Stale Population Growth

Ancient foundations at JerichoWell this is odd: Jeffrey Tomkins’ latest DpSU – Genetics Research Confirms Biblical Timeline – is a rewrite of a story that I’m sure we’ve seen several times before. No new information! I don’t know what’s up, but I didn’t do a great job of covering it the first time so there’s no harm in going over it again from scratch.

Exciting research from the summer of 2012 described DNA variation in the protein coding regions of the human genome linked to population growth.

If really is ‘exiting’ then that might explain why Tomkins has been going on about it long enough for it to be summer in my half of the world now. (On that subject, the Australian bushfires are very impressive this year – it rained ash here on Sunday.)

The subject of this article is really talk origins claim CB620 – “Human population growth indicates a young earth” – disguised as genetics to avoid the explanations provided there.

One of the investigation’s conclusions was that the human genome began to rapidly diversify not more than 5,000 years ago.

Importantly, the are multiple (three) papers that Tomkins’ cites. This one is Evolution and Functional Impact of Rare Coding Variation from Deep Sequencing of Human Exomes, and unfortunately I can’t read enough of it to find the source of the “not more than 5,000 years ago” claim. I can, however, read the ScienceDaily press release, which says:

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.

Now, the creation of the variation being described is tied to population growth. If the trajectory described by ScienceDaily is correct, and is related to the 5,000-year date that is supposed to be in the paper, then what they will be saying is that the more recent acceleration has lead to most of the variation. The keyword, however, is most – there will be some more variation coming from the 10,000-5,000 period, and others from even earlier times which have been around long enough to be nolonger “rare.” Yes, the young Earth creationist date for the creation vaguely matches a time when population growth accelerated (something that has happened multiple times since), but so what?

Let’s get out of Tomkins’ opening paragraph first. He continues:

This observation closely agrees with a biblical timeline of post-flood human diversification. Yet another study, this one published in the journal Nature, accessed even more extensive data and unintentionally confirmed the recent human history described in Genesis.

“Closely agrees” must mean something different to Dr Tomkins than it does to the rest of the world. His “post-flood human diversification” – an extreme bottleneck for which there should be evidence but none exists – was nearer 4,000 years ago, much too late to explain even the 5,000-year increase. Worse, the genetic data is presumably being matched to real time assuming normal lifespans. Back in Noah’s day (i.e immediately post-flood) people supposedly still lived much longer than they do now, which would mean that we would have to consider that period to be even closer to the present to match up with generation times.

The second paper mentioned was Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. This paper is significant as it’s stated aim is closest to what Tomkins wants to do with it – analysing the time of the variants’ creation, rather than looking at their ‘impact’ or similar. Unfortunately for him the paper states:

We estimate that approximately 73% of all protein-coding SNVs [single nucleotide variants] and approximately 86% of SNVs predicted to be deleterious arose in the past 5,000–10,000 years.

That result is even worse for him – realise that ‘recent’ is relative, and need not be convenient for creationists. This is a long way from a confirmation of the biblical narrative.

Differences in human DNA can be characterized across populations and ethnic groups using a variety of techniques. One of the most informative genetic technologies in this regard is the analysis of rare DNA variation in the protein coding regions of the genome. Variability in these regions is less frequent than the more numerous genetic differences that occur in the non-coding regulatory regions. Researchers can statistically combine this information with demographic data derived from population growth across the world to generate time scales related to human genetic diversification.

This paragraph is capped with a cite to the third paper, called Recent Explosive Human Population Growth Has Resulted in an Excess of Rare Genetic Variants (through some devil-work that link actually gives you access to the full paper, in contrast to the other two). Tomkins says:

What makes this type of research unique is that evolutionary scientists typically incorporate hypothetical deep time scales taken from the authority of paleontologists or other similar deep-time scenarios to calibrate models of genetic change over time. Demographics-based studies using observed world population dynamics do not rely on this bias and are therefore more accurate and realistic.

In other words, ‘they don’t use details that we don’t like, so they must be more reliable.’ However, given that “hypothetical deep time scales” to a YEC means anything more than about 6,000 years, this paper #3 also apparently uses “baised” information. A good thing Tomkins doesn’t use this paper to draw any conclusions.

In a 2012 Science report, geneticists analyzed DNA sequences of 15,585 protein-coding gene regions in the human genome for 1,351 European Americans and 1,088 African Americans for rare DNA variation. This new study accessed rare coding variation in 15,336 genes from over 6,500 humans—almost three times the amount of data compared to the first study. A separate group of researchers performed the new study.

This paragraph is confusing and irrelevant, but for clarity the “new study” appears to refer to the second, Nature paper above (citation #3 in Tomkins’ article). It’s possible that this actually is new – i.e. a good reason to cover this topic again – but I’m also confused about when it was publised and it may as well be old for all it matters here.

The Nature results convey a second spectacular confirmation of the amazingly biblical conclusions from the first study. These scientists confirmed that the human genome began to rapidly diversify not more than 5,000 years ago.

I think he’s making the “not more than” part up here – as I said above, this one concluded “5,000–10,000 years.” Tomkins also says:

In addition, they found significant levels of variation to be associated with degradation of the human genome, not forward evolutionary progress. This fits closely with research performed by Cornell University geneticist John Sanford who demonstrated through biologically realistic population genetic modeling that genomes actually devolve over time in a process called genetic entropy.

Ah, Sanford – we manage to get a bit of genetic entropy in. They actually found that the more deleterious mutations tended to be more recent, which if anything shows that natural selection is operating to cull them in apparent contradiction to Sanford’s claim. It is difficult to judge where Tomkins is drawing this conclusion from, but if my suspicions are correct then it’s the equivalent of concluding that “science says that embryos are fully human” from a caption in a textbook stating that the picture above is of “a human embryo at 1 week.” It would be a quote mine if he had actually bothered to produce a quote.

Tomkins concludes:

According to the Bible, the pre-flood world population was reduced to Noah’s three sons and their wives, creating a genetic bottleneck from which all humans descended. Immediately following the global flood event, we would expect to see a rapid diversification continuing up to the present. According to Scripture, this began not more than 5,000 years ago. We would also expect the human genome to devolve or degrade as it accumulates irreversible genetic errors over time. Now, two secular research papers confirm these biblical predictions.

Yeah, no. To summarise, genetic variation (at least in terms of rare variation that hasn’t had time to either drop out of the population or become common) is associated with population growth. The creationist timeline places a “rapid diversification”/start of population growth approximately around one of the earlier periods of acceleration, but fails to explain even earlier growth/variation (which does exist).

There’s also a diagram in this article, which is problematic for a number of reasons. If you’re stuck, remember the correlation between variation and population and read this post from 2011.

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