When you use muscles that you aren't used to using... you get a little sore. It's not that we're so out of shape. It's just that we lacked the certain muscles we used. Due to my epic run up and down Mt. LeConte, my legs were thoroughly sore for not one, but two days. Did it mean I could not move and was tied down in one area? No, it just meant that I felt the soreness throughout my body.
When we do something we're not used to doing, our body 'suffers' from that, and also adapts to what we put ourselves through. Being sore isn't being out of shape, it's just the usage of different muscles that are not usually used. Running up the mountain and stepping on unsteady rocks made me use my legs in a different way. I'm glad that I went through that because my body needed a little shake-down of what was going to happen in a little more than a week. Trail running and road running are too very different things. They both use the same muscles, but the shock absorption and how it's used is very different. It's very important to understand that even with the same muscle, doing something it's not used to doing will cause you to become sore.
In order to be fully prepared for what you're about to embark upon, whether it be the corporate world, or running a 50 miler in the mountains... is to just jump into one and experience it. Let's say you're getting ready to jump into a job that would normally take 80 hrs/week... would you just jump from 0 to 80 in a matter of seconds? Does that make sense? You need to make sure your body is capable of adapting to that, because if you don't, you're going to become very 'sore' minded. In the same way, running 50 miles in the mountains isn't to be trifled with. Which is why I spent that 14.1 miles running up and down LeConte, feeling the pain, and understanding what I was getting myself into.
I remember my first marathon. I wasn't exactly ready for it because I'd never raced that distance before, and as soon as I finished my race... I was sore and literally could not walk as soon as the adrenaline went out of my system. My body was not ready for that... it wasn't ready to go that certain distance at that certain speed. When you have adrenaline and guts pushing you forward, you can do a lot of things... once, but remember that when you go beyond what your body knows it's capable of doing, it ends up getting back at you after you finish... and sometimes, before you finish.
There are different degrees to which you can be sore. One is where you look back at the day before and think, 'that was a great workout' and the other, 'that was a dumb idea'. When you look back and think that it was a great idea, you haven't pushed yourself off the wall like Humpty Dumpty. You might have a lot of cracks, but cracks heal rather quickly compared to breaks.
Cracks will heal up and become stronger.
Shattering takes a longer time and you end up weaker.
Know your limits. Choose wisely and make sure to get the soreness that helps you grow.