Noah's ark is yet another metaphorical story that too many Christians take literally. Christians need to break themselves of this mentality and read between the lines.
The Bible was written to explain our history to a primitive people. What we consider "God" is likely a being that exists beyond the 3 dimensions we occupy. As he would not be bound by the rules of a 3 dimensional universe, he is both impossible for us to perceive while at the same time being what we would consider "almighty". If you look at the Bible from an objective point of view you would see what the flood was all about. God has dissidents on his plane of existence - Satan being a ringleader, as well as Satan's minions. These minions were breeding with humanity and corrupting God's creation.
Genesis 6:4 - "The Nephilim were on the earth in those days--and also afterward--when the sons of God went to the daughters of humans and had children by them. They were the heroes of old, men of renown."
This pissed God off something awful and he wiped everything out, starting once again with pure human DNA through Noah and his family. The "ark" was likely a repository of DNA or embryos of all the species of earth. There is simply no way to fit 2 of "every clean" and 7 of "every unclean" animals on a ~400 foot literal boat. Not to mention the food to keep them all alive, or the lack of ability to deal with the noxious fumes created by all of the urine and feces those animals would produce.
The Bible is full of metaphors because, as I said, it was written to explain things to a primitive people. Examples:
1) Adam was created from the dirt of the earth. Well, is that not true of human beings? If you break your body down to it's basic components, are you not the same as dirt? Calcium, carbon, hydrogen, etc?
2) Eve was created utilizing one of Adam's ribs. Does that not sound like.... cloning? Genetic manipulation?
We ourselves employ this same methodology among for all kinds of things. Think of how you wouldn't explain to a child the intricacies of how babies are made - sex, sperm and egg, chromosomes & the exchange of genetic information. We make up stories, such as babies being delivered by a stork, because the child is simply too young and underdeveloped to understand the actual science. This is why the Bible was written the way it was. However all of the information is there if you care to find it.