Note that we didn't call it junk DNA until we learned a whole lot about how DNA works and formulated a theory in which junk DNA doesn't do anything for good reasons. In a way, lack of understanding prevented us from calling it junk DNA earlier.
Of course it's still possible for the theory to be wrong and the so-called junk DNA being actually important. It's only junk according to our classical, non-quantum and non-relativistic theory of junkiness.
Note that we didn't call it junk DNA until we learned a whole lot about how DNA works and formulated a theory in which junk DNA doesn't do anything for good reasons. In a way, lack of understanding prevented us from calling it junk DNA earlier.
Of course it's still possible for the theory to be wrong and the so-called junk DNA being actually important. It's only junk according to our classical, non-quantum and non-relativistic theory of junkiness.