These are some very deep questions to same the least, but I shall endeavour to do my best explaining it to you.

I think we must start with the question of how we make observations about our universe. The process is known as "abstraction." What this means is that we abstract (choose, pick) a subset of total possible observations and then make conclusions about the whole. If you think about this for a while you will come to realize that this process is fundamentally flawed because it will only produce approximations of reality. The reality is the whole. My observations are merely a part of the whole, and any system which tries to draw conclusions about the whole when it can only assess or observe a part will create problems. That's the first thing to understand.

Therefore, we need to understand that the process of abstraction is fundamentally limited. If we assume that it is not limited, our thinking will run into dead ends. This is the essence of Newtonian concepts of reality.

What does this mean? "Newtonian" is named after Sir Isaac Newton, the brilliant scientist and mathematician who uncovered the three basic laws of motion that every student of physics learns in his lifetime. You probably know them yourself. So what's wrong with these "laws of motion"? They're okay, and they work fairly well...most of the time. Most of the time? Yes, most of the time. You see, Newtonian mechanics (mathematical expressions that describe the motion of bodies) only approximates reality. It works really well for every day objects that we see in our world. But it doesn't work well at all for the very large, nor for the very small. It is a poor mechanical system for atomic scale and for galactic scale objects. This tells us that Newtonian mechanics is only an approximation of the reality. It was formulated by abstraction. Newton picked various pieces of data (observations) from the observable universe and formulated equations that described quite well what he saw. But were his observations universal? No. But it seemed like they were universal for a few centuries. But when the early 1900s can along and atomic physicists began studying the atom, they realized quite quickly that Newtonian mechanics doesn't work at all at that level. Therefore, they needed a more accurate mechanical system. It was more complicated, but it worked well, not only for the very small, but also for the ordinary sized objects. It was called "quantum mechanics." Is it perfect? No. But is it better and more accurate than classical mechanics? Yes, it is. Remember, it was the result of a larger set of abstracted data.

Therefore, with that as a basis, you should be able to understand some of the philosophical implications of these two systems. Newtonian mechanics is based on the notion of absolute concepts of space and time. It works rather well for the basic observable universe you and I work with on a daily basis. However, it is fundamentally flawed. Why? Because it is only an approximation of the universe. Therefore, if we base philosophical premises (i.e. "logic") on this system, we will arrive at flawed conclusions. Thus, Aristotle's system of logic is inherently flawed. It made good sense to the ancient Greeks, but it doesn't make good sense to a 21st century scientist. It is based on the notion of being able to accurate describe the universe in the language of abstractions, i.e. words. But words are not the real thing. Words are abstractions.

Here is another way to look at it. Newtonian thinking is an approximation of the real. If we make philosophical (universal) statements based on an approximation, we're going to run into trouble. We might think we're being totally logical, but we're not. Our logic is flawed. This is very difficult for some people to understand. How could their logic be flawed when everything in their world seems to verify its truth? That's the problem though. Only everything in "their world" seems to verify its truth. What about all the other observations that are not in "their world"? Some of those observations do not verify the truth of their logic, but they don't know that. Nevertheless, the conclusions they make will be flawed because the premise is flawed.

Newtonian thinking would say something like this. Either something is red or is not red. That seems true, doesn't it? But Einsteinian thinking (relativity thinking, non-Newtonian thinking) would ask: What do you mean "red"? What does this abstraction mean? Is there anything objective about "red"? Does "red" exist in the universe? Or does it exist merely in our brains as we interpret various observations about wavelength in the universe?

To put it another way, non-Newtonian thinking would ask, "What do you mean "is"? Does this word mean "equal to"? Are you making a mathematical statement, "Something = red"? If so, what does it mean? In fact, in reality, nothing "is" red. Red is a quality of something, not its essence.

So, that gives you some idea about the philosophical implications of Newtonian and Einsteinian thinking. I slipped in Einstein near the end here because he epitomized non-Newtonian quantum thinking with his "relativity theory." In a certain sense, he showed that not only space was relative, but so was time. They were all dimensions that were observable, and if they were observable, they depended on the observer. Thus, it is impossible to separate the observed from the observer. The observer is always a part of his system. Therefore, the observer can NEVER be totally objective.

In conclusion, reality is not Newtonian. It is closer to being Einsteinian. But, even as Einstein knew, his system wasn't completely universal either. Scientists are still trying to come up with a theory that will explain all phenomena, but they haven't been able to do it yet. Therefore, ALL of our philosophical systems are inherently flawed. Why are they flawed? Because they are based on our thinking (our logic) which is limited by our observations, which as we have seen, creates only an approximation of reality.

If you'd like to understand this further, I'd highly recommend reading the works of Alfred Korzybski. Particularly, his "Science and Sanity."