thus would make analysis of the Tree of Life incomplete.Also, Cytochrome C is not the only gene used to examine common descent; other genetic data is used. Perhaps more importantly, the examination of common descent does not require solely neutral mutations. In fact, researchers have little way of knowing if mutations are detrimental, beneficial, or neutral - unless they perform extensive functional studies, and these are not done for most such common descent studies.In any case, the existence of a detrimental or beneficial mutation in two related species is just as much evidence for common descent as a neutral mutation. An oft-cited example is the "GLO" gene, which is mutated to non-functionality in four known species - fruit bats, guinea pigs, chimps, and humans. Humans and chimps have an identical detrimental mutation in the GLO gene, which is a different mutation than the one in the GLO gene of the fruit bats and the guinea pigs. This is evidence for humans and chimps being more closely related than to other species without that specific mutation. Thus a non-neutral mutation also can demonstrate common descent.Perhaps you are confusing the idea of determining the "molecular clock" with that of determing common descent. The molecular clock method does use assumed neutral mutations to determine when two species diverged from a common ancestor (but not whether or not they did so...)Hopefully this is helpful, let me know if you have questions.