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The first overall context is Milton's CLAIM that there isn't enough hard evidence in existence to remove ToE out of the theory category and into established fact. Part of the basis of this claim is his belief that contrary to popular opinion there is a paucity of transitional bones proving that mankind evolved from an ape/common ancestor. In fact, Milton says the glass case at Kensington is still empty.
Just a reminder. Neo-Darwinian Evolution is not "just" a theory. In science a theory is a generally accepoted best explanation to a problem. Theory has a far stronger meaning in science than in common useage.
Theories do not "grow up" to become facts: they remain provisional, like everything in science
including facts.
However, both the fact of evolution and the theory explaining it are amongst the most securely established in science.
For Whigs admit no force but argument.