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I have come across a sentence, in Crash Course Astronomy, which puzzles me because, as I think, the past perfect has been used in there instead of the past simple.(The sentence is at around 5:40.)

That all changed in 1999. A planet called HD 209458 had been discovered on a very short orbit around its star.

There is a time mark, and there was no any past event that went after the sentence linked to it. I guess the presenter have used the past prefect for emphasis. Tell me please if I am wrong.

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If, in 1999, you opened a copy of Scientific American in August 1999, you might find an article that saiid something like

A planet called HD 209458 has been discovered.

Present perfect is used rather than past simple because discovery has a lasting effect: once discovered, a planet generally stays discovered.

The speaker in this video is reporting what happened in 1999: he can't just use present perfect, otherwise it would sound like it just happened, so he backshifts and uses past perfect.

That all changed in 1999. A planet called HD 209458 had been discovered.

Using simple past in the sentence as it stands does not sound right, because it is missing a crucial piece of information: when it happened.

A planet called HD 209458 was discovered on a very short orbit around its star.

This could be rectified by merging the two sentences, so that the date is directly associated with the simple past:

That all changed in 1999, when a planet called HD 209458 was discovered on a very short orbit around its star.

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Tense usage, or article usage, or any-grammar-phenomenon usage for that matter, tells us about what the speaker means, in and of itself. It need not necessarily be supported by clues in the surrounding text.

In this case, things clearly changed after a certain discovery had been made. A planet is discovered (noticed), and only then is its orbit calculated and certain previously existing assumptions can be shattered (thus changing things).

That said, it wouldn't have been impossible to use Past Simple here—a speaker who would use Past Simple wouldn't have been pointing out this sequence, because it is in fact rather minor. This speaker kept the sequence in the back of his mind; that is why he chose the Past Perfect.

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