This song means so much after attaining Buddhist enlightenment.  ... Atheistic know-it-all's are just as dangerous and close minded as religious fanatics.. "Spirit moves through all things" - There is nothing wrong with that sentence. Spirit does not equal faith/religion, but it doesnt exclude it either, cause we are all made of that same energy (Spirit), no matter what you call yourself.. Can you dig it?
@AJB83: As I understand it, here "science" refers to the domination of nature by the means of technique. Assuming such a meaning, there is little overlap with the "research" mentioned on the other song, and thus no contradiction.
PLEASE DON'T READ THIS. YOU WILL BE KISSED ON THE NEAREST POSSIBLE FRIDAY BY THE LOVE OF YOUR LIFE.TOMORROW WILL BE THE BEST DAY OF YOUR LIFE. NOW YOU'VE STARTED READING THIS. DON'T STOP. THIS IS SO FREAKY. 1. say your name 10 times 2. say your mom's name 5 times 3. say your crushes name 3 times 4. paste this to 4 other songs. if you do this, your crush will kiss you on the nearest Friday. but if you read this and do not paste this, then you will have very bad luck. SEND THIS TO 5 SONGS IN 143 MINUTES. WHEN YOU'RE DONE PRESS F6 AND YOUR CRUSH'S NAME WILL APPEAR IN BIG LETTERS ON THE SCREEN. THIS IS SO FREAKY BECAUSE IT ACTUALLY WORK 
not to go all songmeanings.com on y'all, but I think dmeagle got it, if a little hippy love-ishly. Faith =/= religion (not necessarily). And I don't think SOAD is saying "down with science! Faith cures AIDS!" but that without faith (in life, in human kindness, in music, in the existence of happiness, in the power of questioning, in anything) enriches human life in a way that science can't. And that collectively we have perhaps put too much trust into science alone, because like people have pointed out, science doesn't always lead to good things. It can lead to things like, oh, MK Ultra, Chernobyl, Hiroshima, the ending of One Flew Over the Cuckoo's Nest, to name a few... Like most anything, there can be two sides to science - human progress and environmental damage. Faith can be blindly following a crazed leader or it can be faith that you'll get through the hard day you're having. Just saying.