Just from listening to people talk about their bodies it seems that many people have the wrong idea about how they work. My evidence is when they say things like 'my immune system doesn't like it' or 'your muscles will adapt in order to help you lift heavier next time'. This is actually what's happening and that's a nice way to explain it, but in reality it is actually more complicated than that and the most important distinction is that there is no autonomy on the part of your body. Your body doesn't adapt in order to do anything, rather it adapts because of the way it is built. You're immune system meanwhile isn't made up of lots of little security guards that fly around and zap your germs but rather a host of chemical reactions.
So when you work out what actually happens is that your muscles slightly rip in what is called a microtear. Your body then heals these muscle fibres using the protein in your system (amino acids) and that causes them to come back thicker just like scar tissue. This has the side effect of making them stronger, but it happened just as a result of the way our muscles are built.
Then let's take the example of the immune system. If you remember those educational videos on it from school then you may be under the impression that the immune system is a battle fought out by good white blood cells and evil bacteria - like Star Wars on a microscopic scale. In reality though it again just comes down to chemistry - it's again just a system. Take the protein lysozyme - a useful protein that has a chemical reaction when it comes into contact with the cell walls of bacteria and thereby eradicates them. You get lysozyme from your diet by eating egg whites which contain the protein or it can be administered as medication.
But it's just a system based on chemistry, it has nothing to do with your body trying to help you out (sorry). It all works pretty miraculously and it's pretty hard to imagine it's not based on some kind of autonomy, but it only became such a perfect system thanks to evolution - just another system.
What this all means though is that we can learn how the system works by looking at the chemistry and the biology and that means we can boost or alter it's function. It's all pretty complex though and currently even the top scientists can't honestly say they understand everything. There will come a time though...