Ultraconserved Elements

Another Jeffrey Tomkins post on Designed DNA? Oh, why not.

This one is called Ultraconserved DNA Elements – An Evolutionary Enigma. What are they?

Ultraconserved DNA elements are short chunks of genomic sequence 200 bases or more that are highly similar (conserved) among different types of animals and are generally noncoding (1,2). Hence, they should have very little evolutionary selective pressure acting upon them and evolve rapidly (3).

The first sentence there is correct, or as near to as needs to be,* while the second is not – and with that this post falls immediately.

The problem, in a nutshell, is that noncoding does not mean ‘junk’ (i.e. entirely useless). Indeed, claiming that it was would be so stupid there has been a bit of back-and-forth between Sandwalk and Evolution News and Views recently over whether anyone had ever even said such a thing. “Noncoding” just means that the sequence doesn’t directly turn into protein, and there is a whole world of equally-important regulatory DNA not included in there. While DNA that is ‘useless’ in the sense that it’s sequence doesn’t matter should indeed “have very little evolutionary selective pressure acting upon them and evolve rapidly” – something which is observed –  just because a segment of DNA is non-coding doesn’t mean that this will be the case.

Skipping a slightly problematic explanation of what should happen to said non-sequence critical segments, we read:

The enigma or paradox with ultraconserved DNA elements is that they appear to have minimal functionality, yet they remain unchanged across diverse groups of animals. According to the standard model of evolution, however, they should be highly variable since selective pressures have little influence upon – they should be free to mutate. A quote is posted below from an evolutionary research paper stating this issue.

“Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery.”(4)

This is from the 2007 Science paper Human Genome Ultraconserved Elements Are Ultraselected, the abstract of which (with the quote above bolded) reads in full:

Ultraconserved elements in the human genome are defined as stretches of at least 200 base pairs of DNA that match identically with corresponding regions in the mouse and rat genomes. Most ultraconserved elements are noncoding and have been evolutionarily conserved since mammal and bird ancestors diverged over 300 million years ago. The reason for this extreme conservation remains a mystery. It has been speculated that they are mutational cold spots or regions where every site is under weak but still detectable negative selection. However, analysis of the derived allele frequency spectrum shows that these regions are in fact under negative selection that is much stronger than that in protein coding genes.

For a region to be under negative, or ‘purifying,’ selection there must be a reason: there must be a significant detriment to an organism that has a mutation in the region, preventing it from at least reproducing (such as giving it cancer). Ultraconserved Elements (UCEs) must therefore have some kind of function, where ‘function’ is allowed to be fairly broadly interpreted, and there seem to be plenty of candidatesespecially in development.

So we merely have a case of a class of regulatory DNA defined by being nearly incapable of modification, which is hardly an ‘evolutionary enigma.’ Nevertheless, Tomkins concludes his post with:

Remarkably, the only historically predictive idea that accurately accounts for these types of patterns in life is the text in the book of Genesis in the Bible that specifically states that separate created kinds were made with their own reproductively defined gene pools. Exactly what we observe in modern biology research.

Genesis does not predict this at all. Tomkins could perhaps build up a case if he could show that while the sequences are highly similar between species they did not have any kind of negative selection keeping things that way. That would be a problem – but it’s not what is observed.

The paragraph before that conclusion is a little off-topic, but still interesting:

This enigma is typical of the mosaic observed across the spectrum of life. In cases where organisms have similar nutritional needs, physiologies, body plans, and other shared traits, gene sequences for these traits will often be similar at some level. However, separate types of animals also have DNA sequences and patterns that are unique to that particular organism – these are the types of sequences that defy man’s ideas about evolutionary hierarchies and hypothetical selective processes.

A potential problem for evolution here could be if there were cases where disparate organisms shared genome segments in a way that contradicted how they fall into the tree of life. For example, sharks and dolphins mysteriously having the same genes for something related to swimming, but there being no link between them (all other mammals not having them, and having no sign of having lost them, for example). Of course, convergent evolution is known to occur, but what goes on under the hood to make the organisms superficially similar tends to be very different. Horizontal gene transfer between species may also be a consideration – this wouldn’t be automatic disproof of evolution if it were ever found. Tomkins seems (maybe) to be claiming he knows of such a thing, but he certainly provides no reference.

So, again, we don’t have an ‘enigma’ here, beyond the question of what Tomkins is going on about in a few places (the last sentence in the paragraph quoted just above is particularly nonsensical, unless he has a reference that can clarify). We probably wont see this in DpSU form, but it’s a little better than what we saw last week. But then that’s not hard.

*Caveats include:

One thought on “Ultraconserved Elements

  1. What worries me about Tomkins is that he actually is qualified to talk about genetics, having a PhD in the topic and having spent some years as an assistant professor. So, one of two possibilities arise:

    1. He is actually extremely stupid, which explains why he didn’t get tenure at Clemson and joined the ICR

    2. He is actually extremely clever, and is using his specialized knowledge to bamboozle people.

    I wonder which one it is ——–


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