Thomas,
You make a good argument for why reality can only be understood in terms of its discrete relationships, but it's wrong. With your last paragraph, it's clear you understand your point has its limits, but relegate the wholistic view to mystery. It isn't mysterious at all. It's overlooked because it's so basic. Math says that if you add two things together, they equal two. Well, if that's the case, you haven't actually added them together. Necessarily actually adding things together means you have one of something larger. In basic terms, it's like adding two piles of sand together and having one larger pile, but in reality it's more like components combining to create a larger whole. Whether physics, or biology, we like to take things apart to see how they work, but the fact is that they work together. Much like all the parts of your body add up to a larger whole, or all the components of an atom add up to an atom, not to mention all the various levels between, above and below the atom and the person.
This dichotomy is basic to the difference between eastern and western philosophy. In that we in the west tend to focus on objects and view their actions as emergent. While in the east, there is the contextual view and the particulars within the context are as much a part of the larger whole as your nose is part of you.
One aspect of this that I raise quite frequently and was the subject of my entry in the Nature of Time contest, is that we are looking at time backward. The basis of our rationality and from that, language, culture, history, etc, is the concept of time as the present moving from past to future. So it is natural to include this into our physical theories of how reality functions, but the fact is that it is the changing configuration of what is, the present, which turns the future into the past. We don't travel the fourth dimension from yesterday to tomorrow. Tomorrow becomes yesterday because the earth rotates. It is not that we move from a decided past into a probabilistic future, but that the continuous collapse of probabilities which turns the future into the past. Time is an effect of motion, not the basis for it.
In fact, in eastern cultures, the past is considered to be in front of the observer and the future behind, because both the past and what is seen are known, while what is behind one and the future cannot be seen. Physically we do understand what is in front of us and can be seen is of past events, be they across the room, or across the universe, but we consider ourselves to be moving through our environment, rather than part of it, so we think of ourselves moving from past situations to future ones, as a function of our own spatial action. The irony is that this creates a deterministic view of time, since we only exist at the moment of the present and cannot change the past, or affect the future. On the other hand, when we understand ourselves as fully integrated into our own context, then our actions are part of the process creating these situations and we affect our context, as it affects us.
You do conclude your essay with a nod toward Complexity Theory, with its dichotomy of order and chaos, but I think this relationship can better be described as a dichotomy of information and energy. Energy manifests information, while information defines energy. The information is the top down view of the details, while the energy is bottom up process. They are like two sides of the same coin, such that there cannot be one without the other. They are still opposites though, as energy is fundamentally dynamic, while information is necessarily static.
Think in terms of how you perceive the distinctions you use to define your view of reality: Necessarily you must move from one to the next, otherwise it is that frozen featureless void. So there are the distinctions and there is your movement from one to the next. That is time. Remember the clock has two features; the hands and the face. We think of the hands as moving clockwise, but from the context of the hands, it is the face which moves counterclockwise. The hands represent the present, as it moves from one unit of time to the next.
As I pointed out though, it is the energy of the present which forms and dissolves these units of time. The future becoming the past.
So it is the wholistic present which is creating these discrete units which come into being, grow as long as they absorb more energy then they lose, eventually to lose all energy and fade into the past.
One way to think of this is as a factory: The products go from initiation to completion, but the production line faces the other direction, consuming raw material and expelling finished product.
The mind functions in a similar fashion, as it consumes masses of information, turns it into discrete thoughts, which are then replaced by the next. The brain is physically real, thus it exists in the present. Thoughts coalesce out of the future and fade into the past.
I could go on, but this makes the basic point.
Regards, John