Partitioning intra- and inter-racial genetic variation

Posted by pug on October 25, 2010, 01:30 PM | #

Dasein,

Why not just point out that the split is conceptually wrong in the first place?

Posted by pug on October 25, 2010, 03:54 PM | #

The additive apportionments of variance within and between populations are incommensurable, thus pointless to bring up, save one is an anti-White political agitator.

And, as Lou Jost further notes:

The problems in population genetics start with the misinterpretation of heterozygosity as “diversity”. One of the principal themes of conservation biology is the conservation of diversity. The moment that we begin to conceive of diversity as something that can be conserved or lost by preserving or destroying populations, we implicitly impose subtle mathematical requirements on the concept. For example, if conservation arguments are to be logically consistent, the amount of diversity lost plus the amount of diversity saved must add to the total diversity, at least in highly symmetric examples where other factors that might affect diversity are held constant. Imagine that we are evaluating a conservation plan for an endangered colonial seabird. Its entire population nests on a cluster of twenty small rock islands. Each island contains about the same number of birds, and members of the colonies always return to their home colony to breed. A genetic analysis at a very polymorphic locus shows that each colony (deme) has a heterozygosity of 0.95, and also shows that no alleles are shared by members of different colonies (all alleles are private). The military plans to use 19 of the 20 islands for bombing practice. Geneticsts are asked what effect this will have on the genetic diversity of the endangered seabird. Following standard procedure, geneticists will equate genetic diversity with heterozygosity, and calculate the answer.

Geneticists hired by the military will argue that even if we save just one island, we will be preserving almost all of the genetic “diversity” of the species. The total heterozygosity of the pooled colonies is 0.9975, and the heterozygosity of one colony is 0.95, so the proportion of the colony’s genetic “diversity” saved is 0.95/0.9975 = 95%.

Geneticists hired by an environmental protection group will use the same measures to argue that the military’s plan will destroy 99.9% (0.9974/0.9975) of the colonies genetic “diversity”. The same measures and the same reasoning, applied to the same data, lead to diametrically opposite conclusions depending on which side we are on.

In fact, both results are as fishy as the seabirds’ feces. All the colonies are equally large and equally diverse, and all alleles are private to single islands, so each colony should contribute equally to the total genetic diversity of the species. The loss of 19 of the 20 colonies should cause the loss of 95% (=19/20) of the species’ genetic diversity, and saving one colony should preserve 5% (=1/20) of the species’ diversity. These sum to unity, as they must. If we want to avoid logical contradictions when arguing about conserving diversity, our diversity measure must behave in this way in these highly symmetrical cases. These cases are an acid test of whether our measures match our diversity concept. Heterozygosity fails this test and the others described in Jost (2008).

Thus: if Europeans die out, precisely 100% of the European subset of humanity will die out, and so will a part of humanity. We are irreplaceable. Which is why laws against genocide exist.

Posted by Dasein on October 25, 2010, 05:02 PM | #

pug,

Thanks for the feedback.  I’ve read some of Jost’s work, mostly his critique of Gst/Fst.  My only criticism of Jost would be that, while he presents theoretical cases where Gst/Fst would give nonsense results (like the bird colonies example above), I’m not aware that he has shown examples in human populations where Gst/Fst results are wildly wrong (for example, by systematically comparing his D to Fst- easy enough to do, though, and I might get around to it one of these days).  I know there was a meta-analysis of ecology papers a year or two back that showed that the interpretations were wrong in a substantial percentage (~25%?) of studies because of uncritical use of Gst/Fst, but I’m not aware of any of these studies involving human SNP data.

All this being said, I am not defending the use of Gst/Fst (or AMOVA).  The issue with heterozygosity placing an upper limit on inter-group variation is important, but I don’t know that it’s been demonstrated to be such a problem with SNP data (certainly it would be with microsatellites).  I think the argument against partitioning would be hard to make to the layman, and if it requires understanding that first link of Jost’s, it’s going to be very difficult for the average person to make the case.  But, then again, the average person has no idea what is meant when the 85/15 split is mentioned, nor that it corresponds to average allele frequencies of 0.7 vs. 0.3 (I mentioned this to one person, and their response was “the inter-group variation must be much higher than 15%”).  The ANOVA/PCA stuff I’ve shown above might be just one way to silence the 85/15 squawker.

As for whether the partitioning of variation is meaningless, I don’t believe it is.  Edwards, in his Bioessays article, demonstrated that the ratio of within-population to total sum of squares, using a binomial distribution (I assume it was actually analysis of deviance rather than ANOVA, though I have no experience with this) with p and q of 0.7 and 0.3, respectively, was 0.84.  Basically, the same as what Lewontin found.  So, I think Lewontin’s partitioning is ok, from a statistical point of view.  But, like Jost says, the conclusions Lewontin drew from his results were insane (e.g. if all human groups were wiped out, save Bushmen, 85% of the world’s genetic diversity would be preserved).  And different partitioning techniques (ANOVA, PCA) with large numbers of SNPs can shift the balance of the variation towards the group level.

Posted by seawolf on October 25, 2010, 11:40 PM | #

Based on what I’ve been reading, genetic variation is only a part of the story, and perhaps a smaller part than we ever thought.  Genetic variation is both genes and their expression, which differs so much between people.  Much of our differences is located in the epigenome, which orchestrates (turns genes on and off) phenotype and behavior and makes people and populations (races) vastly different from one another.

Until we’ve actually fully decoded the entire human genome (which we still haven’t done) and identified every single nucleotide variation and fully examined the epigenome and identified every single methyl group affecting gene expression, I think that science will never agree on this issue as it has been polluted by Marxists like Lewontin.

Common sense and observation tell us that there is a hell of a lot of differences to be discovered.

Posted by James Bowery on October 28, 2010, 04:11 PM | #

Science 5 November 1999:
Vol. 286. no. 5442, pp. 1159 - 1162
DOI: 10.1126/science.286.5442.1159
 
Prev | Table of Contents | Next
Reports

Extensive Nuclear DNA Sequence Diversity Among Chimpanzees

Henrik Kaessmann, * Victor Wiebe, Svante Pääbo

Although data on nucleotide sequence variation in the human nuclear genome have begun to accumulate, little is known about genomic diversity in chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). A 10,154-base pair sequence on the chimpanzee X chromosome is reported, representing all major subspecies and bonobos. Comparison to humans shows the diversity of the chimpanzee sequences to be almost four times as high and the age of the most recent common ancestor three times as great as the corresponding values of humans. Phylogenetic analyses show the sequences from the different chimpanzee subspecies to be intermixed and

the distance between some chimpanzee sequences to be greater than the distance between them and the bonobo sequences

.

Max-Planck-Institute for Evolutionary Anthropology, Inselstrasse 22, D-04103 Leipzig, Germany.

Posted by pug on November 05, 2010, 09:43 PM | #

Dasein,

Is it in any way possible that updates to the MR “Race FAQ” are forthcoming (e.g., the inclusion of an European structural cluster as opposed to limited studies concerning the broad Caucasian one), or some sort of centralised effort/resource to debunk the common anti-racial “arguments”/mythologies once and for all?

Posted by Lurker on November 06, 2010, 12:50 AM | #

or some sort of centralised effort/resource to debunk the common anti-racial “arguments”/mythologies once and for all?

Ive said it before - that would a great idea. Too much useful stuff is buried in the posts and comments. The coomonest myths and should be succinctly debunked.

Posted by Dasein on November 12, 2010, 08:15 AM | #

pug,

Yes, the Race FAQ looks like it could do with some updating.  I would need a superadmin to give me privileges to do so.  GW, could you e-mail me and let me know if that’s ok?

From what I can find with a quick Google search, the most popular Race FAQ’s are Goodrum’s and Sailer’s.  Do you (or anyone else) have suggestions for new questions to be covered?  The first thing I would do is expand on the discussion of genetic variation.

Posted by pug on November 12, 2010, 08:36 AM | #

Dasein,

There’s a lot of things that need typing, I guess, though I’m not that good a writer as English is not my native tongue. I may check the opposing views forum section of WN sites to see righteous anti-racist peddle their trash, and some older studies I have saved in my stash dealing with race. An update to human genetic variation studies to include an explicitly European cluster would be great, though. (And although a lot of the stuff is outdated or wrong, one could do with a historical analysis of clustering studies.)

How about inclusion of one of the main arguments I use against the anti-Whites who claim Whites don’t exist?

As we can find out from this study on the status of the race concept in China where a blatantly unsurprising 324 out of the 324 surveyed papers on human genetic variation posited human racial groups, the Chinese have absolutely no ‘problem’ with race.

Why do Chinese have absolutely no ‘problem’ with race? Simple. No Jewfection of biology and their academia is not a kosher playpen where twisted Jews can play out harmful ecological experiments on the Gentile host nations they reside in.

Posted by Dasein on November 12, 2010, 04:17 PM | #

pug,

Thanks for the links.  I had also thought about this sort of a ‘genomics timeline’ approach that would cover major papers, focussing on those since Rosenberg’s 2002 Science paper.  Here is one race-denial site (from the American Anthropological Assocation) that could be used for debunking in the FAQ.

Posted by pug on November 14, 2010, 09:47 AM | #

Dasein,

That website is fairly easy to refute insofar as it is abysmally stupid. All it requires is a correct definition of terms (e.g., race) and pointing out the various obfuscations, which I am happy to help with. Some have actually been pointed out in the literature, e.g., the criticism of ‘race’ for once being ‘essentialist’ a long time ago is crock insofar as the ‘species’ concept (and higher taxa) used to be defined likewise—to no major conceptual detriment except to hair-splitters, I might add—yet no one has a problem with the fairly useless concept of humanity.