The issue is not so much the presence or absence of thought activity during meditation. Rather, the issue is the degree to which ones thought activity is driven, unconscious and fixated.
The great majority of human beings are literally addicted to thinking. Even the most wretched substance abuser can go a few hours between "fixes," but most human beings cannot abide even for a few seconds without some sort of "thought fix." If there's nothing significant to think about, we fill the void with fantasy and trivia.
Simply stated, meditation breaks the addiction to thinking. One is then in a highly desirable situation. When you want to have a complete experience of hearing and feeling (for example as you listen to music), you can do so without being compulsively pulled into thoughts which are not relevant to the music. When you want to have a complete experience of tasting and feeling, as when enjoying a bite of food, you can likewise do so. On the other hand, when it is appropriate to think, you find that your thinking abilities are vastly improved. This improvement in thinking stems from two causes. The first is easy to understand. The second is a little subtle.
Breaking the compulsion to think simply means that the thinking process is no longer scattered by distracting forces. So when you turn your mind to some topic, you can penetrate that topic with great clarity and vigor. To draw a metaphor from the physical world, when thinking is no longer at the mercy of scattering forces, it becomes like a penetrating beam of coherent laser light. I'm quite convinced that this aspect of meditation makes a person a better student and problem solver and may actually raise ones IQ.
Now for the second, more subtle way that meditation improves ones thinking abilities. Here once again a metaphor may be helpful. When a person works through a compulsive eating problem, they certainly don't stop eating. In point of fact they are able to taste and appreciate their food in an entirely new way. Analogously, when a person works through the compulsive need to have answers, the answers begin to come in an entirely new way. The thinking process becomes spontaneous and intuitive. Personal and spiritual insights well up effortlessly of their own. At this point there is no need to stop the thought process in order to be in a state of meditation because the thought process itself has returned to being part of the effortless flow of nature.
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