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[OBG] Nature of Race Full

(2015-May-31, 09:57:34)Duxide Wrote: I post here a review by Kevin MacDonald, recommending publication: https://drive.google.com/file/d/0B7hcznd...sp=sharing


Davide,

With three approvals the paper is publishable.

I uploaded the "final" edition. I set the publication date for June 2. (I will look it over one more time tomorrow.)
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As I feared, the table 4.4 hasn't changed, yet I asked you a million of times to change it...

And I even provided a table model. If a journal accepts something like table 4.4, that's a shame.

Furthermore, it seems there are many things that have changed since the last time I read it. I prefer you hold it a little bit (say, 2 days maximum) before I read it again, although it's unlikely I would ask you to change anything again.
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(2015-Jun-01, 07:48:29)Meng Hu Wrote: As I feared, the table 4.4 hasn't changed, yet I asked you a million of times to change it...

And I even provided a table model. If a journal accepts something like table 4.4, that's a shame.

Furthermore, it seems there are many things that have changed since the last time I read it. I prefer you hold it a little bit (say, 2 days maximum) before I read it again, although it's unlikely I would ask you to change anything again.


Dear Meng Hu,

I tried to fix table 4.4 as you requested, however I was unable to.

And yes, I made a few edits. Specifically, I:

Edited the whole of section I
Completely rewrote section I-I
Rewrote the discussion at the end of II-A on the early subspecies concepts
Added a table to section III-B (on old race/subspecies definitions)
Added to the end of IV-F (a figure and discussion on ancient admixture)
Added section IV-J (on potential human species)
Rewrote section IV-K (on genetic differences)
Added to some of the the tables in IV-K and M (i.e., 4.12 and 4.14)
Heavily edited section V-B (particularly the critique of Templeton)
Reorganized and proofed sections VI-C to F

There were no particularly substantive changes as far as I am concerned. I made the changes because new material came available -- for example some translations of French and Latin texts which I did not have before and some material on phylogenetic concepts.

But, yes, I guess that we will hold off on publication until you look things over again.

Thanks for the interest, by the way.

(I really just could not figure out the table 4.4)
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(2015-May-07, 03:35:54)Chuck Wrote:
(2015-May-06, 10:15:17)Duxide Wrote: First of all, the set of 315 Fst values that I calculated using VCFtools (which employs Weir and Cockeram Fst formula) on 1000 Genomes phase 3 data for 26 populations can be seen here (https://docs.google.com/spreadsheets/d/1...sp=sharing ). I report Fst for 1st and 21st chromosomes (columns C and D). They are practically identical (r=0.995) so either can be used to represent the whole genome. Note that these include SNPs and indels. If you use these Fst values in your paper, please cite my last article (http://dx.doi.org/10.6084/m9.figshare.1393160 ) because they are in the supplementary material there.

THERE IS INDEED MUCH CONFUSION ON INTERPRETING FST AS RELATIVE BETWEEN POPULATION VARIANCE.
It appears that the expected BETWEEN population variance should be 2*Fst, after correcting for the inbreeding coefficient.


Davide,

Would it be possible for you to partition global variance into between continental race, between individual within race, and within individual variance?

See table 4 here for an example.

"To measure the differentiation between populations, the widely used statistic FST [17] and its unbiased estimator [18] were used. FST estimates were averaged over all loci, and 95% confidence intervals (CIs) of the average FST were calculated by bootstrap resampling with 10000 replications...Along with FST, variance components were estimated to reflect intra-individual, inter-individual and inter-population differences in genetic variation."

There appear to be programs which allow for this -- but no one does it. If you need, I will write Nishiyama et al. regarding method/statistical program.

Also, link rot: http://dx.doi.org/10.6084/m9.figshare.1393160


Chuck, I ask you to hold for a couple of days. I have worked hard and spent a lot of time trying to get Vcftools to provide variance components (I had to re-write part of the code) and I am almost done, so I'd like you to have a look at those before you publish this paper. Is it ok?
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John,

Your tables are ugly because you insert them as images. I don't know why you do this. You need to insert them as tables.

In LibreOffice it works like this. Supposing you have the data in a spreadsheet (Calc), then select then region you want and copy it. Then use the special paste in Writer. Select paste as real text format (RTF). Now you have a proper table in Writer.
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(2015-Jun-01, 16:21:27)Emil Wrote: John,

Your tables are ugly because you insert them as images. I don't know why you do this. You need to insert them as tables.

In LibreOffice it works like this. Supposing you have the data in a spreadsheet (Calc), then select then region you want and copy it. Then use the special paste in Writer. Select paste as real text format (RTF). Now you have a proper table in Writer.


Davide,

Sorry, I forgot that you were still working on that.

Emil,

Some of the figures are made by hand using PicPick; so they are naturally inserted as images. Only one table could be formatted otherwise; that is the one which MH mentioned.

I do not know how to use LibreOffice and my file is in Word 2007. I would need a solution using Word. Also, the tables only turn "ugly" when Word --> PDF.
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LibreOffice can open Word files (.doc or .docx).

The solution is presumably similar in Word. Paste special to insert a table as a table. I haven't used Word since I discovered Open Office ~10 years ago, so I don't know exactly.
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(2015-Jun-01, 07:48:29)Meng Hu Wrote: As I feared, the table 4.4 hasn't changed, yet I asked you a million of times to change it...

And I even provided a table model. If a journal accepts something like table 4.4, that's a shame.

Furthermore, it seems there are many things that have changed since the last time I read it. I prefer you hold it a little bit (say, 2 days maximum) before I read it again, although it's unlikely I would ask you to change anything again.


OK, I redid table 4.4 (and Figure 1.3).
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(2015-Jun-02, 00:00:10)Chuck Wrote: Davide,

Sorry, I forgot that you were still working on that.


I am almost done. I am running the code on all the 10 unique pairwise comparisons for the five 1000 Genome Races. I will put the results into Excel spreadsheet, then add the VCFtools + R code to OSF and the output files (hopefully they'll not be too big even after compression). Will post results here soon.
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(2015-May-31, 09:57:34)Duxide Wrote: I post here a review by Kevin MacDonald, recommending publication: https://drive.google.com/file/d/0B7hcznd...sp=sharing


I thank Kevin for his considerate review and for taking the time to read this lengthy and complex paper.

I would like to address two points which he made and to solicit feedback since this may allow me to clarify my arguments and presentation.

Point # 1.

Kevin: "In seeking a useful, non-arbitrary concept of race, he emphasizes that “the underlying natural divisions exhibit small discontinuous jumps in genetic distance between them (Rosenberg et al., 2005).” Such “clusters can be identified objectively at a given grain of focus.These clusters can then be used to infer objectively delineated races” (45). This would yield formal definitions of race as naturally occurring descent groups.

Whether such discontinuous jumps in genetic distance do occur between people separated by distinct evolutionary histories is entirely an empirical matter. He argues cogently against the common complaint that because different, even arbitrary divisions can be made, races don’t really exist (45).
Fuerstaddresses the issue of clines which are often used to argue against the concept of race. It is indeed possible to delineate races based only on clines:
Intuitively, it would seem that without significant discontinuities or at least sharp increases in the slope of the cline, racial designations would be invidiously arbitrary. However, Fuerst solves this by distinguishing between formal races, which do show discontinuities (citing Rosenberg, 2011), and informal races."

................

John: I have distinguished between races as natural (i.e., genealogical/genomic) divisions and clines as character gradients. The two phenomena are fundamentally different. The issue of clines, as originally defined, is largely irrelevant to that of races. The former indexes overall ancestry and genetic kinship, the latter does not.

I have noted that races as natural divisions can be cut out of genomic and population continua just as types of radiation (e.g., visible light) can be cut out of the electromagnetic spectrum. I have pointed out that, historically, intraspecific races were conceived as falling in a population continuum. It was their continuous nature which evidenced that they were not species (e.g., Blumenbach, Prichard, Darwin). I have also pointed out that contemporaneously evolutionary and some phylogenetic taxa subspecies (i.e., formally recognized races) can also be cut out likewise (e.g., Mayr and Ashlock, 1991; Groves, 2004).

There is no justification for requiring races, in general, to exhibit discontinuities.

I have made the point, in line with Darwin, that even if races were biologically arbitrarily delineated, they would still make for nature divisions. They would still cut out groups where members were arranged by genetic relationship. I did note that traditional human divisions nonetheless exhibited genomic discontinuities; thus they can be identified by cluster analysis. I also noted that genomic discontinuities provide support, given contemporaneous conventions, for the position that traditional continental races represent taxa subspecies.

Importantly, I think that "biologically arbitrarily" delineated natural divisions are practically useful, just as "electromagnetically arbitrary" divisions are so. In the former case, individuals are arranged by overall genetic similarity which is what is of importance, both empirically and from the perspective of EGI, to the extent that the latter matters to some. Also, I fail to see how cutting out biologically arbitrarily delineated natural divisions would be invidious. Would defining "family" in a way that acknowledged continuous relations -- nuclear to extended kin -- be likewise? I make this point, because in personal communications, Jiannbin Lee Shiao made a similar case (about invidiousness) -- one which seems to be popular among sociologists; he, however, did not reply to my detailed response. I wish someone could explain so that I might better understand the argument.

Point #2

Kevin: "I suspect that race differences in IQ are influenced genetically, not only for the reasons listed by Fuerst, but also for several other reasons, as outlined by Rushton and Jensen (the worldwide distribution of test scores, g factor of mental ability, heritability, brain size and cognitive ability, transracial adoption, racial admixture, regression, related life-history traits, human origins research, and hypothesized environmental variables”

.....

John: I do not find Jensen and Rushton's evidence compelling. I have myself replicated and extended many of their results. In discussions of those, I have noted the problems. The brain size data is dubious; for example, recently a large multi-country Latin American study n > 7000 showed no association between head circumference and racial genomic ancestry. The regression to the mean and Spearman's hypothesis evidence are compatible with a shared environmental explanation -- I have demonstrated this. The published transracial adoption data shows mixed results and are underpowered; unpublished studies, by myself and Jason Malloy, show ambiguous results. The racial gaps in the UK -- and perhaps in the Netherlands -- have greatly diminished. World-wide scores are often found to be measure non-invariant. Racial admixture data, again which I have written about elsewhere, could in theory be explained by a shared environmental hypothesis. Thus, in the paper, I noted that the evidence is largely indirect and that the issue is still undetermined. Those who feel that Whites -- or e.g., Han Chinese in Southeast Asia -- are being unjustly accused of racism and/or discriminated against should try to establish or find more evidence in support of the position that differences have an evolutionary basis.

Again, I thank Kevin for his thoughtful review. I hope my responses help to clarify some issues.

Sincerely,

John
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