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1) The scientists used the method in numerous studies until 2000.
2) The scientists used the method in numerous studies by 2000.
Better title hint: The scientists used the method....
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Method 1 is the normal way to test for something, but it's time consuming and expensive. Someone, in the year 2000, found Method B. It was better. Now, in 2012, we can say that scientists used method 1 in many studies until 2000. The understanding is that after 2000, they used something else. (Or maybe they just stopped doing studies.)
For a long time, no one knew how to do something that would allow results to be compared. Then, in 1999, someone figured out a way that would allow everyone to do things the same way. It was so popular that scientists had used the method in many studies by 2000. (It only took one year for it be used many times.)
I'm not a teacher, but I write for a living. Please don't ask me about 2nd conditionals, but I'm a safe bet for what reads well in (American) English.