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Under the oldest part of Jerusalem, the area known as the City of David, a maze of tunnels and shafts runs through the rock and deep into biblical history.

In ancient times, the people inside the city walls depended on this system to deliver water from the ever-flowing Gihon Spring outside, thus ensuring a dependable water supply in both war and peace.But nearly everything else about the old underground waterworks, especially their recorded role in two pivotal events in the history of ancient Israel, has left scholars shaking their heads in puzzlement.

Archaeologists and biblical scholars have long wondered if it was these dark, subterranean passages that enabled King David to capture Jerusalem 3,000 years ago.

Biblical accounts suggest that David's general, Joab, surprised the Jebusites, or Canaanites, by sneaking in through a hidden passage. But did any of these tunnels exist at this early time? Were the Canaanites or anyone else then capable of such excavations?

Engineers have long noted that whoever built these passages seemed to go about their task in the most curious way, with no logic in the choice of some routes, slopes and dimensions of the tunnels and many ostensible mistakes in design.

Take Hezekiah's Tunnel. According to the Bible, King Hezekiah, expecting an attack and possibly a long siege by the Assyrians in the eighth century B.C., had a tunnel built to bring water from the spring to an open reservoir within the walled city, which extends south of the Temple Mount.

The siege occurred in 701 B.C. but failed, presumably in no small part because of the tunnel and its secure water supply. But why did the tunnel follow such a serpentine course, extending 1,748 feet, when a straight line of 1,050 feet would have been sufficient and easier to build?

Now, many of these questions can apparently be answered. Previous explanations had been based on the assumption that the tunnels were entirely man-made. Scholars should have consulted a geologist sooner.

A comprehensive geological study of underground Jerusalem has recently shown that the channels and shafts were formed by natural forces tens of thousands of years ago. That means there may have been an underground passage through which Joab infiltrated the Canaanite city. And Hezekiah's Tunnel is winding and irregular because the builders simply modified a natural fissure.

Dr. Dan Gill, a senior geologist with the Geological Survey of Israel, first reported the discovery three years ago in the journal Science. Underlying the City of David, he found, is a well-developed karst system, a geological term for a region of irregular sinks, caverns and channels caused by groundwater seeping through underground rock, mainly limestone and dolomite. Similar processes account for the many caves under the limestone of Kentucky.

In the current issue of Biblical Archaeology Review, Gill has described the findings in more detail and discussed their implications for archaeological research and biblical history. The geology, he said, provides "a simple, consistent and unified solution" to "most of the puzzles that have heretofore stumped researchers."

The extent and peculiarities of the underground water system were discovered and explored in the 19th century. The passages were all connected to Gihon Spring, the Old City's sole source of fresh water and the reason that a city came to be built there. Modern Jerusalem's water supply is piped in from Lake Tiberias.

From Gihon Spring, which is in a cave, there runs a short, irregular tunnel leading to a vertical shaft that goes straight up 37 feet. This is called Warren's Shaft, after the British engineer Charles Warren, who explored it in 1867.

Someone standing on a rock platform at the top of the shaft could drop a bucket on a rope and draw up the cool water. A gently sloping tunnel, and then a steeper one, connect the platform with an entryway at the surface. Though the spring is a little outside the wall, the entryway to Warren's Shaft is safely inside.

Another important component, Hezekiah's Tunnel, was rediscovered in 1837 by Edward Robinson, an American Orientalist. The tunnel, drawing on the same spring, runs from the base of Warren's Shaft until it debouches in an open reservoir known as the Pool of Siloam.

An inscription on the tunnel wall, written in ancient Hebrew script, tells how two teams digging from opposite ends managed to meet in the middle. That was an achievement that scholars found virtually inexplicable because of the winding route the tunnel followed, but the new findings show that the workers were actually following and widening the route of existing passages.