I don't know how to answer that, except to say what you describe sounds like a bad way to build a tower. If we agree for the sake of argument that the tower is leaning, and one day we *realize* it's leaning, what you seem to be suggesting is, "Well, we did all this work. Better than starting over!" and continuing to build on the unsound foundation. No, better to knock down anything we discover is wrong, hit those same questions we answered incorrectly before, and try to get it right.

> ...(2) a powerful entity would have had to deliberately create the genomes of all organisms humans have studied to make it *look* like creatures we think are related in specific ways really are...

Incidentally, if one accepts God in the first place, which one may or may not do, it's not such a big step to go from there to "creation according to a common plan." It seems to be less likely that the same God would create creatures utterly alien to one another to inhabit the same planet, than that this same God would play with variations on a common theme.

It's kind of like doubting the existence of Rembrandt because his paintings are composed of different colors of the same paint, instead of a little blue paint on the left, and a dresser drawer glued to the middle of the canvas, and the upper right corner permanently on fire, and a bit on the lower right that sounds like Bugs Bunny when you pull a string.

Come to think of it, that would be a pretty cool painting.