Among the more esoteric mysteries of the universe you'll find what is also one of its biggest: missing antimatter. The physics of subatomic particles teaches us that the creation of matter from energy, in which some high energy massless particle collides with another particle to create some massive particle like an electron or proton, results in not just the expected particle but a particle pair. One of those particles is of the "normal" sort that comprises most of our cosmic reality, and the other is its antimatter partner.
Think of the collision and resulting matter as knocking out a divot of grass with a golf club. There's the airborne chunk of sod, but also the hole left in the ground. The sod is a typical elementary particle, like a proton or electron, but the hole is its own very real particle as well. The difference is that the hole has entirely opposite properties. It's antimatter, the result of every single reaction that creates matter, from the birth of the universe until eternity.
It's simply impossible to kick out a divot of grass without leaving a hole, and the swing of the golf club must have enough energy behind it to create the mass of both, the regular matter chunk and the antimatter hole. They both have the same mass, and so require the energy to create two equal masses, but some minority of physicists suspect the antimatter particle really has negative mass (which would theoretically give rise to things like antigravity). We see this antimatter/matter pair creation in nature regularly in the upper atmosphere, where high-energy cosmic rays bomb atomic nuclei, resulting in showers of particles and antiparticles.
The not-quite-obvious mystery implied by antimatter creation is that there should be a whole lot of antimatter out there somewhere in the universe, just as much as there is regular matter in fact. However, that appears not to be the case. While it's true that antimatter has the same potential to form into all of the amazing structures of the universe, from black holes to human life, we can reasonably say that what we're looking at out there is regular matter with little to no antimatter interspersed.
Even if we could make out some distant antimatter galaxy, it wouldn't solve the fundamental problem of why some matter continues to exist at all: Equal parts anti- and plain old matter should have left nothing but energy, yet here we are. The imbalance problem is known as baryon asymmetry and it's among the most immediate why are we here?-type physics mysteries. One hope is that by looking very closely at the properties of matter and its antimatter counterparts, we might find some difference beyond simple opposition. Perhaps antimatter charges are slightly different in magnitude, or the antiparticle particles have slightly different masses.
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