Ahhh, that XKCD strip. Still makes me laugh when I think about it; I was almost unable to function on the day it was first written. It was slightly unfortunate that I'm a biologist and my dad's a mathematition though, lots of teasing when he found it.
I can sort of see what your girlfriend's saying. Lemme put this in context: I'm studying microbiology an University, which is a highly chemical based part of biology. Some aspects really are little more than chemical reactions that happen to take place inside cells almost by coincidence, other courses acknowledge that these processes play a small part in keeping a bigger organism alive.
However macrobiology, stuff such as surgery, may blur the line (I really hope my friend doesn't read this and kick my ass before finishing it, he's training to be a surgeon). It moves away from traditional 'science' in labs and testtubes, also leaving little room for experimentation and error since when you try something new, you likely kill someone. However, it does follow the scientific method of observing a thing and seeing what happens when you change one part before attempting to explain that and, for surgery, fix it. It's just that seeing that someone's liver has fallen off and needs a few stitches doesn't need a microscope, which makes some people believe it isn't a science.