Some Genetics

Back in late July I missed – by virtue of being on a school trip for a class I don’t actually take – two articles in a row by Jeff Tomkins. For completeness’ sake, here you go:

First, on the 23rd of July, there was Human DNA Variation Linked to Biblical Event Timeline. This was about a Science paper, Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes, about which Tomkins claims:

A new study reported in the journal Science has advanced our knowledge of rare DNA variation associated with gene regions in the human genome. By applying a demographics-based model to the data, researchers discovered that the human genome began to rapidly diversify about 5,000 years ago. Remarkably, this data coincides closely with biblical models of rapid diversification of humans after the global flood.


The authors wrote, “The maximum likelihood time for accelerated growth was 5,115 years ago.” Old-earth proponents now have a new challenge: to explain why—after millions of years of hardly any genetic variation among modern humans—human genomic diversity exploded only within the last five thousand years?

To begin with it should go without saying that these findings have only been “linked to [the] biblical event timeline” by Tomkins himself, not the study authors. Secondly, the strictest biblical time-line actually has the Flood occurring something like 4350 years ago, showing that the fit isn’t all that perfect after all – and if the young Earth creationists are going to concede 700+ years of flexibility in the form of the dreaded ‘gaps in the chronology,’ they’d probably consider themselves already on the slippery slope to old Earth creationism. Seriously, the adherence to the Ussher chronology seems to have become quite strict of late.

Ashley Haworth-Roberts saved me the trouble of contacting an actual scientist here – it turns out that there are, as you would expect, older mutations than the ones that show a 5000 year old radiation which is more than a little unfortunate for the creationist position. Tomkins is incorrect, on multiple levels, in claiming that it is believed that there have been “millions of years of hardly any genetic variation among modern humans.”

But why did the increase in genetic diversity happen then? The answer, of course, is population growth. From a ScienceDaily article:

How did so many rare variations affecting protein function arise in the human genetic code? The researchers suggest that this excess of rare variations is due to a combination of demographic and evolutionary forces. Both European and African populations grew exponentially beginning around 10,000 years ago, but in the past 5,000 years growth rates accelerated leading to the billions of people living today.

And the reason why that happened is probably the advent of civilisation. Just a hunch.

The second article, from the 25th of July, was Transposable Elements Key in Embryo Development.

If you were (and are) paying attention to the Science and Human Origins saga you should have seen the Chapter 4 part 1 post in Paul McBride’s review, which was published two days after Tomkins’ article. In that post McBride wrote:

I am yet to read Chapter 4, the obligatory ‘junk DNA’ written by Casey Luskin, but I have tried to discuss this topic numerous times with Intelligent Design advocates, as my earlier posts on the topic attest to. The responses are always the same. I’m aware Luskin is not a molecular biologist, so I’m expecting him to do similar, if less thorough job, of presenting the same claims against junk DNA that have been made by Jonathan Wells, and other ID advocates.

Therefore I am predicting that this chapter will:

  1. Conflate junk DNA and non-coding DNA.
  2. Identify functions of non-coding DNA (introns allow alternative splicing, for example) as evidence that junk DNA doesn’t exist.
  3. Present a qualitative argument that because new function is found from time to time (e.g. microRNAs) the base of ‘junk’ is being continually whittled away.
  4. Ignore the quantitative argument that such new discoveries account for a negligible fraction of the human genome, still leaving 90% unexplained.
  5. Make the argument that because active copies of transposable elements can play genomic roles, we can’t discount the importance of any copies of transposable elements.
  6. Ignore that only a handful of copies of transposable elements are actually active, and that most are defunct.
  7. Play up pervasive transcription, while ignoring evidence that spurious transcripts are expected to be produced by error.
  8. Ignore the population-genetic arguments for the existence of junk DNA (e.g. the effectiveness of selection in small populations [Lynch 2007] and the mutational load in mammals [Ohno 1972]).
  9. Ignore the ‘onion test’ i.e. if the junk is truly functional, why do some closely related and ecologically similar species have several times more junk than others?
  10. Broadly, ignore every serious argument that provides support for the inference of junk DNA, and still claim a resounding victory.

Jeff is similarly trying to go after junk DNA, specifically targeting transposable elements (“jumping genes,” as he calls them), and thus points 5, 6, and to a lesser extent 3 and 4, are most relevant here.

Long story short, we already know that transposable elements can have function but the human genome is littered with their corpses (they make up about half of the thing). While MuERV-L – the gene that Tomkins is talking about – may well have a function, it is the mutated duplicates that really need explaining.

In conclusion, you didn’t miss much.


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