I'm a programmer and deal with computers a lot. I can write code and make computers do things, using conditional logic and algorithms. Not so long ago I started to research sleep and am trying to get a grasp of how sleep "works".
I need to start with a good model of how a biological organism operates. As a programmer, I'm tempted to think of an organism as a machine with some software. Is it so at some level? If so, at which level does this analogy no longer hold? I don't want to have pre-conceived notions skew my thinking.
How do biologists think of organisms? Is there such thing as "levels of abstraction" when thinking of a biological organism? For example a motion of a steam engine can be described by classical mechanics, and it gives good approximations of how it works, but if one is to look much more closely one would see quantum physics. Is there a similar way to look at a living organism without getting into individual gene/protein interactions ?