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The loss of useless parts is observed, as Joe pointed out. That's all scaffolding is.

It is not observed. It is speculated. If it were observed, we wouldn't be having these discussions. Scaffolding is just another evolutionary "meme" without testable, verifiable evidence.

It has been observed indirectly. (Examples are already given in this thread : penguin fins, whale fins, parasite organs, cave fish eyes etc...) Why would you simply reject observations like this ? Sometimes celestial objects are discovered by indirect observation also. Even though the object cannot be "seen" because all its radiation is blocked or too weak to be captured by telescopes, astronomers sometimes notice deviations in the motion of other visible bodies. Often they will be able to propose the presence of an invisible body by calculation and comparison of the theoretical results with the observed perturbations. An astrologist could of course claim that the perturbations are caused by supernatural forces. He is perfectly free to refuse all natural solutions, no matter how logical and consistent with the theory of general relativity they are, as long as the hidden body is not "seen". If on top of that, he himself cannot produce any concrete observation for his own supernatural explanation, he should not be surprised if the rest of the astronomical world is reluctant to accept his claim.
Probably most or all sciences use indirect proof at some level. It's a perfectly valid method to gather data.

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