What is the process that creates "Saṅkhāra"
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I found this:
Consciousness is the product of the physiological processes of our body in general, and of the functions of the senses in particular. Or, to speak in the spirit of Schopenhauer: Consciousness is a secondary phenomenom, conditioned by the functions of the cerebral nervous system, based upon the somatic life of the individual: "Only by means of organic life is consciousness possible".
I hope this helps.
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Is it right if I say the origin of Saṅkhāra is not by a natural process of the mind
It is a natural process that when we get feeling born from contact of the faculty with an external object which you react with craving and clinging for a worldly person. You do have control over the process as this point there you can be just see the airing and passing of the feeling born of contact of the faculty with an external object, (phenomena what is felt or known) and be completely be equanimous towards the feeling without clinging and craving. The latter is going against the stream and requires effort. This is going against the natural process this happens.
... but it is a byproduct of Avidyā which dominates the non-arahant mind?
This is a by product of Avidya. It is in short reaction to sensations / feelings with craving and clinging.
The way to overcome this is given in the Pahana Suttas (or the way to let go): Pahāna Sutta, Avijja Pahana Sutta 2. There are times that this process is formalised as understanding 4 Noble Truths.
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