We were asked by an American Christian, "Is God an integral part of the Universe that God created or is God somehow, separate from it, or both?"
Our answer follows:
Before you answer that question you need to answer the questions "What is God?" and "What is the Universe?".
The answer would depend on what is meant by these two words.
And, although people have tried to build various theories about God's essence. The truth is that none of them could be proved, but could be only "believed". They were just the results of their imagination, and could not stand the test of serious "scientific" enquiry. This is why there has been a "conflict between science and religion".
The only thing that can be asserted about God, which also makes sense and can withstand logical "scientific" analysis, is the assertion that "Something has created the Universe, but we do not know what it is, nor what the process of creation was. And possibly (or even certainly), will never know - no matter how our knowledge about the Universe will advance, which can advance without limit".
So unless we want to invent some "fairy tale" about God, as many religions did, we have to accept that God is just a logical concept following from the fact of the existence of the Universe. This can be proved, everything else can be nothing but human fantasies.
So from this point of view, God is "logically" separate from the "Universe". It would be wrong, however, to see this as two separate chunks of anything (matter, spirit, intellect, etc), because the concepts of space, form, shape, size, location, time, etc. are simply inapplicable to the concept of God.
The assumption that God Created the Universe, implies that there was time when God existed and the Universe did not. So, at that time, God could not have been either part of the Universe, or the Universe. So, before the Act of Creation, God was clearly totally separate from the Universe. The Universe did not exist.
To assume that the Universe was created by God out of some parts of Himself, or that having created the Universe, God somehow has merged Himself (or some parts of Himself) with it, you would be making assumptions that you know what God consists of, what was the process of Creation, and which parts of Himself God incorporated into the Universe, all of which you would need to prove. You would not be able to prove this. You can only believe it, if you want to.
Most religions have various theories about the Creation, which the followers of these religions believe to be true. But they are based on the knowledge of the world as prevailed at the time when the creators of these religions advanced their theories about God and the Creation. They played an important part in providing people with a consistent view of themselves and of their place within the Universe.
But as the human knowledge of the world advanced, the theories of God and Creation were becoming incompatible with the more advanced knowledge of the world. And this was leading to Atheism and Agnosticism, and the loss of a consistent view of themselves within the Universe. But now people see, that, while the religious theories of God and Creation are "fantasies", there is more to religion than these theories. In fact these theories are not important - we know no more about the Creation than the people of the times of Abraham. And probably (or even certainly) never will. And the "modern scientific" theories of Creation are no more "scientific", than the theory that the World was created in Seven Days1.
But using the gift of abstract reasoning (or reading the Qur'an) we can now accept the abstract fact of Creation, without the need to paint in our imagination (or on walls and ceilings) a concrete image of God and of the process of Creation. This is just a more honest and "grown up", factual and logical and "scientific" view of the world - which resolves the "conflict between science and religion". And it allows us to benefit from the wisdom of the prophets of the past, rather than throwing it away, as the Atheists did. And we can further build upon this "scientific" legacy of the Prophets, and apply it and develop it further to advance the Human Knowledge of the World and, what is still more important, of ourselves.
One of the most quoted, and least followed, sayings of Jesus is "Know your own self". And the secrete of this self-knowledge is to learn to see ourselves impartially and objectively, as if looking from "outside of the Universe", as God would have seen us, if he were a Man looking at an Ant Hill, and Men were the Ants. This is just a "parable". God is not a Man, nor Men are Ants. But this illustrates how prophets used parables to represent difficult abstract concepts, by visual images, so it would be easier for the people, who lacked the abilities of the prophets, to understand their message.
But people see the concrete visual image, but have difficulties of understanding the abstract message. And then they argue about the Size of the Ant Hill, and the Color of God's Eyes, and whether God looks at the Ants from the East or the West of the Ant Hill. And the "Bad Ants" of the "Ant Hill" are, of course, "Them", and the "Good Ants", of course ,"Us". And then they begin to interpret and use this parable as it is convenient for themselves, rather than seeking to understand the prophetic "message".
And this is why all the history of Mankind has been wars and politics. And, if people want to live in peace and security, they need to abandon politics and learn to govern themselves by Truth and Justice. And this is what the prophetic message is all about.
1) The Qur'an accepts the Biblical version that the world was created in seven days, but it notes that the Prophet was not present at the time of the Creation, and that what people might see as ages, can be be seconds in the eyes of God, and what people see as days could be millenia.