A "mantra" in seed form (bijaskara) is used in yogic meditation as a 
mnemonic device for transcending, to go beyond the the limitations of 
sense perception, in order to experience a fourth state of 
consciousness, which is beyond mere suppositions and discursive 
dialectic; a state of Creative Pure Intelligence, the ultimate, absolute 
reality. According to MMY, the absolute is "knowledge structured in 
consciousness."

So, let's first review what we know so far:

According to MMY, writing in "Beacon Light of the Himalayas" (1955), the 
purpose of the TMer mantras are to fetch the grace of the Hindu gods. 
The Shankaracharya tradition is the custodian of the mantras used in the 
practice of TM. This has been confirmed by SBS, who stated in many 
satsangs that the mantras used in the Shankaracharya tradition are for 
the purpose of establishing an affinity with "istadevata", that is, a 
personal god, represented by the mantra such as Ram, Shyam, Saraswati, etc.

And, it has been established that the mantras given out in TMer 
initiation came from the tradition followed by SBS, from whom MMY 
received the mantras after sitting at the feet of the master. We now 
know that the mantras used by SBS came from his guru, SKS, a Saraswati 
Sannyasin of the Sri Vidya sect, headquartered at Sringeri which founded 
by the Adi Shankara in 810 AD.

The Sri Vidya in turn originated in Kashmere and is related to the 
monist Trika philosophy of Kashmere Tantrism. The Adi Shankara visited 
Kashmere in 811 AD and was initiated into the shakti tantra sect, 
obtaining the Sri Yantra mandala, symbol of the Hindu Goddess 
Tripurasundari (Saraswati), which he then placed on the mandir of 
numerous sacred temples which he founded such as at Sringerimatha, at 
Kanchimatha, and at the Jyotirmatha.

Main purpose of mantra:

There are numerous uses for mantra, such as for protection, 
purification, propitiation, supplication, material gain, and for 
identification. One of the oldest uses of mantra is for clearing the 
atmosphere of malevolent entities, such as for the dedication of 
religious edifice architecture and for preparing the home and hearth for 
human habitation.

But, without doubt, the highest and most pure use for mantra is for the 
purpose of yogic identification with the God of yogins - Ishvara, the 
Transcendental Person, mentioned in Yoga Sutras by Maharishi Patanjali.

So, the main purpose of the mantra is "identification" with istadevata 
in deep meditation, called "dhyana" in Sanskrit. According to Sri Vidya, 
there is no difference between the name of istadevata, and istadevata 
Herself - they are one and the same. By invoking the name of the 
istadevata with mantra, the personal god manifests in the heart (chakra) 
of the sadhak, thus providing the ideal opportunity for the transcending.

According to Brooks, "The srividya, because it consists of 
"indestructible seed" syllables (bijaksara) rather than words, 
transcends such "mundane" considerations as semantic meaning. 
Accordingly, a bija-only mantra is not merely esoteric but inherently 
superior. Because it is purely seed-syllables [bijasaras] it is the 
purest form of mantra. It does not make a request or praise god, it is 
God's purest expression. Gayatri is great but it cannot match Srividya 
because it is still in language; it is Veda and mantra but when 
transformed into the Srividya its greatness increases."

According to Susan Shumsky, a famous TM Teacher, "Within the triangle is 
the mantra known as vagbhava bija (guru seed mantra) aing. This mantra 
embodies an aspect of supreme consciousness."

So, to sum up:

Yoga meditation is a technique that is common all over India, especially 
in the sect of the Sri Vidya and the Kashmere Trika. In that tradition 
they meditate on the bija mantra of Trupurasundari (Saraswati). It's the 
same bija mantra given out in TM initiation. It's the same technique - 
it's a meditation using a bija mantra for the attainment of Absolute 
Knowledge through yogic means (dhyana, mantra, japa, mandala, and puja).

We can assume that the MMY learned meditation from his Master, Swami 
Brahmananda Saraswati who was intiated by his guru, Swami Krishnananda 
Saraswati. All the gurus in the Saraswati lineage meditate on the bija 
of Saraswati at least twice every day. Their headquarters is at Sringeri 
in Karnataka, India.

According to the Shankaracharya of Jyotirmath, H.H. Swami Vasudevananda 
Saraswati, the meditation technique used in TM first originated with the 
Vedic sage Naryana and was passed down through a long line of sages 
including Shakti, Parashara, and Badarayana. It's the same meditation 
that is used by all the Shankaracharyas in that spiritual lineage.

According to Vedanta, Saraswati is considered to be the feminine energy, 
or Adi Shakti of Brahman. Sri Vidya is thus the "Auspicious Wisdom" 
which has three "cities" - waking, dreaming, and deep sleep, and another 
state termed "turyia", which indicates a fourth state beyond the three 
gross states. In Advaita Vedanta, Brahman is considered to be 
Transcendental Absolute. The main religious scripture of the Sri Vidya 
is the Sound Arya Lahari composed by the Adi Shankara which has fifteen 
bija mantras enumerated by the Adi.

"May the Goddess Saraswati, with all power, full of power, further us, 
as the guide of our minds." - Rig Veda VI. 61.9, 11, 3

Works cited:

'Sound Arya Lahari'
Composed by Adi Shankaracharya

'Man Dukhya Karika'
Composed by Sri Gaudapadacharya

'Yoga Sutras of Patanjali'
Commentary by Sri Veda Vyasa

'The Secret of the Three Cities'
by Douglas Renfrew Brooks
p. 95

'Exploring Chakras: Awaken Your Untapped Energy'
by Susan G. Shumsky and K. S. Charak

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