Pseudohelpful Pseudogenes

Pseudo-words abound in this latest Daily (pseudo)Science Update from the ICR. Indeed, it goes beyond the usual pseudoScience element – this is a pseudoUpdate as well. Far from his usual two-week-old news, Brian Thomas is reporting in his latest post – RNA Discoveries Refute Key Evolutionary Argument – on a “recent” study from way back in March.

Have you ever heard of ‘pseudogenes?’ They are the useless copies of genes I obliquely mentioned in my butterfly mimicry post last week. “Uselessness,” you understand, is relative. It seems some of them have functions. Hell, we already knew that – if nothing else, they serve to soak up mutations and turn into useful proteins even via the “non-functional stages” that creationists keep telling us are impossible. Nevertheless, Mr Thomas is trying to spin it that evolution is all wrong because of newer, marginally more important uses more recently found. Indeed:

Pseudogenes, or “false genes,” were initially thought to be mutated and useless genetic “junk” since they don’t code for proteins. When they were first discovered, evolutionists claimed they were leftovers of Darwinian evolution. But ongoing studies clearly show that the evolutionary interpretation was premature and even misleading.

In the circumstances, I don’t see how the idea that these pseudogenes can have a function and, as such, can be selected upon, is any less “evolutionary” than the former – that they are slightly less useless than we now think, have little or no ability to be selected upon and are only there because there has been no pressure to get rid of formaly or never useful gene sequences.

In a study published in the technical journal RNA, Oxford Brookes University biologists reviewed some of the newly discovered functions for pseudogenes. They wrote, “In some cases, what appears to be a nontranslated pseudogene can, in fact, code for truncated proteins.” Also, “evidence that some pseudogenes can exert regulatory effects on their protein coding cousins is mounting.”

You’ll note that the March study – Pseudogenes: Pseudo-functional or key regulators in health and disease? – is using more non-committal language than Brian Thomas is. Basically, some, not all such genes have been seen to do things, but certianly some do. Here’s some more from the abstract:

[S]ome pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys…[W]e describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.

Things aren’t as simple as we thought, is basically. That’s Science for you. Much of this “function” that they have found seems to relate to the ability of some of the genes to sort of work – but not quite – and get in the way of other genes that are doing their jobs properly. That’s “regulation” in the gene world, apparently (and I though the Internet was crazy..). Not entirely unbelievable, nor new – the wikipedia article has a section on the potential functional nature of pseudogenes, and it’s clear that this study isn’t particularly important on it’s own.

So what is the point? Why exactly are the creationists talking about this? And why is it that the time between this DpSU being posted and the publication of this study is five months and twelve days, pretty much exactly 5 months more than usual?

I can’t answer the last one – really, I can’t (must’ve been God then, eh?) – but the point of the rant can be determined (I think) via ‘multiple lines of reasoning’ that point towards the same idea. Creationists – and cdesign proponentsists (can’t leave them out)* – perceive that a “key evolutionary argument” has been demolished.

The argument that they perceive to be destroyed is that pseudogenes are entirely useless, and represent copied forms of other genes, somewhat mutated. The problem here is twofold:

  1. Even if they do have a use, so what? The uses found do not really knock anything out of the situation except the uselessness. Indeed they raise further questions. Why is the regulation of genes in this way so complicated? From a design point of view, that is – I can’t see any problem with this evolutionarily at all. We know that genes get copied and are largely useless when this happens – maybe there is a higher rate of survival among copied genes that still do something, however little that something is. Perhaps sections of code that don’t get much use are more likely to mysteriously “disappear”. Who knows… But why would a designer do this?
  2. Secondly, why does it matter? The whole ‘Junk DNA’ thing is a bit of a meme** in the creationist community, especially among the more highly evolved lot at the Discovery Institute. Here’s Prof Larry Moran of Sandwalk on the subject:

    The IDiots have a bit of a problem. In order to make [Jonathan Wells’s The Myth of Junk DNA] look important they have to first establish that the concept of abundant junk DNA in our genome was a “pillar” of support for evolution. That’s hard to do when their understanding of evolution is so flawed that they don’t see the difference between “Darwinism” and evolution by random genetic drift.
    Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. They been told this but they keep repeating their error. There’s a word for that kind of behavior.
    It’s easy to see how they got confused. It’s because they’re IDiots. It’s partly because they don’t understand that an argument for inheritance of a few pseudogenes is not the same as an argument that more than 50% of our genome is junk. There are plenty of scientists who will use the pseudogene argument to challenge Intelligent Design Creationism but who don’t believe that MOST of our genome is junk.

    The creationists are attacking an argument that for the most part does not exist in the way that they paint it to be. Yes we say that there are (some) useless genes, but that is an argument against creationism, not for evolution, and it remains valid even with these small changes.

Brian Thomas is too busy punching at shadows to go beyond the following as the creationist explaination for the situtation:

The evidence indicates that the vast majority of pseudogenes exists because the cell needs them, not because they evolved. The observation that they perform important cellular functions fits well with the creative engineering genius of the God of the Bible.

So it’s genius to take an existing gene and copy it, degrade it with mutations a bit so that it doesn’t work any more, and set it loose to get in the way of everything else, just to lessen the effect of one gene or another? Programming standards have improved somewhat since creationists made their break with science, I take it…


*That would be by way of being a joke, as it happens. Do tell if you don’t get it…
**Pun intended

One thought on “Pseudohelpful Pseudogenes

  1. Intelligent design? Creative genius? If we programmed like religionuts allege their deity does… we’d a) never get any software created and b) it would be so incredibly inefficient is wouldn’t be good for anything.

    Even when we use genetic algorithms they are optimised so that they basically don’t resemble the origin of the idea. In fact, the things that make biological systems so difficult to model in a computer system is the massive amount of inefficiency.

    It’s… man I wish there was a stronger word than ‘disingenuous’ to describe how ludicrous it is to point to living things and claim they were created by ‘intelligence’.

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