A crucial aspect to this matter is that the actual meaning of the word theory in a scientific sense (based on observation and on the scientific method) doesn't have anything to do with its meaning in common parlance; the colloquial meaning of theory would be equivalent to the concept of a mere hypothesis or conjecture in science.
So in science, a theory is formulated precisely because there is evidence to support it.
And it can be observed and measured too; a greater genetic difference is observed between species, the more apart they are .
And repeated; mutation/selective pressure on bacteria and viruses leading to different strains, etc.
So even if the fossil record disappeared in a puff of smoke, the genetic evidence would lead to the same conclusions (branching apart more and more the further apart two species are in evolution).
And all fossils are transitional. Even the bones in the graveyard are transitional.
That's just my basic understanding of it.
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