In textbook discussions of the empirical content and testability of the theory of universal common descent (UCD — i.e., the monophyletic Tree of Life (TOL), rooted in the Last Universal Common Ancestor (LUCA)), UCD is often held to be testable via the counterfactual of “genes and proteins might have been discovered in groups where they should not exist.” In other words, if we observed genes and proteins occurring in the TOL, with unequivocal homology to the same sequences found elsewhere in phylogenetically distant or divergent groups, UCD would be in trouble. This is a counterfactual expectation — so the logic goes — because, in fact, genes and proteins behave themselves and fall into the nested hierarchy predicted by the TOL and the real existence of LUCA. Nonetheless, such a counterfactual ensures that UCD remains testable, because (in principle) we could observe such anomalous distributions, although we usually don’t.

But UCD always confronts observations with an indefinitely large entourage of helper or auxiliary theories. That by itself isn’t unusual, of course — every scientific theory comes bundled with auxiliary hypotheses and assumptions. UCD’s big entourage only becomes a problem when its members always pay the fines for UCD’s failed predictions, pick up UCD’s tab at restaurants and hotels, and generally cover the empirical shortfalls of UCD.

An Unintentional Case Study

Sooner or later, onlookers will realize that UCD is actually bankrupt. UCD doesn’t pay its bills, because it can’t. An unintentional case study appears now in the journal Molecular Biology and Evolution: “Citrullination was introduced into animals by horizontal gene transfer from cyanobacteria.”

Citrullination is an enzyme-mediated post-translational process whereby arginine residues in proteins are converted to the amino acid citrulline (not part of the “universal 20” set coded for by the genetic code). As Thomas F. M. Cummings et al. write, in the paper:

Citrullination is the post-translational conversion of a protein arginine residue to the non-coded amino acid citrulline and is catalysed by PADI enzymes in a calcium-dependent manner (Sugawara et al. 1982; Wang and Wang 2013). Although citrullination involves a small mass change of only 0.98Da, the removal of a positive charge from the arginine side chain can lead to profound biochemical changes and is known to alter protein structure, sub-cellular localisation and affinity to other proteins and nucleic acids.

But the phylogenetic distribution of citrullination is puzzling, they explain (emphasis added):

Citrullination, a key regulatory mechanism in human physiology and pathophysiology, is enigmatic from an evolutionary perspective. Although the citrullinating enzymes peptidylarginine deiminases (PADIs) are ubiquitous across vertebrates, they are absent from yeast, worms and flies…Here, we map the evolutionary trajectory of PADIs into the animal lineage. We present strong phylogenetic support for a clade encompassing animal and cyanobacterial PADIs that excludes fungal and other bacterial homologues. The animal and cyanobacterial PADI proteins share functionally relevant primary and tertiary synapomorphic sequences that are distinct from a second PADI type present in fungi and actinobacteria.

A Robust Clade? (Just Kidding)

Animals and blue-green algae (cyanobacteria), to the exclusion of everything in between — now there’s a robust clade for you. 😉 Be sure to check out Figure 5 in the paper. What you see in that figure is a graphical representation of the impossibility of testing UCD, because any damn thing can happen in evolution. ANY DAMN THING.

If that language sounds harsh, consider this: there is zero evidence provided in this paper for the horizontal transfer mechanism from cyanobacteria to animals. Moreover, run this thought experiment for yourself: proteins that convert arginines to citrulline are horizontally transferred from cyanobacteria into the germ lines of various animals. One fine day, the proteins wake up in their new metazoan hosts, and start converting arginines to citrullines willy-nilly. 

No problem! Arginine, citrulline, doesn’t matter, evolution is smarter than you are — the animal host’s native proteins, now studded with novel citrullines, will still work just fine. Right? If ever anyone needed evidence of the untestability of UCD, papers like this provide it.