Source: Understanding color & the in-camera image processing pipeline for computer vision
Source: Notes for the course of Color Digital Image Processing
Source: Understanding color & the in-camera image processing pipeline for computer vision
Color Temperatures of the Stars
Source: Understanding color & the in-camera image processing pipeline for computer vision
CIE 1931 XYZ
Source: Understanding color & the in-camera image processing pipeline for computer vision
Source: Human Vision and Color
Brightness, Lightness,Hue, Saturation, and Luminosity
Source: The Brightness of Colour
Brightness has been defined as the perceived intensity of a visual stimulus, irrespective of its source. Lightness, on the other hand, is defined as the apparent brightness of an object relative to the object’s reflectance. Thus increasing the intensity of light falling on an object will increase its apparent brightness but not necessarily its apparent lightness, other things being equal . Saturation is a measure of the spectral ‘‘purity’’ of a colour, and thus how different it is from a neutral, achromatic stimulus. Hue is the perception of how similar a stimulus is to red, green, blue etc. Luminous efficiency, or luminosity, measures the effect that light of different wavelengths has on the human visual system. It is a function of wavelength, usually written as V(l) , and is typically measured by rapidly alternating a pair of stimuli falling on the same area of the retina; the subject alters the physical radiance of one stimulus until the apparent flickering is minimised. Thus luminance is a measure of the intensity of a stimulus given the sensitivity of the human visual system, and so is integrated over wavelength . Luminance is thought to be used by the brain to process motion, form and texture .
Clearly, brightness is monotonically related to luminance in the simplest case: the more luminant the stimulus is, the brighter it appears to be. However, the Helmholtz-Kohlrausch (HK) effect shows that the brightness of a stimulus is not a simple representation of luminance, since the brightness of equally luminant stimuli changes with their relative saturation (i.e. strongly coloured stimuli appear brighter than grey stimuli), and with shifts in the spectral distribution of the stimulus (e.g. ‘blues’ and ‘reds’ appear brighter than ‘greens’ and ‘yellows’ at equiluminance) [1; 5–6].
The HK effect has been measured in a variety of psychophysical studies [7–8] and is often expressed in terms of the (variable) ratio between brightness and luminance.
Title: A Review of RGB Color Spaces …from xyY to R’G’B’
The CIE XYZ and xyY Color Spaces
Douglas A. Kerr
DIVERSE CELL TYPES, CIRCUITS, AND MECHANISMS FOR COLOR VISION IN THE VERTEBRATE RETINA
Wallace B. Thoreson and Dennis M. Dacey
Department of Ophthalmology and Visual Sciences, Truhlsen Eye Institute, University of Nebraska Medical Center, Omaha, Nebraska; and Department of Biological Structure, Washington National Primate Research Center, University of Washington, Seattle, Washington
Physiol Rev 99: 1527–1573, 2019 Published May 29, 2019; doi:10.1152/physrev.00027.2018
Source: Structural color and its interaction with other color-producing elements: perspectives from spiders
Multilayer – 1 D Periodicity
Photonic Crystals – 2 D and 3 D
Quasi Ordered Photonic Crystal
Source: BIO-INSPIRED VARIABLE STRUCTURAL COLOR MATERIALS
1 D Gratings
1 D Periodicity Multilayers
1 D Discrete Periodicity
2 D Gratings
2 D Periodicity
Closed Packed Spheres of Solid Materials
Inverse Opal Analogoues
Source: STRUCTURAL COLORATION IN NATURE
Thin Film Interference
Multi Film Interference
1 D Photonic Crystals
2 D Photonic Crystals
3 D Photonic Crystals
Source: Structural Color and Odors: Towards a Photonic Crystal Nose Platform
Source: PHYSICS OF STRUCTURAL COLORS
Source: PHOTOPHYSICS OF STRUCTURAL COLOR IN THE MORPHO BUTTERFLIES
Source: Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)
Cuticular Multilayer Reflector
Source: Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)
3 D Photonic Crystals
Multilayer reflectors in beetles have also been described as ‘thin-layer stacks’, ‘one-dimensional photonic crystals’ and ‘thin-film reflectors’ (e.g. Parker 1998, 2002; Vigneron et al. 2006). The vocabulary used to describe these structures is somewhat dispersive, as the variously intersecting disciplines of entomology, physics and applied optics (e.g. laser technology, fibre-optic data transmission, telescopes and microscopy) have all developed slightly different suites of terminology. Other synonyms for ‘multilayer reflector’ include multilayer stack, quarter wave stack, interference reflector and dielectric mirror.
We propose that the term multilayer reflector be applied to such structures in Coleoptera; this describes the multilayered nature of cuticular chitin lamellae (which are not true films) and the reflective mechanism by which colour is produced.
The terms ‘metallic colours’ or ‘metallic iridescence’ can be used to distinguish multilayer effects from those produced by other optical structures. Multilayer reflectance can typically be diagnosed as such by its limited palette (usually one or two apparent hues per reflector), blue shift with decreased observation angle and fixed position on the cuticle surface.
Source: Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)
Three-dimensional crystalline structures producing scintillating, gem-like reflectance were described by Parker et al. (2003) in the entimine weevil Metapocyrtus sp. (initially misidentified as Pachyrrhynchus argus); by Welch et al. (2007) in Pachyrrhynchus congestus, and recently in another entimine weevil, Lamprocyphus augustus, by Galusha et al. (2008). The photonic crystals found in the scales of pachyrrhynchine weevils (Pachyrrhynchus and Metapocyrtus) have a close-packed hexagonal arrangement analogous to (mineral) opal, while the photonic crystal of Lamprocyphus has a diamond-based lattice (i.e. a face-centred cubic system rather than a hexagonal one).
Although the term ‘photonic crystal’ applies to any ordered subwavelength structure that affects the propagation of specific wavelengths of light (Parker & Townley 2007), it is the three-dimensionally ordered structures to which the term is most commonly applied. We recommend use of the term ‘three-dimensional photonic crystal’, which distinguishes these structures from the one-dimensional periodicity of multilayer reflectors or Bragg gratings. The terms ‘opal’ and ‘diamond based’ have been used to describe iridescence in weevil scales, but refer to phenomena that are relatively similar from an organismal perspective; it is important to note that these terms refer to crystalline lattice morphology and not the appearance of the scales themselves. Maldovan & Thomas (2004) provided an excellent overview of diamond-based lattice morphology (as observed in Lamprocyphus) in photonic crystals; Yablonovitch (1993) provided a thorough introduction to the photonic band-gap mechanism by which colours are produced in three-dimensional photonic crystals.
Source: Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)
A diffraction grating is any nanoscale array of parallel ridges or slits that disperses white light into its constituent wavelengths (figure 8a shows a grating in cross section). Because white light consists of many different wavelengths, it diffracts into full spectra, creating the rainbow-like reflectance shown in figures 1a,b, 8c and 9b,d. While man-made diffraction gratings can disperse light via reflection or transmission, all beetle gratings are strictly reflection mechanisms.
Source: Gold bugs and beyond: a review of iridescence and structural colour mechanisms in beetles (Coleoptera)
Nature’s Fantastical Palette: Color from Structure
Philip Ball 18 Hillcourt Road East Dulwich London SE22 0PE, UK firstname.lastname@example.org
The changing hues of a peacock’s splendid tail feathers have always captivated the curious mind (Figure 1). The seventeenth-century English scientist Robert Hooke called them ‘fantastical’ because the colors could be made to disappear by wetting the feathers (Hooke, 1665). Using the newly invented microscope, Hooke looked at peacock feathers and saw that they were covered with tiny ridges, which he figured might be the origin of the colors.
Figure 1. The shifting colors of the peacock’s tail have had metaphorical interpretations for centuries.
Hooke was on the right track. The bright, often iridescent colors of bird plumage, insect cuticle and butterfly wings are ‘structural’; produced not by light absorption by pigments, but light scattering from a regular array of objects just a few hundreds of nanometers (millionths of a millimeter) in size (Vukusic & Sambles, 2003; Vukusic, 2004; Wolpert, 2009). This scattering favors particular wavelengths depending on the size and spacing of the scatterers, and so it picks out specific colors from the full spectrum of sunlight. Because the precise hue may depend also on the viewing angle, structural colors are often iridescent, changing from blue to green or orange to yellow. And because they involve reflection rather than absorption, these colors can be startlingly brilliant. The Blue Morpho butterflies of South and Central America are visible from a quarter of a mile away, seeming almost to shine when sunlight penetrates the tropical forest canopy and bounces off their wings.
Structural colors are just one example of how living organisms manipulate and channel light using delicately arranged micro- and nanostructures. These biological designs offer inspiration to engineers seeking to control light in optical technologies, and could lead to more brilliant visual displays, new chemical sensors, and better storage, transmission and processing of information. To make effective use of such tricks, we need to understand how nature creates and deploys these tiny optical structures; indeed, we must learn a new language of color production and mixing.
Rather little is known about how many of these biological structures are put together, how they evolved, and how evolution has made creative use of the color and light effects they offer. But one thing is clear; nature doesn’t have the sophisticated patterning technologies, such as drilling with electron beams, that microengineers can use to laboriously carve such structures from solid blocks. Ingenuity is used instead of finesse; these biological structures must make themselves from the component parts.
If we can master that art, we might develop new, cheap technologies to make such things as materials that change color or appearance, like the camouflage skins of some fish and squid, or fibres that guide and channel light with virtually no leakage, or chemically controlled light shutters. Here I look at some of nature’s tricks for turning structure into color; and the ways they are being exploited in artificial materials and devices (Ball, 2012).
Although the ridges seen by Hooke on butterfly wing scales do scatter light, the bright colors of the reflected light generally come from invisible structures beneath the surface. In the natural world, they offer a robust way of generating color that is not hostage to the fate of delicate, light-sensitive organic pigments.
The colored scales and feathers of birds, fish and butterflies typically contain organized microscopic layers or rods of a dense light-scattering material embedded in a matrix of a different substance. Because the distance between the scatterers is roughly the same as the wavelengths of visible light, the stacks cause the wave phenomenon of diffraction, in which reflected waves interfere with one another. Depending on the angle of reflection, light rays of a certain wavelength interfere constructively when they bounce off successive layers in the stack, boosting the corresponding color in the reflected light (Vukusic and Sambles, 2003; Vukusic, 2004; Wolpert, 2009). It is much the same process that elicits the chromatic spectrum in light glancing off a tilted CD.
In butterfly wing scales the reflecting stacks are made of cuticle; a hard material containing the natural polymer chitin, separated by air-filled voids. In bird feathers, the stacks are platelets or rods of the dark pigment melanin; sometimes hollow, as in the Black Inca hummingbird, Coeligena prunellei, embedded in keratin, the protein from which our hair and fingernails are made (Figure 2). Analogous diffraction gratings made from alternating ultrathin layers of two materials are widely used in optical technologies to select and reflect light of a single color. For example, mirrors made from multiple layers of semiconductors are used as reflectors and color filters in devices ranging from astronomical telescopes to solid-state lasers and spectrometers.
Figure 2. The iridescent blues and greens in the feathers of hummingbirds such as this Black Inca (left; part of blue iridescence highlighted with white box) are created by platelets of melanin pigment punctuated with air holes (right), which act as a photonic crystal to reflect light of a particular wavelength. K=keratin, A=air, M=melanin. (From Shawkey et al., 2009)
The male bird of paradise Lawes’ parotia (Parotia lawesii) has a particularly neat twist on this trick (Figure 3). The barbules (hair-like structures on the feather barbs) of its breast feathers contain layers of melanin spaced at a distance that creates bright orange-yellow reflection. But, as Stavenga and colleagues have recently discovered, each barbule has a V-shaped or boomerang cross-section, with sloping surfaces that also act as reflectors of blue light (Stavenga et al., 2011). Slight movements of the feathers during the bird’s courtship ritual can switch the color abruptly between yellow-orange and blue-green; guaranteed to catch a female’s eye. Stavenga suspects that technologists will want to use this trick for producing dramatic chromatic shifts. “I suspect the fashion or automobile industries will in due time make bent structures or flakes that will exploit these angular color changes”, he says.
Figure 3. A striking color change in the feathers of the male Lawes’ parotia, from yellow-orange (a) to blue-green (b), is caused by the presence of two mirror-like reflectors in the feather barbules (c): layers of melanin rods reflect yellow light, while the sloping faces of the boomerang-shaped barbule cross-section reflect blue at oblique angles. Scale bar in b: 1 cm. (From Stavenga et al., 2011)
The butterflies Morpho didius and Morpho rhetenor obtain their dazzling blue color not from simple multilayer’s but from more complex nanostructures in the wing scales: arrays of ornate chitin ‘Christmas Trees’ that sprout at the surface (Vukusic & Sambles, 2003) (Figure 4). Each ‘tree’ presents a stack of disk-like layers to the incoming light, which acts as another kind of diffraction grating. These arrays may reflect up to 80 percent of the incident blue light. And because they are not flat, they can reflect a single color over a range of viewing angles, somewhat reducing the iridescence; organisms don’t always want to change color or get dimmer when seen from different directions.
Figure 4. The butterfly Morpho didius (left) obtains its dazzling blue color from delicate ‘Christmas Tree’ light-scattering structures (right), made from chitin, that sprout within the wing scales. (Left, courtesy of Peter Vukusic. Right (micrograph) from Vukusic and Sambles, 2003.)
The precise color reflected depends on the refractive index contrast between the nanostructures and the surrounding medium. This is usually air, but as Robert Hooke observed, wetting such surfaces alters the refractive index contrast, and changes the color in a way that is closely linked to the wetting liquid’s refractive index. For that reason, artificial Morpho-like structures carved into solids using microlithographic techniques are being developed by researchers at GE Global Research in New York, in collaboration with others at the State University of New York at Albany and butterfly-wing expert Pete Vukusic at the University of Exeter in England, as color-change chemical sensors that can identify a range of different liquids (Potyrailo, 2011). These might find applications for sensing emissions at power plants, monitoring of food safety, and testing of water purity.
The bright green color of the Emerald Swallowtail butterfly (Papilio palinurus), found widely in southeast Asia, is not produced by green light at all. The wing scales are covered with a honeycomb array of tiny bowl-shaped depressions just a few micrometers across, lined with alternating layers of chitin cuticle and air which act as reflective mirrors. Light bouncing off the bottoms of the bowls is preferentially reflected in the yellow part of the spectrum. But from the sides it is reflected twice before bouncing back, and this selects blue. Our eyes can’t resolve these yellow spots and blue rings, which merge to create the perception of green (Vukusic & Sambles, 2003).
Figure 5. The green of the Emerald Swallowtail butterfly (left) comes from the optical mixing of blue and yellow reflections from tiny bowl-like depressions in the wing scales (right). (Right figure, courtesy of Christopher Summers, Georgia Institute of Technology)
This way of making color has been copied by Summers and coworkers (Crne et al., 2011). To create the tiny bowls, they let water vapour condense as microscopic droplets, called breath figures, on the surface of a polymer dissolved in a volatile solvent. The solvent gradually evaporates to form a solid polymer film, while the water droplets pack together on the surface of the drying solution much like greengrocers’ oranges and apples in crates, sinking into the setting film to imprint an array of holes. By pulling off the top part of the film, Summers and colleagues were left with a surface with hemispherical bowl-like dimples. They then used this structure as a template on which they deposited alternating thin layers of titania and alumina to make a multilayer reflector, like that lining the bowls of the butterfly wing scales (Figure 6).
Figure 6. An artificial micro-structured surface that mimics the green color of the Emerald Swallowtail. Scale bar: 5 µm. (Courtesy of Christopher Summers, Georgia Institute of Technology)
Because each reflection changes the polarization of the light, under crossed polarizing filters the yellow light bouncing back from a single reflection at the bowl centers disappears, while the twice-reflected blue-green light from the rims remains. This could offer a distinctive authentification mark on bank and credit cards. Apparently just a simple green reflective coating, such a material would in fact carry a hidden polarized signature in the reflected blue and yellow light that would be hard to counterfeit. But Summers’ collaborator Mohan Srinivasarao admits that the main reason for seeking to replicate the butterfly’s green color was that “it’s beautiful in its own right”.
Scattering by regular arrays of microscopic objects can, for some arrangements, totally exclude light within a particular band of wavelengths, called the photonic band gap (Vukusic, 2004). These so-called photonic crystals occur naturally, for example, in opal, a biogenic form of silica in which the scatterers are tiny mineral spheres. Artificial photonic crystals can be used to confine light within narrow channels, creating waveguides that might be deployed to guide light around on silicon chips for optical information technology.
Nature has already got there first. Under the electron microscope, the wing scales the Emerald Patched Cattleheart Butterfly (Parides sesostris) display zigzagging, herring-bone arrays: patches of an orderly sponge made from chitin with holes a hundred nanometers or so across. Each patch is a photonic crystal seen from a different alignment. Stavenga and Michielsen have found that these labyrinths in the wing-scales of P. sesostris and some species of papilionid and lycaenid butterflies have a structure known to mathematicians as a gyroid (Michielsen & Stavenga, 2008). In P. sesostris the structure has a photonic band gap that enables it to reflect light within the green part of the spectrum over a wide range of incident angles (Figure 7). Some weevils and other beetles also derive their iridescent color from three-dimensional photonic crystals made of chitin.
Figure 7. The wing scales of P. sesostris (top left, and close-up, top right) contain photonic crystals of chitin (bottom, middle and right) Scale bars: left, 100 µm; middle, 2 µm; right, 2 µm. (Bottom figure, from Saranathan et al., 2010)
Richard Prum and coworkers have figured out how these photonic crystals grow (Saranathan et al., 2010). The molecules in the soft membranes that template the deposition of chitin during wing-scale growth become spontaneously organized into the ‘crystalline sponge’. Biological membranes are made up of long, tadpole-like molecules called lipids, which have a water-soluble head and an oily tail. To shield the tails from water, they cluster side by side into sheets with the heads pointing outwards; the sheets then sit back to back in bilayer membranes. Pores in these membrane induce curvature, partly exposing the lipid tails and therefore incurring a cost in energy. For this reason, the pores in effect repel one another, and this can force them to become arranged in a regular way, an equal distance apart. Periodic membrane structures have been found in the cells of many different organisms, from bacteria to rats (Hyde et al., 1997).
In P. sesostris wing-scale progenitor cells, the outer ‘plasma membrane’ and the folded membrane of the inner compartments called the endoplasmic reticulum, where lipids and other molecules are made, come together to form a so-called double-gyroid structure (Figure 8, left), in which two interweaving sets of channels divide up space into three networks that interpenetrate, but are isolated from one another. One of these is then filled with chitin, which hardens into a robust form while the cell dies and the rest of the material is degraded, leaving behind the single gyroid phase (Saranathan et al., 2010).
It has been suggested that these natural nanostructures might be used as the templates for making artificial ones, for example, by filling the empty space around the chitin with a polymer or an inorganic solid, and then dissolving away the chitin (Saranathan et al., 2010). But it is also possible to mimic the structures from scratch. For instance, artificial bilayer membranes made from lipid-like molecules called surfactants will also form orderly sponges, and so will so-called block copolymers, in which the chain-like molecules consist of two stretches with different chemical composition (Hyde et al., 1997). Ulrich Wiesner and coworkers (Stefik et al., 2012) have mixed liquid block copolymers with nanoparticles of niobium and titanium oxide, and let the polymers form into gyroid and other ordered ‘nanosponge’ structures that usher the nanoparticles into the same arrays. When this composite is heated, the polymer is burnt away while the mineral nanoparticles coalesce into continuous networks (Figure 8, center).
These porous solids could find a wide range of uses. Thin porous films of titanium dioxide nanoparticles coated in light-absorbing dyes are already used in low-cost solar cells. These orderly gyroid networks can offer improvements, partly because the solid material through which light-excited electrons are harvested is continuously connected rather than relying on random electrical contacts between nanoparticles. And the researchers have calculated that double-gyroid nanosponges made from metals such as silver or aluminum, which might similarly be assembled from nanoparticles guided by block copolymers, could have the weird property of a negative refractive index, meaning that they would bend light ‘the wrong way’ (Hur et al., 2011). Such materials could be used to make so-called superlenses for optical microscopes that can image objects smaller than the wavelength of light; something that isn’t possible with conventional lenses.
Inspired by the butterfly structures, Mark Turner and colleagues (Turner et al., 2011) have used laser beams to ‘write’ these intricate three-dimensional photonic crystals directly into a commercial light-polymerizable ‘photoresist’ material (Figure 8, right). Being somewhat ‘scaled-up’ versions of the natural nanostructures, these had photonic band gaps in the infrared part of the spectrum. Current telecommunications operates mostly at infrared wavelengths, and these structures could find uses there; some, for example, have a corkscrew lattice that make them respond differently to circularly polarized light with a left- or right-handed twist.
Figure 8. The gyroid phase (left), and structures mimicking the ‘butterfly gyroid’: (middle) a network of titania organized by self-assembly of a block copolymer, and (right) a larger-scale lattice made by setting a light-sensitive polymer with laser beams (scale bar: 10 µm). (Left figure, courtesy of Matthias Weber, Indiana University. Middle figure, from Stefik et al., 2012. Right figure, from Turner et al., 2011)
Photonic Crystal Fibers
The spines of some marine polychaete worms, such as Aphrodita (the sea mouse) and Pherusa, are tubular structures containing hexagonally packed hollow cylindrical channels a few hundred nanometers across and made from chitin. These arrays act as two-dimensional photonic crystals that reflect light strongly in the long-wavelength part of the spectrum, which gives the Aphrodite spine a deep, iridescent red color (Figure 9) (Parker et al., 2001; Trzeciak & Vukusic, 2009).
Figure 9. The tiny spines of polychaete worms such as the sea mouse (Polychaeta: Aphroditidae; top left) are natural photonic crystals. Seen close up in cross section, they consist of regularly packed hollow channels with walls of chitin. Middle left: cross-section from Pherusa (scale bar: 2 µm); center: side view of channels from Aphrodita; right: the red color of light passing through a spine of Aphrodita. Artificial photonic fibres like this can easily be made by heating and drawing out bundles of glass capillaries (bottom). They can confine light within the ‘solid’ channels even around tight bends. (Note the solid ‘defect’ in the central channel.) (Top, middle center and middle right, courtesy of Andrew Parker, University of Oxford. Middle left, from Trzeciak & Vukusic, 2009. Bottom, from Russell, 2003)
It is not clear if the optical properties of the polychaete spines have any biological function. But there are certainly uses for such light-manipulating fibres in optical technology. For example, Philip Russell and collaborators (Russell, 2003) have made them by stacking glass capillaries into hexagonally packed bundles and drawing them out under heat into narrow fibers laced through with holes. If ‘defects’ are introduced into the array of tubular channels, either by including a wider capillary or a solid rod in the bundle, light can pass along the defect while being excluded from the photonic crystal, creating an optical fiber with a cladding that is essentially impermeable to light of wavelengths within the band gap. Photonic crystal fibers like this can guide light around tighter bends than is usually possible with conventional fibers, where the light is confined less reliably by internal reflection at the fibre surface. As a result, these fibers would work better for guiding light in tightly confined spaces, such as on optical microchips. And because photonic crystal fibers are in general less ‘leaky’ than conventional ones, they could be replace them in optical telecommunications networks, requiring less power, and obviating the need for amplifiers to boost signals sent over long distances.
The splendid blue and green plumage of many birds, while also being physical rather than pigmented colors, lacks the iridescence of the hummingbird or the peacock. Instead, they have the same color viewed from any angle. They scatter light from sponge-like keratin nanostructures; but because these structures are disordered, the scattering is diffuse, like the blue of the sky, rather than mirror-like and iridescent (Dufresne et al., 2009).
In the blue-and-yellow macaw, Ara ararauna, (Figure 10), and the black-capped kingfisher Halcyon pileata, the empty spaces in the keratin matrix of the feather barbs form tortuous channels about 100 nm wide. A similar random network of filaments in the cuticle of the Cyphochilus beetle gives it a dazzlingly bright white shell. In some other birds, such as the blue-crowned manakin, Lepidothrix coronata, the air holes are instead little spherical bubbles connected by tiny cavities.
Figure 10. The blue feathers of the blue-and-yellow macaw contain sponge-like labyrinths of air and keratin (bottom left), which scatter blue light strongly in all directions. Some other feathers derive similar colors from spherical ‘bubble-like’ air holes in the keratin matrix (bottom right). Scale bars: 500 nm. (Bottom figure, from Dufresne et al., 2009)
It is believed that both of these structures are formed as keratin separates out spontaneously from the fluid cytoplasm of feather-forming cells, like oil from water (Dufresne et al., 2009). In liquid mixtures, such as solidifying molten metal alloys or polymers, such phase separation creates different structures in different conditions. If the mixture is intrinsically unstable, the components separate into disorderly, interwoven channels in a process called spinodal decomposition. But if the mixture is metastable (provisionally stable), like water supersaturated with dissolved gas, then the separating phase will form discrete blobs or bubbles that grow from very tiny ‘seeds’ or nuclei. Prum thinks that either of these processes may happen as bird feathers develop, and that birds have evolved a way of controlling the rate of keratin phase separation so that they can arrest the nanostructure at a certain size. Once the cells have died and dried, this size determines the wavelength of scattered light, and thus the feather’s color.
This kind of diffuse light-scattering has been used for centuries as a way of making colors in technology. In milk, microscopic droplets of fat with a wide range of sizes cause scattering of all visible wavelengths, and give the liquid its opaque whiteness. Michael Faraday discovered in the nineteenth century that light scattering from nanoscale particles of gold suspended in water can create a deep reddish-purple color with a precise hue that depends on the size of the particles. Glassmakers had been using alchemical recipes to precipitate nanoscale gold particles in molten silica to make ruby glass ever since ancient times.
Today, engineers are looking at how these random networks and particle arrays can give rise to strongly colored and high-opacity materials. Pete Vukusic and colleagues (Hallam et al., 2009) have mimicked the cuticle of Cyphochilus beetles in random porous networks made from interconnected filaments of the minerals calcium carbonate and titanium dioxide mixed with a polymer and oil liquid binders and left to dry. Guided by the size and density of filaments in the beetle shell, they were able to make thin coatings with brilliant whiteness. Meanwhile Prum, his colleague Eric Dufresne and their coworkers at Yale University (Forster et al., 2010) have mimicked the disordered sponges of bird feathers by creating films of randomly packed microscopic polymer beads, which have blue-green colors (Figure 11).
Figure 11. This thin film of randomly arrayed polymer microspheres mimics the keratin matrix in the blue feathers of the blue-crowned manakin. (From Forster et al., 2010)
One of the most enviable optical tricks in nature is to produce reversible color changes. The reflective, protean colors in the skins of squid such as the Loligidinae family are produced by a protein called reflectin, arranged into plate-like stacks in cells called iridophores, which again act as color-selective reflectors (Figure 12). The color changes are thought to be involved in both camouflage and communication between squid for mating and displays of aggression.
Figure 12. Stacked plates of the reflectin protein (left) in iridophore cells (center) create tunable reflective colors in squid (right). (Center figure, courtesy of Daniel Morse, University of California at Santa Barbara)
Daniel Morse and colleagues have recently figured out how the color changes of iridophores are achieved (Tao et al., 2010). The reflectin proteins crumple up into nanoparticles, which pack together into dense arrays that make up the flat layers. These layers are sandwiched between deep folds of the cell membrane. The color change can be triggered by neurotransmitter lipid molecules called acetylcholine, which activate a biochemical process that fixes electrically charged phosphate chemical groups onto the reflectin protein. These groups largely neutralize the proteins’ intrinsic charge and allow them to pack more closely together, increasing the reflectivity of the layers. At the same time, this compaction squeezes water from between the protein particles and out of the cell, and enables the reflectin layers to sit closer together.
Morse and colleagues (Holt et al., 2010) think that it should be possible to copy some of these tricks in optical devices, perhaps even using reflectins themselves. They have inserted the gene encoding a reflectin protein from the long-finned squid Loligo pealeii into Escherichia colibacteria. When expressed, the protein spontaneously collapses into nanoparticles (Tao et al., 2010). The size of these particles can be tuned by controlling the interactions between charged groups on the proteins using salt. Held between stacks of permeable membranes, these materials might therefore swell and contract, altering the reflected wavelengths, in response to chemical triggers. Morse and colleagues have also taken inspiration from reflectins to develop a light switch based on a wholly synthetic light-sensitive polymer. They use an electric field both to change the refractive index of the polymer and to pull salt into the polymer film to swell it. As with iridophores, this combination of effects alters the material’s response to light dramatically, switching it from transparent to opaque; all without moving parts or high-tech manufacturing methods. The team are currently working with Raytheon Vision Systems, an optics company in Goleta, California, to use this system in fast shutters for infrared cameras.
The Art and Science of Natural Color Mixing
Many of the optical effects found in nature are not purely due to structural colors, but arise from their combination with absorbing pigments (Shawkey et al., 2009). In squid, a thin pigment layer above the reflective layer acts as a filter that can modify the appearance, for example, making it mottled; reflective and absorbing to different degrees in different places. In bird feathers, the physical colors resulting from melanin nanostructures embedded in a keratin protein matrix can be tuned by light-absorbing filters of pigments, such as carotenoids, which absorb red and yellow light. The characteristic green plumage of parrots seems to be produced by laying a yellow pigment over a blue reflective layer of melanin and keratin (Figure 13). And the purple wing tips of Purple Tip butterflies come from red pigments beneath a blue iridescent surface.
Figure 13. Green is a characteristic color of parrots, but their plumage contains no green pigment, nor is it purely a structural color. Rather, it results from ‘structural blue’ overlaid with a filter of yellow pigment.
Chameleons display perhaps the most advanced mastery of these mixing tricks. Their spectacular color changes are produced by three separate systems for modifying the reflected light, stacked one atop the other. The first layer consists of cells containing red and yellow light-absorbing pigment particles, the location of which within the cell determines the color intensity. Below these are iridophores like those of squid, from which blue and white light may be selectively reflected by crystalline layers of the molecule guanine (also a component of DNA). Finally there is a layer of cells containing the dark pigment melanin, which act like the colored ‘ground’ layers of Old Master paintings to modify the reflection of light that penetrates through the first two layers. This combination of reflection and absorption enables the chameleon to adapt its skin color across a wide, albeit species-specific, range to signal warning, for mating displays, and for camouflage (Forbes, 2009).
How pigments alter and adjust the reflected light in such cases is still imperfectly understood. One problem is that the combinations are so diverse; more than 20 different arrangements of melanin, keratin and air have been identified in the plumage of birds. Moreover, melanin is itself a light absorber, creating colors ranging from yellow to black. The bright white markings on the blue wings of the Morpho cypris butterfly are produced by simply removing the melanin from reflective multilayer structures; the mirrors remain, but the pigments do not.
In such ways, evolution has made creative use of the limited range of materials at its disposal to generate a riot of profuse coloration and markings. A better understanding of how this is achieved could give painters and visual artists access to entirely new ways of making colors based on iridescent and pearlescent pigments, whose use has so far been largely restricted to less sophisticated applications in the automobile and cosmetic industries (Schenk & Parker, 2011).
Painter Franziska Schenk has been exploring the mixing of structural and pigmented color during her stay as artist-in-residence in the Department of Biosciences at the University of Birmingham in the UK (Schenk, 2009). With iridescent particles, says Schenk, “the established methods of easel painting no longer apply. Their conversion to painting requires something truly innovative.”
Schenk used iridescent particles to reproduce the starting blue of the Morpho wing in a series of paintings that change color when lit or viewed from different angles (Figure 14). The background color on which the particles are placed is central to the effect. On white, the light not reflected from the blue particles passes through and bounces off the base. This means that when not seen face-on, the blue quickly fades and is replaced by a muted yellow. But on a black background, all non-blue light is absorbed, and the blue is more pure and intense.
Figure 14. Painting of a Morpho butterfly wing by Franziska Schenk, using blue pearlescent pigments. The color changes depending on the angle of illumination, as well as on the nature of the background color. (Courtesy of Franziska Schenk)
Although the brilliance of these colors doesn’t approach that of butterfly wings, it takes advantage of recent improvements in synthetic pearlescent particles. The first of these were made by coating mica flakes with multilayers of metal oxides to generate the diffraction grating. But because the mica surfaces were not perfectly smooth and the grain sizes varied, there was always a range in the precise colors and intensities of the particles. Schenk has used pigments in which the mica substrate is replaced by a transparent borosilicate glass, which is smoother and gives a purer hue. She believes that “iridescent technology is destined to introduce a previously unimaginable level of intensity and depth, thus adding beauty, luster and a dynamic dimension to art”. Schenk’s Studies of Cuttlefish (Figure 15) is a painting that uses iridescent flakes mixed with beads and wax.
Figure 15. “Studies of Cuttlefish” by Franziska Schenk, using iridescent flakes mixed with beads and wax. (Courtesy of Franziska Schenk)
Another series of cuttlefish, “Mantle of Many Colours” (Figure 16), was made with iridescent paint that differs in appearance depending on the conditions and angle of lighting, which results in a compelling chameleon effect that traditional paints simply cannot create. The colors change from greens to purples as the viewing angle shifts. “Still images, together with any attempt to verbally describe the effect, are pretty limiting”, Schenk admits; you have to see these things in the flesh to appreciate their full impact.
Figure 16. “Mantle of Many Colours” by Franziska Schenk, which uses iridescent paint, as seen from different angles. (Courtesy of Franziska Schenk)
“Every day you play with the light of the universe”, wrote the Chilean poet Pablo Neruda, but he had no idea how literally true this would become. Our technologies for transmitting, manipulating and displaying information, whether for work or play, depend increasingly on our ability to control light; to harness and transform color. Some of nature’s most stunning sights depend on such a facility too, and often they show us that beauty can be inextricably linked to utility. We are impressed by plumage, by markings and animal displays, that are specifically designed by evolution to make such an impression. And nature has found ways to make this chromatic exuberance robust, changeable, responsive, and cheap and reliable to manufacture. In shaping color without the chemical contingency of pigments, there seems to be little we can dream up that nature has not already anticipated, exploiting its capacity to fashion intricate fabrics and structures on the tiniest scales. We can only learn, and admire.
Note: The current article is an extended version of Ball P (2012), “Nature’s color tricks”, Sci. Am. 306(5), 74-79.
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Technology of Nanostructures
Colloidal Self Assembly for fabrication of Photonic nanostructures including
Composite and Inverse Opals
Source: Self-assembled colloidal structures for photonics
College of Information Science and Engineering, Northeastern University, Shenyang 110004, China2College of Information & Control Engineering, Shenyang Jianzhu University, Shenyang 110168, China3Melbourne Centre for Nanofabrication, Clayton, Victoria 3168, Australia*Authors to whom correspondence should be addressed.
Viburnum tinus Fruits Use Lipids to Produce Metallic Blue Structural Color
Rox Middleton,1,8,10 Miranda Sinnott-Armstrong,2,9,10 Yu Ogawa,3 Gianni Jacucci,1 Edwige Moyroud,4,5 Paula J. Rudall,6 Chrissie Prychid,6 Maria Conejero,6 Beverley J. Glover,7 Michael J. Donoghue,2 and Silvia Vignolini
In-Plane Direct-Write Assembly of Iridescent Colloidal Crystals
Alvin T. L. Tan, Sara Nagelberg, Elizabeth Chang-Davidson, Joel Tan, Joel K. W. Yang, Mathias Kolle, and A. John Hart
Fabrication of non-iridescent structural color on silk surface by rapid T polymerization of dopamine
In a future post, I will research structural colors.
Color Change in Biology
Color Change using Technology
Smart Food Packaging
Color Change and Technology
Chromic phenomena in dyes and pigments
Some of the major companies are
LCR Hallcrest LLC
Hali Pigment Co. Ltd
Chromatic Technologies Inc.
QCR Solutions Corp.
RPM International Inc.
Good Life Innovations Ltd
FX Pigments Pvt. Ltd
Smarol Industry Co. Ltd
Kolortek Co. Ltd
Kolorjet Chemicals Pvt. Ltd
Smart Hybrid Pigments
The solutions developed by OliKrom involve a new generation of hybrid pigments that combines the proven strength of the metal ions and the flexibility of the molecular material. The change in the structure allow to control the color change as a function of :
Temperature (thermochromic property),
Light (photochromic property),
Pressure (piezochromic property),
A solvent (solvatochromic property),
A gas (chimiochromic property),
The expertise of OliKrom allows for each of these properties:
To adjust the request colors,
To obtain reversible and/or irreversible color-shifting,
To modulate the speed of the color change,
To control the issues of fatigability.
To insert these adaptive pigments in a formulation (paint, ink, masterbatch, …) without altering the properties!
To produce on an industrial scale paintings, inks, master batches, …
Threshold temperature indicators / industrial pipes, thermal mapping.
Plastic toys: decor with changing color, labels, packaging, paper / plastic promotional, “dynamic” advertising inserts.
Cosmetics: Bottles & Jars of cosmetic or perfume.
Smart Textiles: comfort indicator, clarification of the textile with temperature.
Fluorescent Pigments and Phosphorescent Pigments
Source: PHOTOLUMINESCENTS: FLUORESCENT AND PHOSPHORESCENT INKS AND PAINTS / OliKrom
Reversible Thermochromic Material
Irreversible Thermochromic Material
Solvachromes and Chemochromes
Color Change in Biology
Golden Tortoise Beetle
Pacific Tree Frog
Mechanisms for Color Change
Source: Adaptive camouflage helps blend into the environment
Cephalopods such as cuttlefish often use use adaptive camouflage to blend in with their surroundings. They are able to match colors and surface textures of their surrounding environments by adjusting the pigment and iridescence of their skin.
On the skin surface, chromatophores (tiny sacs filled with red, yellow, or brown pigment) absorb light of various wavelengths. Once visual input is processed, the cephalopod sends a signal to a nerve fiber, which is connected to a muscle. That muscle relaxes and contracts to change the size and shape of the chromatophore. Each color chromatophore is controlled by a different nerve, and when the attached muscle contracts, it flattens and stretches the pigment sack outward, expanding the color on the skin. When that muscle relaxes, the chromatophore closes back up, and the color disappears. As many as two hundred of these may fill a patch of skin the size of a pencil eraser, like a shimmering pixel display.
The innermost layer of skin, composed of leucophores, reflects ambient light. These broadband light reflectors give the cephalopods a ‘base coat’ that helps them match their surroundings.
Between the colorful chromatophores and the light-scattering leucophores is a reflective layer of skin made up of iridophores. These reflect light to create pink, yellow, green, blue, or silver coloration, while the reflector cells (found only in octopuses) reflect blue or green.
There are a few animals that have the unique ability to change colors. The ability to change colors can help animals protect themselves against their predators because it allows them to blend into their natural environment. Here is a list of 10 color changing animals.
A chameleon is a unique species of lizard famous for changing its skin color. It does so to camouflage with its surrounding. Sometimes chameleons change their color when they are angry or fearful. To change its color, the chameleon adjusts a layer of specialized cells underlying its skin. Others change color in response to humidity, light, and temperature. Chameleons never stop growing. They keep shedding their skin from time to time. Furthermore, chameleons have excellent eyesight characterized by a 360-degree arc vision. Although chameleons do not hear, their bodies detect sound within the surrounding.
9. Golden Tortoise Beetle
The golden tortoise beetle is an insect that can change its color. The species with this ability include Charidotella sexpunctata and Charidotella egregia. The tortoise beetles change color due to particular events that occur in their environment. Such events include meeting a willing mate and being touched by a curious human being. Hence, when they are mating or agitated, the tortoise beetles change their color from gold to a bright red color. The change of color occurs due to a process referred to as optical illusion.
8. Mimic Octopus
Mimic octopus, scientifically known as Thaumoctopus mimicus, change their color and they can also mimic other sea creatures such as a lionfish, jellyfish, stingrays, and sea snakes. The mimic octopus can pick the color of the sea creature that they intend to mimic. The mimic octopuses change their body shape to avoid potential predators. The change of skin color helps them to adapt to their surrounding. Mimic octopuses can change color and mimic shapes due to their skin which is very responsive to the environment.
7. Pacific Tree Frog
The Pacific Tree Frog inhabits North America. One of its common features is the sticky toe pads. The sticky toe pads enable them to climb trees and plants. The Pacific Tree Frog changes its color to blend in with its surroundings. The change of color is a defense mechanism against predators such as raccoons, bullfrogs, snakes, heron, and many others. Pacific Tree Frogs also change their color based on the seasons and temperature. When the temperatures are high, they turn into a shade of yellow. An example of Pacific Tree Frog species that changes color is Hyla regilla. The process of color change in Pacific Tree Frogs takes 1-2 minutes.
Seahorses, such as the thorny seahorse, are among the marine animals that have mastered changing their color. The purpose of changing their skin color is to camouflage, frighten predators, communicate their emotions, and for courtship. Complex interactions between the brain, nervous system, hormones, and organelles make it possible for the seahorses to change their color. The organelles responsible for these color changes are known as chromatophores. Regarding the speed at which the skin color changes, this depends on the stimulus. For instance, in a life or death situation such as involving a predator, the color changes quickly. But whenever the seahorse is courting a mate, the change takes place slowly.
Flounders are naturally brown. However, they can change color to suit their surroundings. A flounder uses its vision and specialized cells inside the skin to change color. The cells, in turn, have color pigments and are linked to the eyes of the flounders. When a flounder moves to a new environment, the retina in the eyes captures the new color. Consequently, the color seen by the eyes are transmitted to the cells. The cells adjust the pigmentation to match the surface color. Scientists have discovered that flounders depend entirely on their vision to change color. When their eyes are damaged, then they have difficulties in camouflaging to their surrounding. An example of flounder species that changes color is the peacock flounder.
Cuttlefish are cephalopods that change color to feed on prey and avoid predators craftily. They have three mechanisms by which they can change color. Firstly, the cuttlefish skin contains papillae that alter the tone of the fish. The papillae cause the skin to become smooth or rough depending on the environment. Secondly, camouflaging is possible because of the chromatophores in their skin. The chromatophores are sacs of color pigments. To change color, these sacs receive color-changing instructions from the brain and act accordingly. Lastly, cuttlefish have reflecting plates called leucophores and iridophores. The plates enable the fish to change its color.
3. Crab Spiders
Spiders called flower spiders (or crab spiders) change their color. They usually change color to hide from their prey. Consequently, the spiders change color to resemble the flower surface on which they sit through the reflection of light. Some spiders release a yellow pigment that enhances their color changing process. An example of a species of spider with such color changing features is Misumenoides formosipes and Misumena vatia. The color change from white to yellow takes 10-25 days. Hence, the flower spiders patiently wait for the completion of the process before they can attack their prey.
Squids are marine cephalopods. They possess two long tentacles and eight arms. An interesting fact about the squids is that their blood is blue. Furthermore, they have three hearts instead of one like other fish. The squids are uniquely beautiful and able to change color. They change color using chromatophores engraved in their skin. The purpose of changing color is to match the surface they are on so that they can avoid predators. The camouflage also acts as a hunting tactic since it enables them to hide away from their prey.
1. Cyanea Octopus
Known as the big blue octopus or the day octopus, octopus cyabea is found in the waters of the Indo-Pacific. It is known as the day octopus as it is most active during the daytime in contrast to most other octopus species. The cyanea octopusis especially adept at camouflage, able to not only frequently change the color of their skin, but also recreate patterns and textures. On the hunt for crabs, molluscs, shrimp, and fish, the cyanea octopus is able to quickly adapt its appearance to its surroundings, even mimicking moving shadows such as overhead clouds.
Color Change in Plants And Flowers
Color change in Leaves and Flowers
Chlorophyll – Green
Cartenoids – Xanthophylls – Yellow as in Corn
Cartenoids – Carotenes – Orange as in Carrots
Anthrocyanins – Blueberries and Cherries – Blue, purple, red, pink
Flavonols – Pale yellows and whites
Plants change colors
Change in Heat
Change in pH
During the Fall
During the day
Color Fading and Color Metamerism are also important problems but are not discussed in this post.
Source: The science behind why leaves change color in autumn
A rainbow of autumn colors
The green color of chlorophyll is so strong that it masks any other pigment. The absence of green in the fall lets the other colors come through. Leaves also contain the pigments called carotenoids; xanthophylls are yellow (such as in corn) and carotenes are orange (like in carrots). Anthocyanins (also found in blueberries, cherries) are pigments that are only produced in the fall when it is bright and cold. Because the trees cut off most contact with their leaves at this point, the trapped sugar in the leaves’ veins promotes the formation of anthocyanins, which are used for plant defense and create reddish colors.
However, trees in the fall aren’t just yellow and red: they are brown, golden bronze, golden yellow, purple-red, light tan, crimson, and orange-red. Different trees have different proportions of these pigments; the amount of chlorophyll left and the proportions of other pigments determine a leaf’s color. A combination of anthocyanin and chlorophyll makes a brown color, while anthocyanins plus carotenoids create orange leaves.
Source: The science behind why leaves change color in autumn
Can Hibiscus Change Color: Reasons For Hibiscus Turning A Different Color
Can hibiscus change color? The Confederate Rose (Hibiscus mutabilis) is famous for its dramatic color changes, with flowers that can go from white to pink to deep red within one day. But almost all hibiscus varieties produce flowers that can change colors under certain circumstances. Read on to learn more.
Reasons for Color Changing in Hibiscus
If you’ve ever noticed the flowers on your hibiscus turning a different color, you’ve probably wondered what was behind the change. To understand why this happens, we need to look at what creates flower colors in the first place.
Three groups of pigments create the vibrant color displays of hibiscus flowers. Anthocyanins produce blue, purple, red, and pink colors, depending on the individual pigment molecule and the pH it is exposed to. Flavonols are responsible for pale yellow or white colors. Carotenoids create colors on the “warm” side of the spectrum – yellows, oranges, and reds.
Each hibiscus variety has its own genetics that determine what pigments, and what range of colors it can produce. However, within that range, temperature, sunlight, pH, and nutrition can all affect the levels of different pigments in a flower and what color they appear.
The blue- and red-colored anthocyanins are water-soluble pigments carried in plant sap. Meanwhile, the red, orange and yellow carotenoids are fat-soluble pigments created and stored in the plastids (compartments in plant cells similar to the chloroplasts that carry out photosynthesis). Therefore, anthocyanins are less protected and more sensitive to environmental changes, while carotenoids are more stable. This difference helps explain the color changes in hibiscus.
Anthocyanins exposed to hot conditions will often break down, causing flower colors to fade, while carotenoid-based colors hold up well in the heat. High temperatures and bright sunlight also enhance carotenoid production, leading to bright reds and oranges.
On the other hand, plants produce more anthocyanins in cold weather, and the anthocyanins they produce tend to be more red- and pink-colored as opposed to blue or purple. For this reason, some anthocyanin dependent hibiscus flowers will produce brilliant color displays during cool weather or in partial shade, but will fade in bright, hot sunlight.
Similarly, flavonols exposed to high temperatures will fade from yellow to white, while cold weather will cause an increase in production and a deepening of yellow flower colors.
Other Factors in Hibiscus Color Change
Some anthocyanin pigments will change color depending on the pH they’re exposed to within the flower. The pH doesn’t usually change over time within a hibiscus flower because it is determined genetically, but patches of different pH levels can lead to multiple colors occurring within one flower.
So, depending on its variety, your hibiscus changed color because of some combination of temperature, sunlight, nutrition, or pH has taken place. Can gardeners control this hibiscus color change? Yes, indirectly – by controlling the plant’s environment: shade or sun, good fertility, and protection from hot or cold weather.
Anthocyanins and carotenoids… plus some other things.
Flowers come in all shapes and sizes, but what makes them truly stand apart from each other is their vibrant colors. These colors are made up of pigments and, generally speaking, the fewer the pigments, the lighter the color. The most common pigments in flowers come in the form of anthocyanins. These pigments range in color from white to red to blue to yellow to purple and even black and brown. A different kind of pigment class is made up of the carotenoids. Carotenoids are responsible for some yellows, oranges, and reds. (These little guys are what cause the brilliant colors of autumn leaves!) While many flowers get their colors from either anthocyanins or carotenoids, there are some that can get their colors from a combination of both.
Anthocyanins and carotenoids are the main sources of flower coloration, but there are other factors that can affect how colors present themselves. The amount of light flowers receive while they grow, the temperature of the environment around them, even the pH level of the soil in which they grow can affect their coloration. Another factor is stress from the environment. This stress can include a drought or a flood or even a lack of nutrition in the soil, all of which can dampen the coloration of flowers. And then, of course, there is the visual that the eye and brain form together: humans can, for the most part, view all colors in the visible spectrum, BUT every human perceives color differently, so a red rose may appear more vibrant to one person while it appears more muted to another. Beauty (and color!) is in the eye of the beholder.
Silvia Vignolini1,2, Edwige Moyroud3, Beverley J. Glover3 and Ullrich Steiner1
1Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK 2Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK 3Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK
The Mechanism of Color Change in the Neon Tetra Fish: a Light‐Induced Tunable Photonic Crystal Array†
Dvir Gur 1 , Benjamin A Palmer 1 , Ben Leshem 2 , Dan Oron 2 , Peter Fratzl 3 , Steve Weiner 1 , Lia Addadi 4
Codes and conventions are the basis of our social life and from time immemorial have divided the world of culture from the world of nature. The rules of grammar, the laws of government, the precepts of religion, the value of money, the rules of chess etc., are all human conventions that are profoundly different from the laws of physics and chemistry, and this has led to the conclusion that there is an unbridgeable gap between nature and culture. Nature is governed by objective immutable laws, whereas culture is produced by the mutable conventions of the human mind.
In this millennia-old framework, the discovery of the genetic code, in the early 1960s, came as a bolt from the blue, but strangely enough it did not bring down the barrier between nature and culture. On the contrary, a protective belt was quickly built around the old divide with an argument that effectively emptied the discovery of all its revolutionary potential. The argument that the genetic code is not a real code because its rules are the result of chemical affinities between codons and amino acids and are therefore determined by chemistry. This is the ‘Stereochemical theory’, an idea first proposed by George Gamow in 1954, and re-proposed ever since in many different forms (Pelc and Welton 1966; Dunnil 1966; Melcher 1974; Shimizu 1982; Yarus 1988, 1998; Yarus, Caporaso and Knight 2005). More than fifty years of research have not produced any evidence in favour of this theory and yet the idea is still circulating, apparently because of the possibility that stereochemical interactions might have been important at some early stages of evolution (Koonin and Novozhilov 2009). The deep reason is probably the persistent belief that the genetic code must have been a product of chemistry and cannot possibly be a real code. But what is a real code?
The starting point is the idea that a code is a set of rules that establish a correspondence, or a mapping, between the objects of two independent worlds (Barbieri 2003). The Morse code, for example, is a mapping between the letters of the alphabet and groups of dots and dashes. The highway code is a correspondence between street signals and driving behaviours (a red light means ‘stop’, a green light means ‘go’, and so on).
What is essential in all codes is that the coding rules, although completely compatible with the laws of physics and chemistry, are not dictated by these laws. In this sense they are arbitrary, and the number of arbitrary relationships between two independent worlds is potentially unlimited. In the Morse code, for example, any letter of the alphabet could be associated with countless combinations of dots and dashes, which means that a specific link between them can be realized only by selecting a small number of rules. And this is precisely what a code is: a small set of arbitrary rules selected from a potentially unlimited number in order to ensure a specific correspondence between two independent worlds.
This definition allows us to make experimental tests because organic codes are relationships between two worlds of organic molecules and are necessarily implemented by a third type of molecules, called adaptors, that build a bridge between them. The adaptors are required because there is no necessary link between the two worlds, and a fixed set of adaptors is required in order to guarantee the specificity of the correspondence. The adaptors, in short, are the molecular fingerprints of the codes, and their presence in a biological process is a sure sign that that process is based on a code.
This gives us an objective criterion for discovering organic codes and their existence is no longer a matter of speculation. It is, first and foremost, an experimental problem. More precisely, we can prove that an organic code exists, if we find three things: (1) two independents worlds of molecules, (2) a set of adaptors that create a mapping between them, and (3) the demonstration that the mapping is arbitrary because its rules can be changed, at least in principle, in countless different ways.
Two outstanding examples
The genetic code
In protein synthesis, a sequence of nucleotides is translated into a sequence of amino acids, and the bridge between them is realized by a third type of molecules, called transfer-RNAs, that act as adaptors and perform two distinct operations: at one site they recognize groups of three nucleotides, called codons, and at another site they receive amino acids from enzymes called aminoacyl-tRNA-synthetases. The key point is that there is no deterministic link between codons and amino acids since it has been shown that any codon can be associated with any amino acid (Schimmel 1987; Schimmel et al. 1993). Hou and Schimmel (1988), for example, introduced two extra nucleotides in a tRNA and found that that the resulting tRNA was carrying a different amino acid. This proved that the number of possible connections between codons and amino acids is potentially unlimited, and only the selection of a small set of adaptors can ensure a specific mapping. This is the genetic code: a fixed set of rules between nucleic acids and amino acids that are implemented by adaptors. In protein synthesis, in conclusion, we find all the three essential components of a code: (1) two independents worlds of molecules (nucleotides and amino acids), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed.
The signal transduction codes
Signal transduction is the process by which cells transform the signals from the environment, called first messengers, into internal signals, called second messengers. First and second messengers belong to two independent worlds because there are literally hundreds of first messengers (hormones, growth factors, neurotransmitters, etc.) but only four great families of second messengers (cyclic AMP, calcium ions, diacylglycerol and inositol trisphosphate) (Alberts et al. 2007). The crucial point is that the molecules that perform signal transduction are true adaptors. They consists of three subunits: a receptor for the first messengers, an amplifier for the second messengers, and a mediator in between (Berridge 1985). This allows the transduction complex to perform two independent recognition processes, one for the first messenger and the other for the second messenger. Laboratory experiments have proved that any first messenger can be associated with any second messenger, which means that there is a potentially unlimited number of arbitrary connections between them. In signal transduction, in short, we find all the three essential components of a code: (1) two independents worlds of molecules (first messengers and second messengers), (2) a set of adaptors that create a mapping between them, and (3) the proof that the mapping is arbitrary because its rules can be changed (Barbieri 2003).
A world of organic codes
In addition to the genetic code and the signal transduction codes, a wide variety of new organic codes have come to light in recent years. Among them: the sequence codes (Trifonov 1987, 1989, 1999), the Hox code (Paul Hunt et al. 1991; Kessel and Gruss 1991), the adhesive code (Redies and Takeichi 1996; Shapiro and Colman 1999), the splicing codes (Barbieri 2003; Fu 2004; Matlin et al. 2005; Pertea et al. 2007; Wang and Burge 2008; Barash et al. 2010; Dhir et al. 2010), the signal transduction codes (Barbieri 2003), the histone code (Strahl and Allis 2000; Jenuwein and Allis 2001; Turner 2000, 2002, 2007; Kühn and Hofmeyr 2014), the sugar code (Gabius 2000, 2009), the compartment codes (Barbieri 2003), the cytoskeleton codes (Barbieri 2003; Gimona 2008), the transcriptional code (Jessell 2000; Marquard and Pfaff 2001; Ruiz i Altaba et al. 2003; Flames et al. 2007), the neural code (Nicolelis and Ribeiro 2006; Nicolelis 2011), a neural code for taste (Di Lorenzo 2000; Hallock and Di Lorenzo 2006), an odorant receptor code(Dudai 1999; Ray et al. 2006), a space code in the hippocampus (O’Keefe and Burgess 1996, 2005; Hafting et al. 2005; Brandon and Hasselmo 2009; Papoutsi et al. 2009), the apoptosis code (Basañez and Hardwick 2008; Füllgrabe et al. 2010), the tubulin code (Verhey and Gaertig 2007), the nuclear signalling code (Maraldi 2008), the injective organic codes (De Beule et al. 2011), the molecular codes (Görlich et al. 2011; Görlich and Dittrich 2013), the ubiquitin code (Komander and Rape 2012), the bioelectric code (Tseng and Levin 2013; Levin 2014), the acoustic codes (Farina and Pieretti 2014), the glycomic code (Buckeridge and De Souza 2014; Tavares and Buckeridge 2015) and the Redox code (Jones and Sies 2015).
The living world, in short, is literally teeming with organic codes, and yet so far their discoveries have only circulated in small circles and have not attracted the attention of the scientific community at large.
Code Biology is the study of all codes of life with the standard methods of science. The genetic code and the codes of culture have been known for a long time and represent the historical foundation of Code Biology. What is really new in this field is the study of all codes that came after the genetic code and before the codes of culture. The existence of these codes is an experimental fact – let us never forget this – but also more than that. It is one of those facts that have extraordinary theoretical implications.
The first is the role that the organic codes had in the history of life. The genetic code was a precondition for the origin of the first cells, the signal transduction codes divided the descendants of the common ancestor into the primary kingdoms of Archaea, Bacteria and Eukarya, the splicing codes were instrumental to the origin of the nucleus, the histone code provided the rules of chromatin, and the cytoskeleton codes allowed the Eukarya to perform internal movements, including those of mitosis and meiosis (Barbieri 2003, 2015). The greatest events of macroevolution, in other words, were associated with the appearance of new organic codes, and this gives us a completely new understanding of the history of life.
The second great implication is the fact that the organic codes have been highly conserved in evolution, which means that they are the great invariants of life, the sole entities that have been perpetuated while everything else has been changed. Code Biology, in short, is uncovering a new history of life and bringing to light new fundamental concepts. It truly is a new science, the exploration of a vast and still largely unexplored dimension of the living world, the real new frontier of biology.
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CODE BIOLOGY, PEIRCEAN BIOSEMIOTICS, AND ROSEN’S RELATIONAL BIOLOGY
The classical theories of the genetic code claimed that its coding rules were determined by chemistry—either by stereochemical affinities or by metabolic reactions—but the experimental evidence has revealed a totally different reality: it has shown that any codon can be associated with any amino acid, thus proving that there is no necessary link between them. The rules of the genetic code, in other words, obey the laws of physics and chemistry but are not determined by them. They are arbitrary, or conventional, rules. The result is that the genetic code is not a metaphorical entity, as implied by the classical theories, but a real code, because it is precisely the presence of arbitrary rules that divides a code from all other natural processes. In the past 20 years, furthermore, various independent discoveries have shown that many other organic codes exist in living systems, which means that the genetic code has not been an isolated case in the history of life. These experimental facts have one outstanding theoretical implication: they imply that in addition to the concept of information we must introduce in biology the concept of meaning, because we cannot have codes without meaning or meaning without codes. The problem is that at present we have two different theoretical frameworks for that purpose: one is Code Biology, where meaning is the result of coding, and the other is Peircean biosemiotics, where meaning is the result of interpretation. Recently, however, a third party has entered the scene, and it has been proposed that Robert Rosen’s relational biology can provide a bridge between Code Biology and Peircean biosemiotics.