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That also means that there is a potential falsification about the prediction of ToE (not the whole theory)within the DDME development. For instance what if the DDME was found in the earliest mammals. This would be in conflict with the ToE, Right?
You're expecting to work out an awful lot without fossil evidence (or an adequate substitute).
The theory of evolution does not say that the mammalian middle ear evolved in mammals, rather than in their pre-mammalian ancestors - just feathers evolved in the dinosaurian ancestors of birds. In that case the DDME would be found in the very earliest mammals, as feathers are found on the earliest birds. The question is simply not resolvable on purely theoretical grounds.
A better potential falsification would be if there were no evolutionary route to the mammalian middle ear from any potential ancestors. As the article points out, that was once thought to be the case, but the discovery of intermediate forms proved otherwise.
And that is a very strong confirmation of evolution - if evolution were false there is no good reason why these intermediates should exist.