Nice contribution, Yanniru, if the Peanut Gallery may say so.
Y wrote:
Kauffman of the Sante Fe Inst has proposed such a mechanism based on the mathematics of complex systems and developed computer simulations that verify his hypotheses. He says essentially that when molecular structures get to a certain threshold of complexity, then they automatically can reorganize themselves thereby producing new designs and seemingly extra information from nothing. But actually it comes from energy and is consistent with thermodynamics."

This is a plausible physical model where material skepticism will be quite useful in developing further insights. Dr. Ilya Prigogene and others have contributed to this line of thinking for decades and we have partially disuccesed it on astronomy.net. There is no need to refute this point in a discussion of "God."

Y wrote that "that God does not stand outside these mechanisms or laws of the universe, but rather operates through them."

Evolutionarily speaking, the generations will
continue to experience mechanistic variables but there is no guarantee we are going toward fitness in a changing environment. The warriors might find that the "meek" were not the greatest threat to the warriors' survival and that too many stray bombs which harm the meek may actually undermine the survival of the warriors.

Actually, the "God" who is useful to our uplifting is present in ethical discussions and, by the products emanating therefrom, could help us spare sentient (and other) life some of the cruelty and slow steps of animal evolution by enabling transcendently creative progress to help us molecularly develop without some of the experience gained the hardest, most painful ways. I guess this although there is also the potential for great pain in the souls of creating beings and so the comment about pain might not be true.