They precisely calculate flight direction using the angle of the sun and the time of the day, all with brains the size of a grain of sand.

Deconstructing the mechanics of monarch migration down to the molecular level is the work of neurobiologist Steven Reppert of the University of Massachusetts Medical School. His recent findings show how such complex machinery could be shaped by the forces of evolution and offer a glimpse at the development of the internal clocks that play a range of crucial roles in the lives of all sorts of organisms.

Biological clocks appear to have originated very early in the history of life, and can be found in sea urchins, mosquitoes, moths and corals. They are guided by two genes, called cryptochrome 1 and cryptochrome 2 (CRY1 and CRY2).

Of the species studied so far, most have one or the other. Humans and other mammals have CRY2, which is the source of our circadian rhythms, said Reppert. The world's most-studied insect, the fruit fly, has CRY1, and it was presumed to be the standard clock for insects.

In a paper published this month in the journal PLoS (Public Library of Science) Biology, however, Reppert reported that the monarch clock is different.

"It has components of both," he said. "That's why the butterfly mechanism is so cool."

The genes CRY1 and CRY2 hold the codes for making protein molecules that act as the gears of the clock. The proteins are created and destroyed on a regular cycle.

This tells the organism how much time has passed since the clock was last reset. Every 24 hours, the sun strikes some light-sensitive cells with the right intensity and resets the clock to zero.

CRY1 and CRY2 likely started as a single ancestral clock gene, said Adriana Briscoe a biologist at the University of California, Irvine, who was involved with some of the earlier work identifying the two genes. They would have been duplicated by accident in some early life form - probably something that predated the separation of animals from the other kingdoms of life.

Over the course of time the two duplicates evolved slightly different functions. The CRY1 gene's proteins respond directly to the blue wavelength of light, while CRY2 uses indirect input from other light-sensing cells, usually located in the eye.

Eventually, most organisms lost one form and kept the other.

Reppert's discovery that monarchs kept both "has brought tremendous clarity to the field," Briscoe said.

But even a clock with two genes isn't enough to get a butterfly from, say, Upstate New York to central Mexico via Cape May, N.J.

So monarch butterflies also carry what's known as a sun compass - a biological mechanism that senses the angle of the sun. Reppert recently found that the insect's nervous system sends signals between the molecular clock and the compass.

The compass can reveal direction relative to the sun. Since the sun moves over the course of the day, however, a clock is required to set the actual course by helping the butterflies correct for the motion of the sun across the sky, Reppert said.

If the sun is coming from your right side in the morning, for example, then you know you're headed north; the same direction late in the day would mean you're moving south.

Human navigators have the same need to tell time. Since the earth rotates on a regular cycle, knowledge of the sun's position and the time at some standard location will reveal longitude. Sailors had to wait for the invention of good mechanical clocks before they could reliably navigate from east to west and vice versa.

Reppert demonstrated the monarchs' reliance on both clock and compass for navigation a few years ago by tethering butterflies in a sort of flight simulator. It was around the time of the fall migration, and when they were able to see the sun, the monarchs turned toward Mexico.

But when artificial lighting was used to expose the butterflies to altered light-dark cycles, they changed direction to what would have been far off-course.

Even with an accurate clock and other onboard equipment, the monarch's amazing journey still can't be completely explained. For example, they seem to have refined their navigational skills to orient themselves at precise angles.

While Minnesota monarchs automatically aim about 180 degrees - straight south - those from Massachusetts need a compass heading of about 240 degrees. Others know to go almost due west from Atlanta before turning south over Texas.

Butterflies must also correct for wind. A few manage to get blown hundreds of miles off course and still find their way to Mexico.

Scientists expect to get more clues soon from sequencing the monarch's entire genetic code, said Chip Taylor, an entomologist at the University of Kansas. He thinks that will lead to more sweeping insights into the evolution of complex behavior - theirs and ours.

"These systems are going to help us understand some absolutely fundamental aspects of how organisms work," Taylor said.

Reppert is hoping to answer another question as well. Why are some monarchs determined to get to a patch of evergreen forest about 60 miles west of Mexico City while others of the exact same species stay put or head to Florida for the winter instead?

The non-migrating monarchs still find mates and reproduce, he said, so it's not clear that the migrators have any evolutionary advantage, though perhaps they did at some earlier time.

Migrating monarchs, some of which pass through Cape May in the fall, turn off their sexual development during the trip to Mexico, which allows them to live up to nine months. Once sexually mature, they are programmed to die in three or four weeks.

When these longer-lived migrating butterflies reach the ancient pine forest that is their destination, their sheer numbers turn the trees orange as they wait till spring.

Then they go through a delayed adolescence, engage in a mating frenzy, and start flying home in the spring. Now sexually mature, however, they die en route, leaving progeny on the way that somehow know how to complete the trip home.

Several more generations of short-lived butterflies will be born and die before the following fall. Then, the great-great-grandchildren of the migrators will sense the change of season and start a new journey south.

The miracle of the monarch migration, with photos, checklists and guides for would-be butterfly-watchers of all ages: http://go.philly.com/science