Colors of Nature
The rainbow has been an object of mystery throughout recorded history, doubtless having been noted with wonderment by the first two legged apes with three color vision. This is manifest in the legend of the Leprechaun’s pot of gold at its end, wherever that is, and in religion for the sign of the covenant that God made with Noah and “every living creature of all flesh” that rain “shall never again become a flood.”  It is therefore good news when you see one, its ethereal evanescence an object of natural beauty; to go over its chromatic arch puts you somewhere in Kansas or Oz, but not both. Aristotle recorded the first known explanation of the rainbow, asserting that the gods sent its colors as celestial rays of lightness and darkness that interacted with the four essential elements of water, air, earth, and fire. In this the first glimmering of science as observation, it is not too far-fetched. The night sky is black until the sun brings colored light to the greens and browns of earth, the blues and violets of the air, the reds and yellows of fire, and the sparkling refractions of the waters limned in the colors reflected by the firmament. 
Sir Isaac Newton is credited with the first explanation of the rainbow phenomenon as physics, though he acknowledged that the cause and effect of color in light was understood by the more perspicacious of what he calls “the Ancients.” He specifically cites Antonius de Dominus, an Archbishop of Spalato in the early 17th century, who wrote that “the interior Bow is made in round Drops of Rain by two Refractions of the Sun’s Light.” Newton’s treatment of the colors of the rainbow is coda to an extensive study of the properties of light reflection and refraction that was “…not to explain the Properties of Light by Hypotheses, but to propose and prove them by Reason and Experiments.” Starting with foundational axioms that the angle of light’s incidence is equal to the angle of its reflection and in the plane of its refraction, his experiments and careful measurement established the science of optics. Based on observations of sunlight passing through a prism so as to bend or refract the light to form the colors of the rainbow on a white surface, he concluded “the Whiteness of the Sun’s Light is compounded of all the Colours wherewith the several sorts of Rays whereof that Light consists, when by their several Refrangibilities they are separated from one another, do tinge Paper or any other white Body whereon they fall.” (refrangible is the adjectival form of able to be refracted). Absent an understanding of the wave/particle duality of light as photons in the quantum theory of the twentieth century, Newton sought an analogy in nature that would mirror the behavior of light. Choosing sound as a reasonable analog, the octave scale of music became the octave scale of light with the spectrum subdivided to correspond to the seven notes in a scale (do-re-mi-fa-so-la-ti). The result was Red, Orange, Yellow, Green, Blue, Indigo, Violet as the seven octave colors.  Thus ROY G BIV became the mnemonic for the rainbow, supplanted in Shakespearean circles by Richard Of York Gave Battle In Vain (at Bosworth Field).
In reality, there is no line of demarcation from one color to the next as the spectrum is continuous. Indigo is not really even a color, but the common name given to a plant that yields a blue dye. It was not until the 19th century that the wave theory based on the work of Thomas Young and Augustin-Jean Fresnel among others took precedence over Newton’s corpuscular, or particle theory; ultimately the electromagnetic field theory of James Clark Maxwell settled the physics with his eponymous laws. It is now well established that visible light is a relatively narrow frequency band with wavelengths ranging from about 400 to 700 nm (a nanometer or nm is a billionth of a meter) in the expanse of the electromagnetic spectrum that extends from the long meter scale waves of radio to the short wave high frequency X and gamma rays (frequency “f” and wavelength λ are related by f = c/λ where c is the speed of light). Newton’s prismatic spectrum and nature’s rainbow are resolved by the fact that the velocity of light in glass or water varies with wavelength so that the angle of refraction or bending also depends on color, the longer waves at the red end bend less than the shorter waves at the violet end.  So, too do the infrared waves that are longer than the red the ultraviolet waves that are shorter than the violet but humans can’t see them so they are not “visible,” except to many other animals who “see” more than we do.
Newton’s deterministic octave-based color spectrum was unassailable for well over a century; it was considered a faux pas to gainsay the master whose force and motion equations literally governed the universe. Johann Wolfgang von Goethe had another view and was not afraid to challenge him, at least in German. He was roundly vilified by the scientific community who resented the intrusions of a philosopher. Gradually and grudgingly, he was accorded a measure of respect from across the channel. Sir John Leslie noted that Newton’s ideas, after all, “imagined that the primary colours are distributed over the spectrum of the diatonic scale of music,” and were therefore at least partly mystical and not scientific. Goethe argued that color had no intrinsic meaning but was determined according to how it was processed by the brain in response to the perception of the eyes; it was vision that defined color. In his own words: “Colors and light, it is true, stand in the most intimate relation to each other, but we should think of both as belonging to nature as a whole.” He saw color as a dichotomy of feelings, with yellow conveying a sense of action and warmth and blue its opposite in weakness and cold; combining them did not destroy either but became a new quantity as green. While nature produced the colors, they were “modified, specified even individualized” by the act of seeing. Goethe changed the notion of color from wholly determined by the wavelengths of physics to the more nuanced dependence on visual physiology, inaugurating the new science psychophysics.  The nature of color was and still is debatable beyond Goethe’s philosophical emphasis on perception – the use of pigments for art and decoration approached the subject from an entirely different angle.
The use of color to fashion images on rock walls and to adorn earthen vessels dates to at least the Paleolithic Era. Cave drawings in southern Europe using the natural ochre hues of clays are testimony to the emergence of conceptual representation among the early hominids. At the zenith of the Golden Age of Greece, three different methods were perfected to apply pigment: colored paint on wet plaster as fresco; mixing colors in egg whites to apply to wet surfaces as tempura; and the mixing of colors in melted wax as encaustic.  Over time, it was empirically demonstrable that mixing one color with a second color would always produce a third that could be lightened with white or darkened with black. There were some colors, however, that could not be made from combinations. By the eighteenth century, the doctrine was established that “Paintings can represent all visible objects with three colors, yellow, red and blue, for all other colors can be composed of these three …. And a mixture of those three original colors makes a black.” This is now recognized as the subtractive color system – the primary colors of red, yellow, and blue can be combined to make the secondary colors of orange, green, and purple. This contrasts with the additive color system that was the subject of Newton’s prismatic ponderings in which red, green, and blue are the primary colors that combine to make white light. However, Newton’s observation that the color of light is due to its frequency is one of the immutable laws of physics. “White is a Concentrating or an Excess of lights – Black is a Hiding, or Privation of lights.”  In the subtractive system, the color you see is what is not subtracted by the surface; in the additive system, the different wave lengths are added together to produce the final result; red and blue make magenta, blue and green make cyan, and red and green make yellow (if this last one bothers you as it did me, does it make any sense that yellow and blue make green that we all learned in the coloring book subtractive paint system?). Color is complicated.
Vision is even more complicated; how do we “see” color? The moving pictures of life are stitched together pixel by pixel and sent down the optic nerve to be rationalized by the brain’s occipital lobes, one on the left for the right eye and vice versa. How this actually occurs has been a matter of debate for several centuries. Thomas Young was the first to propose that the eye had separate color sensors in a lecture to the Royal Society in 1801. Being careful to tread lightly on Newton’s legacy, he took exception to his hypothesis III, that “the sensation of different colors depends on the different frequency of vibrations, excited by the light in the retina.” As this would require an infinite sensitivity at every point, Young rationalized that “it becomes necessary to suppose the number limited, for instance to the three principal colours, red, yellow, and blue”  What became the trichromatic theory of color was advanced in 1860 by the publication Physiological Optics by Herman von Helmholtz. A follower of Goethe’s psychophysical color theory, he proposed red, green and blue as the three retinal colors, which one of his assistants later demonstrated by making spectral response curves from the eyes of “a cooperative human subject and a color-mixing device of Helmholtz’s design.” Improvements in sensors and techniques advanced the assessment of the anatomy of the eye to the extent that the physiologist Max Schultze concluded in 1866 that there were rod cells sensitive only to light and dark and cone cells that were sensitive to color, correlating to red, green, and blue receptor cells. The trichromatic or Young-Helmholtz theory was thus established and still prevails as one of the two accepted theories of color vision. The other is the opponent-color theory. 
Few things are black or white but there are many shades of gray. Similarly, the vision of color is not a simple combination of red, green, and blue. The three cone type receptors of the retina are not sensitive to one single frequency with its corresponding single color, but rather to a range of frequencies that is called a spectrum. A spectrum is like a probability distribution curve where there is a peak near the center with trailing edges both above and below this maximal point. The three color cone spectra are usually referred to as long (L) or reddish, medium (M) or greenish, and short (S) or bluish according to where their maxima fall along the entire visible light frequency or wavelength range. One way to remember that the red end of spectrum is the long wavelength end is that evidence of the expanding universe is the red shift of light from distant nebulae – as the light moves away the wavelengths are stretched in a sense and become longer and therefore more red. Numerically, the red L cone range is 500-700 nm with a maximum at 570 nm, the green M cone range is 450-630 nm with a maximum at 545 nm, and the blue S cone range is 400-500 nm with a maxima at 430 nm. It is immediately obvious from these measures that the red L and green M cones are very close together in frequency and that the blue S cone is distant and much better defined in a narrow range. The overall visible light range for primates is 400-700 nm  This has significant implications in the evolution of the eye in general and in the evolution of the primate eye in particular.
Sensitivity to sunlight is the foundation of the pyramid of things that are alive. The photon energy of the sun powers plant photosynthesis on which all life ultimately depends. Trees grow upward into leafy canopies and heliotropic plants turn seeking more. The moving animals that followed could not do so without some way to find food, seek a mate, and flee from the predators that eventually established their own niche in the food chain. Vison begins with light sensitive molecules that change shape when they are struck with the appropriate frequency/light, breaking into two parts, one derived from vitamin A (which is why it is so important for good vision) and the other into a protein called an opsin (that is structured very much like a bacterium). Every animal from an annelid worm to a zebra uses opsins, which have the bacterial propensity to penetrate the cell wall of a neuron to send a signal to the brain that corresponds to the color absorbed. It is not unreasonable to propose that vision opsins must then have evolved from a bacterium gaining entry to a cell for nutrition. The “vision” molecules are arrayed on exposed animal tissue in two different ways. Invertebrate eyes are comprised of folded surfaces and vertebrate eyes have bristly extensions from surfaces we call rods and cones for their shapes. As biology ramped up in the early twenty-first century, it was discovered that both types of eyes were found on a type of simple worm called a polychaete, clear proof of their evolutionary connection. And even more surprising is that a single gene called Pax 6 is responsible for the formation of all eyes on all things, and that an eye could be placed anywhere by inserting this gene; mouse derived genes have been shown to grow eyes on fly wings.  The simplicity of a single gene origination seems outlandish in light of the complexity of multicolored vision. It is testimony to the powers of the neural network of the brain that the sum of many pixilated signals creates the three dimensional scene that we see.
Color vision arose about 450 million years ago (mya) with the emergence of the agnathan or jawless fish vertebrates whose only modern survivors are the lampreys and hagfish. The vestigial color scheme was tetrachromatic, having four cone types categorized as LWS, longwave sensitive, MWS, middlewave sensitive, SWS2 and SWS1, both shortwave sensitive in addition to rods for black and white. The first three cones correspond to the same general red-green-blue spectra that comprise human color perception with the addition of SWS1 that extends from 355-445 nm, well into the ultraviolet range. The “four color” physiology has been retained for the vast majority of animals, including most fish, reptiles, amphibians, birds and even insects, which means, counterintuitively, that they “see” more than we do up to and including ultraviolet light. Over the vast stretches of geologic and evolutionary time, the retention of all four color cones (and in a few cases the addition of several more) has been subject to their use for survival relative to other senses. Almost all land mammals are dichromatic, having lost two of their four cones.  The loss of the components of color vision is generally attributed to the “use it or lose it” hypothesis. Smell and sound are vastly more important for night stalkers and their prey on both ends of the survival food chain, sight not so much.
The primates evolved from their two-color cone mammalian ancestors about 50 mya, adding a third cone for reasons that are and always will be subject to conjecture. Unguents eat grasses that are ubiquitous, green, and brown. Carnivores eat anything that doesn’t run down a hole or race up a tree even if it is in the camouflage colors of the forest. Primates solved the predation dilemma by mostly staying in the trees, where they feasted on fruit. The angiosperm or flowering plants solved the problem of reproduction without being able to move by creating fruit as seed package delivery by birds and other tetrachromatic animals. Colors in fruit came about to attract those animals and it is generally believed that primates with improved red-orange fruit finding abilities prevailed.  Three color vision evolved in the Old World monkeys (those emanating from Africa like the genus Homo) with a duplication of one of the two opsin genes to create a third opsin, separating the red from the green. Conversely, the New World monkeys of South America independently evolved an extra color cone as two different alleles on the X chromosome. As a consequence, all male monkeys (since they don’t have the second X) in the Americas are color blind, seeing red and green equally. This raises an interesting question about our primate ancestors … How did the monkeys get across the ocean? Africa and South America separated about 100 mya as a part of the dissolution of Pangea, long before the primates appear in the fossil record as an evolutionary branch. Vicariance is the term used by evolutionary biologists to explain the differences between species caused by a geographic barrier like an ocean. This does not work for monkeys. It is now widely held that a small group or maybe a single gravid female floated over on a tree trunk disgorged from the Congo River after a deluge. This single event phenomenon is called long-distance dispersal and is gaining ground as the operant theory.  When they got there, they evolved trichromatic vision for the same ecological reasons, a phenomenon called convergent evolution. There are marsupial mice in Australia that are unrelated to the placental mice everywhere else.
One of the primate groups that remained in Africa eventually had to come down from the trees and seek a better life on the savanna, probably due to climate change. The colors of the fruited cornucopia were not as important in the struggle to survive in the grass, where danger lurked and food required forage. Homo erectus emerged as the successful design, taking advantage of the efficiency of bipedalism to range far and wide. The brain became the most important organ, growing in size and complexity to make tools as Homo habilis and to make sense as Homo sapiens. The neural network of rod and cone signals from the retinal tissues of the eyes connected the expanding brain to the outside world. Nuances of size, shape, and movement were more important than color in navigating the complex terrain in search of food. The eyes in essence became extensions of the brain that produced digital images compared to the library stored as memory for instantaneous fight or flight decisions. It is this brain processing that sets human vision apart from other animals. The observation of an object’s motion became more important than its color. This can be demonstrated by pointing focused beams of light on individual human retinal cones and recording the sensations. The result is that achromatic signals outnumber chromatic signals.  The complex processing of visual information by the human eye-brain combination was what Goethe was getting at. It eventually took shape as the second theory of human color vision.
The opponent color theory was first proposed by another German psychologist named Ewald Hering in 1872. His hypothesis was rooted in the notion that individuals could not conceive of anything that was greenish-red or yellowish-blue and that these colors must therefore be opposites. He proposed that there must be some mediation between the three sets of opposite colors: green and red, yellow and blue and black and white. This also addresses the interesting observation that red and green make yellow in the additive color system and that blue and yellow make green in the subtractive color system. Black and white always make gray but there is no blackish white. The fact that there is a mediation between two different color cones has been established physiologically. Retinal ganglion cells receive input from two separate color cones to process them before the ultimate signal is sent to the occipital lobe via the optic nerve. While it is not yet completely clear why there is a second tier of processing in the eye’s neural network, it has something to do with being able to cover the entire chromatic space, to see all colors.  It is testimony to the complexity of human color vision that both the trichromatic theory and the opponent color theory prevail equally, just as light can be both waves and particles.
The eyes of other animals have evolved in equal measure to satisfy the mandates of their own survival. While they may not process the incoming multicolor signals with the same degree of integration with the brain as humans, they can see some things we can’t. Changing the color spectrum coverage in reaction to an environmental stimulus is a relatively minor matter of changing one amino acid. Evolutionary color mutations in both primates and birds have been tracked in fossil DNA. “Spectral tuning” so as to cover the entire palette of colors is maximized with trichromacy in primates with a visible range of 400-700 nm and with tetrachromacy in birds with their more extended range of 300-700 nm and including ultraviolet. Most other animals have the four cone color vision of birds. The major exception is non-primate mammals which are dichromatic with a limited ability to detect color on the red end of the spectrum, an evolutionary result of their nocturnal and burrowing behavior. There are some exceptions attributable to changes based on habitat choice. Marine mammals are monochromatic to suit their ocean habitat and penguins are similarly blue-shifted. There are also some exceptions that result from an independent evolutionary path, notably bees and butterflies.
Bees, unlike the majority of tetrachromatic insects, have only three photoreceptors with spectral peaks at 340 nm, 440nm, and 540 nm which means that they can see ultraviolet light quite well but are deficient at the red or long end of the spectrum. So why are roses red and violets blue? Hymenopterans have been around for a very long time, predating the flowering plants by millions of years. Wind pollination was the rule for millennia. The grinding certitude of evolution produced another and sometimes better method. Flowers with sweet nectar pots suspended beneath their pollen-bearing anthers appeared with whatever features were necessary to attract the bees. Some, like the orchids, targeted single species. But they all used color, some with ultraviolet landing pattern indicators pointing to the reward to attract their quarry. Bees begat flowers. Butterflies took a different route, evolving from the nocturnal moths to become day trippers. To cope, many evolved up to eight different color receptors, necessary and sufficient to find food, find a mate, or find a place to lay eggs with a very narrow band wavelength set at the nanometer range for a single hue. We now know the end to the poem: Roses are red, violets are blue, it’s for butterflies and bees, and not for you. 
In nature, every color tells a story. The sky is blue because shorter wavelengths scatter more than longer, redder wavelengths when sunlight hits the gases and particles of the atmosphere – Rayleigh scattering. The grass is green because plants absorb all of the photon energy of the sun except middle wavelengths at the center of the spectrum. Almost all animals are colored in the hues that suit their niche in the complex web of life. Viceroys employ mimicry to appear as poisonous monarchs, red efts announce their own poison with apatetic crimson, rattlesnakes lurk in brown and tan thickets with cryptic splotches, and mammals have fur with mottled hues that accentuate the chiaroscuro surroundings as both predator and prey. According to Gerald Thayer, the premier proponent of protective coloration “The color relations of earth, sky, water, and vegetation are practically the same the world over, and one may read on an animal’s coat the main facts of his habit and habitat, without ever seeing him in his home.”  While color is not mandatory – early cinema and television thrived in black and white – it surely adds to the rich texture of life’s journey, as it surely did for Dorothy when she first ventured out into Oz.
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