Dinosaur soft tissue--just bacterial biofilm?

ResearchBlogging.org 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 (10â15 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

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Bummer. Does this mean I'm not going to get my own T. rex?

By Dan Hocson (not verified) on 30 Jul 2008 #permalink

Blast! One less thing for the next edition of " Of Pandas and People"! Those scientists!

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...

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?

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.

Tara, be very careful in accepting that this paper is the last word on the subject!

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.

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.


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.

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,


Does it mean that chicken,T-rex link is still valid

Appreciatively yours


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.

By BioinfoTools (not verified) on 30 Jul 2008 #permalink

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!

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.

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.

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.


Hi Tara,

Did you see this?

"Oldest Dinosaur Protein Found -- Blood Vessels, More
John Roach
for National Geographic News
May 1, 2009

The fossilized leg of an 80-million-year-old duck-billed dinosaur has yielded the oldest known proteins preserved in soft tissueâincluding blood vessels and other connective tissue as well as perhaps blood cell proteinsâa new study says.

The research was led by the team behind the controversial 2007 discovery of protein from similar soft tissues in 68-million-year-old Tyrannosaurus rex bones."

I wonder why everyone stopped posting the past 2 years! Oh yeah we've now found a Mosasaur, Archaeopteryx and two Hadrosaurs ALL with soft tissue! And it's been confirmed that it's not contamination by major universities (Harvard Medical, University of Mancester, Lund University in Sweden, SMU, North Carolina State and many more)! But what do they know they are just trolls!

So not only is there now evidence refuting the bio-film theories (using immune responses etc.), we have confirmed the presence of dna (using 3 different methods) with histones as well, along with (obviously) bone cells.

Seems like these speculations of "it's not dinosaur soft tissue!", and "it can't possibly be so it must be " were more creations of the mind than actual evidence-base findings, which were used to avoid a nasty conclusion. hehe

But what is remarkable is that the paradigm of evolution still holds. What we see happening is people choosing to change the evidence and not the worldview, at the expense of evidence. Good going fellow scientists! What of scientific integrity?