Color Vision

“Each sense receptor responds to different inputs (electromagnetic, mechanical, chemical), transmitting them as signals that travel along nerve cells to the brain. The signals are then processed in the brain, resulting in immediate behaviors or memories. Changes in the structure and functioning of many millions of interconnected nerve cells allow combined inputs to be stored as memories for long periods of time.” AZ science requirements for middle school


I deeply resented learning (and then forgetting) these pathways in getting my PhD.   I’m not even going to gen into the memories aspect of our sense of sight.    I attended an event at which the speaker asked if any of us could sense when the person sitting next to us had a big heart.  She went on to say that our hearts emit electromagnetic radiation that could be detected by the person sitting next to us.  This is crazy talk when we think about our bodies detect “visible” wavelengths of light.  Memorizing these pathways is for medical and PhD students.  In my opinion, middle school kids should just know that things are complicated and know how to ask questions if they feel interested.  One thing that might be of interest is how light of short wavelengths control

Rods, cones, and more

Our vision is far more finely tuned than just rod and cone pigmented epithelial cells that absorb light.

Photoreception in the retina requires the interaction of multiple cell types.
  • Rod cells are epithelial cells with extensions containing opsins sensitive to low light intensities, i.e. night vision.  They are also responsible for peripheral vision.  We will discuss light absorbing opsin proteins in a bit.
  • Cone cells are also pigmented epithelial cells.  They are less sensitive to low intensity light than rod cells.  They are most concentrated in the fovea, at the center of the retina.  Three different varieties of  opsin are produced by cone cells, each having maximal absorbance in the red, green, and blue regions of the electromagnetic spectrum.  We will discuss individual differences in these options and color perception.
  • Horizontal cells are neurons that provide inhibitory feedback between rod and cone cells.  They allow use to see under both bright and dim lighting.
  • and cones are pigmented epithelial cells at the base of the retina.
  •  Bipolar cells connect the rods and cones to the ganglion cells.
  • Amacrine cells are inhibitory neurons that influence the output of bipolar cells.
  • The ganglion cells have long axons that extend into the hypothalamus and other regions of the brain  in a “tract” of axons known as the retinohypothalamic tract.  Signals are not only relayed to the visual cortex but also to the hypothalamus in charge of our response to circadian rhythms and the dilation of our pupils.

Light absorbance of Rods and Cones

This image is all over the Internet without a good reference for the source. Note the overlapping color absorbance of cone and rod cells.

Teachers may remember a time when fire engines were red, presumably the color of fire.  Nowadays fire engines are what some consider a “lime green.”  According to the APA, this makes them more visible at night when rely on our cone vision.  The color lime is defined as (192, 255, 0) in the (red, green, blue) color scheme.  Lime is a pure spectral color of 564 nm.  Lime is a color that has good visibility with cone vision in the day and rod vision at night.

Opsins and retinal

Opsins are proteins found in the cell membranes of the retinal, melanocytes of the skin, and brain.  This Wikipedia gives far more information than the middle school or high school may need to know about these G-protein coupled receptors that respond to the cis-trans isomerization of retinal.

A chemists’ view of cis and trans


Energy from light switches cis-retinal to all trans-retinal. This switching is transmitted to the protein opsin.

So when someone tells you that they can feel the electromagnetic radiation being emitted from your beating heart, roll your eyes to the back of your head and politelyl ask him or her where the receptors for this radiation are located and how they absorb is heat beat electromagnetic radiation.

Eye movement and attention processing

One level of processing light signals is the response of our eye muscles and attention to signals, be they or rod or cone origin.

The optic nerve carries information from the retina to nuclei of the mid brain as well as the occipital lobes. The nuclei of the mid brain receive input from other sources involved in attention and motor control.

Some references tend to prefer these nuclei in the singular while others use the plural.  This post will simply refer to the nuclei in the plural with the acknowledgement that they may preform functions as a singular unit.

pulvinar nuclei are/is part of the hypothalamus and are involved in visual attention.

lateral geniculate nuclei is/are a relay center(s) for the eyes. These nuclei have six layers of neurons with color specific processing.

superior colliculus  not only receive input from the retina but other parts of the brain including the locus ceruleus.  The superior colliculus is involved in attention to visual cues, orienteering, and decision making.

medial geniculate nuclei are considered part of the auditory thalamus

oculomotor nuclei connects with the oculomotor nerve CN2 that controls eye movement.

trochlear nuclei are relays for cranial nerve 4 which innervate the superior oblique muscles of the eye.

abducens nuclei are relay centers for the abducen nerve (CN6) that controls the movement of the lateral rectus muscle, responsible for outward gaze.


Circadian Rhythms

This retinothalamic tract  image was adapted from a free scientific paper.  Circadian rhythms and sleep seem to have special meaning to middle school kids.   The powers that be that dictate what you should know probably didn’t give much thought to how our sense of sight can affect much more.

Light hitting the retina travels the retinohypothalamic trct (RHT) to the suprachiasmic nucleus (SCN) of the hypothalamus. The paraventricular nuceus relays this signal to the pineal body of the pituitary gland. The pineal gland produces the hormone melatonin, that is released into the blood. The pineal gland also signals the superior cervical ganglion (SCG) that signals the T1/T3 region of the spinal cord. This region feeds back to the pineal gland.

Suprachiasmic nucleus, or SCN, is located in the hypothalamus dorsal to the optic chiasm.

The paraventricular nucleus (PVN) of the hypothalamus secretes many different hormones that have far reaching affects, not just the pineal body/gland.  The PVN also receives input from more than just the SCN including the hippocampus, the heart, and the gut.

The pineal body secretes the sleep hormone melatonin.

The superior cervical ganglion (SCG) is part of the sympathetic nervous system that mediates the flight or fight response.

Melatonin Receptors

Well, middle school kids of Arizona, you are expected to know that signals of our five senses are processed in our brains in ways that result in “immediate behaviors” and memories.

  • We’ve covered how light hitting our retinas may control how our eyes and our attention tract objects we see.
  • We’ve also covered how light controls the production of melatonin.

Melatonin is released into the blood and finds its way to melatonin receptors throughout our bodies, including those in our brains.  Just where are these melatonin receptors?  We can search the gene portal of the National Center for Biotechnologyl Information to find out.  We have two major types: Type 1 ( the MTNR1A gene) and and Type 2 (MTNR1B gene).  It is very confusing when genes and proteins have different names!  Scientists isolate messenger RNA from tissue, sequence the transcripts, and count.  RPKM is an acronym for  “reads per kilo base per million mapped reads.”

Expression of the melatonin receptor 1A gene in different tissues from many different studies.

Note how organs of our digestive and urinary tracts seem to express comparatively large amounts of the melatonin receptor 1A.  Also note the size of the orange error bars.  This means expression of the melatonin receptor 1A is variable.  Also note the variable expression in the testis and prostate.

Expression of the melatonin receptor 1B gene in different tissues .

The Type 2 melatonin receptor (MTNR1B gene)  is expressed in the brain placenta, testis and urinary bladder.

Continue your education on your own!

Some of this may seem boring to you.  Others might find this a little interesting but want a career in science about as much you want be be in a room with flying cock roaches.  I attended a lecture given by Dr. Esther Sternberg, Director of Research for the Andrew Weil Center for Integrative Medicine.  Dr Sternberg mentioned different color of artificial lighting in the work environment to better preserve the circadian rhythms and general well being of workers.   A 2019 Korean study of Kim and others documented bladder dysfunction in shift workers.  So this is what those melatonin receptors in our bladders are are up to?  They control our need to pee while we sleep?

Kim SJ, Kim JW, Cho YS, Chung KJ, Yoon H, Kim KH. (2019) Influence of Circadian Disruption Associated With Artificial Light at Night on Micturition Patterns in Shift Workers. Int Neurourol J.23(4):258-264.  Free Paper

Dr Sternberg mentioned blue tinted lights in the workplace in the morning and red tinted lighting in the evening in her talk at the February 3030 lecture at the biological Society of Southern Arizona mixer.  Do you use your smart phone at night?  Use of a blue light absorbing amber filter may help you sleep better by preventing the blue light from suppressing melatonin secretion.

Mortazavi SAR, Parhoodeh S, Hosseini MA, Arabi H, Malakooti H, Nematollahi S, Mortazavi G, Darvish L, Mortazavi SMJ. (2018) Blocking Short-Wavelength Component of the Visible Light Emitted by Smartphones’ Screens Improves Human Sleep Quality. J Biomed Phys Eng. 8(4):375-380. Free Paper








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