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Adam and the Genome and “Nonfunctional” Pseudogenes

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In Adam and the Genome, which we’ve been considering in this series, theistic evolutionist biologist Dennis Venema argues that another piece of evidence that common design cannot explain is the presence of shared pseudogenes in humans and other organisms, such as apes. At first glance, it seems he may have a point: While common design easily explains functional similarities, non-functional similarities are probably best explained by blind mechanistic processes like mutation.

Pseudogenes are relevant to the question of human/ape common ancestry, but if you define Adam and Eve as an initial couple who were historical people and the progenitors of the entire human race, then you can potentially accept common ancestry yet believe in a traditional Adam and Eve. As such, pseudogenes are not, strictly speaking, relevant to Adam and Eve as the parents of humanity.

Obviously, some believers in the Bible who hold to a traditional, historical Adam and Eve reject common ancestry. But it is possible to accept a historical first couple as the progenitors of humanity, yet also believe in common ancestry. Some scientists associated with BioLogos have promoted this idea, with Adam and Eve as members of a large population of humans that collectively were ancestral to humans. Under this view, they are not the sole progenitors of humanity, but they are progenitors of all living humans, along with others. David Klinghoffer discussed this view here. He notes that it holds to an historical Adam, “but not in the sense that most Christians (and Jews and others who read the Bible) understand — a first couple as the sole progenitors of the human race.” In this sense, pseudogenes are not necessarily relevant to whether Adam and Eve existed.

Having said that, shared pseudogenes would be best explained by common ancestry if (a) pseudogenes are truly non-functional and (b) other explanations like hotspot mutations can never explain these shared similarities.

Venema claims pseudogenes are “nonfunctional.” (p. 34) The problem with his argument from pseudogenes is that there is now good evidence that pseudogenes can have function. Pseudogenes can produce functional proteins, functional RNA transcripts, and even have function if they don’t produce a transcript. The following papers have reported functions for pseudogenes:

  • Zheng and M. B. Gerstein, “The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they?,” Trends in Genetics 23 (May, 2007): 219-224
  • Hirotsune et al., “An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene,” Nature 423 (May 1, 2003): 91-96
  • H. Tam et al., “Pseudogene-derived small interfering RNAs regulate gene expression,” Nature 453 (May 22, 2008): 534-8
  • Pain et al., “Multiple Retropseudogenes from Pluripotent Cell-specific Gene Expression Indicates a Potential Signature for Novel Gene Identification,” Journal of Biological Chemistry 280 (February 25, 2005):6265-6268
  • Zhang et al., “NANOGP8 is a retrogene expressed in cancers,” FEBS Journal 273 (2006): 1723-1730

Indeed, the ENCODE project reported over 850 human pseudogenes that are “transcribed and associated with active chromatin.”

Of course, there are many supposed “pseudogenes” in primate genomes for which we have not yet identified any function. Venema identifies seven other pseudogenes pertaining to olfactory receptors that he claims are “nonfunctional.” And there are many others. The problem for Venema’s argument is that researchers who study pseudogenes caution against assuming that pseudogenes are non-functional, since we’re only starting to understand them.

A 2012 paper in Science Signaling noted that although “pseudogenes have long been dismissed as junk DNA,” recent advances have established that “the DNA of a pseudogene, the RNA transcribed from a pseudogene, or the protein translated from a pseudogene can have multiple, diverse functions and that these functions can affect not only their parental genes but also unrelated genes.” The paper concludes that “pseudogenes have emerged as a previously unappreciated class of sophisticated modulators of gene expression.” (Laura Poliseno, “Pseudogenes: Newly Discovered Players in Human Cancer,” Science Signaling 5 (242) (September 18, 2012).)

A 2011 paper in the journal RNA concurs:

Pseudogenes have long been labeled as ‘junk’ DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins.

(R. C. Pink et al., “Pseudogenes: Pseudo-functional or key regulators in health and disease?” RNA 17 (2011): 792-798)

Because a pseudogene may only function in specific tissues and/or only during particular stages of development, their true functions may be difficult to detect. But a 2012 paper in RNA Biology notes that “pseudogenes were long considered as junk genomic DNA” but “pseudogene regulation is widespread in eukaryotes.” As the paper concludes, “the study of functional pseudogenes is just at the beginning” and predicts “more and more functional pseudogenes will be discovered as novel biological technologies are developed in the future.” (Wen et al., “Pseudogenes are not pseudo anymore,” RNA Biology, Vol. 9 (January, 2012): 27-32.)

Importantly, when we do carefully study pseudogenes, we often find function. One paper in Annual Review of Genetics observed: “pseudogenes that have been suitably investigated often exhibit functional roles.” (Balakirev and Ayala, “Pseudogenes: are they ‘junk’ or functional DNA?,” Annual Review of Genetics, Vol. 37:123-51 (2003).)

Venema assumes that the pseudogenes he’s examining are non-functional. But there are good reasons to question this assumption. It is possible that in the future many more functions will be discovered.

As one famous example, during the 2005 Kitzmiller v. Dover trial, Kenneth Miller testified that the human beta-globin pseudogene is “broken” because “it has a series of molecular errors that render the gene non-functional.” Since humans, chimpanzees, and gorillas share “matching mistakes” in the pseudogene, he testified, this “leads us to just one conclusion … that these three species share a common ancestor.” However, a 2013 study in Genome Biology and Evolution found that the beta-globin pseudogene is functional due to its “conserved” sequence which suggests a selectable function, making it less tolerant of mutations. For details, see:

As another example, Venema cites the vitellogenin pseudogene as supposedly demonstrating common ancestry between humans and birds, such as the chicken. Chickens have three vitellogenin genes which help produce egg yolk. Humans obviously don’t lay eggs so presumably we don’t need genes to produce egg yolk. However, Venema claims that humans have remnants of three non-functional pseudogenes of vitellogenin (VIT1, VIT2, and VIG3) which we inherited from an egg-laying reptilian common ancestor that we share with chickens.

This is not a case where humans have a clear-cut complete (or even semi-complete) non-functional pseudogene clearly matching a functional gene in some related species. Rather, by Venema’s own admission, we have what he calls “pseudogene fragments.” And by “fragments” we’re not talking about large DNA stretches that clearly match large portions of long-lost vitellogenin genes still retained in our chicken cousins. Rather, he notes these are, at best, “very small” and “tiny fragments of sequence.” (p. 39) And importantly, we’ll see below, Ann Gauger reviewed these aligned sequences and found that they are so small that they are “on the borderline of what is detectable as a match,” concluding that “the match is weak.”

Nonetheless, Venema is impressed because “these small fragments are in the correct order and line up with the chicken region.” (p. 40) He argues that this “abundant” evidence for evolution means that people only reject common ancestry “because of prior religious commitments, not for scientific reasons.” (p. 40) But is the scientific evidence so unambiguously clear? Well, let’s examine his citation for these claims.

Venema’s citation for all of his discussion about vitellogenin pseudogenes in humans is a paper by Brawand et al. 2008. Ann Gauger reviewed this paper here and here and found:

This argument was based on the available evidence from the original paper by Brawand et al., mentioned above, that reported the original alignments of the syntenic vitellogenin regions of chick, opossum, and human. (Synteny refers to the alignment of DNA, typically between species, in the same order and with identifiable sequence identity.) That paper reported that there was a vitellogenin gene remnant in human DNA in the region where it should be. Unfortunately they published very little data as the basis for their claim, and I didn’t think it substantiated that claim.

So Venema’s citation of Brawand et al. 2008 does not substantiate his claims that these pseudogenes are present in humans. Gauger later did a more thorough analysis than Brawand et al. did. She found that there is indeed “more similarity between chickens and humans than the Brawand paper reported.” However, she finds:

[D]espite the increased alignment, this is on the borderline of what is detectable as a match. The fact that things vary from alignment to alignment indicates the match is weak. If there ever was a human vitellogenin gene, there’s almost nothing left of the original gene. Swamidass [a theistic evolutionist biologist] tells me that given the long time that has passed since our last common ancestor with chickens, this is to be expected. Yes, I know. But there is an alternate explanation — the possibility that a vitellogenin gene was never there to begin with.

Even after considering the increased alignment, Gauger notes that she wrote her original post “to critique Venema’s claim of strong evidence for a human vitellogenin pseudogene” and “That critique still stands. His illustration greatly overestimates the degree of similarity.” Venema relies upon the same citations in Adam and the Genome that he did in the article critiqued by Ann Gauger. Her critique also stands against his arguments in his book. The evidence in the paper he cites is very weak.

Lastly, Venema claims that common descent is demonstrated because the patterns of these pseudogenes fit a “nested hierarchy” which is consistent with the standard phylogeny for humans and great apes (chimps, gorillas, and orangutans). That may be true — in this particular case. However, there is much genetic data that does not fit the standard phylogeny for higher primates which Venema isn’t talking about.

For example, a 2007 study scrutinized our genomic similarities with chimpanzees and other primates and found that huge portions of our genome don’t fit in the standard “nested hierarchy” of human-ape relationships:

For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place.

(Ingo Ebersberger, Petra Galgoczy, Stefan Taudien, Simone Taenzer, Matthias Platzer, and Arndt von Haeseler, “Mapping Human Genetic Ancestry,” Molecular Biology and Evolution, 24(10):2266-2276 (2007))

For details, see here. Then, in 2012 when the gorilla genome was sequenced, it was discovered that 30 percent of the gorilla genome contradicts the supposed evolutionary phylogeny of humans and apes. As one of the researchers put it, “We can’t just conform to a simple tree on a gene-by-gene basis.”

So, there is plenty of our genome — huge portions in fact — that don’t fit the standard phylogeny. It’s not always the case that “identical mutations … are present before these two lineages separate” (p. 36), as Venema puts it. Sometimes the genetic data contradict the expected pattern of a “nested hierarchy.” So big is this problem that a whopping 23 percent of our genome does not place humans as most closely related to chimpanzees, contradicting the standard evolutionary tree.

In sum, it seems that genetic data fit the standard human-ape phylogeny, except when it doesn’t. As always, evolutionary biologists have their after-the-fact explanations (here, incomplete lineage sorting). The point is that huge amounts of genome data differ strikingly from Venema’s example of some pseudogenes that do fit the standard phylogeny. If the fact that a few pseudogenes fit the standard phylogeny somehow provides evidence for common ancestry, doesn’t the fact that over 20 percent of our genome does not fit the standard phylogeny provide evidence against common ancestry?

Photo credit: pexels, via Pixabay.