In 1989 and 2003, the Vatican issued two documents: Aspects of Christian meditation and "A Christian reflection on the New Age," that were mostly critical of eastern and New Age practices. The 2003 document was published as a 90-page handbook detailing the Vatican's position.[287] The Vatican warned that concentration on the physical aspects of meditation "can degenerate into a cult of the body" and that equating bodily states with mysticism "could also lead to psychic disturbance and, at times, to moral deviations." Such has been compared to the early days of Christianity, when the church opposed the gnostics' belief that salvation came not through faith but through a mystical inner knowledge.[281] The letter also says, "one can see if and how [prayer] might be enriched by meditation methods developed in other religions and cultures"[288] but maintains the idea that "there must be some fit between the nature of [other approaches to] prayer and Christian beliefs about ultimate reality."[281] Some[which?] fundamentalist Christian organizations consider yoga to be incompatible with their religious background, considering it a part of the New Age movement inconsistent with Christianity.[289]
Later developments in the various Buddhist traditions led to new innovations in yogic practices. The Theravada school, while remaining relatively conservative, still developed new ideas on meditation and yogic phenomenology in their later works, the most influential of which is the Visuddhimagga. The Indic meditation teachings of Mahayana Buddhism can be seen in influential texts like the Yogācārabhūmi-Śāstra (compiled c. 4th century). Mahayana meditation practices also developed and adopted new yogic methods, such as the use of mantra and dharani, pure land practices which aimed at rebirth in a pure land or buddhafield, and visualization methods. Chinese Buddhism developed its own methods, such as the Chan practice of Koan introspection and Hua Tou. Likewise, Tantric Buddhism (also Mantrayana, Vajrayana) developed and adopted tantric methods, which remain the basis of the Tibetan Buddhist yogic systems, including the Six yogas of Naropa, Kalacakra, Mahamudra and Dzogchen.[251]
Similarly, Brahma sutras – the foundational text of the Vedanta school of Hinduism, discusses yoga in its sutra 2.1.3, 2.1.223 and others.[121] Brahma sutras are estimated to have been complete in the surviving form sometime between 450 BCE to 200 CE,[122][123] and its sutras assert that yoga is a means to gain "subtlety of body" and other powers.[121] The Nyaya sutras – the foundational text of the Nyaya school, variously estimated to have been composed between the 6th-century BCE and 2nd-century CE,[124][125] discusses yoga in sutras 4.2.38–50. This ancient text of the Nyaya school includes a discussion of yogic ethics, dhyana (meditation), samadhi, and among other things remarks that debate and philosophy is a form of yoga.[126][127][128]
According to Crangle, some researchers have favoured a linear theory, which attempts "to interpret the origin and early development of Indian contemplative practices as a sequential growth from an Aryan genesis",[53][note 4] just like traditional Hinduism regards the Vedas to be the ultimate source of all spiritual knowledge.[55][note 5] Thomas McEvilley favors a composite model where pre-Aryan yoga prototype existed in the pre-Vedic period and its refinement began in the Vedic period.[58]
Samuel states that Tantrism is a contested concept.[183] Tantra yoga may be described, according to Samuel, as practices in 9th to 10th century Buddhist and Hindu (Saiva, Shakti) texts, which included yogic practices with elaborate deity visualizations using geometrical arrays and drawings (mandala), fierce male and particularly female deities, transgressive life stage related rituals, extensive use of chakras and mantras, and sexual techniques, all aimed to help one's health, long life and liberation.[183][266]
^ "application or concentration of the thoughts, abstract contemplation, meditation , (esp.) self-concentration, abstract meditation and mental abstraction practised as a system (as taught by Patañjali and called the yoga philosophy; it is the second of the two sāṃkhya systems, its chief aim being to teach the means by which the human spirit may attain complete union with īśvara or the Supreme Spirit; in the practice of self-concentration it is closely connected with Buddhism". Monier-Williams, A Sanskrit Dictionary (1899)

There is no consensus on its chronology or specific origin other than that yoga developed in ancient India. Suggested origins are the Indus Valley Civilization (3300–1900 BCE)[44] and pre-Vedic Eastern states of India,[45] the Vedic period (1500–500 BCE), and the śramaṇa movement.[46] According to Gavin Flood, continuities may exist between those various traditions:
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Alexander the Great reached India in the 4th century BCE. Along with his army, he took Greek academics with him who later wrote memoirs about geography, people and customs they saw. One of Alexander's companion was Onesicritus, quoted in Book 15, Sections 63–65 by Strabo, who describes yogins of India.[107] Onesicritus claims those Indian yogins (Mandanis ) practiced aloofness and "different postures – standing or sitting or lying naked – and motionless".[108]
Alexander Wynne observes that formless meditation and elemental meditation might have originated in the Upanishadic tradition.[93] The earliest reference to meditation is in the Brihadaranyaka Upanishad, one of the oldest Upanishads.[67] Chandogya Upanishad describes the five kinds of vital energies (prana). Concepts used later in many yoga traditions such as internal sound and veins (nadis) are also described in the Upanishad.[59] Taittiriya Upanishad defines yoga as the mastery of body and senses.[94]
The origins of yoga have been speculated to date back to pre-Vedic Indian traditions; it is mentioned in the Rigveda,[note 1] but most likely developed around the sixth and fifth centuries BCE, in ancient India's ascetic and śramaṇa movements.[8][note 2] The chronology of earliest texts describing yoga-practices is unclear, varyingly credited to Upanishads.[9] The Yoga Sutras of Patanjali date from the first half of the 1st millennium CE,[10][11] but only gained prominence in the West in the 20th century.[12] Hatha yoga texts emerged sometimes between the 9th and 11th century with origins in tantra.[13][14]
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