What did God make the universe from? It seems Himself, since before Creation, only God is. This seems to me to be the most important question for Christianity. NOT why, how, where or who, but what. From what outside or within Himself, could God have made the universe?
As science suggests, the physical universe of time, space, and matter is not eternal. It had a beginning. Thus it was created. It was not arranged or mixed or reassembled, but created out of nothing.
Genesis 1 repeatedly uses the phrase, "God said, 'Let there be...', and there was...". God spoke, and what previously did not exist began to exist. So, specifically, God did not make the universe from anything at all.
Indeed, God did not make the physical universe from Himself, because He Himself is outside the physical universe. In fact, God is spirit. This is in contrast to the idea of pantheism.
In the 11th chapter of Hebrews, we read this:
This ex nihilo power is reserved to God alone. All other creations that mankind does is simply to take what is already made and rearrange it into another form. We never really "make a cake"--we merely assemble ingredients into a different form.
Genesis 1:1-2 (NIV)
It seems from this first creation story pretty clear that God created the universe - there really is nothing more to this universe physically than the heavens (space) and the earth (terra). It also seems apparent that God's spirit was there, "hovering over the waters."
What does the word "create" here mean? Does it mean form from something that was already in existence or create from nothing? It does not spell it out clearly here. However, in John, we have another creation story:
John 1:1-5 (NIV)
"The Word" here means Jesus Christ. God and Christ and the Holy Spirit were clearly in existence before the creation of the universe from what this says along with the Genesis passage above, it appears to me. Here he uses the word "made" and indicates all things were made through Christ. It appears to me from this passage that taken with the Genesis passage that only God, the Father and the Son were in existence, though other parts of the Bible seem to lend creedence to a Heavenly Host as well.
Back to Genesis:
Here, God tells us about the fact that "the Lord God made the earth and the heavens."
Taking this simple statement with all those previous, I just get the strong feeling that indeed "created" and "made" mean from nothing - not like clay being formed into a pot, but through the Word - most literally through speaking things into being through Christ:
Back to Genesis 1:
Genesis 1:3 (NIV)
Genesis 1:6-7 (NIV)
Genesis 1:9 (NIV)
And so on and so forth. God is literally speaking through the Word (Christ) the universe into creation. There seems to me to be no indication of forming from something, other than "through" the Word.
Also, I would add that the single most important question in Christianity is whether you believe Christ died on the Cross for your sins and do you take him as your Lord and Savior. After all, there are only two places that choice can lead you to - eternal paradise, or eternal damnation. That has the biggest ramifications long term for any soul ever in existence, and we seem to forget the fear that we should all have for the unutterable suffering one might face if the choices you make take you to the place no one should want to be.
There's a certain paradox where the uncreated, eternal, infinite God makes a place for the created, finite universe: http://en.wikipedia.org/wiki/Tzimtzum
In essence there's no real way to answer your question. Science takes us back to an instant after the big bang. From there you can either put your faith in some as-yet-undiscovered materialistic process, or the mystical idea that the uncreated, infinite, eternal God reasoned it into existence. I agree that neither is initially satisfying to the intellectually curious.
This dilemma leads us to the truly most important question about creation, which is "why?" We're either here to share in the creative act with God, or we are just really really lucky artefacts of semi-random processes. I spent many years in the latter camp for various reasons, but have since come around to the former because only there is true hope.
One can draw a distinction between creatio ex nihilo (creation from nothing) vs. creatio ex se (creation from Himself)? The later seems to be what you are suggesting.
I can say that traditional Christian (i.e. Catholic/Protestant/Eastern) doctrine certainly favours the former - but there is nothing in the Bible which contradicts the latter. Creatio ex se would imply a form of pan(en)theism - that humanity and divinity are not ultimately separate, but rather that humanity is some kind of lessened state of the divine, but with the potential to return to its original divinity. As Lorenzo Snow, fifth President of the LDS Church said: "As man is God once was, as God is man may be." If all humanity once was part of God, then through Christ all humanity can become God again - and Christ is our forerunner and example in our journey to Godhood.