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Genetics aside, what are the biochemical reasons for the different colours of human irises?
Also, related, how does eye colour change, particularly in childhood? (example: my eyes used to be blue, but are now greenish-hazel).
The colour of human eyes is determined by the pigmentation present and the scattering of light. Variance in the colour and density of the pigments affects how light is absorbed and reflected causing the different iris colours we see. Wiki has a fairly comprehensive coverage on the topic so,I'll use a few of the wikipedia examples to explain how the pigmentation and scattering of light interact to give colours:
Blue eye colour is the result of pigment in low concentration and Rayleigh scattering (or Tyndall effect) of the short light wavelengths (blue is short, red is long).
"There is no blue pigmentation either in the iris or in the ocular fluid. Dissection reveals that the iris pigment epithelium is brownish black due to the presence of melanin. Unlike brown eyes, blue eyes have low concentrations of melanin in the stroma of the iris, which lies in front of the dark epithelium. Longer wavelengths of light tend to be absorbed by the dark underlying epithelium, while shorter wavelengths are reflected and undergo Rayleigh scattering in the turbid medium of the stroma. This is the same frequency-dependence of scattering that accounts for the blue appearance of the sky. The result is a "Tyndall blue" structural color that varies with external lighting conditions.
Brown eyes are the result of higher melanin concentrations which absorbs more of the light, reducing the amount of light being reflected.
"In humans, brown eyes result from a relatively high concentration of melanin in the stroma of the iris, which causes light of both shorter and longer wavelengths to be absorbed."
Green eyes appear to be mid-ground between blue and brown, they have more pigment than blue but less than brown.
"As in the case of blue eyes, the color of green eyes does not result simply from the pigmentation of the iris. Rather, its appearance is caused by the combination of an amber or light brown pigmentation of the stroma, given by a low or moderate concentration of melanin, with the blue tone imparted by the Rayleigh scattering of the reflected light."
More can be read on this in these two studies: study 1 & study 2
What is Rayleigh scattering / the Tyndall effect and why do they turn eyes blue?
I shall refer to this as the Tyndall effect but in the literature both Rayleigh and Tyndall are used because they are apparently very similar though Tyndall occurs with much larger particles. The Tyndall effect is caused by the variable scattering of light by particles depending on the wavelength of the light and relative size of the particles. Shorter wavelength lights are scattered more than the longer ones (so more red light is absorb than blue) which means more blue light is reflected. When more melanin is present in the iris it will better absorb the short wavelength light than when there is little melanin, therefore, people with low melanin levels appear to have blue eyes.
"An analogy to this wavelength dependency is that longwave electromagnetic waves such as radio waves are able to pass through the walls of buildings, while shortwave electromagnetic waves such as light waves are stopped and reflected by the walls."
Why do eye colours change?
Again, wikipedia has a fairly thorough section on this and I will just summarise and directly quote it. Eye colour can change because the melanocytes responsible for the pigments have to continually produce pigment and, just like those causing colour in hair, they can become less productive (which is why we have grey hair) and this happens more with age. Infants often have blue eyes that turn dark, just like yours did, because the melanin is gradually accumulated - it just takes time for enough pigment to build up and allow the eye colour to match it's genetic determinants:
"Most babies who have European ancestry have light-colored eyes before the age of one. As the child develops, melanocytes (cells found within the iris of human eyes, as well as skin and hair follicles) slowly begin to produce melanin. Because melanocyte cells continually produce pigment, in theory eye color can be changed. Most eye changes happen when the infant is around one year old, although it can happen up to three years of age. Observing the iris of an infant from the side using only transmitted light with no reflection from the back of the iris, it is possible to detect the presence or absence of low levels of melanin. An iris that appears blue under this method of observation is more likely to remain blue as the infant ages. An iris that appears golden contains some melanin even at this early age and is likely to turn green or brown as the infant ages. Changes (lightening or darkening) of eye colors during puberty, early childhood, pregnancy, and sometimes after serious trauma (like heterochromia) do represent cause for plausible argument to state that some eyes can or do change, based on chemical reactions and hormonal changes within the body… eye color over time can be subject to change, and major demelanization of the iris may also be genetically determined."
In this study 10-15% of those studied had changes in eye colour beyond childhood so, al though colour is generally stable past childhood, it is not uncommon for eyes to change, and this is likely due to changes in melanin composition. This study is an example of clour change in birds too.
A side note: Animals with other colours
It is common for animals to have other eye colours, for example Blackbirds (Turdus merula) have an Orange eye, which is caused by Carotenoid pigments, rather than melanin as in humans. The reason they have this could be as an indicator of quality in courtship - carotenoids are hard to get, males with bright orange eyes therefore have access to good food resources, and female blackbirds find that attractive. (This section is all from my memory after a talk with a tutor on my undergrad field course in the Isles of Scilly).
What Is the Visible Light Spectrum?
The visible light spectrum is the section of the electromagnetic radiation spectrum that is visible to the human eye. Essentially, that equates to the colors the human eye can see. It ranges in wavelength from approximately 400 nanometers (4 x 10 -7 m, which is violet) to 700 nm (7 x 10 -7 m, which is red). It is also known as the optical spectrum of light or the spectrum of white light.
How Do We See Color?
When light hits an object – say, a banana – the object absorbs some of the light and reflects the rest of it. Which wavelengths are reflected or absorbed depends on the properties of the object.
For a ripe banana, wavelengths of about 570 to 580 nanometers bounce back. These are the wavelengths of yellow light.
When you look at a banana, the wavelengths of reflected light determine what color you see. The light waves reflect off the banana's peel and hit the light-sensitive retina at the back of your eye. That's where cones come in.
Cones are one type of photoreceptor, the tiny cells in the retina that respond to light. Most of us have 6 to 7 million cones, and almost all of them are concentrated on a 0.3 millimeter spot on the retina called the fovea centralis.
Not all of these cones are alike. About 64 percent of them respond most strongly to red light, while about a third are set off the most by green light. Another 2 percent respond strongest to blue light.
When light from the banana hits the cones, it stimulates them to varying degrees. The resulting signal is zapped along the optic nerve to the visual cortex of the brain, which processes the information and returns with a color: yellow.
Humans, with our three cone types, are better at discerning color than most mammals, but plenty of animals beat us out in the color vision department. Many birds and fish have four types of cones, enabling them to see ultraviolet light, or light with wavelengths shorter than what the human eye can perceive.
Some insects can also see in ultraviolet, which may help them see patterns on flowers that are completely invisible to us. To a bumblebee, those roses may not be so red after all.
Isaac Newton discovered that white light after being split into its component colors when passed through a dispersive prism could be recombined to make white light by passing them through a different prism.
The visible light spectrum ranges from about 380 to 740 nanometers. Spectral colors (colors that are produced by a narrow band of wavelengths) such as red, orange, yellow, green, cyan, blue, and violet can be found in this range. These spectral colors do not refer to a single wavelength, but rather to a set of wavelengths: red, 625–740 nm orange, 590–625 nm yellow, 565–590 nm green, 500–565 nm cyan, 485–500 nm blue, 450–485 nm violet, 380–450 nm.
Wavelengths longer or shorter than this range are called infrared or ultraviolet, respectively. Humans cannot see these wavelengths, but other animals may.
Hue detection Edit
Sufficient differences in wavelength cause a difference in the perceived hue the just-noticeable difference in wavelength varies from about 1 nm in the blue-green and yellow wavelengths to 10 nm and more in the longer red and shorter blue wavelengths. Although the human eye can distinguish up to a few hundred hues, when those pure spectral colors are mixed together or diluted with white light, the number of distinguishable chromaticities can be quite high. [ ambiguous ]
In very low light levels, vision is scotopic: light is detected by rod cells of the retina. Rods are maximally sensitive to wavelengths near 500 nm and play little, if any, role in color vision. In brighter light, such as daylight, vision is photopic: light is detected by cone cells which are responsible for color vision. Cones are sensitive to a range of wavelengths, but are most sensitive to wavelengths near 555 nm. Between these regions, mesopic vision comes into play and both rods and cones provide signals to the retinal ganglion cells. The shift in color perception from dim light to daylight gives rise to differences known as the Purkinje effect.
The perception of "white" is formed by the entire spectrum of visible light, or by mixing colors of just a few wavelengths in animals with few types of color receptors. In humans, white light can be perceived by combining wavelengths such as red, green, and blue, or just a pair of complementary colors such as blue and yellow. 
Non-spectral colors Edit
There are a variety of colors in addition to spectral colors and their hues. These include grayscale colors, shades of colors obtained by mixing grayscale colors with spectral colors, violet-red colors, impossible colors, and metallic colors.
Grayscale colors include white, gray, and black. Rods contain rhodopsin, which reacts to light intensity, providing grayscale coloring.
Shades include colors such as pink or brown. Pink is obtained from mixing red and white. Brown may be obtain from mixing orange with grey or black. Navy is obtained from mixing blue and black.
Violet-red colors include hues and shades of magenta. The light spectrum is a line on which violet is one end and the other is red, and yet we see hues of purple that connect those two colors.
Impossible colors are a combination of cone responses that cannot be naturally produced. For example, medium cones cannot be activated completely on their own if they were, we would see a 'hyper-green' color.
Perception of color begins with specialized retinal cells known as cone cells. Cone cells contain different forms of opsin – a pigment protein – that have different spectral sensitivities. Humans contain three types, resulting in trichromatic color vision.
Each individual cone contains pigments composed of opsin apoprotein covalently linked to a light-absorbing prosthetic group: either 11-cis-hydroretinal or, more rarely, 11-cis-dehydroretinal. 
The cones are conventionally labeled according to the ordering of the wavelengths of the peaks of their spectral sensitivities: short (S), medium (M), and long (L) cone types. These three types do not correspond well to particular colors as we know them. Rather, the perception of color is achieved by a complex process that starts with the differential output of these cells in the retina and which is finalized in the visual cortex and associative areas of the brain.
For example, while the L cones have been referred to simply as red receptors, microspectrophotometry has shown that their peak sensitivity is in the greenish-yellow region of the spectrum. Similarly, the S cones and M cones do not directly correspond to blue and green, although they are often described as such. The RGB color model, therefore, is a convenient means for representing color but is not directly based on the types of cones in the human eye.
The peak response of human cone cells varies, even among individuals with so-called normal color vision  in some non-human species this polymorphic variation is even greater, and it may well be adaptive. [ jargon ] 
Two complementary theories of color vision are the trichromatic theory and the opponent process theory. The trichromatic theory, or Young–Helmholtz theory, proposed in the 19th century by Thomas Young and Hermann von Helmholtz, posits three types of cones preferentially sensitive to blue, green, and red, respectively. Ewald Hering proposed the opponent process theory in 1872.  It states that the visual system interprets color in an antagonistic way: red vs. green, blue vs. yellow, black vs. white. Both theories are generally accepted as valid, describing different stages in visual physiology, visualized in the adjacent diagram.  : 168 Green ←→ Magenta and Blue ←→ Yellow are scales with mutually exclusive boundaries. In the same way that there cannot exist a "slightly negative" positive number, a single eye cannot perceive a bluish-yellow or a reddish-green. Although these two theories are both currently widely accepted theories, past and more recent work has led to criticism of the opponent process theory, stemming from a number of what are presented as discrepancies in the standard opponent process theory. For example, the phenomenon of an after-image of complementary color can be induced by fatiguing the cells responsible for color perception, by staring at a vibrant color for a length of time, and then looking at a white surface. This phenomenon of complementary colors demonstrates cyan, rather than green, to be the complement of red and magenta, rather than red, to be the complement of green, as well as demonstrating, as a consequence, that the reddish-green color proposed to be impossible by opponent process theory is, in fact, the colour yellow. Although this phenomenon is more readily explained by the trichromatic theory, explanations for the discrepancy may include alterations to the opponent process theory, such as redefining the opponent colours as red vs. cyan, to reflect this effect. Despite such criticisms, both theories remain in use. A recent demonstration, using the Color Mondrian, has shown that, just as the colour of a surface that is part of a complex 'natural' scene is independent of the wavelength-energy composition of the light reflected from it alone but depends upon the composition of the light reflected from its surrounds as well, so the after image produced by looking at a given part of a complex scene is also independent of the wavelength energy-composition of the light reflected from it alone. Thus, while the color of the after-image produced by looking at a green surface that is reflecting more 'green' (middle-wave) than "red" (long-wave) light is magenta, so is the after image of the same surface when it reflects more "red" than "green" light (when it is still perceived as green). This would seem to rule out an explanation of color opponency based on retinal cone adaptation. 
Cone cells in the human eye Edit
A range of wavelengths of light stimulates each of these receptor types to varying degrees. The brain combines the information from each type of receptor to give rise to different perceptions of different wavelengths of light.
|Cone type||Name||Range||Peak wavelength  |
|S||β||400–500 nm||420–440 nm|
|M||γ||450–630 nm||534–555 nm|
|L||ρ||500–700 nm||564–580 nm|
Cones and rods are not evenly distributed in the human eye. Cones have a high density at the fovea and a low density in the rest of the retina.  Thus color information is mostly taken in at the fovea. Humans have poor color perception in their peripheral vision, and much of the color we see in our periphery may be filled in by what our brains expect to be there on the basis of context and memories. However, our accuracy of color perception in the periphery increases with the size of stimulus. 
The opsins (photopigments) present in the L and M cones are encoded on the X chromosome defective encoding of these leads to the two most common forms of color blindness. The OPN1LW gene, which encodes the opsin present in the L cones, is highly polymorphic one study found 85 variants in a sample of 236 men.  A small percentage of women may have an extra type of color receptor because they have different alleles for the gene for the L opsin on each X chromosome. X chromosome inactivation means that while only one opsin is expressed in each cone cell, both types may occur overall, and some women may therefore show a degree of tetrachromatic color vision.  Variations in OPN1MW, which encodes the opsin expressed in M cones, appear to be rare, and the observed variants have no effect on spectral sensitivity.
Color in the human brain Edit
Color processing begins at a very early level in the visual system (even within the retina) through initial color opponent mechanisms. Both Helmholtz's trichromatic theory and Hering's opponent-process theory are therefore correct, but trichromacy arises at the level of the receptors, and opponent processes arise at the level of retinal ganglion cells and beyond. In Hering's theory opponent mechanisms refer to the opposing color effect of red-green, blue-yellow, and light-dark. However, in the visual system, it is the activity of the different receptor types that are opposed. Some midget retinal ganglion cells oppose L and M cone activity, which corresponds loosely to red–green opponency, but actually runs along an axis from blue-green to magenta. Small bistratified retinal ganglion cells oppose input from the S cones to input from the L and M cones. This is often thought to correspond to blue–yellow opponency but actually runs along a color axis from yellow-green to violet.
Visual information is then sent to the brain from retinal ganglion cells via the optic nerve to the optic chiasma: a point where the two optic nerves meet and information from the temporal (contralateral) visual field crosses to the other side of the brain. After the optic chiasma, the visual tracts are referred to as the optic tracts, which enter the thalamus to synapse at the lateral geniculate nucleus (LGN).
The lateral geniculate nucleus is divided into laminae (zones), of which there are three types: the M-laminae, consisting primarily of M-cells, the P-laminae, consisting primarily of P-cells, and the koniocellular laminae. M- and P-cells receive relatively balanced input from both L- and M-cones throughout most of the retina, although this seems to not be the case at the fovea, with midget cells synapsing in the P-laminae. The koniocellular laminae receive axons from the small bistratified ganglion cells.  
After synapsing at the LGN, the visual tract continues on back to the primary visual cortex (V1) located at the back of the brain within the occipital lobe. Within V1 there is a distinct band (striation). This is also referred to as "striate cortex", with other cortical visual regions referred to collectively as "extrastriate cortex". It is at this stage that color processing becomes much more complicated.
In V1 the simple three-color segregation begins to break down. Many cells in V1 respond to some parts of the spectrum better than others, but this "color tuning" is often different depending on the adaptation state of the visual system. A given cell that might respond best to long-wavelength light if the light is relatively bright might then become responsive to all wavelengths if the stimulus is relatively dim. Because the color tuning of these cells is not stable, some believe that a different, relatively small, population of neurons in V1 is responsible for color vision. These specialized "color cells" often have receptive fields that can compute local cone ratios. Such "double-opponent" cells were initially described in the goldfish retina by Nigel Daw   their existence in primates was suggested by David H. Hubel and Torsten Wiesel, first demonstrated by C.R. Michael  and subsequently proven by Bevil Conway.  As Margaret Livingstone and David Hubel showed, double opponent cells are clustered within localized regions of V1 called blobs, and are thought to come in two flavors, red–green and blue-yellow.  Red-green cells compare the relative amounts of red-green in one part of a scene with the amount of red-green in an adjacent part of the scene, responding best to local color contrast (red next to green). Modeling studies have shown that double-opponent cells are ideal candidates for the neural machinery of color constancy explained by Edwin H. Land in his retinex theory. 
From the V1 blobs, color information is sent to cells in the second visual area, V2. The cells in V2 that are most strongly color tuned are clustered in the "thin stripes" that, like the blobs in V1, stain for the enzyme cytochrome oxidase (separating the thin stripes are interstripes and thick stripes, which seem to be concerned with other visual information like motion and high-resolution form). Neurons in V2 then synapse onto cells in the extended V4. This area includes not only V4, but two other areas in the posterior inferior temporal cortex, anterior to area V3, the dorsal posterior inferior temporal cortex, and posterior TEO.   Area V4 was initially suggested by Semir Zeki to be exclusively dedicated to color,  and he later showed that V4 can be subdivided into subregions with very high concentrations of color cells separated from each other by zones with lower concentration of such cells though even the latter cells respond better to some wavelengths than to others,  a finding confirmed by subsequent studies.    The presence in V4 of orientation-selective cells led to the view that V4 is involved in processing both color and form associated with color  but it is worth noting that the orientation selective cells within V4 are more broadly tuned than their counterparts in V1, V2 and V3.  Color processing in the extended V4 occurs in millimeter-sized color modules called globs.   This is the part of the brain in which color is first processed into the full range of hues found in color space.   
Anatomical studies have shown that neurons in extended V4 provide input to the inferior temporal lobe. "IT" cortex is thought to integrate color information with shape and form, although it has been difficult to define the appropriate criteria for this claim. Despite this murkiness, it has been useful to characterize this pathway (V1 > V2 > V4 > IT) as the ventral stream or the "what pathway", distinguished from the dorsal stream ("where pathway") that is thought to analyze motion, among other features.
Color is a feature of visual perception by an observer. There is a complex relationship between the wavelengths of light in the visual spectrum and human experiences of color. Although most people are assumed to have the same mapping, the philosopher John Locke recognized that alternatives are possible, and described one such hypothetical case with the "inverted spectrum" thought experiment. For example, someone with an inverted spectrum might experience green while seeing 'red' (700 nm) light, and experience red while seeing 'green' (530 nm) light. This inversion has never been demonstrated in experiment, though.
Synesthesia (or ideasthesia) provides some atypical but illuminating examples of subjective color experience triggered by input that is not even light, such as sounds or shapes. The possibility of a clean dissociation between color experience from properties of the world reveals that color is a subjective psychological phenomenon.
The Himba people have been found to categorize colors differently from most Westerners and are able to easily distinguish close shades of green, barely discernible for most people.  The Himba have created a very different color scheme which divides the spectrum to dark shades (zuzu in Himba), very light (vapa), vivid blue and green (buru) and dry colors as an adaptation to their specific way of life.
The perception of color depends heavily on the context in which the perceived object is presented.
Chromatic adaptation Edit
In color vision, chromatic adaptation refers to color constancy the ability of the visual system to preserve the appearance of an object under a wide range of light sources.  For example, a white page under blue, pink, or purple light will reflect mostly blue, pink, or purple light to the eye, respectively the brain, however, compensates for the effect of lighting (based on the color shift of surrounding objects) and is more likely to interpret the page as white under all three conditions, a phenomenon known as color constancy.
In color science, chromatic adaptation is the estimation of the representation of an object under a different light source from the one in which it was recorded. A common application is to find a chromatic adaptation transform (CAT) that will make the recording of a neutral object appear neutral (color balance), while keeping other colors also looking realistic.  For example, chromatic adaptation transforms are used when converting images between ICC profiles with different white points. Adobe Photoshop, for example, uses the Bradford CAT. 
Many species can see light with frequencies outside the human "visible spectrum". Bees and many other insects can detect ultraviolet light, which helps them to find nectar in flowers. Plant species that depend on insect pollination may owe reproductive success to ultraviolet "colors" and patterns rather than how colorful they appear to humans. Birds, too, can see into the ultraviolet (300–400 nm), and some have sex-dependent markings on their plumage that are visible only in the ultraviolet range.   Many animals that can see into the ultraviolet range, however, cannot see red light or any other reddish wavelengths. For example, bees' visible spectrum ends at about 590 nm, just before the orange wavelengths start. Birds, however, can see some red wavelengths, although not as far into the light spectrum as humans.  It is a myth that the common goldfish is the only animal that can see both infrared and ultraviolet light  their color vision extends into the ultraviolet but not the infrared. 
The basis for this variation is the number of cone types that differ between species. Mammals, in general, have a color vision of a limited type, and usually have red-green color blindness, with only two types of cones. Humans, some primates, and some marsupials see an extended range of colors, but only by comparison with other mammals. Most non-mammalian vertebrate species distinguish different colors at least as well as humans, and many species of birds, fish, reptiles, and amphibians, and some invertebrates, have more than three cone types and probably superior color vision to humans.
In most Catarrhini (Old World monkeys and apes—primates closely related to humans), there are three types of color receptors (known as cone cells), resulting in trichromatic color vision. These primates, like humans, are known as trichromats. Many other primates (including New World monkeys) and other mammals are dichromats, which is the general color vision state for mammals that are active during the day (i.e., felines, canines, ungulates). Nocturnal mammals may have little or no color vision. Trichromat non-primate mammals are rare.  : 174–175 
Many invertebrates have color vision. Honeybees and bumblebees have trichromatic color vision which is insensitive to red but sensitive to ultraviolet. Osmia rufa, for example, possess a trichromatic color system, which they use in foraging for pollen from flowers.  In view of the importance of color vision to bees one might expect these receptor sensitivities to reflect their specific visual ecology for example the types of flowers that they visit. However, the main groups of hymenopteran insects excluding ants (i.e., bees, wasps and sawflies) mostly have three types of photoreceptor, with spectral sensitivities similar to the honeybee's.  Papilio butterflies possess six types of photoreceptors and may have pentachromatic vision.  The most complex color vision system in the animal kingdom has been found in stomatopods (such as the mantis shrimp) having between 12 and 16 spectral receptor types thought to work as multiple dichromatic units. 
Vertebrate animals such as tropical fish and birds sometimes have more complex color vision systems than humans thus the many subtle colors they exhibit generally serve as direct signals for other fish or birds, and not to signal mammals.  In bird vision, tetrachromacy is achieved through up to four cone types, depending on species. Each single cone contains one of the four main types of vertebrate cone photopigment (LWS/ MWS, RH2, SWS2 and SWS1) and has a colored oil droplet in its inner segment.  Brightly colored oil droplets inside the cones shift or narrow the spectral sensitivity of the cell. Pigeons may be pentachromats. 
Reptiles and amphibians also have four cone types (occasionally five), and probably see at least the same number of colors that humans do, or perhaps more. In addition, some nocturnal geckos and frogs have the capability of seeing color in dim light.   At least some color-guided behaviors in amphibians have also been shown to be wholly innate, developing even in visually deprived animals. 
In the evolution of mammals, segments of color vision were lost, then for a few species of primates, regained by gene duplication. Eutherian mammals other than primates (for example, dogs, mammalian farm animals) generally have less-effective two-receptor (dichromatic) color perception systems, which distinguish blue, green, and yellow—but cannot distinguish oranges and reds. There is some evidence that a few mammals, such as cats, have redeveloped the ability to distinguish longer wavelength colors, in at least a limited way, via one-amino-acid mutations in opsin genes.  The adaptation to see reds is particularly important for primate mammals, since it leads to the identification of fruits, and also newly sprouting reddish leaves, which are particularly nutritious.
However, even among primates, full color vision differs between New World and Old World monkeys. Old World primates, including monkeys and all apes, have vision similar to humans. New World monkeys may or may not have color sensitivity at this level: in most species, males are dichromats, and about 60% of females are trichromats, but the owl monkeys are cone monochromats, and both sexes of howler monkeys are trichromats.     Visual sensitivity differences between males and females in a single species is due to the gene for yellow-green sensitive opsin protein (which confers ability to differentiate red from green) residing on the X sex chromosome.
Several marsupials, such as the fat-tailed dunnart (Sminthopsis crassicaudata), have trichromatic color vision. 
Marine mammals, adapted for low-light vision, have only a single cone type and are thus monochromats. [ citation needed ]
Color perception mechanisms are highly dependent on evolutionary factors, of which the most prominent is thought to be satisfactory recognition of food sources. In herbivorous primates, color perception is essential for finding proper (immature) leaves. In hummingbirds, particular flower types are often recognized by color as well. On the other hand, nocturnal mammals have less-developed color vision since adequate light is needed for cones to function properly. There is evidence that ultraviolet light plays a part in color perception in many branches of the animal kingdom, especially insects. In general, the optical spectrum encompasses the most common electronic transitions in the matter and is therefore the most useful for collecting information about the environment.
The evolution of trichromatic color vision in primates occurred as the ancestors of modern monkeys, apes, and humans switched to diurnal (daytime) activity and began consuming fruits and leaves from flowering plants.  Color vision, with UV discrimination, is also present in a number of arthropods—the only terrestrial animals besides the vertebrates to possess this trait. 
Some animals can distinguish colors in the ultraviolet spectrum. The UV spectrum falls outside the human visible range, except for some cataract surgery patients.  Birds, turtles, lizards, many fish and some rodents have UV receptors in their retinas.  These animals can see the UV patterns found on flowers and other wildlife that are otherwise invisible to the human eye.
Ultraviolet vision is an especially important adaptation in birds. It allows birds to spot small prey from a distance, navigate, avoid predators, and forage while flying at high speeds. Birds also utilize their broad spectrum vision to recognize other birds, and in sexual selection.  
A "physical color" is a combination of pure spectral colors (in the visible range). In principle there exist infinitely many distinct spectral colors, and so the set of all physical colors may be thought of as an infinite-dimensional vector space (a Hilbert space). This space is typically notated Hcolor. More technically, the space of physical colors may be considered to be the topological cone over the simplex whose vertices are the spectral colors, with white at the centroid of the simplex, black at the apex of the cone, and the monochromatic color associated with any given vertex somewhere along the line from that vertex to the apex depending on its brightness.
An element C of Hcolor is a function from the range of visible wavelengths—considered as an interval of real numbers [Wmin,Wmax]—to the real numbers, assigning to each wavelength w in [Wmin,Wmax] its intensity C(w).
A humanly perceived color may be modeled as three numbers: the extents to which each of the 3 types of cones is stimulated. Thus a humanly perceived color may be thought of as a point in 3-dimensional Euclidean space. We call this space R 3 color.
Since each wavelength w stimulates each of the 3 types of cone cells to a known extent, these extents may be represented by 3 functions s(w), m(w), l(w) corresponding to the response of the S, M, and L cone cells, respectively.
Finally, since a beam of light can be composed of many different wavelengths, to determine the extent to which a physical color C in Hcolor stimulates each cone cell, we must calculate the integral (with respect to w), over the interval [Wmin,Wmax], of C(w)·s(w), of C(w)·m(w), and of C(w)·l(w). The triple of resulting numbers associates with each physical color C (which is an element in Hcolor) a particular perceived color (which is a single point in R 3 color). This association is easily seen to be linear. It may also easily be seen that many different elements in the "physical" space Hcolor can all result in the same single perceived color in R 3 color, so a perceived color is not unique to one physical color.
Thus human color perception is determined by a specific, non-unique linear mapping from the infinite-dimensional Hilbert space Hcolor to the 3-dimensional Euclidean space R 3 color.
Technically, the image of the (mathematical) cone over the simplex whose vertices are the spectral colors, by this linear mapping, is also a (mathematical) cone in R 3 color. Moving directly away from the vertex of this cone represents maintaining the same chromaticity while increasing its intensity. Taking a cross-section of this cone yields a 2D chromaticity space. Both the 3D cone and its projection or cross-section are convex sets that is, any mixture of spectral colors is also a color.
In practice, it would be quite difficult to physiologically measure an individual's three cone responses to various physical color stimuli. Instead, a psychophysical approach is taken.  Three specific benchmark test lights are typically used let us call them S, M, and L. To calibrate human perceptual space, scientists allowed human subjects to try to match any physical color by turning dials to create specific combinations of intensities (IS, IM, IL) for the S, M, and L lights, resp., until a match was found. This needed only to be done for physical colors that are spectral, since a linear combination of spectral colors will be matched by the same linear combination of their (IS, IM, IL) matches. Note that in practice, often at least one of S, M, L would have to be added with some intensity to the physical test color, and that combination matched by a linear combination of the remaining 2 lights. Across different individuals (without color blindness), the matchings turned out to be nearly identical.
By considering all the resulting combinations of intensities (IS, IM, IL) as a subset of 3-space, a model for human perceptual color space is formed. (Note that when one of S, M, L had to be added to the test color, its intensity was counted as negative.) Again, this turns out to be a (mathematical) cone, not a quadric, but rather all rays through the origin in 3-space passing through a certain convex set. Again, this cone has the property that moving directly away from the origin corresponds to increasing the intensity of the S, M, L lights proportionately. Again, a cross-section of this cone is a planar shape that is (by definition) the space of "chromaticities" (informally: distinct colors) one particular such cross-section, corresponding to constant X+Y+Z of the CIE 1931 color space, gives the CIE chromaticity diagram.
This system implies that for any hue or non-spectral color not on the boundary of the chromaticity diagram, there are infinitely many distinct physical spectra that are all perceived as that hue or color. So, in general, there is no such thing as the combination of spectral colors that we perceive as (say) a specific version of tan instead, there are infinitely many possibilities that produce that exact color. The boundary colors that are pure spectral colors can be perceived only in response to light that is purely at the associated wavelength, while the boundary colors on the "line of purples" can each only be generated by a specific ratio of the pure violet and the pure red at the ends of the visible spectral colors.
The CIE chromaticity diagram is horseshoe-shaped, with its curved edge corresponding to all spectral colors (the spectral locus), and the remaining straight edge corresponding to the most saturated purples, mixtures of red and violet.
Parts of the Eye
The eyes sit in a group of bones that make up the eye socket, and muscles attach to our eyes here. These muscles attach to the sclera of our eyes, the outer layer, and this helps keep our eyes in place. The cornea, pupil, lens, and retina are some of the most well-known parts of the human eye. The clear part of the front of your eye is your cornea, and this is the part that initially focuses light coming into the eye. The amount of light that is let in is controlled by the pupil, like the shutter of a camera. The pupil changes size depending on how bright the light is around you if you pay attention, you will notice that your pupils are much smaller when you are in bright light. Surrounding your pupil is the colored part of your eye, which is your iris. The lens focuses the light that comes in onto the retina the retina is in the back of the eye so it can more easily send information to the brain.
How Scientists Study Color Vision in Different Organisms
Humans’ perception of color has shaped how scientists have studied color vision, leading to some misconceptions concerning why and how color vision evolved (Endler 1990 Bennett et al. 1994). The differences between the color vision of humans and the animals that the color patterns are directed toward could mean the difference between assuming an animal that is “brightly” colored is conspicuous, possibly attempting to attract a mate, and that the colors function as camouflage (Marshall 2000). Information gleaned from genetic studies is helping us rethink other assumptions about how animals perceive color. In the past, much of the psychological literature attributed differences between how women and men process color information to environmental factors for instance, young girls’ ability to identify primary colors by name better than young boys was explained by their greater verbal ability and interest in colors. But recent opsin gene analyses show that many females possess more than three photoreceptor pigments, indicating that there may be a genetic explanation for gender-based color perception differences (Jameson et al. 2001, See Fig. 1b) As new techniques and methods of examining colors and color vision are developed that do not rely on human color vision, we learn more about the diversity of colors and color vision across animals. Indeed, we have used these methods to learn more about color vision within humans as well (see above).
The measurement of colors independently of human vision has recently become practical with the use of spectoradiometers. While these devices can make measurements of the physical properties of colors, even the way in which the data is scored can introduce human bias if the measurements are then converted into color codes based on human perception. Scores that are independent of our perception of colors have been developed (see Endler 1990) and make it possible to examine the ability of animals with color vision perception very different from ours. But how do scientists determine the differences between spectra other animals can perceive? Behavioral studies, one of the most reliable methods scientists use to determine what colors an animal can see, do not require complex molecular techniques or sophisticated machines. In the early 1900s, Karl von Frisch, an Austrian naturalist and winner of the Nobel Prize, questioned the commonly held assumption that fish were color-blind. One of his main opponents was Karl von Hess, the director of Munich Eye Clinic, who primarily disagreed with von Frisch’s reasoning that natural selection would act on the senses of animals. Von Frish was able to demonstrate that fish could indeed perceive colors by training minnows to respond to colored objects. Today, scientists still use behavioral color discrimination experiments to determine what colors animals can see. To study the color vision of nocturnal geckos, for instance, researchers trained the geckos to choose between two cues, blue and grey stimuli, rewarding them with untreated “tasty” crickets or negatively reinforcing choices with treated “untasty” crickets (Roth and Kelber 2004).
Not all organisms lend themselves to behavioral studies. Another method to examine the potential for color vision employs molecular genetic analyses to determine what opsin genes an organism possesses. Genes that code for the different retinal photopigments sensitive to particular wavelengths of light can be detected with DNA sequencing. Therefore, it is possible to determine with a small piece of tissue if an animal possesses the genes necessary to make the photopigments to detect different colors. This method helps us learn about animals difficult to study in the wild, like the endangered aye-aye. Researchers who were able to obtain DNA samples of eight aye-ayes available at a few international research institutions gained a better understanding of how this nocturnal primate retained some color vision (Perry et al. 2007).
It is important to note, however, that having a gene for a particular protein does not necessarily mean that the information in that gene is used to actually make that protein. In other words, not all genes that an organism has are expressed all the time, or in some cases ever. Some genes are only expressed during development, and others are not expressed unless there is another gene or a particular environment present. Therefore, a third method to determine color perception of an animal involves postmortem analyses to see if the photopigments necessary to detect certain colors are present in their retinas. This may seem like the ultimate method to answer the question “what colors do animals see?” but it is not. While the number and spectral sensitivities of the photopigments usually give scientists a pretty good idea of what colors an animal can detect, behavioral experiments have shown that this is not always the case. The butterfly Vanessa atalanta has three photopigments but was unable to discriminate colors in the long wavelength range, while Heliconius erato, a butterfly that also has three photopigments, was able to discriminate colors in the long wavelength range (Zaccardi et al. 2006). In the case of these butterflies, the answer to this discrepancy appears to be molecules other than opsins found in the retina cells that can filter light and modify spectral sensitivity. However, it is also possible that the neurological processing of the information provided by the eyes may differ across organisms. Indeed, one study shows that the mammalian brain is flexible enough to readily make use of information from opsin proteins (Jacobs et al. 2007). Jacobs and his research colleagues genetically engineered mice to have an additional, slightly different long-wavelength-sensitive (L) pigment through behavioral tests, they discovered the mice could immediately distinguish a broader spectrum of colors. Therefore, it is important to remember that evidence for color vision is likely best derived from a combination of studies, including molecular, physiological, and behavioral.
Finally, our understanding of the evolution of color vision has benefited greatly from the use of comparative phylogenetic studies. These studies can use the evolutionary relationships among different organisms (represented in phylogenetic trees) to examine the evolution of color vision in relation to the context in which it may have evolved. Even though it is possible to determine how color vision benefits an organism in the present, current function does not necessarily tell us when or in what context color vision initially evolved (Gould and Vrba 1982 Greene 1986 Baum and Larson 1991). Determining the performance advantage that initially selected for color vision requires evidence of phylogenetic congruence between the origin of color vision and the performance advantage (Greene 1986). So, for example, a comparative phylogenetic study was used to determine if primates evolved trichromatic color vision as a means of finding red fruits among the green foliage or to find high-quality mates (see Fig. 3).
Why do we see colors with our eyes closed?
As you settle into bed at night, close your eyes and begin to doze off, you may notice the colorful light show happening inside your eyelids. When you rub the sleep from your weary eyes, the lights suddenly intensify and bursts of bright colors appear all across your field of vision. A few seconds later, the colors settle down again. While you might appreciate the bedtime entertainment, in the back of your drowsy mind you’ve probably wondered what the heck you’re even seeing.
These strange blobs you see have a name they’re called “phosphenes,” and researchers believe that actual light may play a role. But not ordinary light — this light comes from inside your eyes. In the same way that fireflies and deep-sea creatures can glow, cells within our eyes emit biophotons, or biologically produced light particles.
“We see biophotonic light inside our eyes in the same way we see photons from external light,” said István Bókkon, a Hungarian neuroscientist who works at the Vision Research Institute in Lowell, Massachusetts.
Biophotons exist in your eyes because your atoms constantly emit and absorb tiny particles of light, or photons. This photon exchange is just a part of normal cellular function. Your eyes can’t tell the difference between photons from outside light and the biophotons emitted by your own atoms. Either way, your optic nerve simply relays these light signals to the brain, which must then decide if it accurately represents the real world around you, or if it’s just a phosphene.
Our eyes actually produce far more biophotons than we end up seeing as phosphenes. “When you rub your eyes, this generates biophotons in many parts of the eyes,” explained Bókkon. “But they are mostly absorbed locally.” Almost all of the biophotons you see are the ones both emitted and absorbed by atoms in the retina — the part of your eye responsible for detecting light.
Inside the retina, millions of tiny cells called rods and cones collect light and convert it into electrical signals. These signals travel through the optic nerve to a part of the brain called the visual cortex. Here, the brain reconstructs an image using the information received from the eyes. When a reconstructed image looks like nonsense, the brain is quick to label the image as unreal, or a phosphene.
But that information doesn’t always come from your retinas. According to Bókkon, phosphenes can originate in various other parts of the visual system, too. Research has shown that direct electric and magnetic stimulation of the brain can trigger phosphenes, and Bókkon hopes to soon be able to prove that biophotons are responsible for these phosphenes as well.
Depending on where a phosphene originates, it can take on a variety of shapes, patterns and colors. Different atoms and molecules emit photons of different wavelengths, which is why we see different colors. A phosphene with an orderly geometric pattern like a checkerboard may have originated in a section of the retina where millions of light-collecting cells are arranged in a similarly organized pattern. Researchers have also found that different areas of the brain’s visual cortex create certain specific shapes of phosphenes.
In the 1950s, the German researcher Max Knoll at the Technische Universität in Munich came up with a classification scheme for phosphene shapes. He studied phosphenes in over a thousand volunteers and came up with 15 categories, including triangles, stars, spirals, spots and amorphous blobs. He discovered that by prodding different areas of the visual cortex with an electrode device, he was consistently able to induce the same kinds of phosphenes.
In the lab, scientists generally use electric probes and fancy magnetic machines to make people see phosphenes. But the phosphenes we mostly see every day are not related to any type of electromagnetic stimulation. Instead, most phosphenes occur spontaneously when the atoms in our eyes exchange their biophotons. You can also trigger phosphenes yourself by applying pressure to your eyes — but be careful trying this at home!
The most common non-spontaneous phosphenes are pressure phosphenes, like the ones you see when you rub your eyes. According to Bókkon, any type of pressure on the eyes can cause them to emit an “excess of biophotons” that create intense visuals. Sneezing really hard, getting whacked in the head, and standing up too fast (causing a drop in blood pressure) are also ways to trigger pressure phosphenes.
The only people who never see phosphenes are people who have been blind since birth. But people who lose their vision due to illnesses or injuries usually don’t lose all visual functions. Because phosphenes can originate in different parts of the visual system, “theoretically, all blind people who could previously see can retain the ability to see phosphenes,” explained Bókkon.
Researchers have also been studying ways to trigger phosphenes in blind patients to try and figure out a way to potentially restore their vision. If scientists can use technology to make the blind see phosphenes, perhaps they can use similar technology make them see real images.
So next time you crawl into bed, close your eyes and admire the phosphenes. Now that you can appreciate the visual effects in a whole new way, you can just lay back and enjoy the show.
Show/hide words to know
Cornea: is the clear outer surface of the eye the covers the iris, pupil, and the outer chamber of the eye. more
Epithelium: the layer of cells found lining the surface of most surfaces of the body. Epithelium is one of four types of tissues found in human body. The other tissues are connective, muscle, and nervous tissue. more
Fovea: the part of the eye that provides sharp images used for activities like reading, riding a bicycle, and driving. It is located at the back of the eye and has the highest density of cones. more
Iris: in the anatomy of an eye, the iris controls the size of the opening of the pupil. This in turn controls the amount of light that can enter the eye. more
Mitochondria: are the cell’s powerhouse. It packages the energy from food into energy the cell can use to do work. more
Nucleus: where DNA stays in the cell, plural is nuclei.
Photoreceptor: the special type of cell in your eye that picks up photons and then signals the brain. They are located in the retina (a layer at the back of the eye). There are two types, rods and cones.
Pupil: is the hole that allow light to enter the eye. In humans it is round, but other animals like cats and goats the pupil is shaped more like a slit. more
Regeneration: to make something new that was old, damaged, or used. more
A person could have poor color vision and not know it. Quite often, people with red-green deficiency aren't aware of their problem because they've learned to see the "right" color. For example, tree leaves are green, so they call the color they see green. Also, parents may not suspect their children have the condition until a situation causes confusion or misunderstanding. Early detection of color deficiency is vital since many learning materials rely heavily on color perception or color-coding. That is one reason the AOA recommends that all children have a comprehensive optometric examination before they begin school.
If you look at a perched male hummingbird, he might sport a loud patch of red. But if you move your head to the side, suddenly that bird may look purple, or black, or any number of colors depending on his species. What's going on?
This fiery-throated hummingbird in Costa Rica sports brilliant iridescent feathers all over his throat and chest. Click for more detail.
Many birds have colorful feathers because of the pigments contained inside. These are similar to the dyes that give your clothing color. However, you probably don't own any clothes that change color depending on how you look at them, and there's a good reason for that.
Feathers that change colors (called iridescent feathers) look that way because of what scientists call "structural coloration." This means that it is the structure of the feather itself and how it affects sunlight that causes it to look a particular way.
Sunlight is made of many wavelengths of light, which are responsible for all the colors we see. Feathers with structural color reflect, scatter, or absorb different wavelengths in different ways, resulting in changing color.
Additional images via Wikimedia Commons. Hummingbird feather by Brocken Inaglory.