piRNA

Today’s DpSU, by Brian Thomas, is called Newly Found Biochemical Is Essential for Life. With a title like that you could be forgiven for concluding that the élan vital had been discovered. However, the implications of the headline seems to oversell the real discovery more than a little. The angle that Mr Thomas is actually going for is, oddly enough, a variation on the most typical anti-Junk DNA argument.

piRNA is short for “piwi-interacting RNA,” where a piwi is one of a class of regulatory proteins involved in cell division and differentiation. These RNA molecules are slightly longer than miRNA (micro RNA), being made up of a whopping 26-31 nucleotides, they have quite different sequences between species, and, according to Wikipedia, are more complex than miRNA. These kinds of molecule owe their origins to short sections of DNA, which, rather than being transcribed into mRNA (messenger RNA) and then translated into a protein, instead simply preform their function as transcribed RNA strands. piRNA themselves have been known for a few years now – the ‘new’ in the title of Thomas’ article seems to be notably inaccurate. The actual new result is that the inactivation of the “putative RNA helicase MOV10L1 in mouse spermatocytes” prevents the creation of a subgroup of piRNAs which in turn creates further problems down the line, as reported in a recent paper in PLoS Genetics.

To cut to the chase, Thomas seizes on the following:

Mouse sperm cell production stops without piRNAs. The University of Pennsylvania researchers found this out by visualizing the scrambled DNA in such cells. The barrage of mutations occurred after the cells had undergone meiosis—reproductive cell division. The study authors do not yet understand how the presence of piRNAs prevents wanton mutation, only that it does. […] The upshot is that without piRNAs, mice would die in one generation.

Discoveries in the past of miRNAs especially have been used by creationists to argue against the concept of Junk DNA. The arguement runs that non-coding DNA (DNA that does not code directly for a protein) has long been dismissed as ‘junk,’ here’s an example of non-coding DNA that preforms a function, therefore Junk DNA is functional (and not junk). Of course, this falls down due to the fact that ‘non-coding DNA’ is not synonymous with ‘Junk DNA,’ and it has long been accepted that some non-coding DNA has a function and is not junk. However there simply aren’t enough of these little functional segments of DNA being discovered to make it feasible that the entire genome has function. Nevertheless in the days before the ENCODE debacle this arguement was quite common – since then the creationists seem to have convinced themselves that they have defeated Junk DNA, and I haven’t seen it in action very much.

By taking piRNA as evidence that the entire genome must be functional (again, quite the logical leap) Brian manages to come up with an explanation of how the existence or otherwise of non-functional DNA could be even relevant to the issue of evolution vs creationism. This is important because it has been noted from time to time that evolution does not need Junk DNA (or demand that it not exist) and that creationists proclaiming it’s repeated demise as a defeat for evolution are therefore incorrect. Thomas says:

These discoveries present a significant conundrum for evolutionary origins. They demonstrate another vital role for certain “non-coding” DNA—which actually do “code” for piRNAs, though not for protein. Thus, these results reiterate that even DNA sequences that do not code for protein are still vital. How can natural processes generate new DNA code if almost all of that coded genome is required to be fully programmed up-front?

He argues, in effect, that a fully-functional genome would be immutable and would not therefore be able to evolve. I have a number of objections to this. For one, we know that many mutations even to proteins do not have crippling effects – just because a sequence has a function does not mean that it cannot be changed. In addition, we know that bacterial genomes, in contrast to our own, really are streamlined and have little room for non-functioning sequence – this did not prevent the gene duplication and divergence discovered in the Lenski experiment. So even if all DNA had a function that would not, as Thomas seems to think, preclude the possibility of evolution. More importantly, however, it does not seem to be the case that all DNA is functional – even despite the ENCODE results – so the point is moot.

The other claim that Thomas makes is that the system is irreducibly complex:

The biochemical evidence perfectly fits the idea that the entire apparatus for building a new generation of creature from raw ingredients was expertly designed in mice as well as every other creature. It makes sense to think that a Creator tailored all the right biochemical pieces in just the right patterns. After all, every required piece of this apparatus had to have been properly arranged all at once, even as they are in living mice.

The evidence we have is not sufficient to draw this conclusion. Yes, mice today need piRNAs to reproduce – but did their distant ancestors? His explanation may “make sense” to Thomas, but that doesn’t mean it’s true.

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