Because the small knob of cells in vertebrate brains is today separated from the brain and no longer has a clear sensory function, it is known as the pineal body, an isolated bit of tissue with one or two distinct functions. It secretes hormones in some species, while close examination of others shows it contains special sensory cells whose function is still uncertain.
The odd thing is that despite the pineal body's modification in most "higher" animals, such as reptiles, a recognizable middle eye remains in a few lizards. We can still see it -- just barely -- in common anoles, those popular little green and brown lizards incorrectly called chameleons often sold in pet shops. It takes a magnifier to see the median eye in an anole, for it is almost featureless and almost certainly without function as an organ of sight.
There is, however, a pretty good centrally-placed eye on the head of a rare, primitive lizard, the tuatara (Sphenodon), that survives only on certain small islands off New Zealand. The tuatara's median eye is well-developed and easily recognizable, although covered by translucent scales. Within the eye itself clear evidence of a retina remains and the animal responds to light, if not to images.
If a light-sensitive organ, or third eye, is present in certain fishes, frogs, and a few reptiles, what form does its descendant pineal body take in our feathered friends and in mammals, all of which evolved from reptiles? Neither birds nor mammals have the least sign of a median eye in their heads, but they do have a well-developed pineal body attached by a stalk to the rear of a cavity deep inside the brain. Close examination shows it is served by nerves and nourished by blood vessels, evidence that suggests a vital function.
Experimentation reveals that in birds the pineal body is affected by light, even though it is not any sort of eye. It seems to be responsible for detecting (without visual means) the shortening or lengthening of days preparatory to migration. Such sensitivity establishes a biorhythm, or a biological clock. Biological clocks of one sort or another are evident even in us.
The pineal body has sufficient secretory function to be called a gland. In 1958 A. B. Lerner discovered that pineal glands secrete a hormone, melatonin, whose abundance increases in darkness and decreases in light. Melatonin has since been found to be involved in various functions affected by the duration of light, including reproductive cycles in some animals. It is often in the news as a human sleep aid, although the medical profession has not yet fully embraced either its effectiveness or its safety when it is purchased without prescription over the counter.
All nerves produce substances called neurotransmitters, one of which, serotonin, is responsible for producing melatonin in the pineal gland. It is evident that this tiny organ, once part of a functioning third eye in primitive vertebrates, has developed a new, different, and vitally important role in the well-being of higher vertebrates.
If the pineal body in birds is tied in with their seasonal migratory patterns, it has also been found to play a role in both the seasonal and the day-night behavior of other vertebrates. It may have short term effects like sleep cycles, or very long term ones, such as the delayed onset of puberty in humans.
In the animal world there are many instances of one organ evolving into something different from its origins -- a recycling of swim bladders into lungs, fins into arms and legs, fish scales into teeth -- but nothing more remarkable than the refashioning of a tiny part of the ancient brain, once responsible for detecting light and moving objects, to become part of a chemical system that tells a bird to fly to inherited destinations, that eases us into sleep, or that leads a youth through adolescence into adulthood.
The middle eye is gone; the old structure has been lost; still the pineal remnant helps control our growing-up and our daily and nightly rhythm. When you tuck yourself into bed tonight, give a silent nod to an ancient fish and its frog descendants.