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Sakya Explanation
The mainstream Sakya tradition asserts, in a similar manner to Gelug, that when clear-light mental activity is manifest, it gives rise to only pure appearances (dag-pai snang-ba). The habits (bag-chags) of unawareness (ma-rig-pa, ignorance) imputed on the clear-light mind do not give rise to impure appearances (ma-dag-pai snang-ba) at that time. They only give rise to impure appearances when clear-light mental activity is not manifest. In this context, impure appearances refer to appearances that are not beyond words and concepts, while pure appearances refer to appearances that are beyond words and concepts. Sakya calls clear-light mental activity the "causal alaya continuum" (kun-gzhi rgyui rgyud, the causal everlasting continuum of the all-encompassing foundation) and the "ultimate alaya" (mthar-thug-gi kun-gzhi, ultimate all-encompassing foundation). It is the ultimate foundation or source of both impure and pure appearances as defined above. Gelug does not apply the term alaya to clear-light mental activity. Sakya does not explain alayavijnana, then, as a source of impure appearances distinct from the causal alaya continuum. With the attainment of enlightenment, the alayavijnana transforms (gnas-gyur) into the causal alaya continuum, but not in the manner in which a seed transforms into a sprout. Both the alayavijnana and the causal alaya continuum have been ever present before enlightenment. With the attainment of enlightenment, only the causal alaya continuum goes on. The continuity of the alayavijnana ceases.
The provisional alaya (gnas-skabs-kyi kun-gzhi, provisional all-encompassing foundation), uniquely asserted by Sakya, refers to the four mandala-seats (gdan dkyil-khor bzhi): 1. 2. 3. 4. energy-channels, subtle syllables within them, creative energy-drops, energy-winds.
Based on these, the appearance-making aspects (gsal-cha, clarity) of ultimate alayas produce two inseparable quantum levels of appearances of our bodies, speech, minds, and the inseparable simultaneity of the three. The two quantum levels are their gross appearances in our usual human forms and their subtle appearances as Buddhafigures. In this context, impure appearances refer to the former and pure appearances to the latter. The provisional alaya ceases with the attainment of enlightenment and the four mandala-seats transform into the four Buddha-bodies.
Nyingma Explanation
The Nyingma tradition differentiates basis pure awareness (gzhii rig-pa, basis rigpa), as the primordial deepest alaya (ye-don kun-gzhi, primordial deepest allencompassing foundation) from the alaya for constant habits (bag-chags-kyi kungzhi, all-encompassing foundation for habits). The latter is synonymous with alayavijnana. Before enlightenment, the everlasting continuum of basis rigpa has with it a factor of dumbfoundedness (rmongs-cha). This factor is equivalent to the unawareness of not knowing how rigpa exists a type of unawareness included within unawareness regarding all phenomena and preventing omniscience. Because of this factor of dumbfoundedness, basis rigpa functions as an alaya for constant habits and, through a complex mechanism, produces impure appearances, not beyond words and concepts, during conceptual and nonconceptual cognition with limited awareness (sems).
When we access essence pure awareness (ngo-boi rig-pa, essence rigpa), which is the primal purity (ka-dag) aspect of rigpa primally pure of all fleeting stains such as habits basis rigpa does not function as an alaya for constant habits. It gives rise only to pure appearances, beyond words and concepts.