August 4, 2016 | David F. Coppedge

Fossil DNA Stuns Geologists

None of them would have believed DNA could survive over a million years. They have no explanation for its preservation.

An open-access paper in Geology documents the existence of DNA in ocean sediments up to 1.4 million years old in their dating scheme. The DNA appears to be from chloroplasts from algae, such as diatoms (abbreviated cpDNA). There’s less of it in the deeper sediments from two cores drilled into the seafloor in the Bering Sea, but it never disappears, even in the deepest sections. [Note: Ma = million years, ka or k.y. = thousand years.]

The initial decrease in cpDNA reads suggests that most cpDNA decays within 100–200 k.y. of deposition. However, cpDNA from a few phylotypes, including some that match fossil diatoms, are present throughout the cored sediment, ranging in age to 1.4 Ma. The relative fraction of sequences composed by cpDNA decreases non-linearly with increasing sediment age, suggesting that detectable cpDNA becomes more recalcitrant with age.

People become recalcitrant, not organic molecules. What kind of excuse is that? How can DNA remain so long without decaying? They have no idea.

We do not know the mechanism behind the apparent relative slowdown of DNA degradation with age. Whether this decreased turnover is due to decreased lability of residual DNA, an overall decrease in enzyme activity, a decrease in spontaneous decay rates, or some combination of these and other factors remains presently unknown.

Each of the causes listed above has problems:

  1. Decreased lability: why would DNA cease to be flexible?
  2. Decrease in enzyme activity: enzymes are not the only factors causing decay.
  3. Decrease in spontaneous decay rates: what would cause that? It sounds like an empty speculation.
  4. Some combination of these: If none of the factors are good, the combination cannot be much better.
  5. Some combination of other factors: Name one.

They speculate that silica in diatom shells might be preserving the DNA, but they offer no empirical evidence that is possible. Thermal fluctuations alone should destroy DNA over time.

The authors are confident that the DNA is not contamination from recent organisms. This quote mentions previous measurements of DNA of even older age; they call them “poorly constrained” (thus the current study), but if carbon-14 showed the decay of DNA to have a 521 year half-life, it becomes highly implausible it could last a million years.

Without a continuous record that spans long time scales, it is difficult to understand the maximum extent of fossil DNA preservation. Inagaki et al. (2005) inferred the existence of a Cretaceous DNA “paleome” in ca. 100 Ma black shale, based on sequences associated with marine-type sulfate-reducing bacteria. However, these organisms may have inhabited the sediment since its deposition. In contrast, Allentoft et al. (2012) used 14C dating to calculate a 521 yr half-life for mitochondrial DNA in terrestrial bone. These large differences between 100 yr and 100 m.y. time scales illustrate that (1) the relative contributions of fossil versus indigenous materials to DNA pools are poorly constrained, and (2) in marine sediment, we cannot assume all DNA to be non-fossil. In general, genetic studies of material that pre-dates the Quaternary are at odds with the current understanding of DNA preservation, especially in wet environments (Lindahl, 1993). In this study, we examine DNA concentration and composition from continuous sedimentary records as old as 1.4 Ma at two sites in the Bering Sea. The geochemical regime is likely broadly representative of high-productivity continental margins (Wehrmann et al., 2011). In order to separate fossil DNA distributions from living communities in subseafloor sediment, we focus on chloroplast DNA (cpDNA) and assume that it represents ancient material from the sunlit surface world.

The Allentoft paper is open access and measured the DNA half-life in Moa bones to be 521 years. That these earlier finds were “at odds with the current understanding of DNA preservation” motivated their own work. Yet from measuring cpDNA from these cores, they had to conclude that “the preservation of fossil cpDNA over geological time” must be reconsidered. The fact that the DNA does decrease with depth shows that decay does occur. Why, then, would the decay basically stop at some “inflection point”? “At our sites, this inflection occurs at ca. 100–200 ka [ka = thousand years], suggesting that after this point, fossil DNA does not appear to interact at an appreciable rate with enzymes or cells found in this sediment.” Why? They have no idea. In conclusion, they say:

Plankton DNA in marine sediment decays over geologic time (e.g., Boere et al., 2011b). At our Bering Sea sites, the majority of cpDNA sequences disappear within the first 100–200 k.y., but traces are present in sediment of every age sampled (as old as 1.4 Ma). Some of these cpDNA reads match siliceous microfossil taxa previously identified in the same sedimentary sequences, suggesting that microfossils may help to preserve DNA. This persistence of a small relative fraction beyond 1 Ma suggests that residual cpDNA becomes increasingly recalcitrant with increasing sediment age. These results highlight both (1) the potential of fossil DNA for paleoecology studies, and (2) its relative isolation from the biogeochemical processes driven by active subseafloor microbiota.

They know DNA decays. Even if it is relatively isolated from biogeochemical processes, it should still decay. References to some unknown process of “recalcitrance” amounts to mere hand-waving. Here is an anomaly calling for explanation.

The findings make sense if none of the DNA is as old as claimed. Remove the assumption of millions of years. Now look at the data. Below a certain depth, it’s all mostly the same age. It’s all been decaying since deposition. The upper layers include organisms that died more recently. Their cpDNA, therefore, is richer. Believing the millions-of-years scenario, by contrast, requires ad hoc rescue devices, or admissions that the processes of preservation are not understood. These amount to mere post-hoc suggestions to rescue the long-age view.

These are some initial considerations for geologists not enslaved to the geologic column. We encourage such geologists to study this paper and its implications.



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