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There was a study done some three years back on the effect of meditation on the brain and it was observed that during meditation the brains of monks showed increase in brain waves called gamma waves during compassion meditation. There is a new book called Train Your Mind, Change Your Brain by Sharon Begley which has more details on the research in this area.

The question asked by the Dalai Lama was "Can mind shape brain matter" and the answer provided by neuroscientists was that physical states give rise to mental states and not the other way around. Now there is evidence that it can happen the other way as well.

Prof. Davidson then used fMRI imaging to detect which regions of the monks' and novices' brains became active during compassion meditation. The brains of all the subjects showed activity in regions that monitor one's emotions, plan movements, and generate positive feelings such as happiness. Regions that keep track of what is self and what is other became quieter, as if during compassion meditation the subjects opened their minds and hearts to others.

More interesting were the differences between the monks and the novices. The monks had much greater activation in brain regions called the right insula and caudate, a network that underlies empathy and maternal love. They also had stronger connections from the frontal regions to the emotion regions, which is the pathway by which higher thought can control emotions.

In each case, monks with the most hours of meditation showed the most dramatic brain changes. That was a strong hint that mental training makes it easier for the brain to turn on circuits that underlie compassion and empathy.

"This positive state is a skill that can be trained," Prof. Davidson says. "Our findings clearly indicate that meditation can change the function of the brain in an enduring way."[How Thinking Can Change the Brain]