The user starts with a score of 100%. If the user got the card right, the score does not change. Otherwise it is reduced (can't rem the exact function for this - probably need to re-read the article).

If the player gives probabilities instead of choices, you can have him lose points equal to the log of the probability he assigned to what actually happened (minus the log actually, since it'll be negative). In that case giving honest probability estimates is the optimal strategy.