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What science does know for a fact is that the brain is not a static organ. In many of the experiments done, scientist have the ability to see how the brain can change its response to how it is being used both in structure and in function.
For example; if something happened that made you feel angry you could do one of two things. You could focus your attention on those angry feelings to the point where you want to be violent, even if you are not a violent person. Or you could focus you attention on letting go of the event that brought on the angry feelings by focusing on things that bring you peace. Eventually you will feel peaceful.
The reason is simple; when meditation is practiced over and over again the person develops a routine of relaxing the mind and body. They also learn to focus their attention instead of allowing the mind to wander. The mind becomes more and more peaceful and the number of negative thoughts, fears, worries and anxieties subside bringing the person who is experiencing these negative feelings the ability to have more happiness and peace arise within.