Scientists have extracted the hardy, fibrous protein collagen from a 68-million-year-old thighbone that belonged to a Tyrannosaurus rex, jettisoning the long-held belief that ancient fossils could not provide protein samples for analysis. The protein was discovered in a femur (thighbone) unearthed four years ago under a thousand cubic yards of rock on a cliff in the Hell Creek Formation, which spans Wyoming, Montana and the Dakotas in the northwestern U.S.

Simulations over the years have predicted that the protein in bone had a shelf life of just over one million years. Supporting these projections, which were based on the cellular decay and protein degradation in modern organisms, was the total lack of evidence of protein or DNA recovery from bones of organisms over 100,000 years old.

But the successful extraction of collagen peptides (protein fragments made up of multiple amino acids) from the dinosaur bones, as well as those of modern-day animals, turns that notion on its ear. Reporting in two papers in the new issue of Science, a team of researchers announced that a chemical analysis of the T. rex peptides suggests the king of the lizards is most similar to a present-day chicken. Although that is probably not the lineage one might have expected for this mighty and fearsome dinosaur, the complicated methodology that led to the surprising discovery may also help scientists to understand cancer that metastasizes to bone.

"The data from both papers support the hypothesis that original protein may be preserved, but at such low levels they're barely detectable," says study co-author Mary Schweitzer, a molecular paleontologist at North Carolina State University and an associate curator at the North Carolina Museum of Natural Sciences, both in Raleigh. "It's been known for a long time that dinosaurs exhibit wonderful microstructural preservation; this fact has allowed for direct comparison between dinosaurs and living taxa."

In 2005 Schweitzer led a team that reported the discovery of soft tissue in the well-preserved T. rex femur, discovered two years earlier. Soon, she began a new collaboration with Harvard Medical School pathologist and mass spectrometry expert John Asara. In 2002 Asara had sequenced peptide fragments from collagen found in mammoth bone samples sent to him by Schweitzer, which were 100,000 to 300,000 years old.

In the current analysis, Asara used a combination of microchromatography and liquid chromatography to purify and separate out protein components, about 10 to 20 amino acids long, from the "brown, gritty material" he received from Schweitzer. He then fed the purified samples into an ion-trap mass spectrometer, which measures the masses of constituent peptides and then fragments and isolates their component amino acid sequences.

"We were successful in purifying enough peptides in order to cross the threshold of the mass spectrometer and reveal sequences," says Asara, adding that the T. Rex specimen yielded seven sequences. (In contrast, he was able to get over 70 separate amino acid sequences from a 600,000-year-old mastodon sample, which he analyzed concurrently.) "When you look at these set[s] of sequences, they, as a whole set, have the closest similarity to [those of a] chicken, which would support the previous reports that birds evolved from dinosaurs or are closely related at least."

Of the seven sequences, three matched collagen peptide scripts from chickens, one matched a frog and another matched a salamander; the other two matched multiple organisms, including chickens and salamanders. Asara points out that the similarity between dinosaurs and chickens may only be due to the fact that other animals, such as crocodiles and alligators, have not had their proteins or genomes sequenced. But "as far as the hypothesis that protein would not survive more than a million years," he notes, "we have obviously proven that to be false."

Schweitzer says that now that the team has shown that molecular evidence can be extracted from fossils, the door is opening to a number of other investigations that can be made. For instance, relationships between extinct species and modern-day animals can now be clarified, and scientists, she adds," can learn more about patterns of molecular change and the rates and directions of molecular evolution."

Furthermore, says Lewis Cantley, a systems biologist at Harvard Medical School, the techniques used by Asara can help medical researchers learn more about the process of tumor growth in cancers that metastasize on bone, such as prostate and bone cancers. "Our goal would be to take a biopsy of bone from a prostate cancer patient," he says, "and from a very minute amount of material, extracted from a needle, be able to sequence proteins that are at very low abundance—oncoproteins, for example, that drive the tumor—and even identify mutations in the protein sequence that tell us why that person got that disease."