Ancient Enzymes

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Laboratory reconstruction of ancient enzymes has suggested that these enzymes are remarkably similar to enzymes in modern creatures and purportedly indicate what conditions were on the early earth.

“Ancestral sequence reconstruction” is a technique in which DNA known to code for a certain protein in modern-day organisms is used to reconstruct ancestral DNA. The resulting protein sequence can then be synthesized in the laboratory and the properties of the resulting protein studied.

Claiming to have thus reconstructed the enzyme thioredoxin as found in “four-billion-year-old extinct organisms,” researchers were surprised to find that “enzymes that existed in the Precambrian era up to four billion years ago possessed many of the same chemical mechanisms observed in their modern-day relatives.” Furthermore, since the reconstructed enzyme seemed unusually resistant to harsh conditions of heat and acidity, they concluded that the early earth must have been hotter and more acidic.

In fact, however, ancestral sequence reconstruction is only as reliable as the assumptions on which it is based. In this case the researchers “resurrected Trx enzymes belonging to the last bacterial common ancestor” and some other single-celled ancestors. All of these modern organisms were chosen because they “are thought to have inhabited Earth 4.2-3.5 billion years ago after diverging from the last universal common ancestor (quotation from original paper in Nature America).”

While claiming to have avoided making “far-reaching assumptions about ancient life,” the researchers were in fact making unverifiable assumptions about the existence of a particular evolutionary tree as well as the rate at which divergence of species occurred. (Presumably, they have extrapolated backwards using these assumptions to grab a four billion year date, since even the dating methods with their underlying assumptions haven’t suggested dates for fossilized bacteria any older than 2.8 billion years.) Thus the age of this hypothetical ancestor whose protein is to be analyzed in the present form in its descendents is presumed to be about four billion years.

Furthermore, as also pointed out by Paul Williams et al. in “Assessing the Accuracy of Ancestral Protein Reconstruction Methods,”1 the methods chosen for the reconstruction tend to give inconsistent results with regard to such characteristics as thermostability.

Williams’ evaluation would suggest that even the conclusions about the robustness of the enzyme should be taken with a grain of salt.

In the present study, the enzyme’s properties are said to be consistent with the conditions it would have to contend with on the early earth. Yet Williams’ evaluation would suggest that even the conclusions about the robustness of the enzyme should be taken with a grain of salt.

Once again, your presuppositions determine your conclusions.

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  1. Paul D. Williams, David D. Pollock, Benjamin P. Blackburne, and Richard A. Goldstein, “Assessing the Accuracy of Ancestral Protein Reconstruction Methods,” edited by David Hillis, PLoS Computational Biology 2, no. 6 (June 20, 2016): doi:10.1371/journal.pcbi.0020069.


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