Thursday, April 24, 2008

This is so darn cool

In 2003, some guy in Montana digs up a T-rex, one of the last of the thunder lizards to go extinct. In 2007, a gal in North Carolina makes an amazing discovery: recognizable protien fragments are preserved deep within these massive 68 million year old bones. This week Science will publish the report of a medical genetics team at Beth Israel-Deaconess hospital in Boston, directed by a Harvard evolutionary genetics researcher who got strong evidence from protein sequence data obtained in the frail specimens that overlaps sequences in several modern bird species.

Rough and speculative analogies between avian and dinosaur skeletons, pelvis in particular, led to the earliest birds-are-from-dinosaur theories. A few Archaeopteryx fossils were found in 1862 but did not fit perfectly...a lot of missing links had to be postulated. But the last decade has seen a steady flow of fossil discoveries in China that provide virtually all the fossil links paleontologist could want. Fossils are only one chain of evidence.

Genetics are quite another kind of evidence and nothing is sweeter than having more than one completely distinct chain of observations that equally support an hypothesis. But the luck of finding usable protein of that antiquity is amazing. The only way this could not be cool and amazing is if you live in the world manufactured by the god who was manufactured by the creationists. They are left to their ideal worship and the rest of us can concentrate on how frikkin cool this is.

Well, I might be a little biased. Until about the 6th grade, I was positive I wanted to be a paleontologist when I grew up. I am not a paleontologist yet but maybe I am not grown up yet either...its just such neat confirmation. That "guy" from Montana is a scientist named John Horner and I bought one of his books when my kids were in the 6th grade [oh I s'pose I bought it for nostalgic reasons too]. Think I will go re-read the chapter on birds.

By the way, this development does not mean "Jurassic Park" scenarios are immanent. That idea was concocted by a smug fool who only knows enough to be dangerous to people who know even less. [Horner's consulting on that movie must have paid well]


Update: Zinio just delivered my online copy of Science and that linked me to the online materials :
Supporting Online Material for
Molecular Phylogenetics of Mastodon and Tyrannosaurus rex
Chris L. Organ, Mary H. Schweitzer, Wenxia Zheng, Lisa M. Freimark, Lewis C.
Cantley, John M. Asara
Published 25 April 2008, Science 320, 499 (2008)
DOI: 10.1126/science.1154284

They used collagen...that was the protein remnants found in the fossil bones.

Several statistical methods were applied to detect commonalities among amino acid sequences of collagen samples among about 20 living and two extinct species.

MrBayes v3.1.2 (Huelsenbeck and Ronquist 2001) was used for Bayesian inference of
phylogenetic relationships. The prior for the amino acid model set to mixed, in which the
MCMC chain explores 10 fixed-rate amino acid matrices (Poisson, Jones, Dayhoff,
Mtrev, Mtmam, Wag, Rtrev, Cprev, Vt, and Blosum)....The Bayesian tree is identical to the likelihood tree and highly similar to the parsimony tree as well (see below). An additional tree (not shown) was inferred in which all sites (for all taxa) were removed that contained gaps (missing data) in the Tyrannosaurus sequence, resulting in a dramatically smaller dataset. The resulting tree was poorly resolved in multiple areas due to the lack of informative sites for all taxa, though the Tyrannosaurus still grouped with other amniotes. Another tree (not shown) was inferred in which regions containing gaps (missing data) in the alligator, ostrich, and T. rex sequences were removed. This reduced the amount of missing data in the set and produced the same topology, but it did not appreciably change the support for archosaurian nodes.

Phylogenetic trees were generated using Maximum likelihood (Sup. Fig. 1A and B) in PhyML v2.4.5 (Guindon and Gascuel 2003).

The resulting tree properly determines known relationship of species AND locates Tyrannosaurus with birds.:


windy said...

But the luck of finding usable DNA of that antiquity is amazing.

It would be a little too amazing. They didn't get DNA: they sequenced the protein.

GreenSmile said...

Thank you windy. corrections have been applied and credited. I might have to read that Science article when I can get my hands on it.

still a very pretty result, isn't it?

cul said...

Ultimately cool, yes.

My first anecdotal evidence of the bird/dino link came when I looked deep into the eye of a goose I raised from an egg back in the 90's. I had been looking at its feet and saw dino hide written all over it, then the look in the eye test showed me the lizard living inside that bird brain.

Because I was the first animate thing that goose saw after hatching, it (Pip) imprinted on me as its mother and followed me everywhere.

Can you imagine if that egg had held a baby T-Rex?