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What is then Isvara pranidhan in yoga sutras? if there is no isvara?
What then brought the universe to existence? What organized prakriti and purusha? What made an energy to manifest in to the works as we know it?
Exactly, this is a common criticism of Samkhya. There is nothing in Samkhya that can explain how the universe was brought into being, what is the organizing power that is coordinating both prakriti and purusha. Hence in to answer this question Vedanta answers god is the first cause of the universe, god is the organizing power coordinating prakriti and purusha.
Philosophy is not an endless pursuit, it can lead to definite and practical conclusions. One definite and practical conclusion of Samkhya philosophy is Yoga.
Not all Upanishads are Samkhya, Samkhya features more predominantly in the Shvetashvatara upanishad.