Part of the problem with flipping a coin is that it's not uncommon to flip badly. If you don't flip correctly, you will be wobbling the coin, rather than spinning it. This introduces a bias where it is more common for the starting side to come up. I can't find the original article I read, but this one has a little bit on it. Check out this article.
In experiments, the researchers were surprised to find that it's difficult to tell from watching a coin whether it has flipped. A coin toss typically takes just half a second, with the circumference of the coin whizzing around at 3 meters per second. What's more, the coin's spin makes it wobble, often creating the illusion that the coin has flipped.
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