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The DNA of Genius (n=2)
Polygenic scores cannot predict a person's IQ, but can they tell a genius apart from the crowd?
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watson and venter results

A day is a long time in genetics research. Yesterday I made the following prediction about the method that David Piffer has used to estimate racial intelligence:

Prediction: we will need very many more SNPs before we can attempt predictions of individual IQs across different races at better than a correlation of r=0.7

Having made that bold prediction, it struck me I should ask Piffer if his newly enhanced predictive equation could make a fresh calculation as to the intelligence of James Watson and Craig Venter. It was the inability of his method to classify these two leading lights of genetic research which Professor Neil Risch had used to make fun of Piffer when giving his American Society of Human Genetics Presidential Address in 2016. Piffer turned down my request, saying “Well, that would be like carrying out another mini GWAS (or better, a case control study) with 2 people instead of 100,000. No scientific value beyond anecdotal curiosity.”

Ever bold, I championed the cause of anecdotal curiosity. To keep him motivated, I did not say that his getting a positive result was no more likely than bird droppings in a cuckoo clock. An n of 2 is very, very silly, but I am ever a curious person. After a few hours Piffer relented, and this was his reply.

I looked up the 9 SNPs (the “perennial reliables”) for Educational Attainment. Note that these are the same SNPs that Michael Woodley and I used to successfully predict evolution of intelligence since the Bronze Age. They were identified by myself by finding the replicates across Educational Attainment GWAS. They are highly predictive of population IQ (r= 0.9). One of those SNPs was missing from Watson and Venter but the odds ratios and frequencies are in line with predictions.

This is the matrix with allele count and results of Fisher’s Exact test. Not significant (p=0.17) but odds ratios (O.R.= 1.53) are quite good (indicating the overrepresentation of intelligence-enhancing alleles in Watson and Venter’s genomes compared to the average White American (CEU) person.

Intelligence-enhancing allele Intelligence-decreasing allele
Watson and Venter 12 10
1KG CEU (White American) 497 691

Summary statistics: The average frequency of intelligence-enhancing alleles is 47.2% in Watson and Venter’s DNA but only 42.9% for the average White person and 35.6% for the (Nigerian) Yoruba.
watson and venter results

 

In sum, it would appear that even this general method of predicting racial differences in intelligence can be pressed into service to hazard a guess that the two scientists in question are more intelligent than the average European.

I would have been interested if it had been possible to add the DNA of Francis Crick, but you can’t have everything. I presume there is also no DNA for Maurice Wilkins, with whom I worked with very briefly when carrying out a study on the effects of the Christmas Island nuclear weapons tests, but he mournfully declined to add his name to the letter we wrote to the Lancet in 1983 describing that work, saying by way of apology: “Critics say I sign too many letters, so it’s better that I don’t sign this one”. I should have got a buccal swab from him instead.

Onwards and upwards to the sunlit uplands.

 

 
• Category: Science 
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  1. dearieme says:

    Watson thought Crick a very clever fellow. Watson isn’t given to modesty, false or otherwise. So I dare say that Crick was indeed a very clever fellow.

    Does Watson ever chime in here? It would be interesting to hear his view on your jolly jape, doc.

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  2. Older age and incapacity to accept that genius CORRELATES with IQ but it doesn’t mean will be always like that…. indeed, IQ is ONE factor among a combination of other factors, even not so desirable ones…

    C’e triste

    HDD et all talk about intelligence as if they knew EVERYTHING about it, disgustingly stupid!!

    war is peace

    ”intelligence researchers” ”are’…

    Many nursisistic people is moved to ”study’ about intelligence….
    ;)

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  3. Hi Dr Thompson.

    I just finished reading “DNA is not destiny” by Steven Heine and he says the same thing. He doesn’t believe well ever be able to estimate IQ from that either if I recall correctly.

    I also just bought “Genes, Brains, and Human Potential” by Ken Richardson and he hugely critiques the new studies coming out on hits for IQ and education related genes.

    You should pick up both books. They are great reads. Kinda has me thinking, to be honest.

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  4. res says:

    I am having a bit of trouble fully interpreting that first graphic. If I understand correctly, those are standard box plots: http://www.physics.csbsju.edu/stats/box2.html
    That really does not work well with n=2 (and what is the point at 0?), but if I am interpreting it correctly the Watson&Venter plot indicates data points at 0.5 and 1 (inquiring minds want to know which is which ; ) giving an average of 0.75?

    The CEU and (especially) Yoruba plots are much more interesting. CEU looks like a fairly typical normal distribution, but the Yoruba plot has a significant right skew (and extends much higher than the higher median CEU population!). It would be interesting to see a full distribution plot of the Polygenic scores for the Yoruba. Any thoughts on whether this might be a sign of subpopulations? That plot makes a decent case that there are at least some high potential IQ individuals in Africa (disproportionately so relative to the normal curve assumption!). Which is not surprising to me, but leads to further questions about who are they, etc.? This seems highly relevant to the discussions in Chanda Chisala’s blog.

    Would it be possible to see Box plots for all of the populations? Perhaps also full distribution plots, but those would be harder to gather in a small number of plots for easy comparison.

    Thanks to Dr. Thompson and Davide Piffer for motivating/performing this analysis.

    P.S. I have downloaded Piffer’s data and am in the process of trying to replicate his RPub results (previous post) in R so I may be able to generate this myself soon (minus the Watson&Venter bit).

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    • Replies: @Jm8
    Interestingly it seems that some African populations score above some Amerindian ones (e.g. the Mandinka and the Yoruba above the Maya, Pima, and South American Indians; and the Biaka and Kenyan Bantu above the Surui and Karitiana) , and also overall in the "subcontinental average factor scores" where Sub Saharan Africa is just above the Amerindians (and of course the results may also be somewhat confounded by the complication Cochran mentioned; Africans possibly having their own alleles affecting IQ that are not detected—or as much picked up, etc.):

    https://topseudoscience.wordpress.com/2017/06/02/new-genes-same-results-group-level-genotypic-intelligence-for-26-and-52-populations/

  5. Anonymous says: • Disclaimer

    Watson is no genius. He is a smart guy who happened to be in the right place in the right time. It was Crick who was a genius. Wilkins was just ordinary with no spark or an unusual insight on anything. Crick should have won a second Nobel for the contributions to figuring out genetic code. Franklin would have never solved the structure on her own – her understanding of her own narrow field was inferior to Crick’s and she lacked imagination that was absolutely required, given the kind of data obtained from the kind of DNA they were working with.

    Read More
    • Replies: @James Thompson
    Privately, other commentators have come to the same conclusion. Crick, in a word, the others helpful, but no more. The one really left out of the picture was Dorothy Hodgkin, but she got her Nobel for Chemistry anyway.
  6. res says:

    On a related note, it would be interesting to see this Polygenic score included in 23andMe and/or Promethease, etc. reports and get an idea of the frequency distribution in those populations.

    Read More
  7. Jm8 says:
    @res
    I am having a bit of trouble fully interpreting that first graphic. If I understand correctly, those are standard box plots: http://www.physics.csbsju.edu/stats/box2.html
    That really does not work well with n=2 (and what is the point at 0?), but if I am interpreting it correctly the Watson&Venter plot indicates data points at 0.5 and 1 (inquiring minds want to know which is which ; ) giving an average of 0.75?

    The CEU and (especially) Yoruba plots are much more interesting. CEU looks like a fairly typical normal distribution, but the Yoruba plot has a significant right skew (and extends much higher than the higher median CEU population!). It would be interesting to see a full distribution plot of the Polygenic scores for the Yoruba. Any thoughts on whether this might be a sign of subpopulations? That plot makes a decent case that there are at least some high potential IQ individuals in Africa (disproportionately so relative to the normal curve assumption!). Which is not surprising to me, but leads to further questions about who are they, etc.? This seems highly relevant to the discussions in Chanda Chisala's blog.

    Would it be possible to see Box plots for all of the populations? Perhaps also full distribution plots, but those would be harder to gather in a small number of plots for easy comparison.

    Thanks to Dr. Thompson and Davide Piffer for motivating/performing this analysis.

    P.S. I have downloaded Piffer's data and am in the process of trying to replicate his RPub results (previous post) in R so I may be able to generate this myself soon (minus the Watson&Venter bit).

    Interestingly it seems that some African populations score above some Amerindian ones (e.g. the Mandinka and the Yoruba above the Maya, Pima, and South American Indians; and the Biaka and Kenyan Bantu above the Surui and Karitiana) , and also overall in the “subcontinental average factor scores” where Sub Saharan Africa is just above the Amerindians (and of course the results may also be somewhat confounded by the complication Cochran mentioned; Africans possibly having their own alleles affecting IQ that are not detected—or as much picked up, etc.):

    https://topseudoscience.wordpress.com/2017/06/02/new-genes-same-results-group-level-genotypic-intelligence-for-26-and-52-populations/

    Read More
  8. @Anonymous
    Watson is no genius. He is a smart guy who happened to be in the right place in the right time. It was Crick who was a genius. Wilkins was just ordinary with no spark or an unusual insight on anything. Crick should have won a second Nobel for the contributions to figuring out genetic code. Franklin would have never solved the structure on her own - her understanding of her own narrow field was inferior to Crick's and she lacked imagination that was absolutely required, given the kind of data obtained from the kind of DNA they were working with.

    Privately, other commentators have come to the same conclusion. Crick, in a word, the others helpful, but no more. The one really left out of the picture was Dorothy Hodgkin, but she got her Nobel for Chemistry anyway.

    Read More
    • Replies: @Anonymous
    Agree! BTW, Franklin still deserved the Nobel because she was fantastic experimentalist/technician who made a key contribution. That she was able to get any data from the material they had is nothing short of a miraculous. If course, without data any model would have remained just a model for a very long time.

    Hodgkin was top notch on all levels.

  9. Anonymous says: • Disclaimer
    @James Thompson
    Privately, other commentators have come to the same conclusion. Crick, in a word, the others helpful, but no more. The one really left out of the picture was Dorothy Hodgkin, but she got her Nobel for Chemistry anyway.

    Agree! BTW, Franklin still deserved the Nobel because she was fantastic experimentalist/technician who made a key contribution. That she was able to get any data from the material they had is nothing short of a miraculous. If course, without data any model would have remained just a model for a very long time.

    Hodgkin was top notch on all levels.

    Read More
    • Replies: @James Thompson
    I remember sitting next to her at a very small (n=28) Pugwash conference on Nuclear Forces in Geneva in December 1986 , at which the Russian generals were arguing with the American generals about which way the long range Russian radars were pointing, and she fell asleep. She roused herself later, explained who she was very modestly, and we chatted afterwards.
    , @dearieme
    I've seen somebody suggest that a fair outcome would have been the physiology/medicine prize for Crick & Watson, and the chemistry prize for Wilkins & Franklin (had she but survived).

    I have met people qualified to have a view on the matter but they've had other things to talk about.
  10. @Anonymous
    Agree! BTW, Franklin still deserved the Nobel because she was fantastic experimentalist/technician who made a key contribution. That she was able to get any data from the material they had is nothing short of a miraculous. If course, without data any model would have remained just a model for a very long time.

    Hodgkin was top notch on all levels.

    I remember sitting next to her at a very small (n=28) Pugwash conference on Nuclear Forces in Geneva in December 1986 , at which the Russian generals were arguing with the American generals about which way the long range Russian radars were pointing, and she fell asleep. She roused herself later, explained who she was very modestly, and we chatted afterwards.

    Read More
  11. dearieme says:
    @Anonymous
    Agree! BTW, Franklin still deserved the Nobel because she was fantastic experimentalist/technician who made a key contribution. That she was able to get any data from the material they had is nothing short of a miraculous. If course, without data any model would have remained just a model for a very long time.

    Hodgkin was top notch on all levels.

    I’ve seen somebody suggest that a fair outcome would have been the physiology/medicine prize for Crick & Watson, and the chemistry prize for Wilkins & Franklin (had she but survived).

    I have met people qualified to have a view on the matter but they’ve had other things to talk about.

    Read More
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