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The problem was that the Sun should output a lot more electron neutrinos then were measured. This meant that the model describing the interior of the Sun would be wrong, but it was working very well in predicting other things.

It was finally solved when something called neutrino oscillation was discovered. It turned out that (this might be a bit technical) the interaction state of a neutrino was not equal to its mass or propagation state. In short, this meant that electron neutrino's could become muon or tau neutrino's after a while (and change back again after that).

After this people began looking for muon and tau neutrinos coming from the Sun and together with the electron neutrino number they added up to the amount the Solar model predicted. The problem was thus solved; the Sun DOES output more electron neutrino's but some of these change into muon or tau neutrinos before they reach the Earth, and since we were initially only looking for electron neutrinos we missed some.

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