Problem with scientific theory and reality

Before I discuss about the problems that were faced by scientific theories . first I would like to define scientific theory. so scientific theory is a theory which explains about everything through observation, experiments and mathematical calculation. the ancient philosophy and physics was totally on the basis of observation I,e newton/Kepler and all other greatest scientists gave their laws but now a days the scientific theory has reached beyond of our imagination.
Two new theory of science which really became controversial and extends our imagination beyond of our brain capacity. This was really never ever imagined by newton’s throughout his life span the present discovery of science say’s the reality might be working on the principle of relativity or uncertainty. So the question is that how can we believe these facts .it is making us to believe.
The problem with the scientific theory is that it is totally on the basis of ‘observation’ not on ‘participation’. So these two words really makes a difference.
Imagine there are two bags(school bags)(of same sizes same look ) let I assume it as x so if sir will ask me to get that bag . so when the sir will ask me to get that bag the x will strike inside my brain and ripple of waves produced similarly like we are throwing a stone to a river. Then I suddenly realised that sir is asking for the bag then I saw there are two bags near the desk then I was in dilemma with those two bags then finally I took the one bag and gave it to sir but sir said no that he was asking for another  bag which was kept nearer to the bag which i brought
So the sir was observing on the different bag but the x that strikes inside my brain was the different one. So this shows that the observer has different views but the participants has different.

Another example-
If a friend pinch me then I would shout owh…………… he observed that I was in pain but I was the participator he don’t know how much in pain I was in but I know the pain I was in. Similarly it is happening in quantum mechanics we are not electrons we just try to find out the behaviour of electrons by observing it sorry i forgot even we cant observe it we try to understand its peculiar behaviour through our imaginations. the nature is trying to show the different things but we are observing it in different way .we may don’t know the strangeness of nature the reason of the strangeness of nature. Something it may be a force which is hidden to us which makes our nature of life,space and time an illusion. Exploring the secret of universe by many scientists may also be an illusion because it was totally on the basis of mathematical calculation and according to me god doesn’t practice mathematics.