Bioluminescence

Most of the habitable volume of this planet is deep ocean, and it is dark. In that volume, making your own light is not exotic — surveys of open-water animals in Monterey Bay found roughly three-quarters of them capable of it. Bioluminescence is the norm; we are the unusual ones.

The chemistry

The reaction is simple in outline: a substrate called a luciferin is oxidized by an enzyme called a luciferase, and the energy comes out as a photon instead of heat. It is extraordinarily efficient — almost no waste warmth, which is why it is called cold light. “Luciferin” is a job description, not a molecule; the versions used by fireflies, jellyfish, and deep-sea shrimp are chemically unrelated, and the ability has evolved independently on the order of fifty separate times.

Borrowed light

Many marine animals cannot make their luciferin at all. Coelenterazine, the most widespread one in the ocean, is acquired through diet and passed up the food chain. Others outsource the whole apparatus: anglerfish and bobtail squid cultivate symbiotic bacteria in dedicated organs, feeding them and controlling the output with shutters and reflectors, like housing a colony in a lamp.

Hiding by glowing

The least intuitive use is camouflage. In the twilight zone, a predator looking upward sees prey as a silhouette against faint downwelling light. Hatchetfish and many squid counter this with rows of ventral photophores that emit downward at precisely the intensity and color of the water above, erasing the shadow. Some tune the output as surface light changes through the day.

Private wavelengths

Nearly all marine bioluminescence is blue-green, because that penetrates seawater furthest — and so nearly every deep-sea eye is tuned to blue-green and blind to red. The stoplight loosejaw exploits this with a red-emitting organ plus a retinal pigment apparently derived from chlorophyll, giving it a searchlight its prey cannot see. Other animals go the opposite way: a harassed dinoflagellate flashes to advertise its attacker to something larger, a burglar alarm rather than a weapon.

The jellyfish that changed biology

Osamu Shimomura, working through tens of thousands of Aequorea victoria, isolated a protein that glowed green under ultraviolet light. Green fluorescent protein became the standard way to make a cell's inner workings visible — splice its gene onto any protein you want to follow and watch it move. It earned a Nobel Prize in 2008, and it is a reasonable argument that basic curiosity about glowing animals paid for itself several times over.