Evolutionary Tree

[SteveII]

However, if some genes say we are related to chimpanzees and some genes say we are not, and that conflict is not resolved, that would significantly weaken the theory of common descent. My point was and continues to be that if common descent is called into question in the long run, every other part of the overall Theory of Evolution (modern synthesis) that is not an observable fact (in the strong sense of the word) is undermined (which is most of it).

So your point is one huge argument from ignorance. Gotcha.

No, my point was to have a discussion on what happens to the overall Theory of Evolution (modern synthesis) if the theory of Common Descent is permanently undermined due to unresolved gene conflicts. I offered my opinion that if common descent is permanently undermined, everything we have inferred about the overall theory is called into question. In light of feedback and further reflection, it does not matter to the question whether Common Descent is an assumption or a conclusion--only that it is intertwined in many of the sub-theories. The question remains unanswered unless your answer is that it cannot be wrong--in which case that is not a very scientific position.