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Bye-bye, dino soft tissue

A lot of e-ink has been spilled over the claim, primarily by Schweitzer, that intact, ancient soft tissue can be found inside fossilized dinosaur bones. She made some interesting observations of mysterious stuff extracted from fossils, but what it is and whether it’s actually preserved dinosaur tissue has been contentious. It’s baffled me, that’s for sure, since it didn’t jibe with my understanding of chemistry, and I couldn’t imagine some SF stasis field operating inside old bones. Here’s an excellent summary of the problem.

Reports of dinosaur protein and complex organic structure preservation are problematic for several reasons. Firstly, it remains unclear how such organics would be preserved for tens of millions of years. If endogenous, putative dinosaur soft tissues should contain diagenetically unstable proteins and phospholipids, vulnerable to hydrolysis, although the released fatty acid moieties from phospholipids could be stabilized through in situ polymerization into kerogen-like aliphatic structures. At 25°C and neutral pH, peptide bond half-lives from uncatalyzed hydrolysis are too short to allow for Mesozoic peptide preservation, although hydrolysis rates can be decreased through terminal modifications and steric effects on internal bonds. Estimates based on experimental gelatinization suggest that, even when frozen (0°C), relatively intact collagen has an upper age limit of only 2,700,000 years. Secondly, the instances of dinosaur peptide preservation reported are older than the oldest uncontested protein preservation reported by at least an order of magnitude. The oldest non-controversial peptides include partially intact peptides from 3.4 Ma in exceptionally cold environments, as well as short peptides bound to eggshell calcite crystals from 3.8 Ma stabilized via unique molecular preservation mechanisms. The youngest non-avian dinosaur bones are 66 million years old; on both theoretical and empirical grounds, it seems exceptional that original proteins could persist for so long.

Yeah, what he said. Complex molecules like proteins and nucleotides are going to degrade slowly over time, so what’s preventing breakdown in these fossils? Idea like polymerization or chemical modification into more stable molecules have been floating around, but it’s hard to get around the empirical fact that even a molecule as stable as collagen is going to fall apart, eventually.

These authors do an exhaustive analysis of the organic compounds found in ancient fossil bones, and most persuasively, do positive controls with recent bones and bones that are fossilized, but younger, and what they find is that the original organic material degrades steadily and somewhat predictably, and that dinosaur bones are destitute of original dinosaur soft tissue. They can find collagen in, for instance, shark teeth from the Pleistocene-Holocene, but it’s undetectable in older specimens.

So how to explain the spongy soft stuff found by some investigators inside dinosaur bones? Previous investigators failed to take into account the ubiquity of microbes.

Previous studies have often reported purported endogenous ‘soft tissues’ within fossil dinosaur bone. However, these studies often do not fully address fossil bones being open systems that are biologically active. This can be seen in field observations, in Dinosaur Provincial Park and elsewhere, where fossil bone is frequently colonized by lichen on the surface or overgrown and penetrated by plant roots in the subsurface. This forces researchers to consider that subsurface biota (e.g. plant roots, fungi, animals, protists, and bacteria) could contaminate bone. Given that fungi can produce collagen, the need to rule out exogenous sources of organics in fossil bone is made all the greater. Even deeply buried bone has the potential to be biologically active, given the high concentration of microorganisms in continental subsurface sedimentary rock. The analyses presented here are consistent with the idea that far from being biologically ‘dead’, fossil bone supports a diverse, active, and specialized microbial community. Given this, it is necessary to rule out the hypothesis of subsurface contamination before concluding that fossils preserve geochemically unstable endogenous organics, like proteins.

I find the idea that bacteria and fungi can successfully infiltrate rocks and bones far more likely than that bone chemistry can somehow suspend the laws of thermodynamics for a hundred million years. I’m going to tentatively accept the explanation of recent bacterial contamination for the soft tissue in fossil bone controversy.

The study of fossil organics must consider potential microbial presence throughout a specimen’s taphonomic history, from early to late. Microbial communities interact with fossils immediately following death and after burial, but prior to diagenesis. Microbes are known to utilize bone and tooth proteins and fossil evidence of early fungal colonization has even been detected. More recent microbial colonization of fossil bone will occur as it nears the surface during uplift and erosion in the late stages of the taphonomic process. Furthermore, given that microbes can inhabit the crust kilometres below the surface, it might be predicted that bone remains a biologically active habitat even when buried hundreds of meters deep for millions of years. The extensive potential for microbial contamination and metabolic consumption makes verifying claims of Mesozoic bone protein extremely challenging.

Remember, dino fans, “life will find a way”. Bacteria are amazing.

Also, it seems to me that Schweitzer et al. have discovered an interesting and possibly important phenomenon, but it needs to be studied from the perspective of microbiology, not paleontology.

Saitta ET, Liang R, Lau MC, Brown CM, Longrich NR, Kaye TG, Novak BJ, Salzberg SL, Norell MA, Abbott GD, Dickinson MR, Vinther J, Bull ID, Brooker RA, Martin P, Donohoe P, Knowles TD, Penkman KE, Onstott T (2019) Cretaceous dinosaur bone contains recent organic material and provides an environment conducive to microbial communities. Elife. 2019 Jun 18;8. pii: e46205. doi: 10.7554/eLife.46205.

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Comments

  2. says

    That’s too bad. Even though I couldn’t believe it I still thought it was the coolest thing ever. Imagine if we could find intact dino DNA?

  3. Artor says

    I’d thought the report was unlikely when I first saw it, but didn’t the researchers do genetic sequencing on the soft tissue they’d found? Wouldn’t that have shown right away if it were foreign organisms colonizing the fossils?

  4. chrislawson says

    Did anyone try to sequence or analyse the amino acid frequencies of the collagen recovered from late Cretaceous fossils? There are differences between mammal species, so I suspect that it might be possible to tell if the collagen is from an avian ancestor vs. a fungus.

  5. curbyrdogma says

    Of course the creationist takeaway is that soft tissue in dino bones = young earth. So the analysis above still suggests that since collagen molecules couldn’t possibly be preserved for 65 million years, one must surmise that the dino fossils are far more recent.

    It would have to be established beyond a doubt that the “soft tissue” was indeed microbial in origin; otherwise this will persist as a creationist go-to trope, same as the Angkor Wat “stegosaurus” and “fossilized” teddy bears…

  6. says

    There was some attempt at sequencing the protein sequence of the collagen — and it looked like degraded “chicken” collagen. But it could also have been contamination.

  9. wzrd1 says

    @6 Degraded, indeed. Some ignore that bones aren’t a solid, impermeable substance, but with channels for blood to flow into and out of, providing clear pathways for colonization and replacement of soft tissue with degraded tissue-biofilm products that may, at some points, appear to be soft tissue.

    That said, some of the courser structures could become replaced by biofilm products, hinting at the original structure, even when the original structure no longer remains.
    For indeed, life finds a way – to confuse the unwary.

  10. Owlmirror says

    I am not so confident that the question can be dismissed. Schweitzer, et al, do seem to be aware of the hypothesis that they’ve been looking at microbes, and address it in their more recent papers. For example, here’s a paragraph from:
    Schweitzer, MH, et al. Molecular analyses of dinosaur osteocytes support the presence of endogenous molecules. Bone. 2013. :

    The persistence of original cells, retaining morphology, transparency and flexibility comparable to those in living tissues, in fossils dating to the Mesozoic (~250–65 MYA) is highly controversial. It has been proposed, as mentioned above, that the ‘vessels’ and ‘cells’ arise as a result of biofilm infiltration [43]; but no data exist to support this hypothesis. In fact, localized antibody binding to these tissues that show different patterns of binding, using antibodies to proteins microbes do not produce, negates this hypothesis. It has also been suggested that our T. rex sequences are the result of contamination [63] or statistical artifact [64]. These suggestions, however, did not consider all of the data put forth to support the hypothesis of originality, but rather focused on only morphology [43], or on only sequence data [63,64], and in all cases, did not include the immunological data in their critiques. Negative controls of sediments extracted in tandem with dinosaur bone, or buffer blanks, did not produce collagen sequence, and indeed collagen is rarely identified as a contaminant in mass spectrometry analyses. The most parsimonius explanation for all the data presented previously [3,4,38,39,2] is that collagen is preserved in these ancient tissues. Because we have consistently observed microstructures similar in location and morphology to osteocytes and vessels in demineralized bones from various extinct taxa, deriving from different ages, depositional settings and environments [36,37,39], it is also more parsimonious to assume a common source (i.e., endogenous to vertebrate organisms from which they derive) than to invoke identical contaminants in different bones from different environments that consistently produce the same structures; structures that are common in both morphology and immunological response to vertebrate bone components.

    Also:

    Extant osteocytes contain DNA, required for production of proteins involved in bone maintenance. We have shown localized binding of antibodies to DNA, and positive reactivity to PI and DAPI, two histochemical stains for DNA, to internal regions of ‘cells’ from each
    dinosaur, though signal is greatly reduced from that seen in extant cells. More importantly, antibodies to DNA bind dinosaur ‘cells’ in an identical pattern to the histochemical stains, and completely different from antibodies to actin, tubulin and PHEX. Antibody and histochemical staining indicate the presence of material within dinosaur ‘cells’ that is chemically and structurally consistent with DNA. That this is eukaryotic DNA is supported by recovery of histone H4 sequence (Table 1 and Supplemental Fig. S3D–H), and the binding of antibodies to histone H4 in the same pattern as DNA antibodies and histochemical stains (Supplemental Fig. S5). This DNA-binding protein is not found in microbes, thus a microbial source for these microstructures is not supported. It is highly doubtful that contaminant DNA from exogenous sources would localize to a single point inside these cell-like microstructures, and not in other regions.

    These data are not sufficient to support the claim that DNA visualized in these cells is dinosaurian in origin; only sequence data can testify to its source. However, these data suggest that affinity purification using antibodies may provide a means of recovering and concentrating sufficient amounts of DNA to be useful for next generation genomic sequencing. Because only about 15%–20% of cells from the dinosaurs reacted positively, and because reactivity that was observed was minimal relative to extant cells, there may be insufficient DNA present to validate its origin by current sequencing technology.

    Schweitzer et al may still be making some mistakes — maybe the degraded DNA is fungal or protistal, or the collagen they’ve been finding is fungal, as suggested in the above — but they do seem to be trying to avoid mistakes.

    I don’t have the chops to evaluate the biochemical technical work, but maybe someone else does.