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The gratitude spoken of here is of a general nature - a feeling of thankfulness for being alive and endowed with what is described as a "soul": a feeling which often leads man to the realization that this boon of life and consciousness is not accidental, and thus, in a logical process of thought, to belief in God. According to Zamakhshari, this is the reason why "gratitude" is placed before "belief" in the structure of the above sentence.
Naqir = the groove in a date-stone, a thing of no value whatever. Cf. n. 575 to iv. 53.