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Revelation via Natural Metaphore

You know how it is when you get a really great idea? Chances are, someone else was there first. Unfortunately, some really great ideas are not well known, except to a very few people. Finding out whether someone else had your idea before can sometimes be very difficult to do. (I had that experience years ago when I got an idea in the mathematics of the abstract, time-dependent Cauchy problem. I pursued it for 2 years, only to find out someone else had achieved better results with a slightly different idea. I was only 29 at the time, so I was pretty crushed by the experience.) It turns out Pope John Paul II got a really important idea way before I did (and, before him, we can credit St. Paul), and his application of it was immensely more important. I call the idea, revelation via natural metaphor. The late atheist, Carl Sagan, had a very similar idea, which he incorporated in his best-selling novel, Contact. Towards the end of his book, he wrote that the protagonist began to discover a coded message in the decimal expansion of π. If you think about the implications of that, you will begin to appreciate what the idea of revelation via natural metaphor is all about.

The case of the nuptial relationship:

To continue, let me quote from John Paul II's The Theology of the Body:
Man, who "from the beginning" is male and female, should seek the meaning of his existence and the meaning of his humanity by reaching out to the mystery of creation through the reality of redemption. There one finds also the essential answer to the question on the significance of the human body, and the significance of the masculinity and femininity of the human person. The union of Christ with the Church permits us to understand in what way the spousal significance of the body is completed with the redemptive significance, and this in the diverse ways of life and in diverse situations. It is not only in marriage or in continency (that is, virginity and celibacy), but also, for example, in the many forms of human suffering, indeed, in the very birth and death of man. By means of the great mystery which Ephesians treats of, by means of the new covenant of Christ with the Church, marriage is again inscribed with that "sacrament of man" which embraces the universe, in the sacrament of man and of the world which, thanks to the forces of the redemption of the body is modeled on the spousal love of Christ for the Church, to the measure of the definitive fulfillment of the kingdom of the Father. [p. 354]
What clued me in to the significance of this statement was a remark by Christopher West in The Theology of the Body Explained.
Nuptiality is a permanent dimension of love since all love entails some sort of complementarity ("otherness"), mutual self-giving, and fruitfulness. The eternal prototype is found in the Trinity itself: in the God who is love, in the God who is an eternal life-giving Communion of Persons. Of course we cannot speak of sexual difference and communion in the infinitely transcendent, Uncreated mystery of God. As the Catechism observes, "In no way is God in man's image... God is pure spirit in which there is no place for the difference between the sexes. But the respective 'perfections' of man and woman reflect something of the infinite perfections of God." We might say that male-female "otherness" and the call to fruitful communion is an "echo" in the created order of the transcendent mystery of "otherness," communion, and generous fruitfulness found in the Trinity. It is in this image that we are made as male and female. The divine Love is so generous that it bears fruit in the gift and mystery of our creation. [pp. 13-14]
I have emphasized the relevant statements about revelation in bold type in these two paragraphs. Such "echos" of devine self-revelation, it seemed to me some 8 or 9 years ago, occur in atomic and nuclear physics, as well. What got me to thinking about this were two very mysterious phenomena in physics: (1) virtual photons in electron-proton attraction and (2) quark confinement.

The case of virtual photons:

A virtual particle, according to Wikipedia, is a temporary elementary particle, used to describe an intermediate stage in an interaction between particles in quantum field theory.
These virtual particles are responsible for the interactions of the external particles (external legs of the diagram). For example, the electromagnetic interaction (referred to as photons) occurs due to the exchange of virtual photons. The fact that the particle number operator does not commute with the Hamiltonian implies the number of particles in an area of space is not a well-defined quantity, but like other quantum observables is represented by a probability distribution. Since these particles do not have a permanent existence, they are called virtual particles or vacuum fluctuations of vacuum energy. Antiparticles have been proven to exist and should not be confused with virtual antiparticles. Virtual particles and antiparticles arise in Quantum Field Theory as a result of the energy-time Uncertainty Principle. Virtual particles are an artifact of perturbation theory which do not appear in a nonperturbative treatment. As such, their ontological status is questionable.
That is, a virtual particles may or may not exist in reality, but they are a tremendous convenience in understanding the mathematics of quantum physics. Thus, a virtual photon is exchanged (or, we might say, shared) between an electron and a proton, and this exchange determines the physics of electron-proton attraction, i.e., this virtual photon is their binding energy. What is this an "echo" of? Consider specifically the hypostatic union. Christ is divine and human. His divinity is his nature as the Word of God, one of three divine Persons of the Trinity. His humanity is his nature seen by his disciples nearly 2000 years ago in the body of Jesus. His humanity shared divine power with his divinity in the person of the Holy Spirit, and in fact his hypostatic union was accomplished by the power of the Holy Spirit. Thus, I claim that electron-proton interaction is an image or an echo of the hypostatic union. The human part is imaged by the electron while the divine part is imaged by the proton. The combination, Jesus, is still a divine Person. This echoes the fact that a bare proton is still considered to be an atom of hydrogen. The role of the Holy Spirit is "played" by the virtual photon that binds the two together. The mysterious character of a virtual photon hints at the mystery of the Holy Spirit, once described by Jesus this way:
The wind blows where it wills, and you can hear the sound it makes, but you do not know where it comes from or where it goes; so it is with everyone who is born of the Spirit. [John 3:8]
Furthermore, the existence of the Holy Spirit is a matter of faith from revelation. That is to say, its ontological reality has been questioned, just like the ontological reality of virtual particles is in question. There is here, one might say, an "echo" of the inherent hiddenness of the Holy Spirit. More generally, electron-proton interaction may be seen as an echo of Jesus and his Mystical Body, the Church. It may also be seen as an echo of the nuptial relationship between Jesus and one of his saints. In that nuptial relationship, mediated by the Holy Spirit, the saint is "divinized." That is to say, the saint shares divine power with Jesus. The fact that the love between Jesus and one of his saints is viewed as nuptial love is well testified in the literature on mystical union. Of course, the frutfulness of this nuptial relationship can be seen as echoed in the abundance and importance of atoms in the universe.

The case of quark confinement

Quark confinement, according to Wikipedia, "is the physics phenomenon that quarks cannot be isolated." Quarks are held together in a baryon by a force known as the strong interaction. Unlike gravity and electro-magnetic force, which obey an inverse square law of attraction, or the weak nuclear force, which is effectively limited to a sub-atomic distance, however, the strong interaction obeys a direct linear law of attraction. That is to say, the attraction between quarks does not diminish with distance. It is, therefore, impossible to simply knock a single quark loose in any physics experiment. As it is put in Wikipedia,
When two quarks become separated, as happens in particle accelerator collisions, at some point it is more energetically favorable for a new quark/anti-quark pair to "pop" out of the vacuum than to allow the quarks to separate further. As a result of this, when quarks are produced in particle accelerators, instead of seeing the individual quarks in detectors, scientists see "jets" of many color-neutral particles (mesons and baryons), clustered together. This process is called hadronization, fragmentation or string breaking, and is one of the least understood processes in particle physics.
What is this an echo of? It may help us to look now at what quarks are.
Quarks are one of the two basic constituents of matter in the Standard Model of particle physics. (The others are leptons.) Antiparticles of quarks are called antiquarks. Quarks and antiquarks are the only fundamental particles which interact through all four of the fundamental forces. The single most important property of quarks is called confinement. This is the experimental fact that, except for the top quark which decays too rapidly, individual quarks are not seen — they are always confined inside hadrons, subatomic particles like protons, neutrons, and mesons. This fundamental property is expected to follow from the modern theory of strong interactions, called quantum chromodynamics (QCD). Although there is no mathematical derivation of confinement in QCD, it is easy to show using lattice gauge theory.
The most important class of particles composed of quarks are the baryons. According to Wikipedia,
In particle physics, the baryons are a family of subatomic particles including the proton and the neutron (collectively called nucleons), as well as a number of unstable, heavier particles (called hyperons). The term "baryon" is derived from the Greek barys, meaning "heavy," as they are heavier than the other main groups of particles. Baryons are strongly interacting fermions — that is, they experience the strong nuclear force and are described by Fermi-Dirac statistics, which apply to all particles obeying the Pauli exclusion principle. This is in contrast to the bosons, which do not obey the Exclusion principle. Baryons, along with mesons, belong to the family of particles known as hadrons, meaning they are composed of quarks. Baryons are fermions composed of three quarks, while mesons are bosons composed of a quark and an antiquark. The quark model classification of baryons is based on this construction.
Thus, the two main particles of physics, other than electrons, are the proton and the neutron. Together, protons, neutrons and electrons combine to form atoms, all the atoms of the universe. Thus, the portion of atoms that most closely echo divinity, the protons and neutrons, are each composed of three quarks, held together by a mysterious force that does not diminish. Indeed, individual quarks do not occur in isolation. This echos the "internal structure" of the Trinity, also known as the "Immanent Trinity." See "Immanent Trinity vs. Economic Trinity."

Conclusions:

To sum up, one could say that the most salient facts of nuclear physics echo the mystery of the Immanent vs. the Economic Trinity. Thus we have two completely different levels of nature, human sexuality and nuclear physics, each of which naturally echo the theology of the divinity and of divine and human interaction. Each is a kind of metaphor that reveals, i.e., is a revelation of God and of God's plan for creation.