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If I sit in front of my monitor for a long time (most of the day), my eyes get really blurry. It usually happens at night, and it gets to the point where everything is blurry. When this happens, I rub them and then I can see fine....but 2 minutes later they go back to being blurry. Does this happen to a lot of people ?? Is it my monitor's refresh rate ??

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It's perfectly normal, and no, you aren't doing long term damgage to your eyes. You're suffering from eyestrain. The muscles that control the shape of your lens are simply worked beyond their limits. When this happens, it's time to quit, and go do something you don't have to focus on.
All muscles do this. Haven't you ever done an activity that so strained a particular muscle group that those muscles seemed limp, and difficult to control?
You can last longer at the computer by taking regular breaks, and letting your eyes relax by either closing them, or staring off into space without focusing on anything.
If you think it's bad now, wait until you get older
BTW, since you wear glasses, make SURE you get regular check-ups for your lens prescription. If your lenses are even SLIGHTLY off, your eyes will become strained much faster. Also, get "computer glasses." Ask your doctor about these. You measure the average distance from your eyes to to computer screen, and tell your doctor this distance. He then makes glasses unique for this purpose. My Mom got these (I don't wear glasses) and she is MUCH happier.