A great deal of reference material about the physiology of vision is available on the Internet -- for example, in Wikipedia. Rather than trying to duplicate it all here, I will merely review some basics that are particularly relevant to Features of Light and Darkness. Before I begin, let me mention that biology is well-known as a science full of exceptions, so please forgive me if my summary is written with too broad a brush; I will mention a few interesting special cases later on.
The human eye sees light by virtue of four special kinds of light-detecting cells in the retina, which is the layer of cells inside the eyeball on the side away from the lens. Three of these kinds of cells are called cone cells. They are responsible for vision in bright light, and the fact that there are three kinds is what allows us to see colors. (Think "Cones see Color".) Broadly speaking, the kind of cones known as red cones see red light, green cones see green light, and blue cones see blue light.
It isn't really quite that simple. The ranges of color to which the different kinds of cones are sensitive are broad, and they overlap. The actual ranges of sensitivity of these cells are shown in the list of pigments in Features of Light and Darkness, that you get by pressing one of the "Pigments" buttons. Yet the basic idea is there: Colors that preferentially stimulate red cones will look red, and so on. Colors that stimulate more than one kind of cone cell will look like mixtures of primary colors.
Thus in bright light, color vision is a three-parameter system. In bright light, when your eye looks at a uniformly illuminated field of light, whether it is looking at a light source itself or whether that light has reflected off or passed through a colored medium, all your eye knows about it is three numbers; namely, the responses of the red, green and blue cone cells.
On the other hand, light itself is most definitely not a three-parameter system. In principle, you could construct a light source in which the brightness of every different wavelength had an arbitrary value -- a spectrum with lots of narrow bands, each of any brightness you liked. Some of the spectra shown in the list of lights sources of Features of Light and Darkness (that you get by pressing one of the "Lights" buttons) have several bumps and dips in them -- think "like that, but with lots more bumps and dips". With so many spectra to choose from, it shouldn't surprise you that there are usually many ways to make colors that look the same to the eye; that is, there are many different spectra that can stimulate the red, green and blue cone cells in any given way.
The fact that there are many ways to make the "same" color of light is responsible for some of the interesting effects that Features of Light and Darkness can demonstrate. Thus in the scene named Features of Light and Darkness, which is the one that shows when the app starts, the upper and lower lights are different kinds of orange light that are carefully constructed to appear the same to the eye when they reflect off the white pigment that is the background for most of the scene. You can see what the differences are by pressing the "Upper Light" and "Lower Light" buttons when that scene is displayed, and looking at the actual spectra. The point of the scene is that although those two lights by themselves look identical to the eye, when reflecting off the background pigment, they reflect differently off the special greenish-yellow pigment used for the text "Features of Light and Darkness" in the scene, so that lettering looks different depending on what kind of light is shining on it.
Cone cells show all the colors of the world when the light is bright, but they fail miserably in dimmer conditions. Fortunately, the eye has another way to see things, that works when it is nearly dark: It uses the fourth kind of light-detecting cells in the retina, the rod cells.
Let me restate so that we can be clear about what is going on: Cone cells work well in bright conditions, but their ability to see at all fails rapidly as the light dwindles. If your eye had only cone cells, it would "get dark" a lot sooner and a lot faster when the sun went down. You might not be able to see anything at all under dim moonlight or under starlight, and you might not be able to see your food -- or your date -- at a romantic dinner.
Rod cells work well under dim conditions. They are what lets you see at all by starlight or by skyglow, when it is nearly dark. They work so well they turn off completely when the light is bright; if they didn't, your brain might be dazzled by the signal they produced in bright lighting.
There is only one kind of rod cell, which means that in dim conditions, you cannot see color. That is, night vision is a one-parameter system.The only signal that your brain gets is how much the rods are stimulated; it interprets this signal as the brightness of the light. Everything is monochrome. "At night, all cats are gray," and that is why.
There is a catch, and it is fascinating. There is a region of rather low brightness in which the cone cells are not quite turned off but the rod cells have begun to turn on. Furthermore, the range of colors of light to which rod cells are sensitive isn't the same as for any of the cone cells; it is in between the ranges of the green and blue cone cells. Thus in this range of light intensity, your eyes have four active kinds of light-detecting cells. That means that twilight vision is a four-parameter system, which in turn means it is possible to create colors of light that look identical in bright light, with three-parameter vision, but are not the same in twilight, with four parameter vision. The activity of the rod cells allows those colors to be distinguished. That effect is the basis of the scenes Twilight Ink and In Darkness.
Since the rod cells are less sensitive to red, orange and yellow light, it follows that the relative brightness of those colors will diminish, compared to blues and greens, as the light gets dimmer. The scene Purkinje Effect demonstrates this change.
Let mention a few special cases and exceptions to the brief summary description above.
First, the changes in color vision that happen as it gets brighter or darker take time. You probably know that if you step outside at night, leaving a brightly-lit room, it takes a while before you can "see in the dark". That is because it takes a while for your rod cells to turn on and start working. It can in fact take as much as half an hour, or perhaps longer, to achieve full dark adaptation. Furthermore, when you go suddenly from darkness to bright conditions -- perhaps someone turns on the light in a darkened room -- you are dazzled by the brightness for a moment, and can't see anything till your eyes have adjusted. Features of Light and Darkness makes no attempt to deal with such transient effects.
Second, Features of Light and Darkness makes no attempt to deal with how things are seen by people who have one of the conditions collectively known as "color blindness", and the effects the app shows probably will not replicate what such people actually see in the lighting conditions indicated. I am not sure I know enough to simulate such conditions accurately, and I would have no way to check my work if I tried.
Third, there are some reports of people who have more than four kinds of light-sensitive cells in their retinas. Not much is known about them, but quite probably there are conditions in which they can distinguish certain colors of light which the rest of us cannot. Their world is thus perhaps more fascinating than ours, at least when it comes to color.
Fourth, there are certain colors which the eye could in principle sense but which no light can produce. That is not nearly as mysterious as it sounds. If you look at the sensitivities of the three cone cells, you will see that the green cone cell sensitivity is completely overlapped by the red and the blue sensitivity. What that means is that there is no color of light that can stimulate the green cone cells without also stimulating either the red or the blue cones as well. So if you would like to know what color your brain sees when your green cone cells are turned on but the red and blue cone cells are not, there is no way to find out.
(Well, actually, there is perhaps an exception to the exception. Maybe there is a way to see this kind of green, just for a moment. Suppose you stared for a long time at a light that was made of a mixture of a red light way at the red end of the spectrum and a blue light way at the blue end. That light would stimulate your red and blue cone cells, but not the green ones. Then your eye and brain might compensate, and "dial down" the brightness reported by the red and blue cone cells, so that you would not be dazzled. You may have seen this kind of effect when you stare at a patch of some kind of bright colored light for a long time. Then suppose someone suddenly turned off the red-plus-blue light and at the same time turned on a green light. While your vision still had the red and blue cone cells "dialed down", you might for a moment see a very intense green, with your green cone cells fully stimulated and your red and blue cone cells for the moment idle.)
(When I was a child, I read a delightful children's science fiction book called The Wonderful Flight to the Mushroom Planet, that was written by Eleanor Cameron in 1954. In that book, a rather odd scientist, Tycho M. Bass, had discovered a rather odd planet, which no one could see without a special filter because it only shone in infragreen light. The kind of super-intense green described in the last few paragraphs is not "infragreen" in the same sense that "infrared" light is infrared, and I doubt there are any small unknown worlds as close to the Earth as Cameron's creation, but it is interesting to note that in a certain whimsical sense, Tycho M. Bass was on to something.)
Fifth, and somewhat incidentally, there are colors of light which the LCD display on your portable device cannot produce, which means that Features of Light and Darkness cannot show them to you. Don't go blaming Apple or the LCD display manufacturers, though -- they are doing the best they can, and the display technology on these devices is absolutely wonderful. Yet for example, open up the list of "Lights" and look at at "Display Red", "Display Green", and "Display Blue". Those are the spectra that an LCD display will give you if you ask for the primary colors red, green or blue; the best it can do is to provide combinations of those three spectra. Now, can you find a combination that will produce a spectrum that has just a bump at the far red end, or the far blue end, or indeed, any narrow bump at all? The answer is "no", and that is all there is to it.
Hey! Wait a minute! Some of the spectra shown in that list have narrow bumps. How does Features of Light and Darkness deal with them? The answer is, by being sneaky, as we will discuss in another section herein.
In a slightly more abstract sense, the problem here is that an LCD display is also a three-parameter system -- all you get to specify is how much of Display Red, Display Green, and Display Blue get produced. Yet as I have shown above, real spectra are much more complicated than that.
It turns out that LCD displays cannot produce any truly intense colors -- the technical term is "saturated". If you could arrange to shine a real spectrum, made with real sunlight and a real prism, on a white piece of paper next to an LCD screen, you would see that the colors of light on the screen all looked washed out and faded compared to those in the real spectrum.