• Physics
  • Fluorescence
  • Refraction
  • Dispersion
  • Prisms
  • Beam Splitters and Image Combiners
  • Internal Reflection
  • Scattering
  • Coherent Light
  • Polarized Light
  • Why Is The Sky Blue?
• Biology
  • Photoreceptor Distribution In The Eye
  • Is the retina actually a part of the brain?
  • How Do Rods and Cones Work?
  • Types Of Opsins
  • Light and Dark Adaptation
  • Acquired Color Vision Deficiencies
  • Congenital Color Vision Deficiencies (including Color Blindness)
  • Tetrachromats?
  • Why Did Humans Develop Color Vision?
  • Metamers

• Related Pages

The most common cases of fluorescence convert incoming radiation of a short wavelength (e.g. black light) into longer wavelength visible light. The incoming radiation is absorbed by an atom, kicking an electron up into a higher energy level. When the electron falls back down, it doesn't go all the way down to its base state. The radiation that it emits is less energetic, of a longer wavelength.

In some cases, longer wavelength radiation is converted to shorter wavelength, as in the frequency-doubling crystals used to make green LASER pointers from IR LASER diodes. In this example, one low energy photon kicks an electron up, and a second photon kicks the electron even higher. When the electron returns to the base level, it emits energy corresponding to the sum of the two incoming photons - having a shorter wavelength.

Some fluorescent materials are:

• fluor spar
• uranium glass
• calcium sulphide

• visible light
• ultra-violet rays (black light)
• cathode rays (this is how a conventional television lights up the screen)
• X rays
• heat
• etc.

Refraction

Dispersion

When measuring the refractive index of a transparent substance, one must identify the wavelength used in the measurement. The wavelength most commonly used for this purpose is the yellow "D line spectrum" emitted by a sodium lamp. It actually consists of two strong lines in a closely spaced doublet, with an average wavelength of 5.893 nm.

Since the index of refraction is different for different wavelengths, so is the degree of bending. This phenomenom lets us manufacture a "dispersion prism", that breaks down a ray of sunlight into its component colors. In nature, dispersion is responsible for rainbows.

Dispersion has its drawbacks, though. Lenses rely on refraction in order to manipulate light. A plain glass lens will disperse light every place that its maker intended to refract light. This results in "chromatic aberration", where the focal length of the lens is different for different wavelengths of light. This is easily noticed around the edges of cheap one-piece "magnifying glasses". In order to correct this problem, multiple element "compound" lenses are used. [Years ago, I wore spectacles with a strong prescription. They worked fine when looking through the center of the glass, where the angle was small. But looking through the sharply curved edges of the glass would produce a rainbow effect.]

Prisms

• reflecting prisms

  These prisms redirect light beams by total internal reflection. In optical equipment, reflecting prisms can be used to perform the work of mirrors, without having to fine-tune and adjust the relative positions of individual mirrors.

• polarizing prisms

  Polarizing prisms divide incoming non-polarized light into separate components, polarized in orthogonal directions.

• refracting prisms, also known as dispersion prisms

  This is the science fair kind of prism that bends and separates light into its component colors.

For more information than you ever wanted to know about prisms, please see http://www.olympusmicro.com/primer/lightandcolor/prismsandbeamsplitters.html

Beam Splitters and Image Combiners

Internal Reflection

• When N₁ is greater than N₂: the angle of refraction is always smaller than the angle of incidence.
• When the two refractive indices are equal (N₁ = N₂): the light is passed through without refraction.
• When N₂ is greater than N₁: the angle of refraction is always greater than the angle of incidence.

MORE COMING SOON.

Scattering

This picture shows the small sharp dot of a LASER pointer, shining on a big chunk of quartz rock.

Although the light enters at one spot, the beam is scattered again and again, until the whole rock seems to glow with an internal light.

Coherent Light

Remember all those

When all the photons in a monochromatic light beam are synchronized, the beam is said to be "coherent". This is what makes LASER light unique.

Polarized Light

Remember that

This one wiggles up and down (blue axis), while zipping along the green direction.

Another photon in the beam may be wiggling in and out of the page (red axis), while zipping along the green direction.

Envision a bunch of photons, all zipping along the green direction. But each one wiggles in a different direction, along the axis of a different colored arrow.

That's the normal state of affairs in a beam of light.

Think of a polarizing filter as having a slot that only passes light that wiggles in the right direction.

This picture shows a polarizing filter that only allows photons to pass if they are wiggling up and down.

We could twist this filter 90 degrees. It would then only pass photons that wiggle in and out of the page.

This filter is twisted by 90 degrees. It only passes photons that wiggle in and out of the page.

• If you have an object that emits light of various wavelengths, and look at it through a lot of atmosphere, the light will appear less blue than it should look. This is because the other colors headed towards you are relatively unimpeded, but the blue light headed your way gets scattered off of the path to your eyes and doesn't reach you.
  As this beam of multicolor light travels from left to right, more and more of the blue rays are scattered out of the beam.
  
• Some of the light that is scattered on its way to you, eventually comes to you anyway, but from a different angle.
• The more atmosphere that you look through, the more pronounced these effects, because the light has to go further through the scattering medium.
  In this diagram, the red line represents sunlight coming to the Earth; blue represents atmosphere.

  The vertical red line has to travel through much less atmosphere. The horizontal red line must travel through much more atmosphere.
  

Here's what it all means:

• The sky looks blue because some of the blue light from the sun is bounced around and comes at you from other angles in the sky.
• When you look straight up at noon, you are looking through a minimal amount of atmosphere.
• When you look at the setting sun, the light rays that reach you are almost at a tangent to the Earth. They have to travel through much more of the atmosphere, so much more blue light is stolen from the sun, making it look more red.

For more detailed information on the biology and chemistry of vision, please see Kimball's Biology Pages.

After roughtly 30 minutes in the dark, almost all of the photoreceptors are packed with their visual pigments. Everything is ready for optical stimulation. In this "dark-adapted" state, the visual system is amazingly sensitive. A single photon of light can cause a rod to trigger. You will see a flash of light if as few as seven rods absorb photons at one time.

When the lights come on, all the photoreceptors react, making the the illumination almost painfully bright. In the brightly lit room, visual pigment is used up faster than it is regenerated. The longer you stay in the light, the lower and lower the supply of visual pigment. Over the next few minutes, photoreceptors become insensitive as they run low on visual pigment: your overall light sensitivity decreases. Eventually, the rate of visual pigment use is balanced by the rate at which it is formed. This condition is the "light-adapted" state.

Chemical changes make the dark-adapted state about 25,000 times more sensitive than the light-adapted state.

Central Nervous System Changes

In bright light, the pupillary constrictor reflex reduces the size of the pupil. This can cut down the amount of incoming light by a factor of 30.

In dim light, the central nervous system can turn up the amplification of signals along the visual pathway, by a factor approaching 3.

In the discussion of how rods and cones work, I said that each type of photoreceptor uses a different light-sensitive "visual pigment", which is composed of a light-absorbing chemical called 11-cis-retinal, coupled to a protein of the opsin family. Retinal is the same in all cases, but the type of opsin differs for each type of photoreceptor. It is the opsin that "tunes" a photoreceptor to a particular wavelength of light.

The opsin proteins consist of long chains of nearly 350 amino acids hooked together. An individual's DNA contains instructions for building these proteins: it specifies which amino acids are hooked together, and in what sequence they are to appear. If the DNA instructions specify the wrong amino acid, you may still be able to build a protein, but it won't be exactly what you needed. This altered protein would have different chemical characteristics. It might produce an opsin that is tuned to the wrong color of light, or one that just plain doesn't react to light at all.

• When we say "missing cone pigment", the genetic code probably resulted in an opsin protein that doesn't react to light at all, or the reaction is so strange as to be useless.

• When we say "anomalous cone pigment", the genetic code resulted in an opsin protein that reacts to a light, but not the way it should. This produces cones that have a shifted peak sensitivity.

  This isn't necessarily bad. What it does mean is that you're not like average people.

  You could wind up with cone pigments that let you see in the dark, reacting to infrared light. [Opsins responding to ultraviolet are unlikely to be helpful, since much of that part of the spectrum is absorbed by the eye before it gets to the retina.] A person with opsins just a little further towards the ends of the spectrum could see all the colors that an average person can, but would also be able to distinguish additional shades of colors. It is actually likely that such people live amongst us - don't forget that much of our information about color response is based on average values of numerous observers.

Types and Prevalence of CVD

types of CVD	males	females	person	cause
anomalous trichromasy			anomalous trichromat	have all three cone photopigments; but one cone photopigment is anomalous
protanomaly	1%	0.01%	protanomal	anomalous "red" cone pigment
deutanomaly	5%	0.4%	deuteranomal	anomalous "green" cone pigment
tritanomaly	rare	rare	tritanomal	anomalous "blue" cone pigment
dichromasy			dichromat	two functioning cone channels; one cone photopigment missing
protanopia	1%	0.01%	protanope	missing "red" cone pigment
deuteranopia	1.5%	0.01%	deuteranope	missing "green" cone pigment
tritanopia	0.008%	0.008%	tritanope	missing "blue" cone pigment
monochromasy			monochromat	typically totally color blind; may have one cone pathway in addition to the rod pathway.
rod monochromasy	rare	rare	rod monochromat
cone monochromasy	rare	rare	cone monochromat
atypical monochromasy	very rare	very rare	atypical monochromat
overall	~8%	~0.5%

Why do CVD rates differ by cone pigment color?

• The blue-cone opsin gene is located on chromosome 7.

  Everybody has two copies of that chromosome, one from each parent, so two copies of the blue-cone opsin gene.

  If one of the genes is defective, the backup copy of the gene in the other chromosone is available to generate the correct opsin. The backup copy makes the disorder rare - in order to screw up the blue cones, you need to damage two chromosones. Since both males and females have two copies of the gene, they are equally protected against a single mutation, and gender makes no difference for incidence of blue cone problems.

• The green- and red-cone opsins are both encoded on the X chromosome in tandem (next to each other).

  During the process of oogenesis (egg formation), some shuffling around happens. The X chromosomes from the grandmother and grandfather mix with each other in random places to make the egg's brand-new X chromosome that will be contributed by the mother. Since red and green codes are next to each other, cross-contamination between these codes is much more likely than with the blue-cone code. This is why red/green problems are more common than blue problems.

• A change in the red-cone opsin gene has a 50/50 chance of shifting the color response, or rendering the opsin worthless.
• The green-cone opsin gene is overall more delicate than the red-cone opsin gene, because it has a larger total prevalence of problems.
• But the green-cone opsin gene is somewhat more flexible, with a gene change more likely to change its color response, but is less likely to render the opsin worthless.

A recent study found that the gene that produces the red-cone opsin is unusually likely to undergo variations. [Published in "American Journal of Human Genetics", September 2004. Co-authored by Dr. Brian C. Verrelli. Summary at http://www.reuters.com/newsArticle.jhtml?type=healthNews&storyID=5773899.] They studied 236 samples of DNA from around the world and found 85 variations in the OPN1LW gene. They say this is about three times the number of variations one would see in any other randomly selected gene from the human genome. They conclude that, some time in the evolution that led to humans, it was advantagous to generate numerous variations in the red-cone gene. I'll be interested to see what they find when they look into the other color genes.

Why do CVD rates differ by gender?

• The green- and red-cone opsins are both encoded on the X chromosome in tandem (next to each other).

  The 23rd pair of chromosomes determines gender. For females this pair is XX and for males this pair is XY.

  Females, with XX chromosones, have a backup copy of the genes for green- and red-cone opsins, one on each X chromosome. This makes red and green disorders rare for females - in order to screw up either red or green cones for a female, you need to damage two chromosones.

  Males, with XY chromosones, have a single X chromosome. They don't have a spare for either of the green- and red-cone opsin genes.

  This makes red and green disorders more common for males (without a backup) than for females (with a backup).

• The blue-cone opsin gene is located on chromosome 7.

  Both males and females have two copies of that chromosome, one from each parent, so two copies of the blue-cone opsin gene.

  Since males and females have the same number of copies of the blue-cone opsin gene, they have the same prevalence of problems with that gene.

• The Mantis Shrimp has ten types of photoreceptors.
• In at least three species of New World Monkey (squirrel monkey, spider monkey, marmoset) most are dichromats, but a sex-linked color vision factor makes about one-third of the individuals trichromats.
• In addition to different colors, the photoreceptors of bees are sensitive to polarized light.
• Marsupials have trichromatic vision, extending into the ultraviolet. (http://www.sciencedaily.com/releases/2006/03/060325232608.htm)

How do these color receptors develop?

• It has been suggested that "Old-World Primates Evolved Color Vision To Better See Each Other Blush" (http://www.sciencedaily.com/releases/2006/03/060320221839.htm).
• One study (http://www.sciencedaily.com/releases/2004/01/040120033216.htm) suggests that trichromatic vision evolved twice in primates: once in the common ancestor of apes and Old World monkeys, about 23 million years ago, and once in the howler monkey lineage, about 7-16 million years ago. It also suggests that the evolution of color vision corresponds to a decline in the sense of smell.

Other species are tetrachromats and better. Why not humans?

I have seen at least two theories of human tetrachromats.

• James T. Fulton is in the process of writing a book entitled "Processes In Biological Vision". Many sections of the book are available online at "http://4colorvision.com/index.html". Fulton provides a lot of information that meshes with conventional theories of color vision. He also presents some unusual ideas that may be proved in time, or turn out to be crackpot.

  Fulton suggests that all normal humans are indeed tetrachromats, having a photopigment that responds in the UV range. But somewhere along the evolutionary path, the optical components of the eye started absorbing UV light. Fulton suggests that humans are "blocked tetrachromats".

• The article "Looking for Madam Tetrachromat" at "http://www.redherring.com/Article.aspx?a=3941&hed=Looking+for+Madam+Tetrachromat%0a" discusses the search for a human tetrachromat.

  According to their theory, the shifted response of some anomalous opsins can provide four different receptors in females (or even five - females have two X chromosones, so you could have two different reds and two different greens in addition to blue).

  The researchers interviewed in the article think that they have found two tetrachromats, but haven't gone so far as to actually state it for a fact.

  [This theory that females may have extra opsins due to their double X chromosones is also being studied in prosimians, such as lemurs and bush babies. See http://www.sciencedaily.com/releases/1999/11/991109072142.htm]

Let's start in the middle - the optic nerve. There are over 100,000,000 light receptors in the retina. The optic nerve bundle contains approximately 800,000 nerve fibers. The information from many light receptors is boiled down and re-encoded, to be transmitted along fewer nerve fibers. We don't need to speculate that a tetrachromat would need more nerve fibers to carry the new color; it is far more likely that the new color information would be encoded for transmisison along existing pathways.

We're also not suggesting that a tetrachromat has additional cones with the new photopigment. More likely, some of the cones normally dedicated to one pigment would instead be manufactured with the new photopigment. In an individual with normal vision, one finds:

• 16% blue cones
• 10% green cones
• 74% red cones

• 16% blue cones
• 10% green cones
• 37% red cones
• 37% funky red cones

Processing? I'm actually hopeful in this respect. The human eye/brain visual system has an uncanny ability to extract as much visual information as it can from incoming light, even reprogramming its image processing in order to make sense of the image.

• In 1897, George Stratton wore special goggles containing optics that turned his view of the world upside-down. After using the goggles nonstop for six days, Stratton suddenly saw the world right-side up, as the brain had adapted to make proper sense out of unusual input. When Stratton removed the goggles, the world turned upside-down again, until his brain adapted back to "normal".
• Similar goggle experiments with inversion (mirrors) and rotation (prisms) have been performed many times since then with similar results. See: Snyder (1952), Kohler (1962), Harris (1965).
• Some suggest that the visual system remains inverted, and the motor system is inverted to match it. See Linden (1999). Either way, powerful changes are at work to extract usable information from visual data.
• Kaufman (1974) got similar results with lenses made to distort and bend images. After adaptation the bent lines came to look straight. It's rather difficult to blame this on the motor system.
• McCullogh (1965) used color-altering contact lenses to distort sensory input. Once again, the subjects adapted.

A recent article suggests that the brain must learn how to process color information. ["Experience in Early Infancy Is Indispensable for Color Perception", by Yoichi Sugita. Published in Current Biology, Volume 14, Number 14, 27 July 2004, pages 1267-1271. Summary at http://www.sciencedaily.com/releases/2004/07/040727085636.htm] This paper says that monkeys raised under monochromatic light performed differently on color-matching tasks. If it is true that mammals must learn to process or interpret color vision information, perhaps tetrachromats would learn to make use of the additional color information available to them.

I stumbled across a paper describing transplating eyes between different species. The description of prior experiments said "Depending on the species,the grafted eye reportedly could endow the recipient with better visual acuity than the animal exhibited preoperatively." The new work concerned the visually evoked, neuro-endocrine skin camouflage reactions of certain salamanders. ("FOREIGN EYE TRANSPLANTS: Do They Work?" by Paul Pietsch and Carl W. Schneider Indiana University, Bloomington, Indiana, USA and Department of Psychology, Indiana University of Pennsylvania, Indiana, Pennsylvania, USA. http://www.indiana.edu/~pietsch/foreign-eyes.html] If substituting a "better" eye from a different species improves vision, there must be some neurological rewiring going on.

Scientists took mice (normally dichromats), and genetically engineered them to be trichromats. The mice were able to efficiently process sensory information from the new photoreceptors in their eyes. ["Genetic Studies Endow Mice With New Color Vision" http://www.sciencedaily.com/releases/2007/03/070322160852.htm]

• Your dresser drawer contains a bunch of loose socks, some white and some blue. They are made out of the same material and have the same texture. Your bedroom is lit only by a blue party lamp. You carefully pick two matching socks and put them on. When you go to class, everybody thinks you are an idiot because you are wearing one blue sock and one white one. What happened?

  The white sock reflects all light. The only available light is blue, so the white sock reflects only blue light and looks blue.

  The blue sock only reflects blue light. The only available light is blue, so the blue sock reflects the blue light and looks blue.

  You thought that you had a match, but under the blue light, the white and blue socks colors were metamers.

• You are watching television, and the scene shows a yellow rose. It's a beautiful shade of yellow, exactly matching the paint on the wall. But you happen to know that television is based on the RGB color system. Where's that lovely yellow color coming from?

  The television is sending out red and green. This stimulates your trichromatic vision system the same way that true yellow light would.

• how color vision works
• color systems
• color mixing
• coloring light
• advanced light and vision concept [this page]

Thank you for visiting. Your comments are welcome.
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