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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 do not show a "direct correlation with common descent," but rather tell directly conflicting stories about supposed phylogenetic history. Here's a recreation of Table 2 from the paper:

Eukaryotic genes and their closest prokaryotic relative.

Closest eukaryotic relativePercent of total
Cyanobacteria15.3
Alphaproteobacteria8.5
Gammaproteobacteria6.3
Betaproteobacteria2.3
Probable proteobacteria8.4
Other bacteria12.8
Archae9.6
No prokaryotic homolog36.6

(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 homologue-lacking 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."

Regardless, one thing is clear: this data does not show that "Universal biochemical organization and molecular variance patterns in all organisms also show a direct correlation with common descent." If there was such a "direct correlation with common descent," then they wouldn't be resorting to invoking HGT.

Second, let's now look within eukaryotes. Can biochemical similarities between plants and animals be explained by common ancestry? It turns out that they have a highly similar biochemical organization of their respective innate immune systems, but their common ancestor didn't have an innate immune system. Common descent cannot explain these "unexpectedly similar" systems. Consider these striking comments from a paper in Nature Immunology:

  • "Although it seems to be generally accepted that the innate immune responses of plants and animals share at least some common evolutionary origins, examination of the available data fails to support that conclusion, despite similarities in the overall 'logic' of the innate immune response in diverse multicellular eukaryotes."
  • "Although the underlying logic of multicellular development in plants and animals is unexpectedly similar, it seems that multicellularity evolved independently in plants and animals and that the basic molecular mechanisms specifying pattern formation were independently derived."
  • "Although adaptive immunity is unique to vertebrates, the innate immune response seems to have ancient origins. Common features of innate immunity in vertebrates, invertebrate animals and plants include defined receptors for microbe-associated molecules, conserved mitogen-associated protein kinase signaling cascades and the production of antimicrobial peptides. It is commonly reported that these similarities in innate immunity represent a process of divergent evolution from an ancient unicellular eukaryote that pre-dated the divergence of the plant and animal kingdoms. However, at present, data suggest that the seemingly analogous regulatory modules used in plant and animal innate immunity are a consequence of convergent evolution and reflect inherent constraints on how an innate immune system can be constructed."
  • (Frederick M Ausubel, "Are innate immune signaling pathways in plants and animals conserved?," Nature Immunology, Vol. 6 (10): 973-979 (October, 2005) (internal citations omitted).)

The biochemical organization of the innate immune systems of plants and animals is strikingly similar -- but this is a direct non-correlation with common descent. Under their evolutionary thinking, these are forced to call the systems "unexpectedly similar," postulating that the similarities were "independently derived." This type of data is neither anticipated nor explained by Darwinian evolution and common descent. It is anticipated and explained by common design.

Somehow, something tells me not to expect any corrections over at Wikipedia.