The First Stage
The first thing that the meditator experiences is his ever-arising, distracting thoughts. He discovers that his mind is so ungovernable that he can hardly control it even for a very short period of time. Errant thoughts flow on and on like a waterfall, without halting for a single moment. The tyro [novice] feels that he has many more distracting thoughts than ever before – meditation seems to have increased, rather than lessened, them.
Many beginners are seriously baffled and disheartened by this initial experience. In their frustration they begin to doubt the effectiveness of their meditation practice, and become skeptical about the very possibility of attaining Samadhi. Some then change their meditation techniques from one type to another, and end up in utter despair, finally giving up their practice altogether.
The truth is that distracting thoughts are never increased by meditation; meditation only makes one more aware of them. Only a quiet mind can become aware of this thought-flux, which up to now has always been flowing on practically unnoticed. Therefore, this meditation experience is a sign of progress, not of regression. It is said that if the meditator has really gained some progress in his meditation, he may experience many thoughts which come and go within a fraction of a second. This fact has been testified to by Buddha himself, in the Sutra of the Elucidation of the Hidden Profundity.  [Endnote 4-6]
[1. The most important of the Yogacara Sutras. en.wikipedia.org/
The Alaya [Adana] Consciousness is very subtle and profound;
In it all the Seeds flow on like pouring torrents.
I do not introduce this Consciousness to fools and ignoramuses,
For I am afraid that they might cling to it as the True Self.
According to the philosophy of Yogacara, the ever-arising thought-flux experienced in meditation is the bringing-into-play (Chinese: hsien hsing) of the "Impression-Seeds" that have so far been unnoticed in the Store (Alaya) Consciousness. These "Seeds," infinite in number, unlimited in range, and well-preserved in the depository of the Alaya consciousness, are the essential material constituting the basic framework of the human mind. The entire realm of Sangsara is upheld by this Alaya Consciousness and is set in motion by these "Seeds."
The work of meditation is, first, to recognize the action of the "Seeds" which manifests itself as thought-flux; second, to halt the propulsive workings of the Seeds; and finally, to transform or sublimate them into the infinite capacity of Buddhahood. Therefore, one should not be discouraged by the discovery of this ungovernable thought-flow, but continue his meditation practice until he reaches the state of Samadhi.
The Second Stage
If the yogi disregards the initial difficulty of controlling his errant thoughts and meditates perseveringly, he will gradually become conscious of a lessening of the thought-flow, and find it much easier to control than before. In the beginning, wild thoughts gush forth like torrents; but now the flow begins to move slowly like gentle ripples on a wide, calm river. When the yogi has reached this stage, he will probably encounter many unusual experiences; he will see strange visions, hear celestial sounds, smell fragrant odors, and so forth. Most of these visions, according to Tantric analysis, are produced by the Pranas stimulating the different nerve centers. Many of them are of a delusory nature. The yogi is repeatedly warned by his Guru that he should never pay any attention to them; otherwise he will be misled and go astray. The story told below is a typical example of the delusory visions that one is subject to in this second stage of meditation.
On the outskirts of the Par Pong Lamasary in the Derge district of Eastern Tibet, there was a small ashram called the "Meditators' House," where dwelt thirty-six Lama yogis who had vowed to meditate for three years, three months, and three days without stepping outside of the ashram boundary, or sleeping lying down on a bed, or seeing or talking to anyone except their Guru and their fellow meditators at certain limited times. An absolute silence was maintained in the ashram at all other times, and strict discipline was observed.
At the end of the three years, three months, and three days' period of meditation, a great "graduation" celebration was held, in which all the monks in the monastery and the people in the village took part. Then, after the necessary preparations, the next class began. This program had been carried on for over two hundred years in the Lamasary of Par Pong.
In 1937 I studied there for some time, and had an opportunity to talk with a Lama who was one of the "graduates" of the Meditators' House. He told me the following story.
"In the middle of the fifth month of my stay in the House, one day, during my meditation, a spider appeared at a distance of a few feet from my nose. I did not pay any attention to it at the time.
"A few days passed, during which the spider did not vanish, but came closer and closer to my face. Annoyed by its constant presence, I tried in many ways to get rid of it. First, I meditated on Compassion – sending all my good will to the spider; but it would not go away. Then I called for help from the Protector-of-Dharma, and recited his fierce Mantrum in the hope of exorcizing the spider, but that was not effective either. Then I tried to meditate on the illusoriness of all beings, and to understand that this spider was not real, but merely a figment of my own imagination. Even this was of no use.
"A few more weeks then passed, in which, despite all my efforts to drive it away, the spider grew larger and larger, and moved closer and closer to my nose. Eventually it became so large and so close, and frightened me to such an extent, that I could no longer meditate. I then reported the whole experience to my Guru.
"He said to me smilingly, 'Well, it seems that you have tried everything that can possibly be done. I don't think there is anything I can do for you in this case. What would you do next?"
"This so upset me that I said, 'If nothing can help, I have no choice but to kill the spider with a dagger, for as things now stand I cannot meditate nor can the spider derive any benefit from me. Although killing any sentient being is a crime forbidden by our Lord Buddha, the important thing now is that I cannot carry on my pursuit of Enlightenment due to this hindrance. I thus fail both myself and the spider. On the other hand, if I kill the spider, my hindrance will be overcome. Then once more I will have a chance to win Enlightenment, which will certainly bring true happiness to all concerned.'
"My Guru answered, 'Do not be in a hurry! Do not kill the spider today. Wait until tomorrow. Now listen carefully, and do what I say. Go back to your room and meditate again. When the spider appears, mark a cross on its belly with a piece of chalk. Then come back here and see me once more.
"I followed his instructions and, upon the appearance of the spider, marked the cross on its belly as he had bidden me. Then I returned to his room and said, 'Dear Lama, I have done as you told me.'
"My Guru replied, 'Now, let down your apron!' I was very puzzled, but obeyed him. Thereupon he pointed to the lower part of my belly, and said, 'Look for yourself!' I lowered my head and looked. There, to my astonishment, I saw a cross marked in chalk! If I had stabbed the supposed spider, I would have killed my-selfl"
The Third Stage
Thus, if the yogi pays no attention to distracting thoughts, physical discomforts, delusory visions, or other forms of impediment, but persists in his meditation, he will eventually achieve the longed-for accomplishment, and reach the state of Samadhi. From there he may take up the more advanced practice of Prajnaparamita and set his feet on the journey toward Buddhahood.
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