Common Ancestry: Wikipedia vs. the Data

Does the molecular data give evidence of common ancestry? Representing a common view among Darwinian evolutionists, Wikipedia says yes: "Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent." Did you get that? -- "all organisms"! To show why this statement is wildly false, I could give numerous examples to the contrary. Let's consider two:

First, consider a recent paper in Annual Review of Genetics which observes that huge percentages of eukaryotic genes tell conflicting stories about common descent. Here's a recreation of Table 2 from the paper:

Eukaryotic genes and their closest prokaryotic relative.

Closest eukaryotic relative

Percent of total Cyanobacteria 15.3

Alphaproteobacteria

8.5

Gammaproteobacteria

6.3

Betaproteobacteria

2.3

Probable proteobacteria

8.4

Other bacteria

12.8

Archae

9.6

No prokaryotic homolog

36.6

(From Table 2, Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012).)

This table shows that eukaryotic genes send extremely mixed messages about the supposedly closest prokaryotic relative of eukaryotes. (Of course "closest prokaryotic relative" merely means "which prokaryote's version of a gene has the highest sequence similarity to the eukaryotic version of the gene?") Some eukaryote genes are most similar to one type of prokaryote, whereas other eukaryote genes are most similar to another. There's no consensus from eukaryote genes about eukaryote ancestry.

In fact, the largest category of genes here is eukaryotic genes that have no homolog among prokaryotes -- they don't even have any possible candidate ancestors to explain where these genes came from, much less a consistent pattern of similarity pointing to one particular ancestor. All this is the opposite of "a direct correlation with common descent."

Darwinian evolutionists will try to retain common descent and explain away this data by ad hoc appeals to horizontal gene transfer (HGT), or by inventing hypothetical ancestors as needed to donate these non-homologous genes. In fact, this paper explains that evolutionary biologists typically treat phylogenetic conflicts as a very test

 for the presence of HGT:

The classic test for inferring HGT is the phylogenetic congruency test, whereby a gene tree is compared with a species tree (or possibly some other reference tree made up of different genes) and the question is posited: Are the two topologies different and is the difference significant?
(Michael Syvanen, "Evolutionary Implications of Horizontal Gene Transfer," Annual Review of Genetics, Vol. 46:339-356 (2012).)

In other words, if two phylogenetic trees aren't congruent, the problem isn't that common descent is wrong, but rather the conflict is simply evidence of HGT. Let me put it another way: most evolutionary biologists do not treat common descent in a scientific fashion where it is capable of being falsified. If the data doesn't fit with common ancestry, they simply take that as evidence for ad hoc fallback explanations like HGT. Syvanen invokes widespread HGT, but he's uncommonly honest about the data and its implications, offering the radical suggestion that "life might indeed have multiple origins."

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