Evolutionary Tree

[Esquilax]

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.

The trouble is that you're committing the same mistake that every other ID proponent does: you're going negative, when you'd need to go positive.

"We don't know X, Y and Z, we can't resolve this conflict" is not, and will never be, an argument against a theory in science. The reason for that is that theories don't come into existence based on nothing, they arise as the natural consequence of reams and reams of data, from which an explanatory framework for that data can be made which is probabilistically the best fit.

Scientific theories are models that explain things, and they're always incomplete because our knowledge is incomplete. Saying "you can't explain that!" and "evolution doesn't tell us this!" might be viscerally pleasing to your gut, but it doesn't carry the epistemological heft you seem to think that it does. You aren't going to topple this tower in this way: removing three or four bricks, or pointing out a gap here or there, does not erase the foundational observations that constitute the theory of evolution as a whole. At best, you'd be providing something that would subject the theory to revisions, which is something that's already happened multiple times, none of which required that we scrap the entirety of the theory and rediscover everything again.

Evolution would still be the best explanatory model for the phenomenon we've observed even if you took apart common descent, so you're barking up the wrong tree to begin with, but the real trouble is that you're attempting to bark up a tree simply by pissing on another, unrelated tree. It's not going to work, no matter how many arguments from ignorance you chain together.