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It's a good question.
The commentary explains that they arise and cease together, sharing the same sense-object. This is why they are considered to be associated.
But why were they identified to be distinct aggregates in the first place?
I think the distinction of the five aggregates can be experienced and understood in meditation (jhana + vipassana).
They are simply different functions of the mind, that tend to arise and cease together.
Here's an analogy. When you turn the steering wheel, the front tyres of a car turn together. So, they are associated. You cannot differentiate when the steering wheel is turned from when the tyres are turned. But you can differentiate that the steering wheel and the tyres are distinct parts of the car.
From Piya Tan's "M43: Maha Vedalla Sutta":
“Feeling, perception and consciousness, avuso: are these states associated70 or dissociated? And is it possible to separate these states to describe their difference?” “Feeling, perception and consciousness, avuso: these states are associated, not dissociated. And it is not possible to separate these states to describe their difference. For, avuso, what one feels, that one perceives; what one perceives, that one cognizes.
Therefore, avuso, these states are associated, not dissociated. And it is impossible to separate these states to describe their difference.”
Footnotes:
70“Associated” (samsattha). Comy explains as “associated by way of arising together, ceasing together, sharing the same basis (sense-faculty), sharing the same sense-object” (ek’uppāda,eka,nirodha,eka,vatthuka,ek’ārammana- tāya samsatthā) (MA 2:342).
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I think the point here is that they are dependant links, the 5 aggregates are a part of the 12 dependant links of dependant origination that in turn causes suffering (dukkha)
Ultimately they are dependently related and are not really separate, but instead a consistent process of how we experience reality as a sentient being in samsara.
We can conceptualise them by using dependant origination and giving them name and form to perceive them with consciousness etc.
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I would suggest the translation of "nānākaraṇaṁ" as "differentiate" is inaccurate. MN 43 is obviously describing how consciousness, feeling, perception & wisdom cannot occur without each other. Therefore, MN 43 must say, similar to the below:
Therefore these phenomena are conjoined and not disjoined and it is not possible to separate (nānākaraṇaṁ) them and find (paññāpeti) them apart from each other.
Note: for SN 22.82, Bhikkhus Bodhi & Sujato translate paññāpana (from paññāpeti) as 'manifestation' & 'found'. In other words, 'paññāpeti' does not always mean 'to declare'.
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"Feeling, perception, & consciousness are conjoined, friend, not disjoined. It is not possible, having separated them one from another, to delineate the difference among them. For what one feels, that one perceives. What one perceives, that one cognizes. Therefore these qualities are conjoined, not disjoined, and it is not possible, having separated them one from another, to delineate the difference among them." -- Mahavedalla Sutta
The are conceived separately but they exist or arise together. He says, "For what one feels, that one perceives. What one perceives, that one cognizes." Feeling, perception and consciousness are conjoined and you have them all when talking about, for example, a bodily feeling.
Just because something can be conceived doesn't mean it [must] exists isolated from other things. Heat and electrical current coexist together and you can describe each one separately. Sounds to me you have problems with semantic aberration called elementalism:
"... what I call "elementalism," or splitting verbally what cannot be split empirically, such as the term mind by itself and the terms body, space, time, etc., by themselves ." -- The Role of Language in the Perceptual Process
Just because words 'mind' and 'body' exist separately because of the nature of the language, that doesn't means that the mind and body exist separately empirically. Mind and body are one organic unity. Similarly, just because perception or feeling or consciousness can be described separately, doesn't means they exist separately from each other.