Comment by l33tman

It reflects the fact that the measurement apparatus, environment in general and the observer in particular are all also part of the "wave function". Until these are linked to the system to be observed (like the proton), the system has to be analyzed as the full set of possible configurations of its constituents.

After you link it up with the apparatus, it is pulled into the system as a new part of it, and so on. The more stuff you pull into the system, the less number of different configurations you sum over, eventually you end up with a single configuration with an observer that has a clear measurement result in her mind. This process is what is called "wavefunction collapse" in old physics texts (and a lot of modern pop-sci accounts).

What sets this apart from other purely probabilistic theories is that it's non-local, the entire linked system from the proton to the measurement apparatus to the observer has to be taken into account in the calculations if you are to be thorough. In local theories you can separate the parts of the system and handle them separately, like you could say "there is a 1% probability that a charm quark pops out in the upper left part of the proton every second" etc. You can't really do this in QM/QFT, and this is what in essence leads to all of the counter-intuitive results and confusion..