How do Intelligent Design Creationists deal with pseudogenes and false claims?

Some of the people who comment here have pointed out that this is the second anniversary of a post by Jonathan McLatchie on Evolution News & Views (sic): A Simple Proposed Model For Function of the Human Vitamin C GULO Pseudogene.

That post is significant for several reasons. Let's review a bit of background.

Intelligent Design Creationists have a problem with pseudogenes. Recall that pseudogenes are stretches of DNA that resemble a gene but they appear to be non-functional because they have acquired disruptive mutations, or because they were never functional to begin with (e.g. processed pseudogenes). All genomes contain pseudogenes. The human genome has more than 15,000 recognizable pseudogenes.¹ This is not what you would expect from an intelligent designer so the ID crowd tries to rationalize the existence of pseudogenes by proposing that they have an unknown function.

Jonathan Wells devoted a chapter and an appendix to pseudogenes in his book The Myth of Junk DNA. The chapter title was: Pseduogenes—Not so Pseudo After All. I reviewed that section and showed that the argument for the fucntion of pseudogenes was nonsensical [Junk & Jonathan: Part 8—Chapter 5].² McLatchie revived the argument by proposing the the GULOP (GULO) pseudogene could, in fact, be active.

For a description of this pseudogene see: Human GULOP Pseudogene. It's the remnant of a gene that used to encode the enzyme L-glucono-γ-lactone oxidase, one of the key enzymes in the pathway to vitamin C. Unlike most mammals, humans and other primates are unable to synthesize vitamin C on their own and have to acquire if from food.³ Here's a diagram showing the gene fragment in the human genome compared to the intact gene in the rat genome.


Note that the fragment in our genome lacks a promoter and seven of the 12 exons in the intact gene.

McLathie proposed that the human GULOP sequence could produce a functional enzyme through editing of the RNA transcript. It was part of a general argument that pseudogenes could be functional because stop codons and small deletions in the DNA sequence could be altered post-transcriptionally by RNA editing.

Here's the important part. I criticized McLathie's argument by pointing out the obvious: (1) the human DNA sequence isn't transcribed, (2) the pseudogene is missing seven exons making it somewhat difficult to recreate a functional mRNA by RNA editing [How IDiots Would Activate the GULOP Pseudogene]. McLatchie responded by admitting that he was wrong: Unitary Pseudogenes and RNA Editing.

That was pretty amazing. You will note that the original post now has an update⁴ at the top of the post stating ...

Update: Please see the article available at this link for an important correction and revision to the argument entertained here.

Not unexpectedly, the mea culpa was accompanied by a good deal of rationalization explaining why he (McLatchie) had made a honest mistake.⁵ Not only that, the RNA editing argument still could apply to lots of other pseudogenes even though it doesn't work for GULOP [see: What Happens When a Creationist Argument Is Refuted?].

The most important lesson in this little episode is that some Intelligent Design Creationists are serious about debating their ideas and they will respond to scientific criticism. That's encouraging. It's why I think we should continue to refute and debate the scientific claims of Intelligent Design Creationists even though most of the time it seems pointless.

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1. Pseudogenes evolve over time by random genetic drift and fixation of neutral mutations. After about 100 million years, they can no longer be recognized as pseudogenes because their sequences are indistinguishable from other forms of junk DNA.

2. Shocking, isn't it?

3. That's why we get scurvy.

4. It's a bit disingenuous to link to an "update" instead of stating clearly that the original post is completely wrong.

5. It was the fault of the Ensembl Genome Database for not making it clear that the DNA sequence wasn't transcribed and for presumably not making it clear that seven exons were missing. McLatchie also "forgot" to mention that he learned of his error by reading my blog post. We knows that's the case because he commented on my post and admitted he was wrong.