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Scientifically the thoughts are generated from brain. However in spiritual world, from where do they originate?

Also in case if the source of thoughts isn't in one's own control, then why many scriptures talk about controlling thoughts?

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Commentaries on Verse 2, Samadhi Pada of Patanjali Yoga Sutras describe sources for thoughts and Mind stuff in detail and best one would be Vyasa Commentary. Pandit Usharbudh Arya translated it into English but i can't post it here as it is in copyright.

Swami Vivekananda also explained Patanjali Yoga Sutras in detail. Chitta (mind stuff) shows effect on force (explained in commentary in detail) and it is presented at end as "thought". Swamiji explains words like chitta (mind stuff), Vritti (whirlpools or thought waves), Buddhi (determinative factor), Ahamakara (egoism) in detail.

Here is what Swamiji said on verse 1.2.

योगश्चित्तवृत्तिनिरोधः ॥२॥

yogaś-citta-vṛtti-nirodhaḥ ||2|

Yoga is restraining the mind-stuff (Chitta) fromtaking various forms (Vrttis)

Commentary:

A good deal of explanation is necessary here. We have to understand what Chitta is, and what are these Vrttis. I have this eye. Eyes do not see. Take away the brain centre which is in the head, the eyes will still be there, the retinæ complete, and also the picture, and yet the eyes will not see. So the eyes are only a secondary instrument, not the organ of vision. The organ of vision is in the nerve centre of the brain. The two eyes will not be sufficient alone. Sometimes a man is asleep with his eyes open. The light is there and the picture is there, but a third thing is necessary; mind must be joined to the organ.

The eye is the external instrument, we need also the brain centre and the agency of the mind. Carriages roll down a street and you do not hear them. Why? Because your mind has not attached itself to the organ of hearing. First there is the instrument, then there is the organ, and third, the mind attachment to these two. The mind takes the impression farther in, and presents it to the determinative faculty—Buddhi—which reacts. Along with this reaction flashes the idea of egoism. Then this mixture of action and reaction is presented to the Purusa, the real Soul, who perceives an object in this mixture. The organs (Indriyas), together with the mind (Manas), the determinative faculty (Buddhi) and egoism (Ahamkara), form the group called the Antahkarana (the internal instrument). They are but various processes in the mind-stuff, called Chitta. The waves of thought in the Chitta are called Vrtti (“the whirlpool” is the literal translation).

What is thought? Thought is a force, as is gravitation or repulsion. It is absorbed from the infinite storehouse of force in nature; the instrument called Chitta takes hold of that force, and, when it passes out at the other end it is called thought. This force is supplied to us through food, and out of that food the body obtains the power of motion, etc. Others, the finer forces, it throws out in what we call thought. Naturally we see that the mind is not intelligent; yet it appears to be intelligent. Why? Because the intelligent soul is behind it. You are the only sentient being; mind is only the instrument through which you catch the external world. Take this book; as a book it does not exist outside, what exists outside is unknown and unknowable. It is the suggestion that gives a blow to the mind, and the mind gives out the reaction.

If a stone is thrown into the water the water is thrown against it in the form of waves. The real universe is the occasion of the reaction of the mind. A book form, or an elephant form, or a man form, is not outside; all that we know is our mental reaction from the outer suggestion. Matter is the “permanent possibility of sensation,” said John Stuart Mill. It is only the suggestion that is outside. Take an oyster for example. You know how pearls are made. A grain of sand or something gets inside and begins to irritate it, and the oyster throws a sort of enameling around the sand, and this makes the pearl. This whole universe is our own enamel, so to say, and the real universe is the grain of sand. The ordinary man will never understand it, because, when he tries to, he throws out an enamel, and sees only his own enamel.

Now we understand what is meant by these Vrttis. The real man is behind the mind, and the mind is the instrument in his hands, and it is his intelligence that is percolating through it. It is only when you stand behind it that it becomes intelligent. When man gives it up it falls to pieces, and is nothing. So you understand what is meant by Chitta. It is the mind-stuff, and Vrttis are the waves and ripples rising in it when external causes impinge on it. These Vrttis are our whole universe.

The bottom of the lake we cannot see, because its surface is covered with ripples. It is only possible when the rippled have subsided, and the water is calm, for us to catch a glimpse of the bottom. If the water is muddy, the bottom will not be seen; if the water is agitated all the time, the bottom will not be seen. If the water is clear, and there are no waves, we shall see the bottom. That bottom of the lake is our own true Self; the lake is the Chitta, and the waves are the Vrttis.

Swamiji later explains Satva, Rajas and tamas Gunas and how they occur. So, Thoughts or Vrittis occur in Chitta.

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