I had a conversation with someone recently who thought that Intelligent Design was a scientifically applicable idea. I tried my best to explain that it wasn't, but I don't think I reached her.
Intelligent Design is the basic idea that where there is design there must be a designer. So a newt looks the way it does because it was designed by a higher power. This belief is all fine and dandy until you get into scientific aspects of it. Intelligent Design as a scientific theory offers that the gaps in the evolutionary theory (such as why the newt's earliest legged ancestor started to develop legs in the first place) can be explained in the simple sentence that 'God did it' with the premise that it's that way because God designed it that way. This way of explaining things is counterproductive to science.
Science, especially biological science, gets into the nitty gritty details of it's subject and asks all the questions. The answer 'God did it' isn't good enough. Whether or not God did it, science asks the question of HOW it was done regardless of whether or not God was involved.
Personally, I believe that God has a lot to do with why the universe is here and how it came to be. But, I also recognize that in order for science to work, God needs to step out of the theoretical picture. Because God offers no real evidence for his existance other than the emotional connection between him and humanity's subconscious, God has to step out of the realm of science until evidence for his existence is found.
Until then, Science is the study of how rather than why. Religion is the study of why. When the two get intermingled with one another, people get pissed off as evidenced by the evolution vs Young Earth Creationism debate. In my opinion that whole debate is almost worthless. What Young Earth Creationists don't realize is that the world didn't have to come into existance six thousand years ago in order for God to exist or for life to have meaning.
What that whole debate boils down to is Biblical infallibility which is a subject heading for later.