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Because the ocean basins really are short-lived features on geologic times scale, reconstruction the world’s geography by backtracking along the hot-spot trail works only for the last 5 percent or so of geologic time.

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    "or so" - imprecise but fairly close to correct; in this case, it means "about 5 percent of geologic time" – Violette Jun 27 '16 at 18:38
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Or so is an idiom that means "approximately". So the author is saying that this method works for approximately five percent of geologic time.

You see this idiom used a lot with numbers where the exact number is unknown or unimportant. For example,

He had asked a dozen or so people. ... At half past seven or so there would begin the buffet dinner...

Louie had seen a few tarantulas during his years in the business, although he couldn't recall one in the past ten years or so.

Digital photography has been in use for three decades or so...

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