From experience, I have learned that the best students don't always make the best teachers. Someone who is a little slow in the uptake appreciates the finer points a little more than someone who just "gets it."
I've been running since I can honestly remember. And I have never ever been good at it. According to Google Earth's distance calculator, the first distance I can honestly remember running was a whopping 200 metres. I think I was about 10 or 11 years old.
So although I was never good at it, I did do it a whole lot, and over a very long time (if my 11 years old estimate is correct, a good 14 years on and off at the time of this writing). So that, at least, gives me the right to offer a pedestrian perspective.
First, though, I need to clear out a few well-spread misconceptions about "exercise."
1. Exercise is good for you
2. Exercise makes you burn calories
Exercise is Good for you
Actually, no. In the short term, exercise is fundamentally damage, and nothing more. Good exercise is merely controlled damage.
The only thing that makes exercise "good" is the healthy body's capacity to heal from the damage, over time.
The karate masters who break blocks of wood with their fists develop stronger bones with gradual practice. Their bones incur microfractures, small hairline cracks. When they heal, they come back stronger.
The human body is a self-healing machine, and it's the process of recovery after exercise that makes it so good for you.
Exercise Makes you Burn Calories
Actually, no. Well, yes, it does, but it doesn't really matter all that much when you look at the big picture. The number of calories exercise burns is really just a fraction of the number of calories you burn throughout the day, just to stay alive and functioning.
The body burns calories even while sleeping: the heart still has to pump blood a good 1-point-something metres around the body, which is no mean feat. The lungs still have to continue pumping air in and out. The liver still has to detoxify that McDonalds you just had for dinner, and goodness knows the kidneys are still filtering our blood.
For the body, there's always work to do. And that work requires energy.
Where exercise really helps is raising your metabolism, the amount of energy your body burns just to keep itself going. And when that rate goes up, it goes up 24/7, which really adds up over time.
Unlike the human mind, the human body will never invest in something it doesn't need. If it doesn't need muscle (which is a huge, energy-consuming machine that requires resources to not only build, but to maintain day to day), it won't keep it. It will slowly be eaten away (and is excreted through the urine, as it so happens), until it reaches equilibrium at the point at which you utilize it.
So it's the overall level of activity that dictates how much muscle your body has invested in.
Now, Back to Running...
From what I've seen (and painfully felt), running depends on three things: solids, liquids, and gases. Bones (solids), muscles (liquids)**, and breath (gases).
During an honest run, either of these three things will give way before you have to stop. The chain is only as strong as it's weakest link. When the weakest link breaks, it doesn't matter how much stronger the other links were. There's no A for effort here, this is the real world.
Whichever one you push to the limit, will probably not hurt as much the next time you go back out, provided you've given yourself enough time to heal.
And that's really all I wanted to say on the matter. I've discovered this through personal experience: bones can hurt quite badly the first time you start running. I started running as a child, and I remember my legs used to keep me awake at nights when I first started out.
Muscle pains are more easily manageable, especially the muscles in the legs, which are big and can take the hit.
Breathing is also quite painful, but less so in sheer magnitude. It is just as debilitating, though, which is what we're measuring here. The diaphragm, the muscle-controlled pull-valve that expands the lungs forcing air in, has a big role to play in it. It needs to be strong to be able to continuously push and pull air in and out so the lungs can quickly oxygenate the blood and get pumped back around the body.
Running is Hard
Well, nobody said it was going to be easy. In most of the things that are really worth having, there are no shortcuts.
Humans are optimized for running, though. Over generations, we have evolved to be very efficient runners.
Of all terrestrial mammals, humans run the longest distances voluntarily. We can outrun even horses, who will never go as far unless pushed. Cheetahs and big cats will overheat very quickly because of their fur and lack of sweat glands. After a certain point, they simply will not run. And although they run very fast, they can't stay that fast for long, so they don't get too far.
Humans on the other hand, are relatively hairless, and sweaty, so we can cool down more easily. We have a fleshy bottom, which is connected via thick muscles to long legs which gives them power. We have a tendon that goes from our heels up our legs that we don't seem to really need for walking, but helps add spring to a run by allowing us to powerfully push our feet. We have a chord (called the nuchal chord) that runs down the back of our heads, which allows us to keep our heads upright while we run, a feature shared only by running mammals. Since humans are upright, we have a smaller base area, which makes it easier to topple over if the centre of gravity shifts during long strides (Why does a bottle turned upside down topple over more easily than one standing on the base? The area of contact with the surface decreases when it is upside down). To cope for that, we have independent shoulder motion relative to the head, so we can adjust our centre of gravity and keep our balance when making long strides. This is something no other primate has, and something that makes humans an order of magnitude more mobile.
And so it is! So lets get to it. Like Darth Vader said... it is... our destiny.
** Muscles are technically not liquid. They are what physicist Eric Drexler calls "machine-phase," neither solid nor liquid, but still a cohesive, functioning unit. But lets not split hairs.