T. rex analysis supports dino-bird link, etc

First an earlier article, that no doubt others have blogged on, as I work down through my backlog of unread science news articles.

[Above: Tyrannosaurus rex femur from Montana's Hell Creek formation, MSNBC]

T. rex analysis supports dino-bird link, MSNBC, Alan Boyle, April 12, 2007 ... For the first time, researchers have read what they say is the biological signature of a tyrannosaur - a signature that confirms the increasingly accepted view that modern birds are the descendants of dinosaurs.

The signature doesn't come from studying the shape of the 68 million-year-old dinosaur's fossilized bones, but from analyzing the organic material found inside those bones. It's not DNA [but] ... collagen proteins that were isolated using techniques on the very edge of what's possible today. Those techniques, detailed in Friday's issue of the journal Science, could open up "a new window into an entirely new approach" for paleontology ... Mary Schweitzer, a paleontologist at North Carolina State University ... and her colleagues emphasized that the protein analysis was just the first step in what could become a worldwide effort to categorize extinct species according to their molecular makeup.

Famed paleontologist Jack Horner, another member of the research team, said he would embark on a world-girdling series of expeditions this summer to see if further samples could be found. ... The tale of the T. rex began with Horner, back in 2003: He and his team found the tyrannosaur's massive leg bone beneath 1,000 cubic yards of rock at the Hell Creek fossil site in Montana, but had trouble fitting the bone inside their helicopter for the airlift back to the lab. When they broke the bone into pieces for transport, they were amazed to find that some of the dinosaur's soft tissues appeared to be preserved within. Previously, paleontologists had thought all the tissues of a fossil turned to minerals over the course of millions of years.

After analyzing the tissues under a microscope, Schweitzer reported in 2005 that they looked similar to the cells and blood vessels found in ostrich bones. But at that time, "we could not directly address what that material was made of," she said ... Schweitzer suspected that some of the material was preserved collagen protein - which is the main organic constituent of bone, left behind when the minerals are removed. She said the material looked like collagen, and it reacted like collagen when chicken antibodies were applied to a sample.

But to confirm her suspicions, Schweitzer turned to John Asara, a specialist in mass spectrometry at Harvard Medical School .... Mass spectrometry is a technique for identifying minute quantities of a substance by measuring its atomic properties, molecule by molecule. ... After removing the minerals and impurities from the bone samples that Schweitzer provided, Asara had less than a billionth of a gram of protein to work with. Nevertheless, he and his colleagues were able to decode seven strings of protein molecules. Those sequences were compared with a large database of collagen data - including sequences that Asara and his team isolated from a modern ostrich and from mastodon bone fragments that were 160,000 to 400,000 years old. ... The researchers took pains to make sure that they had the right sequences to compare, going so far as to create and analyze synthetic proteins that were modeled on the natural proteins in order to check their results. ...

Asara's team had only those seven T. rex protein sequences to work with, and it turned out all of them matched up with modern-day sequences. "Out of seven total sequences, we had three that matched chicken uniquely," Asara told reporters. "We had another that matched frog uniquely, one that matched newt uniquely, and a couple that matched multiple sequences." The bottom line was that the T. rex's biological signature was most like a bird's, at least based on the first fragmentary data. "It looks like chicken may be the closest among all species that are present in today's databases for proteins and genomes," Asara said. ... The researchers said they were heartened to see that different sequences matched the unique signatures of more than one species. That "pretty much convinced us this was very unlikely to be due to contamination," Asara said. ...

The close link to birds was also reassuring, said Thomas Holtz, a paleontologist at the University of Maryland at College Park who was not involved in the research but was familiar with the findings. "It would be totally astonishing if it were any result but that," he [said]. ... Horner told journalists that the findings already have strengthened the dinosaur-bird connection: "It's the first way we can test the hypothesis of relationships. ... This is a test, and we have failed to falsify that dinosaurs and birds are related. It changes our hypothesis to a theory now." ...

The successful test could lead to changes in the way fossil-hunters do their work. Schweitzer and her colleagues speculated that the tissue within the Hell Creek leg bone was so well preserved because the fossil was created in sandstone, where water and chemicals that might have destroyed the proteins could leach away more easily. Also, Horner's team did not apply preservatives to the broken bone that might have destroyed the proteins.

"The big issue here is that these are special fossils," Phil Andrews, an expert on protein analysis at the University of Michigan ... [said]. "These Hell Creek fossils are exceptionally well preserved, and that's what makes this possible." Horner's expedition, involving more than 100 people on nine field crews, would be aimed at finding other fossils that fit the specifications for biological samples. "We're going worldwide looking for exquisite preservation ... looking for specific specimens that are deep in sediments," he ... said ...

See also ABC/Reuters, CBS, FOX News, Livescience, NCSU press release, New Scientist, NewsWise, New York Times, Scientific American , USA Today & Yahoo.

This is further evidence that birds and dinosaurs shared a common ancestor (which I accept), but it is not necessarily evidence that birds are descended from dinosaurs (they could both be descended from earlier non-dinosaur reptiles). For example, they also found proteins "that matched frog [and] newt uniquely" but no one is suggesting that birds descended from frogs or newts, but that they all shared a common ancestor.

Nor is it evidence for evolution since common ancestry is not the same as evolution.

The only way it would "have strengthened the dinosaur-bird connection" would be they had tested (or will in the future) ancient non-dinosaur reptile (eg. archosaur) proteins and found no match to bird proteins. Or if the proteins shared by T-rex and birds are not shared with living represenatives of ancient reptiles, such as crocodiles. Indeed that point was made in a Nature News article which is now no longer free (but still available free online here):

"This is in keeping with the dominant view that birds and dinosaurs are closely related. But the researchers hasten to point out that this does not mean that T. rex's closest modern relative is the chicken - just that the chicken is the closest relative for which collagen sequence is available in public databases. Crocodile and alligator collagen sequences, for example, were not available for comparison."

While this a noteworthy (and newsworthy) achievement, with the exception of a test of non-dinosaur reptile fossil proteins above, I doubt that recovering fragments of ancient protein will add significantly to what systematists can already deduce about ancestral relationships from fossils, comparative anatomy and molecular comparisons. As Holtz said above, "It would be totally astonishing if it were any result but that." And as paleontologist and leading birds-from-dinosaurs proponent Mark Norell said, "I think it's a really great experiment ... But is this going to change the way we look at dinosaurs? Well, probably not."

Cosmologically Speaking, Diamonds May Actually Be Forever, ScienceDaily , April 26, 2007 ... If you've ever wondered about the ultimate fate of the universe, Lawrence Krauss and Robert Scherrer have some good news - sort of. ...

[Right: Measurements of supernovae showed the Universe is expanding at an increasing rate, NASA]

In a paper published in the journal Physical Review D, the two physicists show that matter as we know it will remain as the universe expands at an ever-increasing clip.

That is, the current status quo between matter and its alter ego, radiation, will continue as the newly discovered force of dark energy pushes the universe apart. "Diamonds may actually be forever," quips Krauss ... "The discovery of dark energy has changed everything, but it has changed the view of the future more than the past. It is among the worst of all possible futures for life," says Krauss, who has spent the last few years exploring its implications. In an eternally expanding universe there is at least a chance that life could endure forever, but not in a universe dominated by vacuum energy, Krauss and ... collaborator Glenn Starkman have concluded.

As the universe expands, the most distant objects recede at the highest velocity. ... When their recessional velocity reaches light speed, they disappear because they are traveling away faster than the light that they emit. According to Krauss and Starkman, the process of disappearance has already begun: There are objects that were visible when the universe was half its present age that are invisible now. However, the process won't become really noticeable until the universe is about 100 billion years old. By ten trillion years, nothing but our local cluster of galaxies will be visible.

From the perspective of future civilizations, this process puts a finite limit on the amount of information and energy that will be available to maintain life. Assuming that consciousness is a physical phenomenon, this implies that life itself cannot be eternal, Krauss and Starkman argue.

So if one wants "life ... eternal," the Universe cannot provide it. But Jesus can:

"For God so loved the world that he gave his one and only Son, that whoever believes in him shall not perish but have eternal life" (John 3:16)!

Stephen E. Jones, BSc. (Biology).

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Exodus 24:12-18. ¹²The LORD said to Moses, "Come up to me on the mountain and stay here, and I will give you the tablets of stone, with the law and commands I have written for their instruction." ¹³Then Moses set out with Joshua his aide, and Moses went up on the mountain of God. ¹⁴He said to the elders, "Wait here for us until we come back to you. Aaron and Hur are with you, and anyone involved in a dispute can go to them." ¹⁵When Moses went up on the mountain, the cloud covered it, ¹⁶and the glory of the LORD settled on Mount Sinai. For six days the cloud covered the mountain, and on the seventh day the LORD called to Moses from within the cloud. ¹⁷To the Israelites the glory of the LORD looked like a consuming fire on top of the mountain. ¹⁸Then Moses entered the cloud as he went on up the mountain. And he stayed on the mountain forty days and forty nights.