An Exaptated Pseudogene

Appropriately, for this attempt to return to timely updates, the first new DpSU – Pseudogene Plays Important Role in Cell Cycle, by Jeffrey Tomkins – is again related to junk DNA, just as the last one I did was about ENCODE. This article, however, is of the old type – it’s about a genetic feature, once “dismissed as junk DNA,” that has now been shown to have a function. Or, to quote Tomkins:

Once again, DNA sequence that was once thought to be nothing but a genomic fossil has shown itself to be vital to human survival. In this case, if the so-called pseudogene is not functioning properly, cell cycle dysfunction and cancer is the almost certain outcome.

A pseudogene looks like a gene – often another gene in the same organism – but has lost its original protein-coding function. The pseudogene of interest here is called “ψPPM1K,” and is a processed pseudogene. To make such a gene a normal gene (here, PPM1K) is transcribed into mRNA and the introns are stripped out as normal in the process of protein synthesis. However, instead of progressing further the mRNA is transcribed back into DNA which is inserted back into the chromosome. The result is a partial clone of the original gene, generally lacking introns and possibly other parts. The paper Tomkins is talking about (open access) says:

PPM1K (NM_152542.3), located on chromosome 4q22.1, produces a 3725-nt mRNA encoding a mitochondrial matrix serine/threonine protein phosphatase shown to regulate the membrane permeability transition pore (MPTP) essential for cell survival and organ development (59). Pseudogene PPM1K (ψPPM1K) (Supplementary File S1), 474 bp in length, is partially retrotranscribed from PPM1K and is also located on chromosome 4 (Figure 2a). Transcription of ψPPM1K is supported by mRNA and EST evidence (Supplementary Figure S2), and bases 155–456 of the ψPPM1K transcript show >79% similarity to the antisense-strand of PPM1K (Figure 2b). Multiple alignments of the 5′- and 3′-ends of ψPPM1K DNA sequences in 44 vertebrate species revealed a high degree of conservation among rhesus, mouse, dog and elephant. The ψPPM1K sequence also contains SINE and Alu repeat elements (Supplementary Figure S2).

(Emphasis added) The sequence of this pseudogene is highly conserved, meaning that natural selection is likely acting to preserve it, so it’s not surprising that some degree of function would be found. According to Tomkins:

This amazing pseudogene is actively transcribed and found to produce an RNA product that can be further processed into two different smaller RNA molecules—which in turn form elaborate secondary structures. These regulatory RNA molecules were shown to target and control many different cellular genes. Most importantly, they control a number of key genes involved in regulating the cell’s cycle and cell growth in the body.

This pseudogene could therefore be said to be exaptated: it has been evolutionarily co-opted to a new function. There’s nothing impossible about that – gene duplication produces new genes that can evolve new functions, so too can partially duplicated genes produce “pseudogenes” that have new and entirely different functions. This does show that this pseudogene is not entirely nonfunctional, but it doesn’t make this true:

Once more, the errant predictions of the evolutionary paradigm have been destroyed by the advance of scientific discovery. The PPM1K pseudogene is not a defunct genomic fossil produced by random evolutionary processes, but rather a key feature designed by the Creator to keep our cells in check. If this so-called pseudogene malfunctions, serious health consequences—some even fatal—are the result.

Tomkins concludes:

Clearly, humans should be looking at the genome from the perspective of pervasive functionality and incredible bioengineering—the product of an Omnipotent and Wise Creator.

As I’ve been reading over old DpSUs I’ve seen a lot of use of the word “clearly.” These things rarely are – it makes for a good red flag when it comes to looking for utterly unsupported claims.

There are two other points in this article worth mentioning. First, Tomkins talks about another psuedogene, related to beta-globin. This is an allusion to an article Tomkins published a couple of weeks ago, which should appear in the catch-up series around the end of the week (though I do have to write it first).

The second is a mention of “orphaned” retrogenes:

Despite the still prevalent myth that processed pseudogenes are largely non-functional genomic fossils, scientists have been identifying important functions for these retrogenes in mammals since 1985. This little known scientific truth includes the prevalence of functionally active “orphan” (unitary) retrogenes that have no discernible parent gene from which they supposedly originated and they are also often species specific—utterly defying the macro-evolutionary presuppositions of common descent surrounding their presence.

This latter claim is cited to a paper in Molecular Biology and Evolution from earlier in the year, called ““Orphan” Retrogenes in the Human Genome” (also open access). An orphan retrogene is like a processed pseudogene, but the new gene entirely replaces the original.

That paper is quite interesting, because it mentions quantitative numbers on how many of the genes in the human genome that have arisen in these kinds of ways are actually functional. It may be true that “scientists have been identifying important functions for these retrogenes in mammals since 1985” but it seems that much less than 10% are actually transcribed, which would make it rather difficult for the remainder to be functional as Tomkins claims.

Tomkins’ description of orphaned retrogenes is in fact quite misleading. The 25 genes found by this paper were previously considered perfectly normal genes, with a well-studied function and all the rest of it. The findings can be described as the discovery – via comparisons with the same genes in different animals – that those genes are actually impostors: retrogenes that have replaced their parent gene, thus escaping prior categorisation as such. This is completely opposite from a situation where function has been found for a known pseudogene, and in no way does it “defy” common-descent.

If it’s not clear, this isn’t a catch-up post. The first of those (about fossil bird eggs) is due in a little less than nine hours, and more will follow every 24 hours after that. Don’t forget to check back!

One thought on “An Exaptated Pseudogene

  1. “Despite the still prevalent myth that processed pseudogenes are largely non-functional genomic fossils, scientists have been identifying important functions for these retrogenes in mammals since 1985.”

    Those would of course be *creationist* scientists doing the work, right? Because we know that all “evolutionists” are just people like Richard Dawkins, not those actively engaged in the lab work.


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