Lucapsa,
First of all, we aren't making the Bible out to be another deity. It is the Word of God, period; nothing more, nothing less.
Look at what you said. "Word of God". Now go to John 1. What is the "Word" with a capital "W"? It's not the Bible, is it?
Thank you for proving that you are making the Bible into your god.
Second of all, God created this universe ex nihilo.
That is one interpretation in the history of Christianity. Many Christians read that God created the earth from pre-existing material "the earth was without form".
Scientists today claim that the amount of matter/energy is a constant, and has always been a constant; whereas the Bible portrays a starting point of zero matter/energy, that steadily increases over a period of six days, until it reaches its current amount.;
You have a misstatement of science there.
1. Yes, the amount of energy/matter in the universe NOW is constant. However, at some point there was NO matter/energy (or spacetime)
2. You are using Genesis 1. However, in Genesis 2:4 scripture states that God created the heavens and earth in ONE day, not 6. The Hebrew is very specific. Also, some of the entities you say God created ex nihilo in Genesis 1 (and thus increases matter/energy) such as animals and people, Genesis 2 says were formed from existing matter. So you have 2 contradictory accounts of creation. Since they contradict, one or both of them must be wrong.
Thirdly, nature currently is hostile to God and His creation. Look around. All you see is death, destruction, and decay, sometimes packaged as a beautiful spectacle, as in nebulas and novas. Nature is a killer that demands absolute obedience to its laws; but as Paul points out, it does so against its intended purpose.
1. There was always death in creation. Look at Genesis 1:27. God gives humans plants to eat. Why? Why do we have to eat? So we don't starve
to death.
2. Nature can't be hostile to God.
God created nature. How can nature turn hostile to God? Why in the world would God permit such a thing?
3. As MrGoodbytes pointed out so well, how do you get from "nature is in pain" to "nature is hostile to God"? That's a complete non sequitor and misinterpretation.
There is coming a time when God is going to intervene and return nature to its amicable state, starting with the elements on the Periodic Table (as Peter makes clear).
Where does Peter make that clear? Paul says in Romans 8 that God is going to intervene and take everyone to heaven.
Since Jesus Himself is the One behind the strong nuclear force (Colossians 1:17), all He has to do is release His hold, and the events of 2 Peter 3:10 will take place.
How do you get from "And he is before all things, and by him all things consist." to "strong nuclear force"?
Colossians 1:17 is making a common theological statement that is a bedrock of Christianity (but is ignored by creationists): God
sustains the universe. This is not limited to the strong nuclear force.
Now, as to 2 Peter, what were the "elements" in Peter's day? Earth, fire, water, air! Peter is saying that God will eventually destroy the earth. Again, this is a theological statement, not one of science. 2 Peter is reaffirming what is stated in Genesis 8: that the next time God destroys the world it will be by fire.
Didn't anyone ever tell you that it is invalid to quote out of context?
You do realize that you are cherry-picking science here, right? You take science when you think it is backed by the Bible, but reject it when you think science contradicts the Bible. That's called Special Pleading and is invalid.
Fourthly, Genesis 1 is a detailed account of the Creation, in chronological order. Genesis 2 simply contains 20 words in verse 19 that are considered out of sync, but could easily be parenthetical, not contradictory.
You've got worse problems than that. But forming the animals out of the ground is not parenthetical. After all, once they are formed, God takes them to Adam to name and see if they are fit companions. If the animals had existed before, God wouldn't have to form them, just take them to Adam. In Genesis 1:25, the Hebrew has God forming men and women (both plural) together. Obviously this isn't how it happens in Genesis 2. Also, Genesis 1 has everything
spoken into existence, doesn't it? As you said, it is ex nihilo. But in Genesis 2 the animals, Adam, and Eve are formed from existing matter. And there is also that contradiction in timing. Don't forget that the name of God changes between the 2 also. In Genesis 1 it is "Elohim". In Genesis 2 it is "Yahweh". All these tell you that you have 2 different creation stories from 2 different sources.
Take Romans for example. There are three whole chapters that are parenthetical (4,5, and 6 - I think). Do we throw the book of Romans out because of it? --- The book of Proverbs is another example. It contains two back-to-back verses that [supposedly] contradict each other: [bible]Proverbs 26:4[/bible][bible]Proverbs 26:5[/bible] Should we throw that book out too, as some suggest?
Have I suggested throwing anything out? No. I'm telling you the contradictions, when read literally, are signals to tell you not to read them literally! The creation stories are not histories; they are theological stories.
And yes, Proverbs 26:4 and 26:5 do contradict.

We have 2 very good sayings put side by side. Am I suggesting throwing out the entire book? No.
We take claims one by one. Not by a group. That those 2 sayings contradict does not mean that each of them is not good and true to some extent. It simply means that there are 2 different ways to look at the situation.
Jesus said that man shall live by every word: [bible]Matthew 4:4[/bible] And since our God is a jealous God, He jealously guards and protects It from even nature itself, which is currently hostile to It.
1. Notice that you capitalized "It", as though the Bible is God. More evidence you worship the Bible and not God. It is you who guard the Bible, not God.
2. You took Matthew 4:4 out of context. Jesus is being tempted. He answers by a direct quote from the Torah. Jesus' ministry shows that he did NOT advocate "every word". Mark 10 and Matthew 14 has Jesus throwing out Deut 2:1. The story of Jesus at the well in John and preventing the crowd from stoning the prostitute has him throwing out words of the Bible.
3. Note that YOU don't live by "every word". You don't obey the dietary laws, do you? Are you a farmer? Do you obey the laws about farming where it says that you must keep fields fallow? Do you forgive all debts every 7 years? Do you sell your daughter into slavery? Do you obey all the laws concerning work on the Sabbath?
You pick and choose.
God in His Creation says that your interpretation of the Bible is wrong. Instead of listening to God, you reject Him. That is wrong for a Christian to do.