Greta Christina Says this so well:

When you look at the history of the world, you see thousands -- tens of thousands, arguably hundreds of thousands or more -- of phenomena for which a supernatural explanation has been replaced by a natural one. Why the sun rises and sets; what thunder and lightning are; how and why illness happens and spreads; why people look like their parents; how people got to be here in the first place... all these things, and thousands more, were once explained by gods or spirits or mystical energies. And now all of them have natural, physical explanations.

Natural explanations, I should point out, with mountains of solid, carefully collected, replicable evidence to support them.

Now, how many times in the history of the world has a natural explanation of a phenomenon been supplanted by a supernatural one?

As far as I am aware, exactly zero.

...

Given this pattern -- thousands upon thousands upon thousands of natural explanations accurately supplanting supernatural ones, zero supernatural explanations accurately supplanting natural ones -- doesn't it seem that any given unexplained phenomenon is far more likely to have a natural explanation than a supernatural one?

I guess that's why I'm not bothered by the things that science hasn't explained. How did life begin on Earth? What was the universe like before the Big Bang? We don't know. Some people look at those gaps in our knowledge and assume that God must be responsible. My 5-year-old daughter made that argument to me this week. First she tried peer pressure and told me that I was the only person who didn't believe in God, but when I listed some other people she changed tactics. She asked where people came from and where the Earth came from if God didn't make it.

I told her that she was asking good questions, then I asked her who made God, if he's responsible for making everything else. She said that there were people before God that made him. Who made them? And so on.

The pattern shows that the gaps are closing. This is an issue that any believer needs to think about and any apologist needs to account for. Why has religion been on the wrong side of issues of knowledge so consistently?

One way of dealing with this, and it has always failed miserably, is to attempt to deny and discredit new knowledge. The Church did it with Galileo and some are trying to do it now with evolution. The religious viewpoint just ends up looking stupid in the eyes of history.

Another way to deal with this is to say that the religion was never meant to answer scientific questions. The believer may claim that those parts of the holy book are not meant to be taken literally and the religion only answers metaphysical questions (e.g., What's the meaning of life? How should we treat each other? What actions are immoral?) There are four problems with this.

1. History proves this assertion wrong. Religion has always tried to explain the way the physical world works and how things began. As much as the more reasonable Christians may hate to admit it, the Creationists are part of a long chain of religious groups who try to promote supernatural explanations for the world, even in the face of overwhelming evidence for the natural explanations.

2. After such a long record of being wrong about the world, why would religion be considered authoritative on any subject? Not to mention the parts of the Bible that condone genocide. Do you really want to take ethical advice from a book like that?

3. If Genesis and Revelation don't have to be taken literally, then why does any book between need to be taken literally? If the creation story was just a human author's attempt to explain where the world came from, then aren't the 10 Commandments another human's attempt to prescribe how people should behave?

4. Why shouldn't we see these questions as one more area for natural explanations? Some scientific disciplines, like geology and biology, are limited to the way the physical world works. Others address the mind, society and even meaning. Psychology, ethics and philosophy, though not as exact, do take an essentially scientific approach to the deep questions that humans ask. They gather evidence, propose theories and test them, like the harder sciences. They're self-correcting and they've also replaced some supernatural explanations. I would much rather take advice on issues of morals and meaning from someone using this approach than from an ancient, pre-scientific religious book.