A Johns Hopkins University professor who has traced hundreds of years of the Chesapeake Bay's history by studying the mud at its bottom received one of the highest honors for bay scientists earlier this month.

Grace Brush, whose specialty is called paleoecology, was awarded the Mathias Medal. The award is named for former U.S. senator Charles "Mac" Mathias from Maryland, a father of the modern movement to clean up the bay.

The medal is given by the Maryland and Virginia Sea Grant programs and the Chesapeake Research Consortium. It has been awarded only five times since its creation in 1990.

Jonathan G. Kramer, director of the Maryland Sea Grant program, said Brush's work has provided goals for the efforts to restore the bay because it shows what the bay looked like before the arrival of European settlers.

"She's really set the historical record for what's happened and how the bay's responded," Kramer said.

Brush's work involves plunging long plastic tubes into the bay's muddy bottom and pulling out a tall, thin "core sample" of mud. A sample just one meter tall can contain layers of sediment that were deposited over hundreds or even thousands of years.

Brush and her graduate students usually slice those samples into pieces about one centimeter thick.

Then they look inside them for an array of very small things: seeds, pollen, microscopic plankton -- even the preserved jaws of tiny worms, which measure only a couple of millimeters wide.

Brush, who lives in Columbia, was one of the first women to work in her field, and has been studying core samples in the Chesapeake since the 1970s. She said she realized her work could affect the save-the-bay movement when she heard people saying in the late 1970s that underwater grasses seemed to be declining.

She realized, "We can test that hypothesis because we can look for the seeds in the sediment."

She concluded that the grasses had declined rapidly in the early 1970s because of cloudy and polluted water. It was not part of nature's regular boom-and-bust cycles, she said, but something that "had not happened at any time prior."

In any small slice of mud, Brush said, there can be hundreds of seeds and hundreds of thousands of pollen grains. But to Brush and her graduate students, every little thing tells a story about changes in the bay.

If they find an abundance of ragweed pollen, it means the mud around it dates to the early 1700s. That was a time when much of the forested land around the bay was cleared for farming, creating open land that was prime habitat for ragweed.

When they stop finding pollen from the American chestnut, it means the mud was deposited after the 1930s, when a blight nearly wiped out the once-common tree.

When they find cesium, it means the mud dates to the 1950s, when nuclear weapons tests sent fallout all over the world.

Brush's work also found that, at some point after Europeans settled in the area, one kind of plankton became much less prominent, and another was found more often.

The reason: The disappearing variety of plankton lived mainly on the bay's bottom, which was becoming more inhospitable as agricultural pollution blocked out sunlight in the water.

"What that's showing is that the water was very clear before settlement, so plants could grow" on the bottom, Brush said.

In recent years, she said, she has seen another troubling trend: a new kind of microscopic algae that is not eaten by other creatures in the bay. Instead, this algae -- which is fed by pollution from farms and sewage plants -- blocks out sunlight and eats up underwater oxygen.

Brush said she is often asked whether her research shows the bay is getting better or worse. Her answer is unequivocal.

"It began to change after settlement, and it's certainly not . . . improved whatsoever," she said.