Here's today's evolution column. It also ran in today's Philadelphia Inquirer on the front of the Health and Science section:

The eye was a puzzle to Charles Darwin, who thought natural selection must have produced this complex machine but didn't know how. Creationists still sometimes issue an old taunt — "What use is half an eye?" — unable to envision a way organisms might use parts of what became our eyes.

In the last few years, new insights have filled in the gaps in some surprising ways. Many of the components of the eye, for example, quietly evolved during the 3.4 billion years that life existed as single cells. Some of the pigments that color our worlds were inherited from bacteria, said neurobiologist Jay Neitz.

"Why should a single-celled organism have color vision?" asked Neitz, who works in the ophthalmology department at the University of Washington in Seattle, in partnership with his wife, Maureen. "Answering that led us on an adventure," he said, which included a study of timekeeping among fish and, later, the use of gene therapy to give a normally color-blind species of monkey the ability to see red and green, much as humans do.

Scientists have known since the 1980s that bacteria capable of photosynthesis carried light-sensitive pigments in addition to chlorophyll, said Neitz. The pigment, called rhodopsin, evolved before chlorophyll and looks a lot like the pigments we and other animals use to detect color. But nobody knew whether the resemblance was a coincidence or the result of common ancestry.

So he and his colleagues investigated by taking samples of rhodopsin from frogs, alligators, whales, rats, rabbits, dogs, pigeons and several fish, including the famously primitive "living fossil" known as the coelacanth. By measuring small differences in these pigment molecules from animal to animal, he was able to estimate how fast rhodopsin changes over evolutionary time. That comparison pointed to a very early common origin for rhodopsin — going back to a common ancestor living more than a billion years ago. The Earth at that time was populated only by single-celled life.

"The thing that shocked us was that it goes back to before the Cambrian explosion, which is the first time we saw fossils that had eyes," Neitz said.

How could color vision predate eyes?

His theory is that the bacteria needed these pigments to tell time. While the intensity of light can change depending on shade or depth in the water, the color of the sky reliably reflects whether the sun is high overhead or angled low. By sensing color, bacteria can differentiate the red-orange hues of the morning and afternoon sky from the bright blue sky of high noon. In some latitudes and seasons, the midday sun can fry many organisms (including some humans) with intense ultraviolet light. A good color-sensing "clock" can help prompt bacteria to swim farther down the water column when the sun rises dangerously high.

Some of these bacteria used their color-detecting ability to adopt a circadian pattern called crepuscular, said Neitz. People tend to think of living things as nocturnal (night creatures) or diurnal (day creatures), he said, but crepuscular organisms are most active in the morning and late afternoon, using the midday to take a siesta.

Crepuscular lizards determine when to seek shelter by collecting light from a sensitive organ on the tops of their heads, he said. Signals go to the pineal gland, which is excited by the orange light of the low-angled sun and suppressed when exposed to the light of noon.

To further investigate the value of color vision for timekeeping, Neitz and his wife started experimenting on crepuscular fish known as cichlids. First, the researchers tried changing the intensity of light to mimic what happens in nature but left the color of light the same all day and night. The fish switched their pattern, becoming nocturnal, he said. But when the researchers also varied the color to mimic what happens in nature, the fish returned to their morning-afternoon rhythm, even when the intensity of light was kept constant.

The color vision system that we and the fish inherited from bacteria allows us to see the colors yellow and blue. That ancient system is still intact in most people with so-called color blindness, who usually carry mutations that prevent them from seeing reds and greens. Most mammals, including dogs and cats, also see yellow and blue.

We inherited our red-green color system from monkeys that lived about 50 million year ago. Birds, fish, and insects independently evolved new dimensions of color vision. Creationists often claim that "good" mutations are nearly impossible, but the acquisition of red-green color vision shows how it can happen without any magic. That's a story to be continued next week.

Contact Faye Flam at 215-854-4977 or fflam@phillynews.com; or follow on Twitter @fayeflam;