POORLY WORDED THEORIES TO POP HOLES IN YOUR THEORIES!
Everything can be explained, and eventually is. To take your examples:
1.) Newton’s laws of motion state that an object in motion, stays in motion till an equal or opposite force is applied. This theory works as well in real life with both good and evil (( Corny I know)) positive and negative, cause and effect. But I think I have discovered a middle ground. A Anomaly to that rule.
There are always exceptions to rules, and these are explained rather easily, with either "It doesn't cover it." or "It has changed because we have found something different." Good and Evil are merely perceptions, used in stories to add "Flavor." We are all, technically, on the middle ground, so the anomalous behavior would be to be completely good or evil. There are always middle grounds to positive and negative based, again, on perception.
For example: We're in a fight with a giant rhino. The Rhino breaks it's legs and it's neck. It's positive for us, and Negative for the rhino. It might also be negative for us because the rhino will now die, and it might be good for the rhino because it doesn't have to fight.
2.) For every thing in this world, there is at least one thing that can not be explanned, for every rule. This thing being un explainable through both science and faith. Science dictates that without a spine, you are unable to walk. Yet I have a father who walks straight, and tall, without a single sign of pain on his face. His spine is snapped clean in half. The doctors cant figure out how he can do that, and they cannot attach it back.
Rules which cannot be explained are simply rules that have not been fully explored and exploited or tested. According to the truly faithful, EVERYTHING can be explained through faith. Without a spine, you are unable to walk, yes, but I have met your father, (Who hates me for good reason.) He doesn't show pain because he needs to be strong for you guys, and his strength translates to his spine. His spine is broken in half, yes, but his nerves are still attached, and his muscles are holding it in place, and therefore, he can still walk. Inside, he is still hurting, but you and your brother make him numb it. YOU are his strength, Brother, YOU are his pride and joy, his greatest accomplishments, his legacy. Just remember that. He is tougher on YOU because YOU are the firstborn, his first and best. You represent him and his skills when you leave later in life, so he forges you to take his place in his stead.
TL;DR, Everything is explained eventually, you just have to look harder and think harder.
Also, Ghosts are formed from paranoia, and when people can't find any evidence about the "strange" happenings, just remember that everything has evolved to accommodate their needs.
Rats, for example, are very good at hiding because they need to be.
