What Happens When a Creationist Argument Is Refuted?

A few days ago, Jonathan McLatchie published an article on evolution News & Views (sic) where he claimed that humans embryos synthesize the enzyme that makes vitamin C [A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene]. This is important for creationists because the gene for that enzyme is a classic pseudogene—a formerly active gene that has lost it's function.

Intelligent Design Creationists don't like pseudogenes because they are junk and their intelligent designer would not fill up the human genome with junk. Hence, pseudogenes must have some function that has yet to be discovered.

Unfortunately for Jonathan McLatchie, his argument was ridiculous. He proposed that RNA editing could resurrect the GULOP pseudogene during embryogenesis. What he failed to notice was that the pseudogene is not transcribed and, furthermore, it is missing seven exons. It's very difficult for RNA editing to recreate seven exons in a nonexistent transcript [see How IDiots Would Activate the GULOP Pseudogene].

To his credit, McLatchie realized that he was wrong and he posted an update that linked to a revised post. Let's look at this mea culpa to see how creationists respond to criticism [Unitary Pseudogenes and RNA Editing].

In a previous article, I argued that pseudogenes could be rendered functional by post-transcriptional RNA editing. I used the specific example of the vitamin C GULO gene and suggested the possibility that the human GULO pseudogene may be functional in utero but subsequently turned off. Such a hypothesis requires that GULO produce an mRNA transcript. I had consulted the Ensembl Genome Database regarding the GULO pseudogene in humans, and that database reported that it produces a transcript but no known protein product.

Upon further investigation, however, I've discovered that the Ensembl database appears to be inaccurate on that point, and it's not confirmed that the GULO pseudogene produces a transcript (indeed, clicking on "Supporting evidence," one finds that there is "No Transcript supporting evidence for this transcript"). Part of the reason for this is that the GULO pseudogene lacks a canonical promoter. However, that doesn't necessarily mean this pseudogene produces no RNA transcript. Many metazoan loci possess non-canonical promoters that, moreover, can be millions of base pairs upstream of annotated exons (e.g., see Manak et al., 2006). A further complication with the proposed hypothesis is that some exons are absent from the GULO pseudogene, and it's not entirely clear to me how they could be created by RNA editing. While my original hypothesis is probably incorrect with respect to this particular pseudogene, it remains possible that the human GULO pseudogene yields RNAs that perform some other function in the cell.

That's not bad as far as confessions go but it does raise some questions. If Jonathan McLatchie really was interested in pseudogenes then why didn't he do the appropriate research BEFORE publishing his original post? He might have found my original 2007 post on the subject, complete with references to the scientific literature [Human GULOP Pseudogene] or he could have found the scientific papers directly by searching PubMed.

Maybe he doesn't trust scientists? In that case, he could have read the Appendix to Jonathan Wells' book The Myth of Junk DAN. The papers giving the correct structure of the pseduogenes are all referenced in that creationist book.

The important point here is that the GULOP pseudogene really is a pseudogene and no amount of special pleading is going to resurrect it. It's very unlikely that human embryos can synthesize the enzyme L-glucono-γ-lactone oxidase in spite of the "evidence" that McLatchie presented in his original post. (He doesn't mention that in his mea culpa post.)

That means that creationist really do have to come to grips with the idea that our genome contains dead, inactive, genes that used to be functional in our ancestors. And the fact that our closest relatives, the chimpanzees, contain a similar GULOP pseudogene cries out for an explanation. So far, Intelligent Design Creationism, has not produced an explanation. It made a prediction: namely that pseudogenes are actually functional, but that prediction has not borne fruit.

So, in the face of an argument that has been soundly refuted, what is an IDiot supposed to do? Here's how Jonathan McLatchie responds ....

Moreover, there's a much more important point to take note of, which I hope is not lost in this discussion -- namely that my original hypothesis could be more generally applicable. What I proposed might be happening in the GULO pseudogene could very well be happening in other unitary pseudogenes. Unitary pseudogenes are genes that have been disabled by mutations such as frame shift mutations, deletions, or point mutations resulting in premature stop codons.

Yes, it's a remote possibility that a gene could become a pseudogene by acquiring mutations that affect the coding region but not transcription. As long as the pseudogene is transcribed and no coding region is deleted, it is possible that a specific RNA editing system could evolve that would make the gene capable of producing a functional protein.

Of course if there was strong selective pressure to reactivate the gene there are probably easier ways to accomplish that goal. Furthermore, it probably wouldn't have been inactivated in the first place.

This is a classic example of special pleading. There's no scientific reason whatsoever to imagine that pseudogenes could be reactivated by RNA editing. It's all speculation motivated by a desire to avoid the obvious conclusion: pseudogenes are dead gene.

McLatchie failed utterly to give us a plausible example when he discussed the GULOP pseudogene and his hand-waving references to RNA editing are useless unless he can point to another specific example. But that's what counts as legitimate argument on the creationist blogs. All they need to do is raise doubts about evolution and it doesn't really matter if their arguments make sense. McLatchie's error was to pick a specific example that could be easily refuted. Most creationists don't make that mistake. I think Jonathan McLatchie has learned the lesson. We probably won't see much science from him in the future.

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[Photo Credit: The photo is from the Apologetics 315 website. Follow the link to hear the interview with McLatchie.]