On intelligence quotient and race

I wrote this as a comment on IQ and racial differences some months ago.

I think that IQ is real in that it measures a form of intellectual prowess. We all know people who are more and less intelligent and IQ seems to correlate with that. IQ almost certainly does not measure wisdom (knowing what is good and right).

I also think that an IQ difference between races is feasible. Certain tribal groupings differ in height, weight, eye colour, hair shape, on average.

However it seems to me that IQ likely is associated with many more genes than these other features. I also suspect that IQ is influenced by education despite claims otherwise. There is also evidence of IQ changes over time within a racial group. Therefore I very much doubt that there are significant, if any, differences between races.

So my position is there could be an IQ difference but there probably isn't. IQ does not measure morality. Having a higher IQ is a benefit, probably like being tall, or running fast. Racial differences are averages and do not apply to an individual. And IQ is only one metric, so it cannot be used for a general claim of racial superiority. We are equal before God because of our imago Dei, not because of our skills. And the man who is strong or fast or smart should never boast in this, but boast in the Lord.

DNA in dinosaur bones

A recent study published in Bone (doi:10.1016/j.bone.2012.10.010) shows evidence of residual dinosaur DNA in dinosaur bones. They retrieved osteocytes (bone cells) from the bone and stained it for DNA.

The dinosaurs were Tyrannosaurus rex and Brachylophosaurus canadensis.

Row 1 (ABC) is T. rex. Row 2 (DEF) is B. canadensis. Row 3 (GHI) is ostrich.

Column 1 (ADG) is a anti-DNA antibody stain. Column 2 (BEH) is propidium iodide, a DNA stain. Column 3 (CFI) is 4′,6′-diamidino-2-phenylindole dihydrochloride, a DNA stain.

Note that the stains are limited to the nucleus of the cell.

They also identified several proteins including histones which are closely associated with DNA.

They have not yet sequenced the DNA, though that would be of considerable interest.

In your faces evolutionists

We have been long told that most of the DNA we have is junk, useless leftovers with no function after millennia of mutation and selection. Apparently only gene coding DNA is functional. Thus it was in the 1980s, and 1990s, and even 2000s though some of the more astute were suspicious.

The creationists were more circumspect. Perhaps gene coding DNA was a small component of the genome but, they protested, all that DNA is there for a reason. We are designed and we are very complicated. Our lack of knowledge does not preclude that the rest of the DNA is functional, we just aren't finished looking. So the junk DNA scenario was disputed by creationists decades ago. Pseudogenes, they said, probably had a function and were not left over relics from our primate, mammalian or reptilian past. Other codes beyond the triplet codon to amino acid likely existed.

This week Nature published 6 papers of several they aim to publish on the ENCODE project, along with other related material at their site.

The publication has made this news though much of this kind of information has been known to several researchers. The importance of introns has been known for some time. That polymerases produce far more RNA than is translated into protein is documented, even if the reason the this has been elusive. Gene regulators and promoters have been known of for decades, though it turns out that enhancers do not exist solely adjacent to the gene, but at distances of hundreds of thousands of bases distant. Why? Well because the 3 dimensional configuration of DNA means that a distant "file" location may happen to be physically nearby.

Interestingly the design advocates were long claiming unknown function for junk DNA. After all, while a few mutations have accumulated since creation, 95% of our genome housing junk is not consistent with design, even broken design. Creationists were dismissed, but it turns out they were correct all along. And the evolutionists who insisted that our genome was predominantly junk are left looking the fool. So much for the off quoted adage,

Nothing in biology makes sense except in the light of evolution.

Though I don't expect them to be questioning their dogma soon, rather adding some evolutionary spin,

Why evolution would maintain large amounts of 'useless' DNA had remained a mystery, and seemed wasteful. It turns out, however, that there are good reasons to keep this DNA.

Age estimate for chromosome divergence

JS Allen mentioned a couple blog posts concerning the time the Y chromosome may have gone thru a bottleneck.

• How old is Y-chromosome Adam?
• The father of us all: 142 thousand years ago

The second refers to the article A Revised Root for the Human Y Chromosomal Phylogenetic Tree: The Origin of Patrilineal Diversity in Africa.

Dienekes first post suggests that the divergence of the Y chromosome was 40,000 years ago, the second mentions recent data pushing the date back to 140,000 years. This material is something that Dienekes follows, whereas I am only moderately familiar with it. The journal article covers material on genetic anthropology and my reading on genetics is focused more on disease, but I wish to identify a few assumptions that mean I do not agree with the dates suggested.

My post was on the variation of autosomes, sex chromosomes and mitochondria based on a bottleneck of 3 brothers and their wives. The issue of dating a bottleneck, while related, is a different question. The later requires knowledge of

1. the variation currently and the likely original sequences; and
2. molecular clock rates.

Both have significant assumptions and I differ from the authors in several of them.

The article mentions that they attempted independence with regard to 1 then they discuss assumptions relating to using chimp Y chromosomes and human X chromosomes

We obtained a strict-consensus MP [maximum parsimony] tree, which was rooted with respect to either orthologous chimp MSY [male-specific region of the human Y chromosome] sequence... or paralogous human X chromosome sequence...

This hardly seems independent. I reject the use of other species sequences as having relevance, and I do not know whether my assumption of 8 X's to 1 Y at the bottleneck affects the second. So the resulting phylogeny is not necessarily correct.

The problem with molecular clocks is they are not independent either. Dienekes mentions a calibration of 70,000 years for a split but what is this based on? More to the point, in his 2010 post he raises the problem with molecular clocks.

Age estimates vary overall between 6,530 years and 535,755! It is obvious that fast/medium mutating markers provide unbelievably small age estimates (most of them are less than 20 thousand years). However, if we limit the analysis to slow mutating markers, most age estimates are in excess of 300,000 years!

In short, you can arrive at any age estimate you want, by choosing a particular mix of slow and fast mutating markers.

He says (correctly) that we mustn't average different clocks. He rejects throwing them in the trash and argues for identifying the correct clock.

But that is equivalent to having a number of different clocks, some of which tell you that 3 seconds have transpired, and some which tell you that it's been a whole minute. The rational thing to do is not to take an average, but to throw the clocks in the garbage, or figure out what's wrong with them.

I agree, but we are likely to differ on what we consider reliable. I suspect mutation is more rapid than accepted by evolutionists, if so then the clocks are going faster than anticipated. I would like to see some data obtained with fixed dates and generation numbers.

These are just 2 problems with the interpretation. There is also the interbreeding question, the targeted DNA changes versus random mutation, the incompleteness of the data (both complete Y DNA and adequate sampling of the populations). Further data will be interesting.

The greater issue is that (hidden) assumptions markedly affect interpretation. While  interpretations such as given in the paper will be seen as evidence for the evolutionary scheme, so much of the evolutionary paradigm is assumed that it becomes very circular. This is not intrinsically bad, but lack of awareness of assumptions can have the effect that you think your interpretation is stronger than it really is. This can be a potential issue for creationists also, though given their strong focus on identifying underlying assumptions, and that they are working within a paradigm they generally disagree with, I think they are often more attuned to this issue.

Postdiluvian genetic variation

This article from Robert Carter raises some interesting ideas concerning genetic variation.

People have 2 sets (diploid) of chromosomes. Many of our genes are identical, but several have variants. Consider the maximum variation at creation. Adam had 2 sets of autosomes, 1 X chromosome, and 1 Y chromosome. Eve was made from his side. God could have kept the autosomes, doubled the X chromosome, and removed the Y chromosome. But God could also have created Eve with her own set of chromosomes. Several genes may have been identical, but if we consider the maximum, then the original variation in Adam and Eve was (a maximum of) 4 alleles for each gene in all the autosomes, 2 from Adam and 2 from Eve; 3 alleles in the X chromosomes, 1 from Adam and 2 from Eve; 1 allele in the Y chromosome, from Adam; and 1 mitochondrial allele per gene from Eve. This assumes that all Eve's mitochondria had identical DNA. Sperm have mitochondria but these are not incorporated into the embryo so only the female's mitochondrial DNA is passed on.

Mutation and recombination would have increased the number of alleles in Adam's descendants to the time of the Flood. Carter discusses the genetic bottleneck at the time of the deluge and mentions the maximum number of variants this would entail.

On the Ark we have Noah, his wife, their 3 sons, and their sons' wives. The genetic material of the sons is determined by their parents, and the genetic material of the wives is potentially independent; depending on their relationship to Noah's bloodline. Thus we have 4 sets of autosomes from Noah and his wife, 3 X chromosomes, and 1 Y chromosome, 2 mitochondrial lineages. The sons could potentially inherit all 4 autosomes, both Xs from their mother (but not their father's X), 1 Y from their father, 1 mitochondrial from their mother. The sons' wives could have 6 autosomes, 6 Xs, no Ys, and 3 mitochondrial. Considering the offspring of Shem, Ham and Japheth and their wives there is a maximum of:

• 10 autosomes;
• 8 X chromosomes;
• 1 Y chromosomes; and
• 3 mitochondrial chromosomes.

The mitochondria of Noah's sons (from their mother) will not be passed on. The mitochondrial variation may be somewhat more as several mitochondria are passed on and they may not all be identical within a single person.

The descendants of Shem, Ham and Japheth encompasses the entire human race. Carter considers the variation we currently find.

[We] are potentially looking at a huge amount of genetic diversity within the X chromosomes of the world.

Does this fit the evidence? Absolutely! It turns out that Y chromosomes are similar worldwide. According to the evolutionists, no “ancient” (i.e., highly mutated or highly divergent) Y chromosomes have been found. This serves as a bit of a puzzle to the evolutionist, and they have had to resort to calling for a higher “reproductive variance” among men than women, high rates of “gene conversion” in the Y chromosome, or perhaps a “selective sweep” that wiped out the other male lines. For the biblical model, it is a beautiful correlation and we can take it as is.

The evidence from mitochondrial DNA fits our model just as neatly as the Y chromosome data. As it turns out, there are three main mitochondrial DNA lineages found across the world. The evolutionists have labeled these lines “M”, “N”, and “R”, so we’ll refer to them by the same names. They would not say these came off the Ark. They claim they were derived from older lines found in Africa, but this is based on a suite of assumptions (I discussed these in detail in a recent article in the Journal of Creation). It also turns out that M, N, and R differ by only a few mutations. This gives us some indication of the amount of mutation that occurred in the generations prior to the Flood.

Let’s assume ten female generations from Eve to the ladies on the Ark. M and N are separated by about 8 mutations (a small fraction of the 16,500 letters in the mitochondrial genome). R is only 1 mutation away from N. This is an indication of the mutational load that occurred before the Flood. Given the assumption that mutations occur at equal rates in all lines, about four mutations separate M and N each from Eve (maybe four mutations in each line in ten generations). But what about R? It is very similar to N. Were N and R sisters, or perhaps more closely related to each other than they were to M? We’ll never know, but it sure is fascinating to think about.

One more line of evidence crops up in the amount of genetic diversity that has been found within people worldwide. Essentially, much less has been found than most (i.e., evolutionists!) predicted. The general lack of diversity among people is the reason the Out of Africa model has humanity going through a disastrous, near-extinction bottleneck with only about 10,000 (and perhaps as few as 1,000) people surviving. However, the reason for this lack of diversity is twofold. First, the human race started out with only two people. Second, the human race is not that old and has not accumulated a lot of mutations, despite the high mutation rate. Third, there actually was a bottleneck event, Noah’s Flood!

Mummy KV55 identified as Akhenaten

Historical inscriptions state that Pharaoh Akhenaten was the son of Amenhotep 3 and the father of Tutankhanem. Akhentaten's wife was the famed Nefertiti, though he also had other wives. A mummy found in 1907 in tomb KV55 has been confirmed by genetic testing as Tutankhamen's father, and the son of Amenhotep 3.

Two years of DNA testing and CAT scans on 16 royal mummies conducted by Egypt's Supreme Council of Antiquities, however, gave the firmest evidence to date that an unidentified mummy — known as KV55, after the number of the tomb where it was found in 1907 in Egypt's Valley of the Kings — is Akhenaten's.

The testing, whose results were announced last month, established that KV55 was the father of King Tut and the son of the Pharaoh Amenhotep III, a lineage that matches Akhenaten's, according to inscriptions.

Previous assertions that KV55 is Akhenaten were dismissed based on the supposition that the age of the KV55 mummy at death was too young, but this has since been revised.

Akhenaten ruled during the 18th Dynasty, traditionally dated in the 14th century BC. He promoted worship of Aten the sun-disk in preference to the god Amun. He changed his own name from Amenhotep (4) to Akhenaten, removed the name Amun from several inscriptions and destroyed Amun's temples, and built the city Akhetaten for Aten.

It is claimed by some that Akhenaten was a monotheist, antedating and anticipating Moses. This is incorrect for several reasons: theological and chronological. Though Akhenaten may have been a monotheist of sorts, it appears that he was devoted to Aten in preference to Amun whom he rejected. But he tolerated other deities, all his animosity was directed solely at Amun.

Neither did Akhenaten antedate Moses. Even with traditional Egyptian dating one needs also to hold to a shortened Hebrew chronology placing Moses in the 13th rather than the 15th century BC. Scripturally, 200 years between Moses and David is too short. All the arguments for a late exodus are extra-biblical.

But the traditional dating of Akhenaten is incorrect. Finding synchronisms between Israel and Egypt based on matching individuals rather than spurious dates places the beginning of the 18th pharaonic Dynasty around the time of King Saul. Akhenaten is not mentioned in the Bible by any name. His great-grandfather may have been. Akentaten was the son of Amenhotep 3, son of Thutmose 4, son of Amenhotep 2. Amenhotep 2 is identified as Zerah the Cushite (2 Chronicles 14) by Immanuel Velikovsky and David Down. Zerah attached Judah c. 900 BC which would place Akhenaten some time in the late 9th century BC. The Armana tablets from the time of Amenhotep 3 and Akhenaten are correspondence between Egypt and northern countries. They include correspondence from Samaria (which is erroneously ascribed to Sumer) and Jerusalem.

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Picture of Nefertiti bust in Berlin museum.