I really don't see what the problem. If things were quite different, the theory would be quite different or completely replaced by something that could deal with the observations. If there were no nested hierarchies, the Theory of Evolution would have to change to reflect that but the resultant theory would probably not resemble the current one all that much. It may have the same name but it would not be the same theory.
There is a moderate amount of plasticity in the current TOE but that is about it so whats the problem?
Dizredux
The problem is that we were going to have a "Theory of Evolution" no matter what the data was.
Evolution is a religious creation story that steamrolled its way into the scientific institutions while progressively enveloping itself around the data... all while being carefully protected from potential falsification itself.
It is a cunningly devised fable (2 Peter 1:16) to lead people away from the truth of the Bible and Jesus Christ.
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