A perspective on the evidence for keratin protein preservation in fossils: An issue of replication versus validation

Abstract

The preservation potential of biomolecules within vertebrate integument through deep time has recently been subject to much research and controversy. In particular, the preservation potential of proteins, such as collagen and keratin, is currently debated. Here, we examine claims from a recent study (Schweitzer et al., 2018, PLoS One), which concludes that feather keratin has a high preservation potential. We argue that this work provides insufficient evidence for protein preservation due to issues of methodology and data interpretation. Additionally, we contrast their approach and claims to those of other recently published studies in relation to the question of keratin protein preservation in fossils. We worry that most of the perceived evidence for Mesozoic polypeptide survival stems from repeated replication of methods prone to false detection, rather than triangulation by validating these claims with alternative methods that provide independent lines of evidence. When alternative explanations exist for the evidence cited as support for dinosaur proteins far exceeding their predicted preservation limits, it is most parsimonious to reject the more extreme taphonomic hypotheses. The evidence is instead more consistent with a mode of preservation in which keratinous structures do not fossilize organically as polypeptides, but rather as largely pigment and/or calcium phosphate remnants, which were originally held within the keratin matrix that is now lost. Unsupported taphonomic models (e.g., keratin polypeptide preservation) have the potential to influence our interpretation of fossil data, potentially resulting in erroneous paleobiological or evolutionary conclusions, as illustrated in another recent paper (Pan et al., 2019, PNAS) that we also discuss.

Sediment-encased pressure-temperature maturation experiments chemically simulate natural diagenesis of melanin

“…We hypothesise that, like natural diagenesis, P/T-maturation favours hydrolytic loss of integumentary proteins -evidenced by signi cant volume loss leading to voids/impressions as noted in prior work 28,30 .…”

“…An alternative view 57 suggests that brown stains in fossils can be readily produced by remnant proteinaceous components oxidatively condensing with sugar/lipid moieties to yield N-linked melanoidin-like heterocyclic polymers (i.e., advanced glycation end products [ 60 (i.e., extensively waterlogged, reducing lacustrine or marine settings). In contrast, the use of a pressurised setup in this study inhibits water from boiling off, instead directing proteins along hydrolytic reaction pathways.…”

“…Mass calibration of ion peaks was conducted by identifying C-cluster peaks from C 1 -C 9 . Previously published spectra for melanin reported 55 characteristic negative secondary ion peaks 13,60 , and these were used in our analysis. These peaks were normalised based on total-ion m/z counts for a given spectrum and mean-centred using the formula: -Σ(ion count i -μ ion count ).…”

“…Closed system maturation involves sealing tissue samples inside tiny Au/Ag capsules (~2 mm diameter) that are welded shut and placing them inside water-pressurised autoclaves. In contrast, tissues of larger sizes have been wrapped in aluminium foil, a highly open system, and subjected to heat and pressure in Ar-gas-pressurised autoclaves, but samples have been known to completely leak out of foil, leading to irretrievable products 29,30 . These setups represent unnatural extremes in closed vs.…”

The Society of Vertebrate Paleontology’s Publication Policy Is Inconsistent With Scientific Epistemology

“…Repeating the same analysis or using the same methods can help us judge whether the previous execution of those methods was successful and can help us assess variability in the sampled population of data or the precision of the method. However, replication alone does not ensure the accuracy of the conclusion if the method used is inappropriate for the question at hand -a point I have previously made with respect to conclusions about molecular preservation in fossils 15 "These efforts [to replicate results] are laudable, but insufficient. If a study is skewed and replications recapitulate that approach, findings will be consistently incorrect or biased... replication alone will get us only so far.…”