Recently, our physics color commentator Rob Sheldon took issue with the use of the term “half-life” to describe the survival of DNA in fossils. He says the term has a specific meaning with respect to radioactive decay that just does not apply to other events in nature.
In the biology paper at issue, with “half-life” in the name, the authors explain and use the concept in connection with radiocarbon dating:
Abstract: Claims of extreme survival of DNA have emphasized the need for reliable models of DNA degradation through time. By analysing mitochondrial DNA (mtDNA) from 158 radiocarbon-dated bones of the extinct New Zealand moa, we confirm empirically a long-hypothesized exponential decay relationship. The average DNA half-life within this geographically constrained fossil assemblage was estimated to be 521 years for a 242 bp mtDNA sequence, corresponding to a per nucleotide fragmentation rate (k) of 5.50 × 10–6 per year. With an effective burial temperature of 13.1°C, the rate is almost 400 times slower than predicted from published kinetic data of in vitro DNA depurination at pH 5. Although best described by an exponential model (R2 = 0.39), considerable sample-to-sample variance in DNA preservation could not be accounted for by geologic age. This variation likely derives from differences in taphonomy and bone diagenesis, which have confounded previous, less spatially constrained attempts to study DNA decay kinetics. Lastly, by calculating DNA fragmentation rates on Illumina HiSeq data, we show that nuclear DNA has degraded at least twice as fast as mtDNA. These results provide a baseline for predicting long-term DNA survival in bone.
Allentoft Morten E., Collins Matthew, Harker David, Haile James, Oskam Charlotte L., Hale Marie L., Campos Paula F., Samaniego Jose A., Gilbert M. Thomas P., Willerslev Eske, Zhang Guojie, Scofield R. Paul, Holdaway Richard N. and Bunce Michael 2012 The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils Proc. R. Soc. B.2794724–4733 http://doi.org/10.1098/rspb.2012.1745
But Sheldon points out,
The paper does explain the environmental conditions of 13.1C, ph=5.0 and 158 moa bone assemblage, which is the data needed to make sense of the claim. They even pointed out that this halflife=521 years was 400X slower than the test-tube numbers bandied about in the literature (which would have been 1.3 years?).
But after saying all that, they said the data had a correlation coefficient of R2 = 0.39, which is the lowest value I have ever read in the literature used to support a correlation. Normally if R2<0.5, the paper is rejected by the editors as not showing a correlation.
That is to say, even after correcting for pH, temperature, species, type of bone, location, (burial to remove cosmic rays), and chromosomal variation—they still had a variable half-life of (my eyeballing their plot), somewhere between 100 – 2000 years. In the body of the paper they bandy about correction factors of 5 and 73 for things like temperature and pH. So indeed, 1.2 million year mammoth DNA is quite reasonable if we plug in -5C and ph<7.5. But then the use of “half-life” as a some sort of constant number is meaningless.
So I stand by my statement. Biologists should use this paper as a warning about the uselessness of a half-life number for DNA, especially for predicting DNA preservation or dating artifacts. You would be better served by casting lots.
Rob Sheldon is the author of Genesis: The Long Ascent and The Long Ascent, Volume II.
See also: Does DNA really have a “half life”? Physicist Rob Sheldon is sceptical. Sheldon: “As a physicist, I would like to point out that biologists are misusing the word “half-life”. DNA does NOT have a half-life of 521 years. Radioisotopes have a half-life, because the nucleus is unstable to natural decay through the weak force (for isotopes of interest).” He goes on to say that the weak force of the universe “is unaffected by temperature, pressure, time, or chemicals.” Not so for DNA.