Unitary Pseudogenes and the RTB Model

I recall that in his 11/6/10 critique of the RTB Creation Model, Dennis Venema made a then valid observation that “Unitary pseudogenes remain highly problematic for RTB, and becoming vague on this point does not overcome the difficulty they pose for the RTB model.”

I’m wondering if this critique still stands, or perhaps needs to be revised, in light of this 5/8/19 observation by Fazale Rana concerning unitary pseudogenes’ functionality:

“Creationists and intelligent design proponents had little to offer by way of evidence for the intentional design of genomes. But all this changed with the discovery that virtually every class of junk DNA has function, including all three types of pseudogenes (processed, duplicated, and unitary).
If junk DNA is functional, then the sequences previously thought to show common descent could be understood as shared designs . The competitive endogenous RNA hypothesis supports this interpretation. This model provides an elegant rationale for the structural similarity between gene-pseudogene pairs and also makes sense of the widespread presence of unitary pseudogenes in genomes.”
https://www.twr360.org/blog/details/2774/pseudogene-discovery-pains-evolutionary-paradigm

Rana’s citations to evidence are quite underwhelming. There are approximately 13,000 pseudogenes in the human genome, and biologists are completely on board with the idea that a meaningful number would have been exapted to new functionality. The figures I have seen bandied about in research papers are on the order of 10%, although I would welcome any corrections from biologists.

So biologists would expect roughly 1300 pseudogenes in the human genome to have some sort of exapted functionality (again, assuming I have read the literature correctly).

Then I look at Rana’s article. One pseudogene, FAAH, was discovered to have a specific function. Also, a Harvard study found “a number of gene-pseudogene pairs in which both must be intact and transcribed for the gene to be expressed properly.” [emphasis mine]

FAAH. “A number.” As long as that number is less than or equal to 1300, nothing has been overturned.

Time to move along.

My $.02,
Chris

EDIT: Corrected number of pseudo-genes in human genome. The correct number is roughly 13,000, not 200,000 as I had previously written.

Another thing is that the functionality of pseudogenes has nothing to do with their very strong evidence for common ancestry. It’s essentially a red herring. For example this quote from @DennisVenema in a separate article:

Part of evolutionary theory is the expectation that occasionally some sequences, after losing their original function, may come under natural selection to be repurposed to another function. The technical term for this process is exaptation , and many examples of it are known. Certainly a long, non-coding RNA gene could arise at this location in the human genome and this sequence could be exapted as a regulatory sequence

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I have a “layman’s proposal” to run by those in the know here, about whether the following analogy is an accurate way to view the pseudo-gene (and whole “junk-dna”) situation.

Engineering thinkers seem prone to black-and-white thinking regarding a tool or a machine-part’s usefulness. If it’s broken or obsolete - get rid of it. If it’s useful - it should be perfectly useful for its intended (designed) purpose. But in contrast to that … perhaps our DNA is like the tools scattered around an old woodworker’s shop.

The woodworker has had a lot of tools through his hands over his long career. He’s sold or lost some of them, but being the miser that he is, he doesn’t throw anything out. So he’s got a lot of stuff around his shop. A curious observer coming in to interview the woodworker might ask him if such-and-such over there in the corner is still useful. The woodworker hems and haws - he won’t say no even though he hasn’t touched it in years. Instead he hedges and says “yeah, I’m thinking I might need that for a project coming up.” The frustrated observer (who wants to help the woodworker clean out his shop) has trouble getting straight yes-or-no answers from him on whether or not they can just get rid of things. Some things are no longer being used for what they were originally for. A heavyish broken gadget is serving as a doorstop. Other gadgets are partially malfunctioning, but still useful with slight modifications, and others yet are being creatively used in other ways than when they were new. He’s got a drill that would work, except that he lost his bit set that goes with it (unitary pseudogene?) So what the would-be helper finally gathers from his woodworking mentor is that “usefulness” is not an on-or-off concept, but a very elastic one instead. The woodworker can remember the past usefulness of every dusty back-shelf item even though the likelihood of it being used the same way again is nearly nil.

Does that sum up the junk DNA situation?

It certainly describes my workshop! I usually find a use for that piece of junk I saved for 7 years…the week after I threw it away!

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Seriously, I understand that some are calling DNA segments functional if they are transcribed, but often no useful function has been demonstrated. Is that correct or is that a figment of my imagination?

I’ve only just skimmed Rana’s article, but as far as I can see this is not a unitary pseudogene. It’s a gene and a corresponding pseudogene made from the RNA of the gene in question that was reverse transcribed and inserted into the genome (i.e. a processed pseudogene). It’s well known that processed pseudogenes can come to be regulators of their parent genes.

One of the reasons I called out Rana way back when is because he tends to talk up processed pseudogenes and give the impression that we have similar findings for all pseudogenes. Nope. There was a reason I specifically emphasized unitary pseudogenes, which are unique sequences in a genome that correspond to functional genes in related species. The most well-known examples are the GULO (vitamin C) pseudogene and the vitellogenin pseudogenes in the human genome.

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It seems that he is still making the exact same arguments today (or well last month):
https://www.reasons.org/explore/blogs/the-cells-design/read/the-cells-design/2019/07/17/does-old-earth-creationism-make-god-deceptive

A few comments from me on the article:

  • I would say there’s a false dichotomy that is inherently dangerous to much of Christian writing on this topic. It’s either evolution or design (i.e. God). And thus, the lie is propagated that the two are necessarily mutually exclusive.
  • The ‘but vestigial structures/genes have function’ red herring is all over the article. The reason it is a problem is that it is exactly what is expected with common ancestry. That’s is some ancestral gene is tweaked a little bit and sometimes all we get are deactivated remnants depending on how long ago it was lost, but other times we get a completely new function from existing genetic material. Without saying it, this is a very strong argument for common ancestry!
  • His argument against the deceiver god objection is identical to how YEC’s do it. Here’s a nice example from AiG: https://answersingenesis.org/astronomy/age-of-the-universe/mature-for-her-age/. Basically the deal is to go ahead and list some of the things that you think scientifically cast doubt upon the science that is challenging you. In AiG’s case it is attack the assumptions, radiometric dating something or rather and then the other things they think challenges an old earth. For Rana it is the theory of evolution can’t explain x, y or z therefore he must be right!
  • He claims that his objections to evolution are scientific and not theological. I’d like to believe him but actually don’t.

Also @nicktavani I’ve been going through this paper on unitary pseudogenes and enjoying it so far:

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Rana is a very intelligent person, and he has been shown the evidence many times. I believe he understands it and where the weight of the evidence lies.

It’s also very interesting to me how Rana starts the article with a quote from one of RTB’s former followers who has abandoned the RTB camp exactly over this issue. I’ve often thought that OEC is an “endangered species” if you will - their adherents (a) are open to scientific evidence, since they accept the age of the earth, and (b) the evidence for common ancestry is just as compelling as that for an old earth. I doubt that OEC is gaining many new adherents. I suspect it’s just the old guard who hang on. Young people who are open to science are not very likely to accept the evidence for the age of the earth and then suddenly shift into denial mode for the evidence for evolution.

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