Three genetic variants linked to IQ, and they vary by race

[ApostateAbe]

We know from uncomfortable studies of identical twins that variants in IQ are much more genetic than we would like it to be. Identical twins reared in entirely different households tend to have much more similar IQ than unrelated children reared in the same household. About 50% more similar. Why is this uncomfortable? IQ is not just a number. It is strongly related to everything we typically associate with intelligence, including educational achievement, income, and high-intelligence professions. Maybe there are a few professionally-licensed engineers with an IQ below 80, but they would be extremely rare. Your own high intelligence isn't much due to the elite parenting skills of your parents, no, but to their bad f***ing skills. Their greatest parenting accomplishment was letting the condom slip off.

This means gene variants must exist that cause greater intelligence, and we have only recently begun to find them. Last year, a study was published in the Proceedings of the National Academy of Sciences that identified three such gene variants. The study by Rietveld et al is titled "Common genetic variants associated with cognitive performance identified using the proxy-phenotype method," analyzing the genes and IQ of over one hundred thousand people, and three gene variants (SNPs) were identified as having a small relationship to IQ: rs1487441, rs7923609 and rs2721173. According to the study, each SNP accounts for only less than half of an IQ point. There are thousands more to find before we have a complete montage of the gene variants that influence IQ variants.

The study does NOT discuss racial/ethnic differences in the allele frequencies. However, the 1000 Genomes Project has made freely available on the web a searchable browser of their database, of every human allele, mapping each of them by frequency with each major race (and sub-race). So, you can guess what I did next. You can see the results in my table below.

The first allele has a strong positive correlation with Richard Lynn's values of median racial IQs (correlation of 0.91, on a scale between -1 and 1). The second allele has a minor negative correlation. And the third allele has a moderate positive correlation. The allele with the strong POSITIVE relationship with median racial IQs is strikingly large, but the allele with the small NEGATIVE correlation of course would be at odds with the idea that genes account for racial differences in IQ. Far from a deal-breaker--if there are thousands of genes that contribute to intelligence, then most of them would be expected to contribute to the racial patterns, but not all.

My analysis of these three SNPs do not prove that intelligence variations among the races are genetic. However, it makes it more plausible. Maybe, after we find all the alleles related to intelligence variations, we will find that they just happen to equal out on the whole, predicting equal intelligence for all races given equal environments. But, why would we expect that? Because the universe caters to our deepest wishes? Because biological evolution is guided by social justice?

We need to be prepared for the identification of all genetic variants related to intelligence. After they are found, they will be mapped to the races just as easily as I have done with those three SNPs, and we need to expect that the results will tend to favor the races of high measured intelligence, just as with those three alleles (average correlation: 0.39). Impulsive denials of the biology of race, the biology of intelligence or both will no longer be politically effective. Don't become an anti-scientific conspiracy theorist, and don't become a full-blown racist, either. White supremacists will try to lay sole claim to this science. Be rational about it, and don't let them. Genocide does not follow from gene differences.

Data of the heritability of IQ: http://s10.postimg.org/ocn7w10ix/Erlenmeyer_Kimling_and_Jarvik_via_WF_Bodmer_and.png, from Erlenmeyer-Kimling and Jarvik via WF Bodmer and Ashley Montagu, "Race & IQ," page 326.
Rietveld et al: http://www.pnas.org/content/111/38/13790.full.pdf
1000 Genomes Project Browser: http://browser.1000genomes.org/index.html
Richard Lynn's IQ data: "The Global Bell Curve," 2008.

 

[ApostateAbe]

I believe I made a mistake. The correlations of the second two alleles are actually NEGATIVE, not positive, according to Rietveld et al. The signs of the second two correlations, should be reversed, and the average correlation becomes lower: 0.21.

 

[ApostateAbe]

And it matters little, because somebody already beat me to it and did it better. The latest papers of Davide Piffer analyzed many IQ-linked alleles by population frequency and population median IQ, and, yes, they are mostly positive correlations! This is the beginning of something both good and evil.

https://www.researchgate.net/profile/Davide_Piffer/publications

 

[rjh01]

The table is worthless. To relate genes to intelligence I would expect to see a table that says that the average IQ of people with a certain gene is equal to a certain number. The above table introduces an irrelevant variable (race). Worse the author does not appear to be a researcher.

 

[ApostateAbe]

The table is worthless. To relate genes to intelligence I would expect to see a table that says that the average IQ of people with a certain gene is equal to a certain number. The above table introduces an irrelevant variable (race). Worse the author does not appear to be a researcher.

As intelligence is a vastly polygenic trait, each genetic variant having a tiny effect on IQ, we should not expect much value in averaging the IQ of all carriers of a single variant. Race is not an irrelevant variable, but a central component of the theory of evolution. Genetic divergence would be impossible without races. Vast arrays of gene frequencies including the genes for intelligence are expected to diverge when populations geographically diverge.

 

[fromderinside]

The table is worthless. To relate genes to intelligence I would expect to see a table that says that the average IQ of people with a certain gene is equal to a certain number. The above table introduces an irrelevant variable (race). Worse the author does not appear to be a researcher.

As intelligence is a vastly polygenic trait, each genetic variant having a tiny effect on IQ, we should not expect much value in averaging the IQ of all carriers of a single variant. Race is not an irrelevant variable, but a central component of the theory of evolution. Genetic divergence would be impossible without races. Vast arrays of gene frequencies including the genes for intelligence are expected to diverge when populations geographically diverge.

I wonder how many speculations, caveats, intervening variables, and the like, one have to interpose between those two items to produce a theory that would hold up like, say theory of motion.

Just askin'

 

[ApostateAbe]

As intelligence is a vastly polygenic trait, each genetic variant having a tiny effect on IQ, we should not expect much value in averaging the IQ of all carriers of a single variant. Race is not an irrelevant variable, but a central component of the theory of evolution. Genetic divergence would be impossible without races. Vast arrays of gene frequencies including the genes for intelligence are expected to diverge when populations geographically diverge.

I wonder how many speculations, caveats, intervening variables, and the like, one have to interpose between those two items to produce a theory that would hold up like, say theory of motion.

Just askin'

OK, I would like to understand your question sufficiently. What "two items" do you mean?

 

[rjh01]

The table is worthless. To relate genes to intelligence I would expect to see a table that says that the average IQ of people with a certain gene is equal to a certain number. The above table introduces an irrelevant variable (race). Worse the author does not appear to be a researcher.

As intelligence is a vastly polygenic trait, each genetic variant having a tiny effect on IQ, we should not expect much value in averaging the IQ of all carriers of a single variant. Race is not an irrelevant variable, but a central component of the theory of evolution. Genetic divergence would be impossible without races. Vast arrays of gene frequencies including the genes for intelligence are expected to diverge when populations geographically diverge.

This sounds like complete garbage.

 

[ApostateAbe]

As intelligence is a vastly polygenic trait, each genetic variant having a tiny effect on IQ, we should not expect much value in averaging the IQ of all carriers of a single variant. Race is not an irrelevant variable, but a central component of the theory of evolution. Genetic divergence would be impossible without races. Vast arrays of gene frequencies including the genes for intelligence are expected to diverge when populations geographically diverge.

This sounds like complete garbage.

Then I have a challenge for you: try making sense of the process of evolutionary divergence without biological races. Tell me how it works.

 

[ronburgundy]

Looks a lot like the pattern expected if the average correlation across all the relevant alleles was zero: Some by chance being positive, some negative, some near zero.

In fact, an t-test shows that the average correlation of those the values is not significantly different from zero, and won't differ from zero if the next couple dozen alleles continue to show a similar pattern.

 

[ApostateAbe]

Looks a lot like the pattern expected if the average correlation across all the relevant alleles was zero: Some by chance being positive, some negative, some near zero.

In fact, an t-test shows that the average correlation of those the values is not significantly different from zero, and won't differ from zero if the next couple dozen alleles continue to show a similar pattern.

Yes, that's right. More precisely, these results can be expected from just about any genotypic IQ distribution. But, what can NOT be concluded is that every race has exactly the same alleles for intelligence. Maybe a race lacks some alleles for intelligence and compensates perfectly with other alleles. There is no reason we should expect that but for ideology or wishful thinking, but it is a possibility all the same. Davide Piffer's analysis included a few more alleles for intelligence, he broke down the races in much more detail, and he came up with a stronger correlation, but even that does not yet prove the genetic hypothesis of racial IQs. It won't be long before it is either fully proved or fully disproved, and I think it would be most rational to expect that the genetic hypothesis will be proved, not disproved. Such an expectation would be on the side of both the phenotypes and Piffer's trend. We should not be letting mere wishful thinking affect our probability judgments.

 

[Trodon]

Individual and racial differences in native intelligence have legitimate policy implications. For decades I have been appalled at the way the discussion of these differences and their implications has been suppressed. I look forward to scientific research that will vindicate Charles Murray. I hope he will still be alive when the truth can be proven and stated safely in public.

 

[ronburgundy]

Looks a lot like the pattern expected if the average correlation across all the relevant alleles was zero: Some by chance being positive, some negative, some near zero.

In fact, an t-test shows that the average correlation of those the values is not significantly different from zero, and won't differ from zero if the next couple dozen alleles continue to show a similar pattern.

Yes, that's right. More precisely, these results can be expected from just about any genotypic IQ distribution. But, what can NOT be concluded is that every race has exactly the same alleles for intelligence. Maybe a race lacks some alleles for intelligence and compensates perfectly with other alleles. There is no reason we should expect that but for ideology or wishful thinking, but it is a possibility all the same.

It is not wishful thinking, it is supported by your own data which shows that the relationships cancel out and the net effect is not different from zero. Random error differs most from zero with small samples, so the odds are much greater that the net effect will approach zero as the samples of alleles gets larger. It is quite plausible that the correlations with IQ differences between races are non-causal and spurious and that is why they are so unreliable and all over the spectrum from high to low to negative. IOW, even if those alleles have a causal impact on within group differences in IQ, they might have no causal impact on between group difference and the correlations for individual alleles are spurious products of third variable factors.

 

[ApostateAbe]

Yes, that's right. More precisely, these results can be expected from just about any genotypic IQ distribution. But, what can NOT be concluded is that every race has exactly the same alleles for intelligence. Maybe a race lacks some alleles for intelligence and compensates perfectly with other alleles. There is no reason we should expect that but for ideology or wishful thinking, but it is a possibility all the same.

It is not wishful thinking, it is supported by your own data which shows that the relationships cancel out and the net effect is not different from zero. Random error differs most from zero with small samples, so the odds are much greater that the net effect will approach zero as the samples of alleles gets larger. It is quite plausible that the correlations with IQ differences between races are non-causal and spurious and that is why they are so unreliable and all over the spectrum from high to low to negative. IOW, even if those alleles have a causal impact on within group differences in IQ, they might have no causal impact on between group difference and the correlations for individual alleles are spurious products of third variable factors.

There is large random error given any proposed distribution for such a small set of alleles. If the results are expected from distributions of alleles equal to 0 IQ differences, that point would be hardly relevant if they are likewise expected from ANY distribution. It is night, and the closet is dark and black--exactly what we expect if there is a monster lurking in it.

 

[EgalitarianJay]

This sounds like complete garbage.

Then I have a challenge for you: try making sense of the process of evolutionary divergence without biological races. Tell me how it works.

Race has roughly the same meaning as "lineage", "kind" or "subspecies."

Race in zoological taxonomy refers to variation below the species level. A race is a population on the cusp of speciation. Race may be an end result of evolutionary divergence but you don't need races for micro-evolution to occur.

This article debunks the notion that "IQ genes" are differentiated racially.

Race, Genomics and Intelligence:Slight Return



Joseph L. Graves Jr.

Joint School for Nanosciences & Nanoengineering,
North Carolina A & T State University & UNC Greensboro,
Greensboro, NC, US
​

Abstract


The notion that genetic/genomic differences among racial groups are responsible for observed differences in measured intelligence is recurring. Certainly, genetics, race, and intelligence arguments have been advanced with each increase in the sophistication of genetics (Graves 2005a). Not surprisingly this has continued in the modern genomics era. The reader must be aware that are significant definitional issues that impact this argument. The first refers to the notion of race. The second definition that must be considered is the notion of intelligence. I refer the reader to Sternberg (2012) for a good review of the intelligence question. Surprisingly (not too surprisingly once we familiarize ourselves with the history of the race and intelligence debate; see Graves 2005b), measurers of intelligence have not effectively addressed racial definitions. In the main, they have focused their attention on differences between groups of people that are clearly socially defined, but not so clearly biologically differentiated in ways that would support their claims. Thus this chapter will first discuss and describe human biological genetic differentiation, specifically with how this variation impacts genetic causal factors that purportedly impact intelligence, and finally modern genomic approaches to the genetic influences on intelligence.

Full Article

 

[ApostateAbe]

Good to have you back, Jay. Looks like Dr. Graves is sharing the Word docs of his articles with you!

 

[EgalitarianJay]

Good to have you back, Jay. Looks like Dr. Graves is sharing the Word docs of his articles with you!

Indeed. Actually he shared a PDF version as well which I find to be more readable.

Link

 

[ApostateAbe]

Thanks! I have that article in my Dropbox folder since you shared it with me.

Graves cites Sewall Wright. I have seen many conflicting claims about Sewall Wright and F_ST concerning race. Even within the literature of Graves, I see conflicting claims. I bought the most commonly-cited book of Wright to sort out the facts. It turns out that Graves lied. I would hesitate to use such strong language, but I know that Graves likewise has Wright's book, he is literate, his critics have corrected him on this point many times, and such hostile language is not beneath Graves, as you are aware (i.e. Joseph Graves and Terri Place's, "Race and IQ Revisited: Figures Never Lie, but Often Liars Figure," 1995). The spurious claim is as follows:

The population subdivision statistic (F_ST) compares the allelic diversity of each of the subpopulations against a pooled total population. Since Wright’s invention of F coefficients, which examine the proportioning of genetic variation between different levels within a species, population geneticists have utilized a minimum value of differentiation between subpopulations and the total species as the threshold for identifying the existence of biological races (F_ST> 0.250). Wright chose this value to maximize the probability that the subgroups were actually fixed for alternative different alleles at various loci.​

He cites this book by Wright, which I have in my possession:

Wright, S. (1978). Evolution and the Genetics of Populations, Vol. 4: Variability within and among Natural Populations, Chicago, IL: University of Chicago Press.​

Now, to be fair, Graves does not claim that Wright used a threshold of F_ST> 0.250 for races. No, he claimed that anonymous "population geneticists" do, in the context of talking about Wright. But, he has no source for this claim about population geneticists, so a reader is led to think that this is Wright's threshold for biological races. If Graves intended that "population geneticists" use this threshold though not Wright, then he needs a source. But, that would be impossible, because no population geneticist has ever apparently used this threshold for identifying "races." That is the lie.

It reminds me of Matthew 2:23.

"...and [Jesus] went and lived in a town called Nazareth. So was fulfilled what was said through the prophets, that he would be called a Nazarene."

There is no ancient Jewish prophecy to be found anywhere that anyone would be called a Nazarene. It was apparently made up, though it is difficult for a critical reader to conclusively falsify, as the "prophets" remain anonymous.

So, this isn't a direct misattribution of Sewall Wright. It is evolution away from his earlier lie, found in "Against racial medicine," 2006, where he really did directly misattribute F_ST> 0.25 as Wright's "minimum threshold for the existence of racial differentiation." The claim was in direct conflict with Sewall Wright's cited book. Wright used 0.25 as the threshold for "very great differentiation," not racial differentiation, and he wrote in the same book that human races would be counted as subspecies by taxonomists by the standards common among taxonomists, except for a custom of vocabulary, though Wright also stated that the F_ST of human races was about 0.12.

Joseph Graves seems to be one of the two authors who have created a very common myth about F_ST and race. The other guilty author is Alan Templeton, who has repeatedly misrepresented his only source, Smith, Chiszar, and Montanucci, "Subspecies and Classification," 1997.

I have focused on this point because it is one I have taken special pains to investigate. But, maybe it isn't the most important point for you. If not, then what point of Graves do you find most relevant?

 

[ApostateAbe]

Interesting statement on page 2:

"Rushton spent a great deal of time attempting to demonstrate the existence of biological races in the human species (Rushton, 2000). His views on this issue were widely accepted by psychometricians."

When I make the claim that the majority of intelligence researchers believe that racial differences in intelligences are largely due to genetics, I have met with a lot of skepticism--not just on the point that there are racial intelligence differences due to genetics, but on the point that a majority of intelligence researchers believe it. People enter the debate believing that I am the one in the pseudoscientific fringe. Since we have last talked, all of my threads on the topic have been moved and restricted to the "Pseudoscience" forum.

 

[EgalitarianJay]

ApostateAbe,

I will email Dr. Graves and ask for a source on population geneticists using the value of 0.25 as the threshold for classification of biological races.

I have focused on this point because it is one I have taken special pains to investigate. But, maybe it isn't the most important point for you. If not, then what point of Graves do you find most relevant?

The most relevant point for this thread is that genetic variants which account for the distribution of intelligence are not differentiated racially.

At least 1/3 of the 20,000 genes of the human exome are actively expressed in the human brain (Institute of Neurological and Brain Disorders, 2012). Given that brain function undoubtedly has something to do with cognitive performance, the notion that we can identify a small number of candidate genes which will capture the majority of the variation in the normal range of human intelligence is absurd. Clearly there are a number of mutations which occur in specific genes that reduce intelligence. These mutations have high penetrance and have pleiotropic impacts on a variety of physiological systems. Such pathological mutations have been well-studied and we know a great deal about how natural selection acts to reduce the frequency of such alleles. In this regard, the brain is no different from any other organ. However, comparing high penetrance mutations that are pathologic in character to genetic variants which account for normal variation in cognitive function is like comparing apples and watermelons.

Source: Race, Genomics and Intelligence: Slight Return by Joseph Graves

Interesting statement on page 2:

"Rushton spent a great deal of time attempting to demonstrate the existence of biological races in the human species (Rushton, 2000). His views on this issue were widely accepted by psychometricians."

When I make the claim that the majority of intelligence researchers believe that racial differences in intelligences are largely due to genetics, I have met with a lot of skepticism--not just on the point that there are racial intelligence differences due to genetics, but on the point that a majority of intelligence researchers believe it. People enter the debate believing that I am the one in the pseudoscientific fringe. Since we have last talked, all of my threads on the topic have been moved and restricted to the "Pseudoscience" forum.

When he says "psychometricians" I believe Graves is referring to hereditarian racialists who happen to be psychometricians and not the majority of intelligence researchers. This is based on personal communication with him.

Here is an example from published literature supporting my point:

In 1999, Transaction Publishers released an abridged version of J. Philippe Rushton’s Race, Evolution, and Behavior: A Life History Perspective, the unabridged version having originally been published in 1995. The new, abridged version has been sent to a number of scholars, particularly anthropologists at universities throughout Canada and the United States. It has been hailed by all the leading proponents of genetically determined racial hierarchy: Arthur Jensen, Thomas Bouchard, Linda Gottfredson, Hans Eysenck, and Richard Lynn. They champion Rushton’s views because their program lacks any specific or credible evolutionary genetic rationale that could possibly explain why ‘race’ specific differences in IQ should exist.

Source: What a tangled web he weaves: Race, reproductive strategies and Rushton's life history theory Anthropological Theory 2002; 2; 131