An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)--researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented "proof" that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of "soft tissue = dino blood" were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren't actual vessels and cells, but are instead iron-rich bacterial biofilms. More on that below.
First, a bit about biofilms. These are the sticky structures that form when bacteria adhere to a surface and form "communities" of organisms (as opposed to their free-living, "planktonic" stage). The plaque on your teeth and tongue; the scummy ring around your bathtub; the slippery coatings on ocean rocks are all composed of biofilm, which itself is made up of not only bacterial cells but also the matrix they produce that allows them to adhere to the surface (and also provides them protection from the elements around them). Though we've studied bacteria in their planktonic state for much of the history of microbiology, this is quickly changing as we realize the ubiquity of biofilms not only in the environment around us, but also within our own bodies (where biofilm-associated bacteria are much more resistant to the effects of antibiotics, for instance).
So, biofims are everywhere--but *inside* bone? That was the question examined in the new paper. To do this, researchers fractured a number of specimens from different ages and locations and examined the hard and soft tissue they found inside. They found remarkably similar structures in each case after examining them with scanning electron microscopy (SEM), which allowed them to view the surface and shape of the soft tissue material; and with energy dispersive spectroscopy (EDS) and Fourier Transform Infrared Spectroscopy (FT-IR) to look for molecular "fingerprints."
What they found provides an alternative hypothesis to the previous "dino blood" findings. The iron present (and thought to have come from blood cells) could be explained by the presence of iron-containing framboids: spheres commonly found in sediments. Blood vessel-like structures were found but also could be attributed to biofilm, and when compared by FT-IR to lab-grown biofilms, the chemical signature of the fossil structure more closely resembled modern biofilms than modern collagen. The authors argue that the biofilm hypothesis better explains the data, including the ubiquity of these structures in fractured fossils:
This investigation contends that iron-oxygen spheres are far too common in many formations to be the result of extraordinary preservation. Framboid morphology and elemental signature may superficially make them appear to be related to biological structures but they are, in fact, an inorganically produced mineral feature often found in association with organic matter.
Arrows on this electron microscope image indicate biofilms, or slime, peeling away from the walls of vascular canals in dinosaur bone. Credit: Thomas Kaye.
But what about the dinosaur collagen claimed to be found in a prior study? The authors explain that as well:
Recent protein work by Asara et al. examined ground tyrannosaur bone under a highly sensitive mass spectrometer. This resulted in seven recovered protein sequences attributed to the original tyrannosaur but only in femptogram quantities (10−15 gram moles). The additional detection of bacterial proteins, identified at the species level as the decomposing bacteria Rhodococcus sp. showed conclusively that bacterial contamination was present, even though the original bone was deeply buried. Rhodococcus sp. exhibits morphological differentiation and can be found as both cocci and filaments consistent with forms found in lacunae from this survey (Fig. 10). Recent discoveries of collagen-like proteins in bacteria and viruses add to the problem of unambiguous identification of vertebrate biomolecules.
This paper seems to deal a pretty convincing blow to the "dino blood" theory, but I'm anxious to see what the dino experts have to say about it, including the original proponents of the hypothesis.
Kaye, T.G., Gaugler, G., Sawlowicz, Z., Stepanova, A. (2008). Dinosaurian Soft Tissues Interpreted as Bacterial Biofilms. PLoS ONE, 3(7), e2808. DOI: 10.1371/journal.pone.0002808
Life Science
Comments
Bummer. Does this mean I'm not going to get my own T. rex?
Posted by: Dan Hocson | July 30, 2008 12:56 PM
Blast! One less thing for the next edition of " Of Pandas and People"! Those scientists!
Posted by: Scott | July 30, 2008 1:20 PM
Disappointing, but also a great example of how science is dynamic. We now have a competing theory on the origin of organic material inside fossil bones. Will further evidence bear it out, versus the original hypothesis?
Unlike cdesign proponentstists, scientists are actually working to determine that...
Posted by: wright | July 30, 2008 2:03 PM
Tara, be very careful in accepting that this paper is the last word on the subject! Some of the new findings do contradict some of the older findings, but there is much about this new paper that isn't satisfactory (and doesn't address admitted problems with the older findings). For example, why are the framboids not nucleating around iron-rich sources, such as blood cells? Wherever there's a source of iron (be it blood or anything else), iron crystals can form diagenetically. Why are these biofilms dating so recently, despite all the different ages of the source materials? Did they all somehow predict "Hey, in the next couple hundred years, someone's going to break us open and look for biofilms -- better get some!" How did the biofilms form such uniform tubular structures, especially if water levels inside the bones fluctuated and varied? Why did the previous collagen findings have chemical signatures more similar to chickens than anything else (reacted with chicken antibodies)...are we now supposed to accept that this reaction indicates that tyrannosaurs are more closely related to Rhodococcus bacteria than to chickens?
I'm not saying this new paper is bad; certainly it's a good attempt to come at some previous conclusions another way, which is what science is supposed to do. But this new approach examines structures; much of the previous work examined chemistry, and I don't think one can adequately contradict the other. That they point at different results only means that there's a lot more work to do. The field of examining fossilization at this scale is so new that there's basically now two data points. Would any scientist be comfortable making pronouncements on such tiny quantities of data?
Posted by: Jerry D. Harris | July 30, 2008 2:42 PM
This actually sounds more fascinating than 'just' recovered dinosaur tissue. Those darn bacteriums - always springing surprises on us.
Too bad MS can only detect proteins - I'd love to see if it'd be possible to date the bacteria based on genetic drift compared to contemporary Rhodococcus sp.
Posted by: Sili | July 30, 2008 2:55 PM
Oh, I don't think that at all. As I mentioned, I'm anxious to see what the Schweitzer group will come back with, and I'm also interested in seeing what the biofilm folks have to say about it (as Kaye noted somewhere that's not his field). I think we're much closer to the beginning of this story than the end. It'll be a fascinating area to watch in the coming years, and I'm sure Kaye isn't the only one who tried to replicate Schweitzer's findings, so I'm sure there are other ideas out there as well.
Posted by: Tara C. Smith | July 30, 2008 3:09 PM
Hello All,
Tom Kaye here from the paper. Since this seems to be the blog with the most activity, I will offer to answer any questions for the group.
Tom
Posted by: Tom Kaye | July 30, 2008 5:11 PM
Hi Tom--
Thanks for stopping by! There's also a good discussion over at Panda's Thumb, where I cross-posted this. If you can ignore the trolls (the creationists etc.) there are some good questions you may be able to respond to over there also.
Posted by: Tara C. Smith | July 30, 2008 5:56 PM
Dear Tara--
One answer I didn't get from the Panda's thumb is whether there are other molecular or protein evidence for common ancestry between dinosaurs and birds?
I know the fossils fit perfectly with what we would expect, but I also like to see molecular evidence too, so disappointed if it isn't.
PS. Tom told me in the Panda thumbs thread that his team didn't examine the specimen from this study,
http://www.sciencedaily.com/release[...]24140418.htm
Does it mean that chicken,T-rex link is still valid
Appreciatively yours
Don
Posted by: Draconiz | July 30, 2008 9:26 PM
I keep meaning to read these papers, but never get around to it...! Nice to see a potted update on what's happening. My own interest, apart from the general story, was to look into what is know about these "protein sequences" in case there is something I can look into for a little work-related leisure. (I realise in a vague way that there are issues about them being "protein sequences".)
In the spirit of a little fun: what if there is both biofilm and T. rex soft material?!
I'm reminded a little of how bacteria can get "through" what is superficially solid material when viewed at a larger scale. My favorite example of this, although probably not quite a fair comparison, is the endolithic colonies.
Tara: Thanks for the link to the Panda thread. Read your older articles that included references to Hendra viruses, good reading.
Posted by: BioinfoTools | July 30, 2008 9:39 PM
whoa I'd hit that
Posted by: LaQuyn | July 31, 2008 12:10 AM
Hi Tara,
on biofilms, which came first, the planktonic mode or the biofilm mode? I would think that some OOL theories would favor development on a substrate, surrounded by a concentrated slime of organic chemicals.
ps - yes you are still the hottest science blogger!
Posted by: David vun Kannon, FCD | July 31, 2008 12:29 PM
I'm curious to know if this will affect any other studies that had apperently discovered preserved fossilized tissue. I was thinking specifically about the material that was extracted from neanderthal fossils that had shown no direct relation between them and modern humans.
Posted by: Susan | August 1, 2008 4:37 AM
Good question, and I'm not well-versed enough in the evolutionary history of biofilms to answer. I'd think planktonic because there seem to be a lot of specializations associated with biofilm formation, and it also can be a suicidal activity for a portion of cells involved. Plus, mechanisms used to form biofilm include a measurement of the density of other cells around them--obviously not possible if there weren't other cells...however, how much of that is secondary adaptation I'm unsure.
Posted by: Tara C. Smith | August 1, 2008 9:54 AM
thanksss you .. veryu good sites
Posted by: liseli kızlar | February 13, 2009 6:44 PM
Tara,
This is interesting.
Now comes a further announcement by Schweitzer and others, in the prestigious journal Science, of substantial additional evidence to bolster her previous findings.7 The specimen on this occasion was a piece of fossil hadrosaur (duckbilled dinosaur) bone (Brachylophosaurus canadensis) regarded by evolutionary assumptions as being 80 million years old.
In short, the researchers found evidence of “the same fibrous matrix, transparent, flexible vessels, and preserved microstructures she had seen in the T. rex sample”.8 Only this time they went to exceptional lengths to silence critics.
Critics said that her claims, which given the millions of years perspective are indeed “extraordinary”, required extraordinary evidence. But this is a cliché; in reality, they just require evidence, and that has been amply provided. Yet the critics demanded additional protein sequencing, super-careful handling to avoid claims of contamination, and confirmation from other laboratories. So Schweitzer and her team set about doing just that when they looked at the leg bone of this hadrosaur encased in sandstone.
Extraordinary measures were taken to keep the sample away from contamination until it reached the lab. They used an even more sophisticated and newer mass spectrometer, and sent the samples to two other labs for confirmation. They reported finding not just collagen, but evidence of two additional proteins—elastin and laminin. They also found structures uncannily resembling the cells found in both blood and bone, as well as cellular basement membrane matrix. And there were, once again, hints of hemoglobin, gleaned from applying hemoglobin-specific antibodies to the structures and seeing if the antibodies would bind to them.
Some scientists are still skeptical about the hemoglobin, which is “difficult to identify with current technology”. Dr Pavel Pevzner of the University of California, was quoted as saying that if it is not a contaminant, it would be “much bigger news [than the confirmed discoveries of blood vessels and other connective tissues in] this paper.”9
Even leaving aside the hemoglobin, the Schweitzer et al paper is huge news. Pevzner had been critical of the technique used in Schweitzer’s analysis of the T. rex protein, but now he says that her new study “was ‘done the right way,’ with more stringent controls to guard against contamination”, for one thing.
There were eight collagen proteins alone discovered from the hadrosaur fossil, which revealed twice as many amino acids as the previous tyrannosaur specimen. These were compared with sequences from animals living today as well as from mastodon fossils and her T. rex sequences. The hadrosaur and tyrannosaur collagens were closer to each other than the others, and each were closer to chickens and ostriches than to crocodilians, for instance—results which would also confirm her previous identification of T. rex collagen.
The samples were identified as collagen by both sophisticated mass spectroscopy and antibody-binding techniques. They were also examined via both light and electron microscopy, which confirmed that they had the appearance of collagen as well.
As Schweitzer says, “These data not only build upon what we got from the T. rex, they take the research even further.”
Pretty amazing. I hope that I am not considered a "creationists troll". Oh well, I have been called much worse,
Tom Severson
Posted by: Tom Severson | June 10, 2009 12:20 PM
Now comes a further announcement by Schweitzer and others, in the prestigious journal Science, of substantial additional evidence to bolster her previous findings.7 The specimen on this occasion was a piece of fossil hadrosaur (duckbilled dinosaur) bone (Brachylophosaurus canadensis) regarded by evolutionary assumptions as being 80 million years old.
Posted by: 2009 ÖSS Sonuçları | June 27, 2009 8:34 PM
2009 ÖSS Sonuçları
Pretty amazing. I hope that I am not considered a "creationists troll". Oh well, I have been called much worse,
Tom Severson
Posted by: 2009 ÖSS Sonuçları | June 27, 2009 8:36 PM