The other theory, a more prevalent one since the debut of genetic testing, is that modern humans evolved in Africa and migrated into Europe and Asia.
Just after the announcement, however, Radien Soejono, the senior archaeologist at the Jakarta-based Indonesian Centre for Archeology, signed agreements to hand the specimens over to Jacob's lab, some 275 miles (440 kilometers) away.
Because of the growing controversy, the team's co-leader, Mike Morwood of the University of New England, Australia, was apprehensive. He told Nature magazine, "We thought we would never see them again." He added that his colleague, Peter Brown, the lead author on the paper announcing the discovery, took careful measurements and photos of the specimens before they were transported.
The situation heated up earlier this year as Jacob kept possession of the remains for about two months longer than he had agreed, and after it was discovered that some of the bone material was removed for further genetic analysis by a German lab.
On February 23 Jacob's lab returned all but three leg bones and a portion of the cut jaw.
In the meantime, the hobbit continued to dominate archaeology news. Paleoneurologist Dean Falk announced research findings in early March at a press conference hosted by National Geographic.
Her team created an endocasta virtual, 3-D view of the interior of the skull showing detailed features, including the size, shape, and vascular structure of the brain. Falk, a professor at Florida State University, said that the research concluded that the hobbit, despite her grapefruit-size brain, could have been capable of higher forms of intelligence and reasoning.
Now the hobbit is again at the epicenter of news, this time over the damages that were documented after their return from Jacob.
The Indonesian Center for Archeology, which now has the remains, believe that most damage resulted from improper techniques in making molds, said the center's director, Tony Djubiantono.
The molding procedures stripped anatomical detail from the base of the cranium and broke a portion of the skull. Two teeth in the jaw were removed and glued back in. Those damages could deprive researchers of critical information.
Researchers also reported that a mandible showed long, deep cut marks along the lower edge on both sides where material to make the molds was trimmed.
Jacob has denied that his lab caused the damage while the specimens were in his possession. Attempts to contact him by phone, fax, or e-mail have been unsuccessful.
Djubiantono, though distressed by the condition of the bones, is reluctant to point the finger of blame directly at Jacob, and he declined to sign a draft letter from Morwood and others. However, in a phone interview, he said he had had a serious discussion with Jacob.
Falk said the incidents surrounding the hobbit are regrettable.
"It sounds awful. If these were damagedand I have no reason to think otherwise, because Morwood is a credible sourcethen the loss could be substantial," Falk said, adding that casting, a common procedure, can be extremely destructive to the specimen.
While some have called for a formal investigation, it doesn't appear that such an action will occur. Falk, like several other researchers, said that she hoped the paleoarchaeological community will take a stand and express their collective concern.
Djubiantono said the remains in repository at the center will never again be shared off-site. "We have hope that the information that may have been lost to the damage can be filled in with what we continue to learn. We have found other skeletons at the general area of the excavations. We believe it will tell us much more."
Among the things they hope to discover are clues that would reveal how the small creatures lived their lives and interacted with others of their species.
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