The problem with your analysis, IzzyR, is that “pseudogenes serve no purpose” isn’t an assumption. It’s a theory.
- The vestigial organs argument is typically said to go like this: vestigial organs serve no purpose. God wouldn’t make something that serves no purpose. Ergo, vestigial organs prove creationism wrong.
Formulated in that fashion, it’s an example of the fallacy of argument from ignorance. It basically says, “We can’t find a use for this, so it must have no use.” But you can’t really say for sure whether it’s the case that you just haven’t found a use yet, and that a use might be found in the future.
BTW, I’m not sure that that formulation of the vestigial organs argument isn’t a creationist strawman. A much better version of the argument goes like this:
Here’s an organ which looks like something else, but has been jerry-rigged to serve a different purpose. Since God could make any organ from scratch to perfectly serve its purpose, this jerry-rigging proves evolution.
It’s what I call the “Isn’t it funny?” argument. Evolutionists point out that whales have vestigial legs. Creationists declare that those legs aren’t “vestigial”- they serve a purpose! They are support structures for the whales’ genitals. Isn’t that funny? The perfect genital-supporting structure just happens to look like a shirvelled-up leg, not an arm, not a wing, not a skull, but exactly what evolution would have jerry-rigged into service.
By contrast with the classical vestigial organs argument (i.e., it serves no purpose, therefore creationism is wrong) we have the pseudogenes argument:
- Here is some data. Here is an evolutionist explanation for that data, which makes testable predictions, and those predictions are borne out by further experiment. Creationists cannot explain that data at all. Therefore, evolution is right and creationism is wrong.
Yes, the evolutionist explanation happens to involve pseudogenes serving no function, but there’s a world of difference between argument #1 and argument #2.
In argument #2, we just don’t say, “See? look- we can’t find any function. Creationism is wrong.” We say this:
here we have some things that look like extra copies of regular genes.
They have all the earmarks of normal gene-copying processes, such as (in the case of processed pseudogenes) the marks left by splicing RNA back into the genome.
Ok, my hypothesis at this point is that these genes were produced by normal copying processes, instead if by creation ex nihilo. How can we test this? For one thing, there’s the question of the arrangement of genes in the hemoglobin cluster, which I discuss in the FAQ. Also, so far as I know, retroposition of RNA has been seen in vitro, and it’s definitely been seen in a clinical setting. So clearly we have good reason to think that pseudogenes arose by natural processes.
We also find:
- They have mutations which would prevent them from being turned into full-length proteins.
From which we expand our hypothesis: these must be extra gene copies which got switched off by those mutations. Therefore, they don’t serve a coding function.
How can we test this? If it’s right, then the mutation rate should be higher for pseudogenes that for regular genes, and should be comparable to the mutation rate for introns and other noncoding regions. And, as a matter of fact, it is. (For that matter, the mere existence of consistent mutation rates proves common descent, because the rates are measured across different ‘kinds’ with reference to the fossil record.)
And, since we don’t know of any function pseudogenes could possibly serve, we can conclude that they serve no function.
Now, your news story reports that someone has found that one class of junk DNA serves a purpose. So? What does that have to with pseudogenes? If that class of junk DNA has a mutation rate that is comparable to that of pseudogenes, then it says something about the constraints on noncoding regions, and we’d have to posit that pseudogenes might serve a noncoding function which was subject to very loose evolutionary constraints. But that’s just a minor modification to what we’ve said thus far: pseudogenes are copies of normal genes, produced through naturalistic physical processes, which have had their coding function destroyed by mutations, and which therefore accumulate mutations more quickly than real genes, in a pattern consistent with the fossil record. And, BTW, creationists still can’t provide an explanation for pseudogenes.