- By 2008, the percentage of students choosing science subjects had decreased markedly.
Why don't we use "in" instead? I'm a non-English native speaker, and I don't know the differences between those two prepositions when they go with year.
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'In' as applied to a year refers to something which occurs or occurred in that year. For example "The last London Olympics took place in 2012". 'By' has the meaning of 'up to' or 'up to and including'. For example "The internal combustion engine was invented in the late 19th century and by 1930 was the main power source for mechanised road vehicles".
The use of 'by' in the quotation you gave suggests that the there has been a decline in the percentage of science students over a number of years. If 'in' had been used it would have implied that the decline took place between 1st January 2008 and 31st December 2008.