On the side of rationalism, it is very difficult for any reasonable person to deny the edifice of natural law which humankind has built. Kepler observed that the planets sweep equal areas in equal times. This fact cannot be denied, it is there for anyone who cares to repeat the observations. Newton observed that the gravitational force is proportional to the product of the two masses involved and inversely proportional to the square of the distance. Again, this is undeniable fact; it has been verified in the orbits of the planets and in the trajectories of our spacecraft. The universe has regularities everywhere we look. Of course, we are constantly refining our theories as our powers of observation are constantly refined. The fact remains that the universe has order. One of the primary goals of science is to discover the laws of nature. Despite the general impression, science does not seek to explain why the universe exhibits its symmetries. It only seeks to discover them, to characterize them, to describe them, and ultimately to make predictions based on them.
The theory of evolution is a case in point. Darwin sought a mechanism to explain the origination of species. He sought a process which would give rise to the diversity of plant and animal species observed in the world today. That process he termed natural selection, whereby environmental pressures influence and change the characteristics of species, sometimes to the point of creation of new species from old. The fossil record which science has discovered bolsters the theory. The record of the evolution of humankind from more primitive primates is incontrovertible. One can rely on faith in scripture and ignore the facts, but to be truly honest one must take these facts into account. One must see evolution as a natural process which does indeed exist.
The most striking thing about the natural laws in the universe is that they exist at all. Why should the universe obey these laws? Why should these regularities exist? Science does not address these questions. Science seeks to describe, not explain. Ultimately, that is the most compelling reason for having faith in the process of science; that it seeks only to explain the explainable, the objective, while leaving more subjective modes of thought for others. It is the honesty of science which is its strength.
To address the question of the existence of natural order, we must leave science behind and proceed to the spiritual realm. Natural laws exert an influence on the universe. They seem to be some mysterious meta-force beyond those described by science. That force is God, or rather what we can observe of God. Nature is God's way of getting things done. God decided to create light and so he arranged that certain physical processes be put in place and there was light. God decided to create thinking beings who might contemplate His nature, and so He set in motion a majestic process in which simple organisms evolve into ever more complex ones, a process taking billions of years. Evolution is not incompatible with God; it is the means by which God accomplishes His goals. When we observe natural order we are observing a reflection of God Himself. Natural law is the order which God imposes on the universe. There has to be a force underlying natural order; for without it there is only chaos. Something causes objects to obey inverse square laws, something causes charged particles to obey Maxwell's equations. To say that it is in their nature is not enough. Why is it in their nature? What is this mysterious influence which causes them to have this nature? This overriding influence is our glimpse of God.
Chaos itself is observed to have properties and regularities. We normally tend to think of chaos as the absence of any and all predictable qualities. In recent times, however, we have discerned some kinds of order even in randomness. Chaotic systems may be self-similar at different magnitudes of observation. Chaotic systems may take unpredictable paths through phase space and yet still revolve about an attractor. Systems may exhibit regular behavior up to a certain breaking point, at which they break into chaotic behavior. What dictates even these examples of orderliness? Why aren't chaotic systems truly chaotic; that is, totally random with no predictable behavior patterns? Again, there is some underlying influence dictating the way even chaotic systems behave.
The most interesting example of this underlying influence is life itself. Why should organic molecules evolve over time, each seeking to survive by adapting to the environment? Why is survival important to an organism? One might answer in a rationalist way by observing that only the longer living species are detectable; that the unfit species do not last long enough to observe. Therefore survival is nothing more than lasting longer than your neighbors, that the importance of survival to the organism is a happy coincidence but otherwise entirely subjective. There are different levels of stability, and the most stable species are the most observable. But stability is an example of orderliness in the universe and stability is a deeper matter than survival. I agree with the rationalists that survival is merely a matter of stability, but I ask why is there stability? There exist forces in the universe which conspire to make some physical systems more stable than others. Scientists seek to formulate mathematical laws describing the energy states in systems in order to model these systems. I ask why do these mathematical laws exist? Why Schrodinger's equation? Why Planck's Constant? The answer again has to be because these laws are God's will; it is how He accomplishes His goals.
God is a craftsman. He desires to create. He gathers his tools and creates a canvas, the universe. He applies his raw materials, the quarks, leptons, and gluons, and assembles them into a wonderful tapestry using natural law to give structure. Atoms built into molecules, molecules into cells, cells into organisms. Primordial matter into Solar Systems, Solar Systems into galaxies, galaxies into clusters. It is not a static creation; it is at least four dimensional. Processes evolve in time according to the laws laid down by God; unicellular organisms evolve into human beings. We get a glimpse of God everyday in the fall of an apple from a tree; in the simple act of switching on a light.
Scientists tell us that there are four fundamental forces in the universe -- the gravitational force, the electromagnetic force, the weak nuclear force, and the strong nuclear force. These forces, and these alone, account for all interactions between particles. Any influence of one particle over another can be explained as a consequence of one or more of these forces. However, there is a natural law called the Pauli Exclusion Principle. This principle is the quantum mechanical equivalent of the maxim that no two bodies can be in the same place at the same time. The Pauli Exclusion Principle states that no two particles can exist in the same quantum state, where "quantum state" is a description of the momentum and energy of the particles. Now the Pauli Exclusion Principle seems to be an interaction between particles. If particle A is in quantum state X, it won't let particle B be in the same quantum state. If this is an interaction, then is it electromagnetic, gravitational, strong, or weak? It cannot be gravitational, since gravitation is far too weak for subatomic particles to affect each other so strongly. It cannot be electromagnetic, since, for example, neutral particles such as the neutron also obey the Pauli Exclusion Principle. It can't be either of the nuclear forces, since electrons and other non-nuclear particles obey the principle. If it's not an interactions between particles, what is it? Scientists would answer that it just is. It's axiomatic. We accept it without explanation. It is a first principle from which we can derive useful results.
There are other principles, axiomatic laws of nature which we accept as readily as day and night. There are the conservation laws of energy, momentum, and charge. We don't explain them. We don't ask why they seem to hold true everywhere. We just have faith in them and in their universal validity. This is the hallmark of science; that starting with a small set of axioms we can build up an elaborate theoretical framework to describe the universe.
But the very existence of these principles begs the question -- why do they exist? By it's very nature science cannot answer this question. In scientific reasoning one must start with unexplained axioms. Otherwise one cannot build a logical edifice on top of them. Science can perhaps dig deeper and integrate seemingly disparate principles into a single underlying principle, as in the case of Maxwell's unification of electricity and magnetism, or in the case of Weinberg's unification of electromagnetism and the weak force. However, science must always have a foundation to build upon. Even if we were to discover a "Theory of Everything", we would find axioms beneath the theory.
If we use science to explain science; if we use axioms to explain axioms, then we end up in a never-ending free fall through layers of description. From atoms to nucleons to quarks to the murky depths below, we will never reach an end, precisely because we must always have a foundation upon which our theories stand.
I believe that, beneath it all, at the absolute foundation of all rational thought, there is God. God may be infinitely far away from our current foundation, but He is there. He is the ultimate explanation. He transcends the rational because He is the end of an infinite process. He is the explanation of all first principles. He mandates the conservation laws, the Pauli Exclusion Principle, and the laws governing the forces of nature. He is the reason beneath all explanations. We can go no further in our explanations, because by definition our explanations require axiomatic foundations, and God is the ultimate foundation. If we try to go deeper and ask "Why does God exist?" then the only answer is that God wills it.
This idea requires an act of faith. One might be tempted to reject the idea of an ultimate foundation and prefer an infinity of layers of description. That's okay, if that's the way you like your universes. I just respond by saying that beneath your infinity stands God.
The order in the universe is a natural consequence of God's goals. By observing this order we can get some feel for how He accomplishes His goals, and we can even discern something about the nature of those goals. This is done by observation; not by faith. Faith we reserve for other things. We must have faith in ourselves, in our methods of observation, that the laws of the universe are immutable. Once we accept that faith, we can apply it to the task of determining the nature of God.