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Science is unique. Instead of making guesses, scientists follow a system designed to prove if their ideas are true or false. They constantly reexamine and test their theories and conclusions. Old ideas are replaced when scientists find new information that they cannot explain.

What do "they" in the last sentence refer to? Old ideas or scientists? Or could it mean both?

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It could mean both but I take meaning from the context. The reader is given a forceful sequence (almost a cadence) of notions: scientists; their ideas; they reexamine; they test; they replace; they find. Why break the sequence by suddenly assuming that they cannot explain refers to ideas?

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There is indeed a syntactical ambiguity within the sentence, but that ambiguity does not affect its overall point, as there is no real difference between saying

the old ideas cannot explain it

and

the scientists cannot explain it [by using these old ideas].

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