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Exclusive interview with genomic researcher Davide Piffer

19 Sunday Jan 2020

Posted by pumpkinperson in Uncategorized

≈ 101 Comments

Tags

ancient DNA, cold winters, Davide Piffer, ethnicity, IQ, John Hawks, Michael Woodley, mutations, Neanderthals, polygenic scores, race, Richard Lynn

I am extremely honored that Davide Piffer (who has a blog) was kind enough to give our community an exclusive interview. While the leading geneticists in academia have explained only about 10% of the variance in IQ (or its proxy education) at the individual level, Piffer working on his own has reported near perfect correlations between the mean IQs of entire ethnic groups and their polygenic scores, making him a rock star in the HBD community. Virtually no one else on the planet is doing this kind of cutting edge research (at least not publicly).

In retrospect it makes perfect sense that aggregated data should correlate much better than individual level data. Imagine you visited every country in Eurasia and asked only the first person you met in each country their height. Such a small sample size (n = 1) from each country would tell you nothing about which individual country was taller than which, but if you averaged all the heights from the European countries and compared them to the average heights from the Asian countries, you’d learn a lot about which continent was taller. That’s because the small sample size at the level of individual countries is multiplied by the large sample of countries in each continent.

It’s the same with genomically predicting IQ. The small sample of single nucleotide polymorphisms (SNPs) sampled in each individual is multiplied by the large number of individuals sampled in each ethnic group, so while individual predictions are weak, group predictions are strong because individual error cancels out in the aggregate.

Below is my exclusive interview with Piffer. The interview has been lightly edited to remove typos and other mistakes. I began by asking him about table 5 in a 2019 paper he wrote. My statements are in red, while Davide’s are in blue.

Table 5 from the paper Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data

PP: I’m very impressed by your work. But the correlation between PG score & mean IQ is so high in table 5 of Piffer (2019) that it seems too perfect. What would you say to skeptics who think you cherry-picked SNPs or manipulated your formulas to get such perfect results?

DP: Thanks. I didn’t cherry pick SNPs. I used the polygenic score provided by Lee et al and you can see that different PGS construction methods lead to same results… I used EA, EA Mtag, etc, weighted and unweighted..they all give same results. Also my paper replicates my previous findings and what I had predicted from theory years ago. The IQs aren’t cherry picked either because I used the same as I used in previous papers to avoid post hoc results.

PP: In table 1 of Piffer (2019), Peruvians & Colombians seem to have higher polygenic scores than the black populations, yet in Figure 11, Africa scores higher than the Americas. So who has higher polygenic scores: sub-Saharan Africans or Amerindians?

top part of table 1 from the paper Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data
rest of table 1 from the paper Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data
Figure 11 from the paper Evidence for Recent Polygenic Selection on Educational Attainment and Intelligence Inferred from Gwas Hits: A Replication of Previous Findings Using Recent Data

DP: Peruvian and Colombian aren’t pure. They are substantially mixed with Europeans. The groups in figure 11 are natives, so they better reflect the unadmixed population. Also the latter are from low coverage genomes with fewer markers so less reliable. I am working on a high coverage version of same datasets but it will take a while due to my limited funds.

Do you have some basic experience in bioinformatics? I am just looking for someone who could run the code on their laptop because it’s taking me a week to impute each chromosome. So I need to run it on multiple computers. But hey no bother…I will do it myself, it will just take it longer.

PP: No sadly I do not have experience with bioinformatics. But I can ask my blog & twitter readers if anyone has such experience and is willing to volunteer their time.

On table 5 of Piffer (2019) the African American PGS (GWAS sig) is 1.836 lower than the NW European PGS. But since African Americans are only 76% non-white (Bryc et al. 2015), can we roughly infer that un-mixed blacks would be 1.836/0.76 = 2.416 below NW Europeans, giving them a PGS score of 46.834?

DP: yes…also you have unmixed native Africans in the other tables. Kenyans, Yoruba, Mende Sierra Leone, etc

PP: In table 5 Latinos have a PGS (GWAS sig.) of 48.654. Do you think this could be used to estimate the PGS of unmixed Amerindians because according to Bryc et al, 2015, Latino Americans are 65.1% white (mostly southern European), 6.2% black, 18% Amerindian, and 11% unassigned, though the unassigned is broader East Asian/Amerindian so should probably be counted as Amerindian. Since you report the PGS for Southern Europeans and since I estimate the the PGS for pure blacks at 46.834, using simple algebra, I estimate unmixed Amerindians would have a PGS of 47.510.

DP: yes, but you should also cross-check these with the other table with scores for Peruvians and Mexicans and see if they converge.

PP: Good point. In one of your data sets you find a 0.57 correlation between PGS and latitude. Do you agree with Lynn’s cold winter theory of how racial differences in intelligence evolved?

DP: in part, yes. but it doesn’t explain the low Amerindian IQ because Native Americans were in Siberia during the Last Glacial Maximum and then they moved to North America at the end of it, which is also a cold region…So I think most of the differences are due to farming and civilization

PP: Well Lynn argues the anomalies can all be explained by population size. Low population races like Arctic people, Amerindians, Australoids, Bushmen, & pygmies have lower IQs than their climates predict because there weren’t enough positive mutations. Meanwhile high population races like East Asians, whites, South Asians, and West Africans have higher IQs than their climates predict. This would also explain why Neanderthals had lower IQs than their climates predict.

DP: but these SNPs are common among the races..the differences are explained by these common SNPs, not pop specific mutations. pop size is probably related to it through higher competition for resources selecting for higher IQ.

PP: I see…so then it was probably farming and civilization as you say. Just as cold climate boosted IQ because it was a novel environment to adapt to, so was farming, civilization and the literacy and numeracy requirements it imposed. Of course Amerindians also independently created civilization but most remained hunter-gatherers.

DP: yes… plus we don’t know how many of these SNPs are just life history or personality traits like C. stuff that farming selected for. most of them are related to g but a subset will also be related to conscientiousness. Emil et al in their Psych paper vetted their association with g in a sample though so I guess they must be genuine associations with IQ for the most part.

PP: Yes, because no one has given a huge sample (n = 1 million) of genotyped people a highly g loaded test. A perfect study would get a sample of 1 million people (from all over the world) and give them an extremely culture reduced test with many subtests to maximize g loading (i.e. block design, draw a person in the sand, name as many body parts as you can in 1 minute in your own language, pictorial oddities etc) and then enter the composite score, DNA and human development index of each person into a computer and have machine learning create a multiple regression equation predicting IQ using HDI & genomic variants as independent variables. By using such a diverse and global sample, one finds the genomic variants that correlate with IQ everywhere and thus are most likely to be causal.

DP: yes.

PP: Now that the neanderthal genome has been published, why haven’t you tried to estimate their polygenic score? Richard Klein argues that before about 50 kya, modern humans and neanderthals had similar intellect, but suddenly around 50 kya there was a genetic brain change that allowed modern humans to leave Africa, colonize every continent, replace neanderthals & invent art & complex technology. Testing this hypothesis was the main motivation to sequence the neanderthal genome so there’s enormous interest in their intelligence, even in mainstream science.

DP: yes that’s the next step…we’re analyzing genomes from Bronze age now, but Neanderthal would be good. But funds are limited for this kind of research and I am not working in academia.

PP: Above you rejected Lynn’s population size mutation theory on the grounds that all races have all the known IQ related genomic variants, however it also seems you have no high coverage genomes from low population isolated groups like pygmies, bushmen, australoids, arctic people & pure Amerindians. Is it plausible that high coverage genomes of these groups would show they are missing some of the IQ enhancing mutations that appeared in the last 15,000 years?

DP: What I am saying is that you can see a difference even at the common SNPs in their frequencies. I cannot rule out that they are also missing these mutations but that would be an additional factor.

PP: Do you agree with John Hawks’s theory that positive selection in the last 5000 years has been a hundred times faster than in any other period of human evolution because of the explosion of new mutations & environmental change? This is the exact opposite of Gould who argued we have the same bodies and brains we’ve had 40,000 years ago and all subsequent change has been cultural not biological.

DP: from a purely theoretical point of view, yes, but one would need to study ancient genomes to empirically vet that hypothesis.

PP: Is there any strong evidence in support of Michael Woodley’s theory that white genomic IQ has declined by 10 or 15 IQ points since the Victorian era?

DP: I computed the decline based on the paper by Abdellaoui on British [Education Attainment] PGS and social stratification and it’s about 0.3 points per decade, so about 3 points over a century.

It’s not necessarily the case that IQ PGS declined more than the EA PGS..if anything, the latter was declining more because dysgenics on IQ is mainly via education so I think 3 points per century is a solid estimate

Thank you Davide Piffer for this interview. As mentioned above, you can find more of Davide’s thoughts on his blog.

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A near perfect correlation between ethnic IQ & ethnic DNA

17 Friday Jan 2020

Posted by pumpkinperson in Uncategorized

≈ 40 Comments

Tags

Davide Piffer, ethnicity, IQ, polygenic scores, race

Davide Piffer looked at 2,404 genomic variants found to predict education (a rough proxy for IQ) and used these to create polygenic scores of eight ethnic groups reared in First World conditions. He then compared the polygenic scores with the mean IQ of each group and found a 0.979 correlation.

Table 5 from Evidence for Recent Polygenic Selection on
Educational Attainment and Intelligence Inferred
from Gwas Hits: A Replication of Previous Findings
Using Recent Data
by Davide Piffer, 2019

The line of best fit allows us to predict the mean IQ of any group from their PGS (GWAS sig.):

Mean IQ = 9.31(PGS (GWAS sig.)) – 358

Given the 0.979 correlation, genotype predicts IQ remarkably well: Finnish 102, Ashkenazi 108, Southern Europe 99, Estonia 100, NW European 100, African American 83, Latino 95, East Asians 105.

So while our genomic predictions of IQ remain poor at the individual level, Piffer is showing we can predict the mean IQs of ethnic groups with incredible precision, at least when they’re all reared in similar countries.

Because we have only found a tiny fraction of the genetic variants associated with IQ (or its proxy education), the margin of error for predicting any one person’s IQ remains high. But when you try to predict the average IQ of an entire ethnic group, the overestimates and underestimates cancel each other out, and there’s a near perfect correlation between the mean polygenic score and the mean IQ.

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Correcting ethnic IQ differences for nutrition

01 Wednesday Oct 2014

Posted by pumpkinperson in Uncategorized

≈ 41 Comments

Tags

ethnicity, Flynn effect, IQ, nutrition, race, Richard Lynn

Readers of the New York Times have long known that there might be genetically based ethnic differences in IQ, but few people appreciate that nutrition also plays a huge role in IQ. For example, thanks to malnutrition, British whites in the 19th century had real IQ’s around 76 (on modern norms), though this was spuriously pushed down to IQ 66 by lack of schooling (see the Flynn effect). By comparison, in his book Race Differences in Intelligence, scholar Richard Lynn reports the following IQ’s for 10 major populations:

North East Asians: IQ 105
Europeans: IQ 99
Arctic peoples: IQ 91
Southeast Asians: IQ 87
Native Americans: IQ 86
Pacific Islanders: IQ 85
Non-white Caucasoids: IQ 84
Sub-Saharan agriculturalists: IQ 67
Australian aboriginals: IQ 62
Sub-Saharan hunter/gatherers: IQ 54

How much of these scores were affected schooling? Probably not much because virtually all the samples were school children. A major exception being sub-Saharan hunter’gathers, but Lynn estimated their IQ largely by comparing them to equally unschooled neighboring agriculturalist who score IQ 67 with schooling. Since the Bushmen scored about a dozen points lower, it was reasonable to assume that with schooling, Bushmen would score in the mid 50s. Although IQ tests are supposed to measure native ability, few tests are 100% culture fair so it’s necessary to control for schooling when comparing disparate cultures.

So if schooling did not affect these scores, what about nutrition? Although Lynn concedes that malnutrition adversely affects the IQ’s of third-world peoples, no attempt was made to correct the IQ’s for this effect. However on page 184, Lynn provides a table showing the prevalence of malnutrition for various geographic regions. The table lists several measures of malnutrition (i.e. percent underweight, percent wasted, percent stunted, percent anemic) and averaging across the different measures that are provided, implies that as of 1996, malnutrition afflicted 30% of Sub-Saharan Africa, 14% of the Middle East & North Africa, 45% of South Asia, 21% of East Asia & Pacific, and 16% of Latin America & Caribbean. Elsewhere in the book he claims that 25% of Australian aboriginals are malnourished.

I estimated that for each percentage of the population that is nutritionally deficient enough to be proclaimed malnourished, the average IQ of the population is lowered by 0.43 IQ points. This estimate is based on the fact that Lynn notes that African Americans with virtually no white admixture have IQ’s 13 points higher than their genetic counterparts in sub-Saharan Africa, 40% of whom are malnourished. Thus 40 multiplied by 0.43 lowers a population’s IQ 13 points below its potential. So correcting the IQ’s of all the ethnic groups for the level of malnutrition in the regions that they live, gives the following:

Northeast Asians: IQ 105 (no corrections, they live in first world countries)

Europeans: IQ 99 (no corrections, they live in first world countries)

Southeast Asians: IQ 96 (corrected for 21% malnutrition in East Asia & the Pacific Islands)

Pacific Islanders: IQ 94 (corrected for 21% malnutrition in East Asia & the Pacific Islands)

Arctic people: IQ 91 (no corrections, they live in first world countries)

Non-white Caucasoids: IQ 90 (corrected for 14% malnutrition, since they mostly live in the middle east/North Africa)

Native Americans: IQ 89 (many live in Latin America which has 16% malnutrition, others live in first-world North America, I split the difference & corrected for 8% malnutrition)

Sub-Saharan agriculturalists: IQ 80 (corrected for 30% malnutrition in Sub-Saharan Africa)

Australian aboriginals: IQ 73 (corrected for 25% malnutrition mentioned by Lynn)

Sub-Saharan hunter/gatherers: IQ 67 (corrected for 30% malnutrition in Sub-Saharan Africa)

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Caste & IQ in India

29 Monday Sep 2014

Posted by pumpkinperson in Uncategorized

≈ 62 Comments

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castes, ethnicity, evolution, India, IQ

Blogger Alcoholicwisdom wrote on this blog:

Are there any studies on IQ differences between indian castes?

I am in strong favor of the idea that there are IQ differences between castes, of course we need some studies. In every society there are castes, classes, based on intrinsic abilities and intelligence. Nobody would accept a priest which cannot even understand basic religious subjects. Religion at that time was like philosophy which requires a high intelligence, and the smartest people were probably brahmins. The smartest jews are also from rabbi families (my belief). The priests were like scientists, philosophers of their times. Nowadays, the picture is different, as the religions lost their smartest kids mostly to hardcore sciences.

I would seriously doubt there have been any published studies on IQ and caste in India, but there’s a fabulous expert named rec1man who posted on Steve Sailer’s old blog. rec1man did the following analysis of India’s potential IQ:

25% Dalit and Tribal = 80 IQ
15% Muslim = 85 IQ
40% Backward Caste = 95 IQ
15% Upper Caste = 110 IQ
The only item missing is the 5% brahmins

…Making a worst case assumption that
Brahmin IQ is no more than Upper caste IQ , would give a brahmin IQ estimate of 110

My private real numbers are a lot higher, but I wont stir up a controversy , until we reach a consensus on average Indian iQ

Average Indian IQ = 0.25*80 + 0.15*85 + 0.40*95 + 0.15*110 + 0.05*110 = 92.75

The upper caste + brahmin segment = 20% of 1.1 billion = 220 million
at near Ashkenazi levels

Note that rec1man is obviously estimating what India’s IQ would be if India had a first-world environment, because India’s actual IQ is 82 not 93. But as I explained in my last post, India, like sub-Saharan Africa, is probably functioning 13 IQ points below its genetic potential because of sub-optimum nutrition, so a genetic IQ in the mid 90s is realistic (just keep in mind that all of rec1man’s numbers are about a dozen points higher than current phenotypes reared in India).

In other words, India’s genetic IQ distribution looks very much like the United States. The U.S. also have an average IQ in the mid-90s (97 to be precise). This may sound confusing to people who are used to reading that America’s IQ is 100 by definition, but rec1man appears to be using the old IQ scale (which has become popular again thanks to scholar Richard Lynn) in-which IQ 100 represents the average of only people’s of Northwestern European ancestry. Since the U.S. is not overwhelmingly Northwestern European, they are 97 on this scale.

The United States also resembles India’s genetic IQ in that the U.S. also has some social groups with IQ’s around 110 and others around 80 in their purest form. For example the New York Times cites research showing Ashkenazi Americans have IQ’s around 110.

The only thing I find strange about rec1man’s numbers is the assertion that Indian Muslims are 8 points lower than the average Indian intelligence. I don’t buy the Islamophobic crap about Islam making people stupid or violent. Not because I’m some liberal, but rather because I believe real intelligence is a biological variable that is virtually insensitive to cultural influences. I could be completely wrong about that, but my belief is based upon research.

If you agree with the New York Times article about some ethnic IQ differences being potentially genetic, you should know that Indians are not exactly one ethnic group. The original Indians were probably proto-Australoids taking the Southern route from sub-Saharan Africa to Australia. Ancient Australoid genes probably drag India’s IQ down because this population branched off the human-evolutionary tree prematurely. According to Richard Lynn Australian aboriginals have an IQ of 62 but in my opinion this is greatly depressed by sub-optimum nutrition.

India’s average IQ got a huge boost when it was invaded by the non-white Caucasoids who genetically mixed with the native proto-Australoids. According to Richard Lynn, non-white Caucasoids have a respectable average IQ of 84 (but even this IQ, high as it is, would be even higher if the Arab world had first-world nutrition which it doesn’t, despite it’s great oil wealth).

India’s IQ might have got yet another boost if there was an Aryan invasion. We don’t know anything about the ethnicity or IQ’s of the ancient Aryans and they probably weren’t exactly white as we define it today, but as stated above, Richard Lynn estimates North-Western Europeans have a mean IQ of 100. If we average all three groups together, we get India’s current IQ of 82.

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