The element of harmonium · 4:22am Dec 20th, 2016
Ok, let's get this part out of the way - while I am working on stories occasionally, there is no foreseeable updates coming to any of my stories anytime soon.
With that done, let's get to the point of this post - presentation of a half-dreamt, half-imagined idea that someone might want to turn into a detail in a story one day. Keep in mind, this seemed good when I was half awake.
What is the source of magic. Have a clue? Some faint idea? Either way, some readers will expect some kind of explanation. Here's one that sounds just magically scientific enough to work: a stable isotope of technetium, known to pony chemists as harmonium. This isotope is exceedingly rare, but is found in dectectable quantities in certain materials on and near Equis, such as unicorn horns, gemstones, and solar plasma, as well as a part or two per quadrillion in the atmosphere. When heated (such as in the sun), it emits vast amounts of photons, mainly visible light, but some with a wavelength of just a few Plank lengths (For those less scientifically minded, that's the absolute minimum length), or "omega radiation", as pony physicists call it. This radiation causes otherwise impossible things to happen, and such things would appear to be magic to the layman (or laypony, as the case may be).
Some more details:
Harmonium is strongly self-attracting, and reacts energetically to any omega radiation, glowing bright enough to be seen through walls. Certain unicorns, like Rarity, can use this to find otherwise hidden deposits, which are mainly gems. In fact, it was this property that dragged her out into the wilderness the day of Rainbow's first Sonic Rainboom.
The Rainboom itself was the result of compressing harmonium in the air to a certain point. The Rainboom at the wedding was partially Celestia's doing - instead of relying on luck to have enough, she released a fixed amount above the castle at the right time. A mellenium of governing will give you a feel for dramatic timing, it seems.
Alicorn horns are denser than unicorn horns, mainly due to the increase in the isotope present. This greatly increases their magical potential.
Six gemstones are especially rich in harmonium - the elements of harmony, from which the isotope got its name. The tree of harmony, which gave fruit to the elements, is not a plant in any sense, but instead an incredibly large deposit of this isotope, attracted over the lifetime of the planet. Rumor has it that Discord himself planted the seed crystal in the ground.
Speaking of Discord, it could be that he is the last of an ancient species, granted immortality and power over omega radiation by that selfsame power. He has been driven mad over time, losing all that he cared for, and watching the world change in such a strange yet predictable fashion. Perhaps he figured that enough radiation would eventually make another like him. At the very least, it would make things more interesting.