Living the Scientific Life (Scientist, Interrupted)

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Repeated analysis of proteins from a fossilized Tyrannosaurus rex reveal new evidence of a link between dinosaurs and birds: Of the seven reconstructed protein sequences, three were closely related to chickens.

Image: NYTimes

ResearchBlogging.org

It was once thought impossible to obtain actual soft tissue, such as proteins, from fossils, but the impossible has happened and now, two research teams who published reports in this week’s Science describe their findings: the closest relative to the fearsome Tyrannosaurus rex is .. a chicken.

Scientists recovered and identified several proteins within a well-preserved thighbone from T. rex that was fossilized 68 million years ago. Fossilization occurs when minerals replace the constituents of bone, turning them to stone. In this case, the proteins deep within the bone were protected from both degradation and fossilization by the outer layers of fossilized bone. As a result, exploration of the molecular-level relationships of ancient, extinct animals, is now possible using advanced research techniques, instead of relying solely on skeletal remains.

“It has always been assumed that preservation of [dinosaur bones] does not extend to the cellular and molecular level,” said co-author Mary Schweitzer, from North Carolina State University in Raleigh.

The proteins discovered in the T. rex bones are collagens, which are tough but elastic connective fibers that connect muscles and other tissues within the body. Collagen comprises most of the organic material in bone, which consists of both minerals and protein. When the minerals are removed from bone, a flexible collagen matrix remains behind.

“The pathways of cellular decay are well known for modern organisms. And extrapolations predict that all organics are going to be gone completely in 100,000 years, maximum,” explained Schweitzer.

Previously, the oldest ancient proteins identified were from mammoths that died about 300,000 years ago. The researchers have not found any DNA, which is more fragile than proteins, and is necessary for genetic studies and for cloning experiments.

“But proteins are coded from the DNA, they’re kind of like first cousins,” Schweitzer added.

The oldest confirmed fragments of DNA have been found in Neanderthals that lived 30,000 to 50,000 years ago.

“The goal of obtaining sequences either from proteins or DNA for extinct [organisms] has been a long-standing goal to test evolutionary links and processes, or even functional information,” stated Brooks Hanson, an editor at Science.

This work builds on an earlier discovery of soft tissue — including blood vessels — made by Schweitzer’s team in the same, incredibly well-preserved T. rex fossils. Repeated analysis of the preserved T. rex proteins from these bones revealed yet more evidence for a link between dinosaurs and birds, a widely-held but sometimes contentious hypothesis based on similarities in bone structure.

“Most people believe that birds evolved from dinosaurs, but that’s all based on the architecture of the bones,” said John Asara of the Harvard Medical School and Beth Israel Deaconess Medical Center in Boston and leader of the second team. “This allows you to get the chance to say, ‘Wait, they really are related because their [protein] sequences are related.’ We didn’t get enough sequences to definitively say that, but what sequences we got support that idea.”

Three of the seven reconstructed T. rex collagen protein sequences were most similar to chicken collagens (collagen, pictured below)

Collagen proteins [Bigger and more readable image]

The first research team, headed by Schweitzer, reconstructed fragments of several dinosaur proteins found deep within the T. rex femur, or thighbone (pictured below). For example, collagen-1, the main organic (protein) component of bone, was found. Peptide fragments of the complete protein were pieced together into strands comprising the seven protein sequences. Three of these reconstructed sequences reacted with antibodies to chicken collagen. Two other reconstructed proteins appeared to be related to a frog and a newt.

The second research team, led by Asara, independently confirmed the presence of protein in the bone. To identify any proteins that could be present, this research team subjected samples of the material extracted by Schweitzer to examination by mass spectroscopy, which breaks down material into its basic components to determine its mass and chemical composition. This technology is used in medical research to precisely identify the nature of disease-causing agents.

Co-author on the second study, Lewis Cantley of Harvard Medical School, noted that this work is still in its infancy, and when it is improved he expects to be able to isolate more proteins and seek more matches.

“Knowing how evolution occurred and how species evolved is a central question,” Cantley said.

Tyrannosaurus rex thighbone. Image: BBC News.

The dinosaur fossils were unearthed from rock in the Hell Creek Formation of eastern Montana, by a team headed by Jack Horner, from the Museum of the Rockies in Bozeman, Montana and co-author on the first paper. They included a skull, two thigh bones and both tibiae — lower leg bones.

“To get specimens like that involves excavating enormous amounts of material, covered with tens of feet of rock,” Horner explained. “The T. rex was under a thousand cubic yards of rock and therefore in a position not to have been invaded by bacteria or groundwater.”

As a result of these research successes, dinosaur fossil hunters are planning nine expeditions for this summer to search for more well-preserved specimens for similar tests. Additionally, several large dinosaur bones already in laboratories will also be examined for surviving traces of organic matter.

“I think we’re learning an important lesson here — that if we do get specimens like this, we spend a lot of time getting as deep into the sediment as we can in places where there has been very little atmospheric or water contamination,” Horner observed.

Matt Lamanna, a curator at the Carnegie Museum of Natural History in Pittsburgh, said the finding was “another piece in the puzzle that shows beyond the shadow of a doubt that dinosaurs are related to birds.” Lamanna was not part of either research team.

All dinosaurs, excluding birds, disappeared 65 million years ago. They are thought to have died after an asteroid impact which struck off the present-day Yucatan peninsula in Mexico.

Sources

Schweitzer, M.H., Suo, Z., Avci, R., Asara, J.M., Allen, M.A., Arce, F.T., Horner, J.R. (2007). Analyses of Soft Tissue from Tyrannosaurus rex Suggest the Presence of Protein. Science, 316(5822), 277-280. DOI: 10.1126/science.1138709.

Asara, J.M., Schweitzer, M.H., Freimark, L.M., Phillips, M., Cantley, L.C. (2007). Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry. Science, 316(5822), 280-285. DOI: 10.1126/science.1137614.

BBC News (quotes, image).

Daily Herald (quotes).

Comments

  1. #1 RSG
    April 13, 2007

    No wonder snakes and lizards (and alligators) taste like chicken!

  2. #2 jhay
    April 13, 2007

    I still find it funny when people find it hard to believe that today’s birds are more related to dinosaurs than any other organism.

  3. #3 Azkyroth
    April 14, 2007

    Two questions I’d be interested in hearing the answers to: how many bird species (in how many higher taxa) were the bones tested against, and was finding them to be most closely related to chickens specifically a surprise?

  4. #4 Alan Kellogg
    April 14, 2007

    I see Science Made Stupid was ahead of its time.

  5. #5 Bob O'H
    April 14, 2007

    I did enjoy the caption to the picture of the chicken and the T. rex in the BBC’s story:

    The resemblance may not be immediately obvious

    Bob

  6. #6 Tabor
    April 14, 2007

    I also wondered if finding this relationship was a surprise to those doing the research.

  7. #7 llewelly
    April 14, 2007

    Azkyroth, PZ has additional details .
    I do not see any indication that the T-Rex collagen was compared to any other (than chicken) bird collagen, and I take that as a reason chicken was the most similar – it was the only bird.

  8. #8 Chardyspal
    April 14, 2007

    Do you think they compared to chickens because they belong to one of the older order of birds? I would be interesting to see a comparison to ostrich or other paleognaths (did I spell that incorrectly…sorry).

    I thought it was very cool that Mary Schewitzer seems to have been vindicated…It occurs to me that in the 1990s she was subjected to some criticism re her analysis of fossil beta keratin.

    Chardyspal

  9. #9 GrrlScientist
    April 14, 2007

    the proteins were only compared to chicken (well, and to representatives from several other main taxonomic phyla, such as newts and frogs), not to any other bird species. it is possible that they chose chicken because it is from one of the more ancient groups of birds or because its genome has been sequenced, or both.

  10. #10 biosparite
    April 14, 2007

    I’ll never recover my love for T-rex. Chickens are SO dumb. I once walked into a chicken’s field of view as I passed a stock barn, and the chicken was so startled it flew right into the side of the barn with a loud thwack. Hopefully T-rex manifested more ijntellectual powers than that. I recall Garry Larson’s cartoon on why the dinosaurs really went extinct, showing various types, incuding T-rex, lighting up.

  11. #11 Susan Och
    April 15, 2007

    Not all chickens are dumb. There are many breeds of chickens. Some are as dumb as you note, but some are pretty smart and resourceful. I’ve had mother hens who were hyper-aware of their surroundings, softly calling the chicks back under her wings well before I noticed the hawk overhead or the cat lurking.

    I always thought that a chicken running across the yard looked a lot like the typical movie image3 of a T-rex.

  12. #12 Chris' Wills
    April 15, 2007

    …and the chicken was so startled it flew right into the side of the barn with a loud thwack. Hopefully T-rex manifested more ijntellectual powers than that….. Posted by: biosparite

    I suspect that if T-Rex ran into a barn that the barn would come off worst :o)

  13. #13 Michael Wells
    April 15, 2007

    An evolution “skeptic” at another forum that shall remain nameless made the following gripe:

    “this AP article describes research that looked at seven fragments of protein and determined three matched chickens, two matched “several species” (ducks, whales, naked mole rats?!!?), one matched newts and one matched frogs. [...] that is about as conclusive as grabbing seven items at random from a supermarket, discovering four contain chicken and declaring the supermarket is a chicken ranch.”

  14. #14 Michael Wells
    April 15, 2007

    An evolution “skeptic” at another forum that shall remain nameless made the following gripe:

    “this AP article describes research that looked at seven fragments of protein and determined three matched chickens, two matched “several species” (ducks, whales, naked mole rats?!!?), one matched newts and one matched frogs. [...] that is about as conclusive as grabbing seven items at random from a supermarket, discovering four contain chicken and declaring the supermarket is a chicken ranch.”

    I’m too tired and preoccupied right now to figure out in detail why this guy is wrong. (Other than that it’s silly to propose that the scientists who did this are clueless or lying, and that the other scientists and science writers who weren’t involved haven’t noticed or are all playing along). It’s like an itch I can’t quite scratch. Drivin’ me nuts. Can anyone here do better at identifying his logical holes and factual misunderstandings?

  15. #15 Chris' Wills
    April 16, 2007

    ….Drivin’ me nuts. Can anyone here do better at identifying his logical holes and factual misunderstandings? Posted by: Michael Wells

    My best guess is that your evolution skeptic is being deliberately disingenuous.

    I don’t have access to the actual paper, but from the BBC & Herald sites

    Herald Site: He (Asara) was able to identify seven different dinosaur proteins from the bone and compared them with proteins from living species. Three matched chickens, two matched several species including chickens, one matched a protein from a newt and the other from a frog.

    BBC site: Chicken-like
    When the scientists compared the protein sequence pattern to those of living animals in a database, it was found to be structurally similar to chicken collagen, and there were also similarities with frog and newt protein.

    Dr Schweitzer said the similarity to chickens was exactly what one would expect given the relationship between modern birds and dinosaurs.”

    So we have 7 proteins: 3 match chickens, 2 match several species including chickens & 2 didn’t match chicken (frog & newt).

    So 5 out of 7 match up with chicken, this strikes me as a fairly stunning match given the millions of years seperating the two species. I would have been less impressed and guessed that something was wrong if there was a 100% match.

    I would suggest that Dr Schweitzer’s comment is not worded well (it seems to assume that the relationship is true), the relationship between dinosaurs and birds is an hypothesis that predicted that this type of relationship should exist would seem more accurate and a stronger claim.

    The supermarket analogy is strange; if I did pick seven items at random in a supermarket (say a large Tesco with 10,000 different items) and 5 contained chicken I would be very suprised and would guess that the selection wasn’t random.

    P.S. I have no biological expertise and would be interested if anyone could advise how many distinct collagen proteins a chicken has.

  16. #16 Owen
    April 18, 2007

    I wouldn’t worry too much about the lack of comparison with other birds. It seems pretty clear to me that Chicken was used since it’s the bird for which the most genome sequence data is available. With only 7 peptides they’re not going to be able to make too accurate a comparison in any case, but it does look as if T.rex is more closely related to birds than to mammals or amphibians.

    What struck me as odd is the almost passing reference to hydroxylated glycine residues that they observed not only in the Mastadon and T.rex sequences but also in the reference ostrich sequence in the supporting material. As far as I know this is the first ever description of (presumably) alpha-hydroxyglycine in a protein, other than as an unstable intermediate during the reaction to produce C-terminal amidation. I’m not a collegen expert so I’m curious to know what replacing an achiral glycine with a chiral hydroxyglycine at the first position in the collagen triplet would do to the structure of a collagen molecule.