Dinosaurs=birds and DNA tests

[samclem]

I think I checked and didn't see anything about this.
Tests Confirm T. Rex Kinship With Birds .

The research, being published Friday in the journal Science, yielded the first molecular data confirming the widely held hypothesis of a close dinosaur-bird ancestry, the American scientific team reported. The link was previously suggested by anatomical similarities.

In fact, the scientists said, T. rex shared more of its genetic makeup with ostriches and chickens than with living reptiles, like alligators. On this basis, the research team has redrawn the family tree of major vertebrate groups, assigning the dinosaur a new place in evolutionary relationships.

My question is, how are proteins able to survive in usable form for 68 million years inside a dinosaur bone, at least enough to enable scientists to do DNA tests, confirming a link between birds/dinosaurs?

I never took biology, so this kind of thing is always interesting to me.

[Crescend]

Originally Posted by samclem

My question is, how are proteins able to survive in usable form for 68 million years inside a dinosaur bone, at least enough to enable scientists to do DNA tests, confirming a link between birds/dinosaurs?

I never took biology, so this kind of thing is always interesting to me.

The bones were found in a site called Hell Creek. I can't speak for the preservation conditions necessary to keep soft tissue around, but apparently this is currently being actively researched.

On the other hand, I can talk about the methods they used to analyze the sample. The current mass spectrometric methods used for proteomics are very, very sensitive. A modern instrument has attomole sensitivity - that's 10⁵ molecules (a mole is 10²³ molecules). The particular protein that they detected in the T. rex sample was collagen, the most abundant protein in the body. Also, they were looking at protein fragments, not whole proteins. That technique is called 'bottom-up proteomics', and is far more sensitive than trying to detect whole proteins ('top-down proteomics'), though it gives less information about what was in the sample.

From the materials and methods section of their original paper (published last year, by the way - the recent paper was just a phylogenetic analysis), they took ~2.5g of bone from the fossils (though they mentioned that the T. rex bones required significantly more extract - but they never said exactly how much). They took this stuff, purified it through a number of methods, digested it with an enzyme that cut it at predictable locations (trypsin) then ran it through a separation platform (liquid chromatography). The separations were done in a microcapillary, so that should tell you how tiny the volumes we're talking about here are. They then electrosprayed the resulting solution into an ion trap mass spectrometer (crappy mass accuracy, extremely high sensitivity and speed) and measured their mass-to-charge ratios. They then fragmented the detected ions by collisions with helium gas (collision-induced dissociation) and again measured their mass-to-charge ratios.

By inferring the masses of the intact peptides and the masses of various fragments, it's possible to reconstruct the sequence of the intact peptides. Then, by matching these peptides to databases of known protein sequences, it's possible to reach an identification of exactly what they are. The sequences matched most closely to bird collagen.

[jovan]

Originally Posted by Crescend

From the materials and methods section of their original paper (published last year, by the way - the recent paper was just a phylogenetic analysis), they took ~2.5g of bone from the fossils (though they mentioned that the T. rex bones required significantly more extract - but they never said exactly how much). They took this stuff, purified it through a number of methods, digested it with an enzyme that cut it at predictable locations (trypsin) then ran it through a separation platform (liquid chromatography). The separations were done in a microcapillary, so that should tell you how tiny the volumes we're talking about here are. They then electrosprayed the resulting solution into an ion trap mass spectrometer (crappy mass accuracy, extremely high sensitivity and speed) and measured their mass-to-charge ratios. They then fragmented the detected ions by collisions with helium gas (collision-induced dissociation) and again measured their mass-to-charge ratios.

Is it just me, or does this read like it wouldn't be out of place in the last act of a Star Trek TNG episode?



(Thanks for the informative post, though!)

[Pleonast]

In fact, the scientists said, T. rex shared more of its genetic makeup with ostriches and chickens than with living reptiles, like alligators. On this basis, the research team has redrawn the family tree of major vertebrate groups, assigning the dinosaur a new place in evolutionary relationships.

What is new about this? I thought it was generally accepted that birds are dinosaurs and alligators are not. And that alligators and birds are separate from reptiles like lizards and turtles. What are they proposing to redrawn?

[mwbrooks]

Originally Posted by Pleonast

What is new about this? I thought it was generally accepted that birds are dinosaurs and alligators are not. And that alligators and birds are separate from reptiles like lizards and turtles. What are they proposing to redrawn?

Sounds like they scratch out "widely-held hypothesis based on anatomical similarities" and ink in "confirmed by molecular data." Not really drawing, but the graphic artist who does it gets paid anyway.

[mwbrooks]

Originally Posted by samclem

My question is, how are proteins able to survive in usable form for 68 million years inside a dinosaur bone, at least enough to enable scientists to do DNA tests, confirming a link between birds/dinosaurs?

From previous posts, it seems like they aren't testing DNA directly. As for molecules surviving... From Science News:

Registered subscribers only: Salty Old Cellulose: Tiny fibers found in ancient halite deposits (4/5/2008)
Researchers have recovered microscopic bits of cellulose from 253-million-year-old salt deposits deep underground.

Prehistoric bacteria revived from buried salt (6/12/99)
By drilling into pockets of ancient seawater trapped in salt crystals, scientists found—and then revived—bacteria that may be 250 million years old.

[Darwin's Finch]

Originally Posted by Pleonast

What is new about this? I thought it was generally accepted that birds are dinosaurs and alligators are not. And that alligators and birds are separate from reptiles like lizards and turtles. What are they proposing to redrawn?

Apparently the research team wasn't up on its cladistics studies. Those Linnaean types will have to change their hierarchies in order to fit birds in under Dinosauria, but we cladists have been doing that for years

[Johnny L.A.]

Sorry for the hijack, but I found this at another place:

Chickens have always been chickens. The article is absurd Jesuit propaganda.

It's like saying snakes could grow feathers, or iguanas.

Those time periods never existed either.

What you have there is a religion, don't try and sell it as science.

[Northern Piper]

samclem, you might find this article from Discover magazine a few years ago to be helpful:

Schweitzer's Dangerous Discovery: When this shy paleontologist found soft, fresh-looking tissue inside a T.rex femur, she erased a line between past and present. Then all hell broke loose

[John Mace]

Originally Posted by Pleonast

What is new about this? I thought it was generally accepted that birds are dinosaurs and alligators are not. And that alligators and birds are separate from reptiles like lizards and turtles. What are they proposing to redrawn?

I don't know if that was poor reporting or too much hype on the part of the scientists or a little bit of both. In fact, this latest news is simply a refinement of similar data that was released last year. At any rate, as DF noted above, the whole idea that we suddenly now know birds are more closely related to dinosaurs* and we didn't before is nonsense.

*or that they are dinosaurs.