Universe from Nothing?

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The Universe that we can measure and observe is one ruled by laws and order.

Whilst this may appear to be true there are whole parts of the universe that do not appear to follow rules or laws. There are parts of the universe we can, currently neither measure nor observe - merely deduce. These parts are apparently enormous (dark matter - 70% of the universe, dark energy 30% of the universe) which leaves a mere 1%, give or take, that is everything we can observe.

At the same time the idea that God needed to establish rules and laws for his creation is somewhat at odds with his ability to magic the universe out of nothing. Magic, by definition, cannot follow rules and laws.

This is part of the modern dichotomy of God. In the early days (of the church) there was, to all intents and purposes, no science. Everything was regarded as magic - God did it was enough.

As science progresses and explains more and more of how God did it the magic of God diminishes.

If we ever get to the point of solving exactly how he did it - to the point that we can make out own - does that make us Gods?

The very smallest elements which we can study have ordered forms, and follow laws which allow us to predict many, though not all behaviors.

Simply not true. Once you get down to sub-electron level things appear to be very chaotic indeed. We still do not know if there is a smalest elemental level (such as in string theory) or an infinite regression of ever decreasing size (the classical model).

Order itself, law itself cannot exist on its own; it requires something of a higher order to give it. A legal universe requires God for its origin.

Well bearing in mind the above we are somewhat redefining God. Again, why did God need to establish physical rules if he can magic things into existence? Surely he could have them behave as he wants with no discernible rhyme or reason for it?

In summary - if the question is - why is the universe as it is with specific rules, laws and constants and why can we understand those? The answer of God is not an answer.