The backhoe full of human skulls and bones that workers scooped up last spring at an Eastern Shore home site may have looked a bit grisly, but to anthropologists it was beautiful. The remains appeared to be those of 30 to 40 Choptank Indians who lived along the Chesapeake Bay between the years 900 and 1400. Their bones, the scientists said, offered a sort of snapshot of ancient Choptank life. Not since the early 1960s had anyone in Maryland found one of these mass burial pits, or ossuaries. But to Indians, the prospect of scientists handling the bones -- possibly cutting into them for sophisticated laboratory analysis -- was disturbing, if not horrifying. "I certainly don't want to see my relatives' bones on a shelf," said Bobby Little Bear, of Columbia, a member of the Osage tribe. "Ask somebody else if they want to see their grandmother's bones in a glass case." Indians welcomed the state's excavation of the remains to save them from the bulldozers, but because of a dispute over what to do next, the bones have been sitting in 18 boxes in an office in Annapolis. Archaeologists want to conduct several months of nondestructive analysis. Indian leaders, including one man who said he is descended from Choptanks, want to rebury the bones immediately. "What if a scientist said, 'We want to do a study of people in Arlington National Cemetery?' " said Kevin Harley, of Waldorf, who heads the Maryland Commission on Indian Affairs, a state advisory group. "People would say that's a sacrilege and never allow it." The Caroline County discovery has inflamed in Maryland an emotional conflict that has been heating up across the country over who has the first claim to Indian skeletal remains: scientists who see them as precious links to the past or Indians who feel they are ancestors to be returned to Mother Earth. In Maryland, no law addresses the matter, and with the increase in development and consequent excavation, similar disputes are bound to arise. In the last year, increasingly vocal Indian groups have wrested away some of the estimated 600,000 remains in the nation's museums, universities and even roadside tourist attractions. Last month, for example, the Smithsonian Institution agreed to allow Indians to reclaim materials from the museum's 35,000 American Indian remains and artifacts. Recently, the Calvert County Museum approached Maryland's Indian commission offering to return a skull. "Museums have had these remains for so long. They got them from back when Indians were killed on the battlefield," said Patricia L. King, executive director of the state's Indian commission. "They hacked away at the bodies; there was no science to it." Maryland archaeologists and state officials, however, said their analysis will be professional and respectful and could be completed in about six months. They said they understand Indians' belief that the bones must disintegrate for the souls to complete their journey to the Great Spirit. "But the journey being interrupted a month versus six months is about the same, as far as I can see," said J. Rodney Little, the state's director of historical and cultural programs. Members of the commission appealed Little's decision to analyze the bones to his boss, Jacqueline H. Rogers, secretary of the Maryland Department of Housing and Community Development. She ruled this month in favor of Little. The Indians, she decreed, could draw up some guidelines to ensure that the analysis is respectful. She also established the policy that the state would excavate remains only if they are somehow threatened. "This is an issue where people's feelings run very deep," Rogers said. "Both sides are pretty polarized." The debate quickly rekindled Indians' abiding outrage over their treatment by European settlers. That the very bones of their ancestors should be unceremoniously dug up for a shopping center or subdivision seems the final indignation, they said. "It's the last thing left to do to us," said Mervin Savoy of Indian Head, tribal chairwoman for the Piscataway-Canoy Confederacy and Sub-tribe. "Our people have suffered too much at the hand of progress. No other people in the world are on display." It is a painful dispute, as well, for archaeologists and physical anthropologists, who said they cannot understand how their scientific curiosity has made them vulnerable to charges of everything from ethnocentrism to grave robbery. "Indians who don't know . . . their religion and claim this reverence to the past are in an all-out war with me and my colleagues, who have devoted our lives to studying them," said Al Luckenbach, Anne Arundel County archaeologist. "It does make me feel uncomfortable," said Richard B. Hughes, chief archaeologist for the department's Division of Historical and Cultural Programs. "You would think we would be the most likely groups to work together, but we're at loggerheads on this one." The commission estimated that 25,000 Indians live in Maryland, about 7,000 of them in Prince George's, Charles and St. Mary's counties and the rest in Baltimore and on the Eastern Shore. Most Maryland Indians are Piscataway, but other native tribes include Nanticokes, Susquehannas, Shawnees and Delawares. The burial battle is posing problems for federal and local officials, as well as museum directors. Several bills protecting Indian remains are pending in Congress, and several states have enacted legislation. In Maryland, the Caroline County back yard bone cache has made clear the need for some legislation establishing who has the right to unmarked burial remains, both sides agreed. "There's got to be something done because there will be more and more development," King said. "Suppose a site is disturbed by a developer -- can archaeologists excavate? Who's going to pay for it? Who pays for reinterment?" Little, the Indian commission, historians, archaeologists from the Maryland Historic Trust and others have been trying to draft a state law to protect both marked and unmarked graves. They are tackling dozens of thorny issues: Must an Indian show some direct lineal descendance from remains to claim them? Should artifacts found at Indian burial sites also be reinterred? Should Maryland research institutions give up their collections of Indian remains? In the Caroline County case, the analysis will be conducted by a physical anthropologist under contract with the state who will measure and sort the bones, in hopes of determining the age, sex and stature of the people, as well as evidence of their diseases, injuries, diet and other physical characteristics, archaeologist Hughes said. Some Indians are skeptical about the value of the research. "What could this analysis tell me? How some Choptank woman lived? That she ate wild rice? Well, so do I. Big deal," Savoy said. Others, such as Little Bear, see the value of research "as long as some cute little archaeologist doesn't stick {any bones} in his pocket." But they almost all abhor the idea of "destructive analysis," in which pieces of bone are subjected to laboratory tests. Some archaeologists, however, said that such testing, which is still being developed, could provide insights into Indians' genetic makeup and antibodies. The sacrilege, they said, is not in disturbing the bones, but in reburying them. "If these materials are {reburied} we would lose the chance to use these techniques," said Douglas H. Ubelaker, curator of anthropology for the Smithsonian. The state's archaeologists wanted to reserve the right to conduct destructive analysis, but now they say they won't do it, Rogers said. When both sides try to step away from the immediate battle, they analyze the larger war the same way -- as the age-old conflict between science and religion. "An emotional conviction that they have some relation to the bones is not enough," Luckenbach said. "It's the old struggle between science and superstition. It's religion impinging itself on science." Harley sees that conflict, but argues that religious beliefs are valid too. "These people go to college to study these things in a scientific way and this is all they do. I think they have to justify their existence," he said. "Indian people are people of feelings; we think in a more human way. Maybe we have to settle for a compromise."