There is a profound principal in the universe that says there is no central entity or notion anywhere, and that everything has no special significance than any other things in physics terms. This principal dispelled 'earth-centric' idea and later the Newtonian absolute time-space concept. It is a universally accepted principal in modern science. If math and physics are intertwined inextricably then it seems natural numbers ought to have an equal standing as any other numbers, irrational, complex, or even numbers yet to be invented.
Is there any physical underlying reason for natural numbers' special status? Or are the natural numbers just a convenient way for people to count and were invented by macro intelligent beings like us?
Since all natural numbers are mere derivatives of the number '1', so let's look closely at what this number one really means. There are two broad meaning of the number one. First it registers a definitive state of some physical attribute, such as 'presence' or 'non-presence'. We can find its application in information theory, statistical physics, counting and etc. The second interpretation of number one is that it denotes the 'wholeness' of an entity.
In physics, natural numbers virtually have no sacred places prior to the establishment of quantum mechanics. After all, we don't need any natural numbers in our gravity functions or the Maxwell electro-magnetic wave functions. Some sharp observers would argue that the 'R squared' contains a natural number 2. However on close examination the number 2 is merely a mathematical notation for a number multiplying by itself, and it has no actual physical corresponding object or attribute. The fact that there is no natural number in the formulae represents the idea that time-space is fundamentally smooth. For instance there is no such law in physics that requires 7 bodies (non quantum mechanical) to form a system in equilibrium.
Had we obtained calculus capability before we can count our fingers, we probably would have been more familiar with the number e than 1-2-3. We might have used e/2.718 to represent the mundane singletons. There is no logical requirement that we couldn't or shouldn't do it. It is all due to the accident that people happened to need to count their fingers earlier than the invention of calculus. There is no physical evidence that the number '2' is more significant than the any other numbers in the natural world.
However with the standard model of quantum mechanics, energy is quantized, that is, it can only take natural numbers. This idea profoundly altered the status of natural numbers in physics and is a direct contradictory of the notion of 'no center in the universe' principal. In this sense it is far more unorthodox than the two relativity theories combined because the latter in fact enhance the 'no center in the universe' law. Why does the quantum have to be integer times of a certain energy level, and not an irrational number like square root of 17, or the quantity e? Does it really mean there are aristocrats in the number world, where some are nobler than others? Were the ancient Greek mathematicians right after all, who worshiped the sacredness of natural numbers and even threw the irrational number discoverer into the sea?
From this standpoint we can almost say that quantum theory has some bad taste among all branches of natural science.
Before the quantum theory got its germination, actually people should have noticed the unusual role natural numbers play in rudimentary chemistry. For instance, why two hydrogen atoms and not five, are supposed to combine with one oxygen atom to form a water molecule? If scientists are sharp enough back then they ought to be able to be alarmed by the oddity underlying the strange status of natural numbers. It could almost be an indirect way to deduce the quantized nature of electrons.
Fundamentally if natural numbers indeed play a very unusual role in nature, then nature resembles a codebook not just from a coarse analogy standpoint. It is the ultimate codebook filled with rules for a limited number of building block codes. The DNA code is an excellent example.
If it's a codebook, inevitably it takes us to surmise if information itself is the ultimate being in the universe. It is probably not electrons, strings, quarks or whatever 'entities' people have claimed. It is the information that is the only tangible and verifiable entity out there. Everything else is a mirage or manifestation of some underlying information, the codebook.
In this sense physics has somewhat gone awry by focusing on the wrong things, the 'attributes' such as momentum, position and etc. Instead, information is what contemporary physicists talk about and experiment with. Otherwise, the physicists would have no right to laugh at the medieval scholars who based their intellectual work on the measurement of the distance between a subject and God's throne.
The nature has revealed her latest hand of cards to us. It looks like it's the final hand but no one can be sure of course.