Much of the ambiguity to explain the character of wholes in both physical reality and biology derives from the assumption that order exists between or outside parts. But order complementary relationships between difference and sameness in any physical reality as forwarded through physical events is never external to that event - the connections are immanent in the event. From this perspective, the addition of non-locality to this picture of the dynamic whole is not surprising. The relationship between part, as quantum events apparent in observation or measurement, and the undissectible whole: Having revealed but not described by the instantaneous correlations between measurements in space-like separated regions, is another extension of the part-whole complementarity in modern physical reality.
If the universe is a seamlessly interactive system that evolves to higher levels of complexity and if the lawful regularises of this universe are emergent properties of this system, we can assume that the cosmos is a single significant whole that evinces progressive order in complementary relations to its parts. Given that this whole exists in some sense within all parts, one can then argue that it operates in self-reflective fashions and is the ground for all emergent complexity. Since, human consciousness evinces self-reflective awareness in the human brain and since this brain, like all physical phenomena, can be viewed as an emergent property of the whole, it is not unreasonable to conclude, in philosophical terms at least, that the universe is conscious.
But since the actual character of this seamless whole cannot be represented or reduced to its parts, it lies, quite literally, beyond all human representations or descriptions. If one chooses to believe that the universe is a self-reflective and self-organizing whole, this lends no support whatsoever to conceptions of design, meaning, purpose, intent, or plan associated with mytho-religious or cultural heritage. However, if one does not accept this view of the universe, there is nothing in the scientific description of nature that can be used to refute this position. On the other hand, it is no longer possible to argue that a profound sense of unity with the whole, which has long been understood as the foundation to religious experience, can be dismissed, undermined, or invalidate with appeals to scientific knowledge.
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