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[OBG] Nature of Race Full

There are many grammar errors, but I don't want to wait until I finish with those details, so I re-approve and will send the corrections to Chuck by mail.

Concerning the modified/added content, I don't see anything I really think is wrong and I also appreciate the fact that the idea that subspecies (unlike intraspecific races) were thought as involving taxonomic categories has been expressed in a better, and more insisting way (so, in a sense, Krom's comments have been useful in this regard). The response to Pigliucci & Kaplan (2003) in section 5 has also been improved.
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Publication of this paper is currently on hold until we solve the Fst issue (related to the a,b,c) components. It's our (Chuck and mine) belief that this is an important point that it cannot be ignored. I am working on a solution (I am almost done, just one small last issue to solve) and Chuck in the meantime can make the necessary corrections to grammar errors.
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Removing children from family trios (N=24) did not alter the results, which were pretty much identical. Variance components are provided in table 1 and can be seen also at this link: https://docs.google.com/spreadsheets/d/1...sp=sharing
Please credit my work as:
Piffer, Davide; Dall'Olio, Giovanni Marco (2015): Using Vcftools to calculate Weir and Cockerham's variance components for 1000 Genomes phase 3 data. Figshare.
http://dx.doi.org/10.6084/m9.figshare.1450792
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(2015-Jun-16, 22:46:04)Duxide Wrote: Removing children from family trios (N=24) did not alter the results, which were pretty much identical. Variance components are provided in table 1 and can be seen also at this link: https://docs.google.com/spreadsheets/d/1...sp=sharing
Please credit my work as:
Piffer, Davide; Dall'Olio, Giovanni Marco (2015): Using Vcftools to calculate Weir and Cockerham's variance components for 1000 Genomes phase 3 data. Figshare.
http://dx.doi.org/10.6084/m9.figshare.1450792


Thanks. I mentioned and cited the results.

The final copy is attached for publication.

[Versions removed -- to preclude confusion -- but view-able at OSF.]
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(2015-Jun-17, 03:53:12)Chuck Wrote:
(2015-Jun-16, 22:46:04)Duxide Wrote: Removing children from family trios (N=24) did not alter the results, which were pretty much identical. Variance components are provided in table 1 and can be seen also at this link: https://docs.google.com/spreadsheets/d/1...sp=sharing
Please credit my work as:
Piffer, Davide; Dall'Olio, Giovanni Marco (2015): Using Vcftools to calculate Weir and Cockerham's variance components for 1000 Genomes phase 3 data. Figshare.
http://dx.doi.org/10.6084/m9.figshare.1450792


Thanks. I mentioned and cited the results.

The final copy is attached for publication.


References should include a doi, when it's an electronic journal and it has a doi.

In this instance you don't even mention the journal name, making it impossible to cite it:

Piffer, D. (2015a). Estimating the genotypic intelligence of populations and assessing the impact of socioeconomic factors and migrations. Journal? Doi?

This is how you should cite it:

Piffer, D. (2015a). Estimating the genotypic intelligence of populations and assessing the impact of socioeconomic factors and migrations. The Winnower. DOI: 10.15200/winn.142299.93508

Also these articles have doi but you don't report it:

Piffer, D (2015b): A review of intelligence GWAS hits: their relationship to country IQ and the issue of spatial autocorrelation. Figshare. http://dx.doi.org/10.6084/m9.figshare.1393160

Piffer, D. and Dall'Olio, G. M. (2015): Using Vcftools to calculate Weir and Cockerham's variance components for 1000 Genomes phase 3 data. Figshare. http://dx.doi.org/10.6084/m9.figshare.1450792

Finally, you give the wrong reference for this paper, whose final version was published on Mankind Quarterly and not on IBC. This is the correct reference:

Piffer, D. (2013). Factor Analysis of Population Allele Frequencies as a Simple, Novel Method of Detecting Signals of Recent Polygenic Selection: The Example of Educational Attainment and IQ. Mankind Quarterly, 54, 168-200.

There are other omissions and incorrect statements.
When intra-individual variance was partitioned out, roughly the same percent of genetic variance was located between subpopulations as between individuals within subpopulations. The decomposition is shown in Table 4.10 below. Interestingly, Piffer and Dall'Olio (2015) found similar results when decomposing variance between major human races using 1000 Genomes phase 3.

1. Why do you not report the table in Piffer and Dall'Olio (2015)? So much work was spent on this just to give a brief (and totally inaccurate) mention?
2. That is an incorrect statement. The percent of genetic variance between subpopulations is much bigger than that between individuals, after variance within individuals has been accounted for. I have provided columns in my table showing variance in relative terms (%). % variance of between populations: Weighted Fst is a/(a+b+c) or within populations (B=relative proportion or b/(a+b+c). The average Weighted Fst is 0.0807 (roughly 8%), but the average B is 0.0049 (0.49%). So the variance between populations is roughly 20 times greater than that between individuals if we partial out the between gametes within individuals variance.

There is also an incorrect part in this statement, relative to improper citation of Minkov et al: "Third, frequency differences in specific cognitively associated alleles have been shown to predict aggregate national and racial IQ differences (Piffer, 2015a; Piffer, 2015b; Minkov et al., 2014).".

Citation of Piffer is correct because I had actually correlated allele frequencies to IQ scores. But Minkov et al. never did that. Their SNPs have only INDIRECTLY been associated with IQ at the within population level, unlike the SNPs reported by Piffer which were associated with g. As the authors state: "The serotonin-transporter gene is not an IQ gene, however. Holmberg and Lesch (2011) point out that S-allele carriers do not perform better on some typical IQ tasks, such as mental rotation.
In a study of 572 Chinese college students, He et al. (2010) did not find a clear association between 5-HTTLPR alleles and performance on standard IQ tests, such as Raven’s Advanced
Progressive Matrices and a Chinese Version of Wechsler’s Revised Adult Intelligence Scale."
I will publish after these errors and inaccuracies will be corrected.
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Davide,

Yes, I didn't know how to properly cite those papers. I have made the corrections.

As for Minkov et al., If you read closely what I said, you will see that I said nothing incorrect. I also provided a clarifying footnote which you must have missed:

[95] These alleles are not necessarily general cognitive ability associated ones. For example, Minkov et al. (2014) note that: “The literature reviews and analyses by Dobson and Brent (2013) and Holmberg and Lesch (2011) suggest that S-allele carriers outperform L-allele carriers on a variety of cognitive tasks, such as financial decision making, probably because of their hyper vigilant decision-making style… The serotonin-transporter gene is not an IQ gene, however.” The frequency differences nonetheless evidence historic selection pressure on cognitively related traits in general; if there generally was such selection pressure, it would likely, though not necessarily, have acted also on general cognitive ability. The alleles discussed by Piffer (2015a) have been shown to be reliably associated with educational attainment and education achievement scores.

I didn't say IQ scores because at the time I wrote this, they had not been reliably so associated. I changed the last sentence to:

"The alleles discussed by Piffer (2015a) have been shown to be reliably associated with educational attainment, educational achievement test, and intelligence test scores."

As for, Piffer and Dall'Olio (2015), with the statement "Piffer and Dall'Olio (2015) found similar results when decomposing variance between major human races using 1000 Genomes phase 3," I meant similar results with respect to: "They found that between 96.7 and 99.6% of the variance was located within individuals." That is, you both found that most variance was within individuals.

I will clarify the point by changing this to: "Interestingly, when decomposing variance between major human races using 1000 Genomes phase 3, Piffer and Dall'Olio (2015) also found that most variance was located within individuals."

As for your question:

"1. Why do you not report the table in Piffer and Dall'Olio (2015)? So much work was spent on this just to give a brief (and totally inaccurate) mention?"

What I said was not "totally inaccurate", perhaps misleading. I did downplay your results. This was because they fly so far in the face of theory that reporting them makes my discussion look suspect. If you want me to add the table, then request that I do as a reviewer. Doing so as an editor, oversteps your role.
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(2015-Jun-17, 13:37:10)Chuck Wrote: Davide,

Yes, I didn't know how to properly cite those papers. I have made the corrections.

As for Minkov et al., If you read closely what I said, you will see that I said nothing incorrect. I also provided a clarifying footnote which you must have missed:

[95] These alleles are not necessarily general cognitive ability associated ones. For example, Minkov et al. (2014) note that: “The literature reviews and analyses by Dobson and Brent (2013) and Holmberg and Lesch (2011) suggest that S-allele carriers outperform L-allele carriers on a variety of cognitive tasks, such as financial decision making, probably because of their hyper vigilant decision-making style… The serotonin-transporter gene is not an IQ gene, however.” The frequency differences nonetheless evidence historic selection pressure on cognitively related traits in general; if there generally was such selection pressure, it would likely, though not necessarily, have acted also on general cognitive ability. The alleles discussed by Piffer (2015a) have been shown to be reliably associated with educational attainment and education achievement scores.

I didn't say IQ scores because at the time I wrote this, they had not been reliably so associated. I changed the last sentence to:

"The alleles discussed by Piffer (2015a) have been shown to be reliably associated with educational attainment, educational achievement test, and intelligence test scores."

As for, Piffer and Dall'Olio (2015), with the statement "Piffer and Dall'Olio (2015) found similar results when decomposing variance between major human races using 1000 Genomes phase 3," I meant similar results with respect to: "They found that between 96.7 and 99.6% of the variance was located within individuals." That is, you both found that most variance was within individuals.

I will clarify the point.

As for your question:

"1. Why do you not report the table in Piffer and Dall'Olio (2015)? So much work was spent on this just to give a brief (and totally inaccurate) mention?"

What I said was not "totally inaccurate", perhaps misleading. I did downplay your results. This was because they fly so far in the face of theory that reporting them makes my discussion look suspect. If you want me to add the table, then request that I do as a reviewer. Doing so as an editor, oversteps your role.


Indeed I did not request that you add the table. I suggested it and I clarify it now, I suggest that as a reviewer. I do not think your paper would benefit from hiding results. You can present the table and then discuss why the results are so paradoxical but burying them is not very honourable. As editor I can only request that you make the changes to the references section. As a reviewer and a human being who has spent a lot of time working out the decomposition of Fst components, I would not approve of a paper who does not report the table.
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(2015-Jun-17, 13:45:53)Duxide Wrote: Indeed I did not request that you add the table. I suggested it and I clarify it now, I suggest that as a reviewer. I do not think your paper would benefit from hiding results. You can present the table and then discuss why the results are so paradoxical but burying them is not very honourable. As editor I can only request that you make the changes to the references section. As a reviewer and a human being who has spent a lot of time working out the decomposition of Fst components, I would not approve of a paper who does not report the table.


I originally started to, which was why the title still reads:

"Table 4.10. Total genetic variance partitioned into variance between subpopulations, among individuals within subpopulations, and within individuals in a Japanese sample and in 1000 Genomes"

As can be seen, I forgot to delete the "and in 1000 Genomes".

Do you mind if I include just the big three: Africans, Europeans, and East Asians? Since I have three Japanese groups, doing so would be more symmetrical.
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(2015-Jun-17, 13:54:27)Chuck Wrote:
(2015-Jun-17, 13:45:53)Duxide Wrote: Indeed I did not request that you add the table. I suggested it and I clarify it now, I suggest that as a reviewer. I do not think your paper would benefit from hiding results. You can present the table and then discuss why the results are so paradoxical but burying them is not very honourable. As editor I can only request that you make the changes to the references section. As a reviewer and a human being who has spent a lot of time working out the decomposition of Fst components, I would not approve of a paper who does not report the table.


I originally started to, which was why the title still reads:

"Table 4.10. Total genetic variance partitioned into variance between subpopulations, among individuals within subpopulations, and within individuals in a Japanese sample and in 1000 Genomes"

As can be seen, I forgot to delete the "and in 1000 Genomes".

Do you mind if I include just the big three: Africans, Europeans, and East Asians? Since I have three Japanese groups, doing so would be more symmetrical.


Ok that should be fine
 Reply
(2015-Jun-17, 13:56:49)Duxide Wrote:
(2015-Jun-17, 13:54:27)Chuck Wrote:
(2015-Jun-17, 13:45:53)Duxide Wrote: Indeed I did not request that you add the table. I suggested it and I clarify it now, I suggest that as a reviewer. I do not think your paper would benefit from hiding results. You can present the table and then discuss why the results are so paradoxical but burying them is not very honourable. As editor I can only request that you make the changes to the references section. As a reviewer and a human being who has spent a lot of time working out the decomposition of Fst components, I would not approve of a paper who does not report the table.


I originally started to, which was why the title still reads:

"Table 4.10. Total genetic variance partitioned into variance between subpopulations, among individuals within subpopulations, and within individuals in a Japanese sample and in 1000 Genomes"

As can be seen, I forgot to delete the "and in 1000 Genomes".

Do you mind if I include just the big three: Africans, Europeans, and East Asians? Since I have three Japanese groups, doing so would be more symmetrical.


Ok that should be fine


Updated. Please publish.
...

Version with updated publication date below.
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