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Bioluminescence is a way of living organisms to emit light. It is employed by nearly all Pandoran animals. Even the Na'vi have patterns of glowing dots that are unique to each individual. To avoid being detected by predators or prey, animals can damp down their own light. The RDA exploited it as another resource in the form of exotic jewelry and clothing.
Most of Pandora's flora and fauna emits only one single color, often green, blue, indigo, or violet. There are exceptions like the Warbonnet Fern. Its leaves are illuminated by a broad band of red near their stems and by an iridescent blue near their tips. On Pandora, there is also a bioluminescent moss that is touch-sensitive. It will send out rings of blue-green light as a reaction to footsteps.
Bioluminescence is an enzymatic reaction that produces so called cold light. This reaction raises the valence electrons in the molecules of an organic compound to an orbit of higher energy. While decaying to its original state the electrons emit photons of visible light. It is a highly efficient reaction as it converts nearly all energy into light.
The reaction can occur within the metabolism of the creature or within symbiotic organisms that live inside of specialized organs, receiving food and oxygen from their host, and producing light in return.
Eywa is the guiding force and deity of Pandora and the Na'vi. The Na'vi believe that Eywa acts to keep the ecosystem of Pandora in perfect equilibrium. It is sometimes theorized by Earth scientists that all living things on Pandora connect to Eywa through a system of neuro-conductive antennae; this often explains why Na'vi can mount their Direhorse or Banshee steeds and ride them immediately without going through the necessary steps required to domesticate such wild animals.
Some believe that this interconnectedness, which on Earth is merely a spiritual concept, exists in a physical and tangible way on Pandora, in the form of a strange, collective psionic consciousness embedded in the planet, drawn from all Pandoran life. It is, in a way, a bit like a huge biological internet; the trees being computer servers that store information. The Na'vi can upload or download memories from it using their queues and it can even be used for mind transfers in certain cases.
Iknimaya is a treacherous but fundamental rite of passage in which a young Na'vi must select, capture, and successfully bond with one of the ikran who nest in the Hallelujah Mountains.
To connect the queue between the rider and the animal to create the bond, a Banshee Catcher is snapped around the eyes and snout of the ikran. Thus temporarily blinding the animal, a young Na'vi may leap onto its back and connect queues. In this moment, sealed by the subsequent first flight, a lifelong bond is established that allows the Na'vi and banshee to ride through the sky with elegant, seemingly effortless coordination.
A Woodsprite (Na'vi name: Atokirina') is a seed of the Tree of Souls that lives on Pandora. These seeds, according to the Na'vi, are considered very pure and sacred spirits. Furthermore, these seeds are believed to be auspicious wheresoever they choose to rest. They are similar in appearance to small deep-sea jellyfish, but they float on the wind like dandelion seeds, possibly aided in this by the denser atmosphere on Pandora. Woodsprites also hold ritual importance. The Omaticaya Clan plants one of these seeds with the body of a deceased Na'vi, so the Na'vi's consciousness will become part of Eywa.
Strangely, despite the Woodsprite's omnipresence, no other Trees of Souls appear in the movie. This may imply that the seeds are actually infertile or serve another purpose besides reproduction. This would make the Tree of Souls a truly unique entity, since its seeds could not be used to germinate another one in the scenario that original tree was destroyed, damaged, or captured.