Category: genetic variation

Failure of Fst/Gst

Population genetics.

Both “movement” fetishists as well as anti-racist liars like to misuse Fst/Gst in genetic distance discussions (*) to promote their respective agendas.  Unfortunately for them, Fst/Gst is not really a (direct) measure of genetic distance, and particularly fails even as an indirect proxy when comparing populations that exhibit different levels of heterozygosity (e.g., human ethnies) and/or when considering loci with more than two allele variants.  To have the ill-informed trying to parse differences of, say, Fst/Gst = 0.0060 vs. 0.0065 and trying to make relevant conclusions from that is laughable.  The following are a small sampling of links to cite the next time some idiot tries to play such games (emphasis added):

See here.

See also here:

Likewise, when diversity is equated with heterozygosity, standard similarity measures formed by taking the ratio of mean within-subpopulation diversity to total diversity necessarily approach unity when diversity is high, even if the subpopulations are completely dissimilar (no shared alleles). None of these measures can be interpreted as measures of differentiation or similarity. 

At Wikipedia:

Also, strictly speaking FST is not a genetic distance, as it does not satisfy the triangle inequality. As a consequence new tools for measuring genetic differentiation continue being developed.

And this article here:

One underutilized approach is the coupling of indirect metrics of gene flow (e.g. F-statistics, Dest_Chao) with more direct measures such as kinship or parentage analyses (e.g. Loiselle et al. 1995; Selkoe et al. 2006; Buston et al. 2009; Christie et al. 2010; Palsbøll et al. 2010). Broadly speaking, kinship analyses provide an index of the relative relatedness of all genotyped individuals in a data set, and parentage is a distinct case of kinship whereby the most likely parents of individual juveniles are identified (Vekemans & Hardy 2004; Jones & Arden 2003; reviewed in Blouin 2003; Jones et al. 2010). Kinship coefficients (also known as coefficients of coancestry) are widely interpreted as the probability of identity by descent of the genes, but they are more properly defined as ‘ratios of differences of probabilities of identity in state’ (Hardy & Vekemans 2002, p. 23) from homologous genes sampled randomly from each pair of individuals (Hardy & Vekemans 2002; Rousset 2002; Blouin 2003; Vekemans & Hardy 2004).

By comparison, F-statistics and Dest_Chao are often blind to the relatedness of individuals; different population samples with the same kinship structure can have very different levels of genetic differentiation among them and vice versa.

*True, Salter used Fst in On Genetic Interests, but only because there was no other data available for that purpose at that time.  And Salter makes clear in the book that the proper approach would be to use data from global assays of genetic kinship which did not (and still do not) exist for human ethnies.  It is interesting that population geneticists and ecologists will calculate genetic kinship for plant and non-human animal species, but are either too lazy or politically-motivated to do so for human population groups. However, anecdotal evidence from the genetic kinship data that companies such as 23andme and DeCode used to present to their customers suggest that human genetic kinship findings would not be to the liking of either the fetishists or the anti-racists. 

Behold the Parasite

Jews and net EGI.

Of course, Jews are neither wasps nor fungi, nor do they stand in the same relationship to us as do the parasitic wasps and fungi to their hosts just mentioned. Jews are either a closely related species to us, or are a subspecies of the same species. In either case, as repulsive as are parasites, and as loathe as we may be to admit it, Jews are genetically quite similar to us and are in fact extensively cross-bred with us. Doesn’t this effectively rule out their being biological parasites upon us? 

No, not at all. In fact, it makes it even more likely. In 1909, an Italian entomologist named Carlo Emery discovered what is now known as Emery’s Rule. The rule states that that social parasites (that is, parasites of social species — and Homo sapiens is certainly a social species) tend to be parasites of species or genera to which they are closely related. Matt Johnston of the University of Arizona states that, “One explanation for the apparently close relationship between social parasites and their hosts is that in order to get past the hosts’ defenses, the parasite needs to have evolved communication systems similar to the host. This may be more likely if the two share a close evolutionary history.”

This is why I talk about the importance of net genetic interests (not that anyone listens). If all you care about are gross genetic interests, then you would simply measure the genetic distances involved, calculate the child equivalents, and conclude that since Jews are genetically quite similar to, and cross-bred with, Europeans, then their presence in Western societies does not exert much of an EGI cost at all. However, Jews are a highly specialized, evolved parasitic ethny with interests that are incompatible with that of Europeans, and as such Jewish behavior exerts a significant fitness cost on Europeans, so that the net effect on European EGI is enormous. Therefore, net EGI takes into account all factors that affect the genetic interests of an ethny, and provides a final tally of the outcome. If Jews promote mass alien immigration, desegregation, miscegenation, and overall societal degeneration (that imposes severe costs on, among other things, family stability and reproductive success), then their presence is extremely destructive to host EGI regardless of what the relative genetic distances are between Jews and White Gentiles. Further, if Jews consider themselves a different group than are White Gentiles, and pursue a group evolutionary strategy of their own, they would not care that their behavior damages the interests of an ethny relatively genetically similar to their own. Of course, Identity is based upon more than just genetic distances, and issues of Identity, by influencing behavior, directly affect genetic interests.

More HBD Stupidity, 8/17/16

Breezy and Razib.

Steve Sailer gives us important empirical data here:
For example, in 1982, when I had just moved to Chicago, I was headed into the Century Mall on N. Clark St., when a black teen rushed out, followed by two twenty-something Hispanic security guards in close pursuit. I watched them head up Clark Street with the teen in sneakers pulling away from the guards in shiny black leather shoes.

Then we have Razib:

One peculiar thing population genetics teaches us that non-adaptive traits are more heritable.

Yeah, that’s great Razib. Question: if the traits are non-adaptive, how are they heritable (over evolutionary time) when genetic drift, regression to the mean, etc. resulting from the vagaries of sexual reproduction, random events, bottlenecks, etc. will constantly act. Why should extreme outliers be maintained over time?

This is due to the fact that selection tends to remove variation, selecting for fitter individuals.

Right. So, after so many eons of human evolution, and selection for fitter individuals, there must be little to no human variation left, eh? There goes the entire foundation of HBD! Of course, environments and selective pressures change over time, and variation is inherent in the process of sexual reproduction. It’s all very simple – simple that is unless you’re a Brown Cogelite trying to impress the rubes by how very erudite you are.

Look, fast running speed in Negroes was likely adaptive in their ancestral environment. The bell curve of Negro speed is right-shifted compared to that of other races, and that, we can assume, is a result of selection and adaption. A bell curve has, naturally, its outliers, and Bolt is at the extreme right end of the Negro bell curve for speed. So, no, specifically running as fast as Bolt is not necessarily adaptive, but the existence of speedy Negroes such as he is a natural outcome of the adaptive trait of fast Negro speed.
Let us not forget that Razib is the Brainiac who once confused “homologous chromosomes” with “sister chromatids” which I guess makes him the “go-to-HBD-guy” when it comes to biology/genetics.

Shoup on Difference and the Emergence of Reality

Important theoretical science.

I want to give Bowery credit for alerting me to this important Shoup paper.

Sometimes, with the emphasis in science and technics in drilling down into highly specialized details of any given sub-sub-sub (etc.)-discipline, the bigger picture is disregarded.  Getting back to first principles and more fundamental understandings will likely yield important insights and discoveries, as I fear that an increasingly Judaized and Asianized science (it’s all about dem dere papers and grants) is causing us to miss the forest for the trees.

That’s science and technics.  With respect to racial activism, all the pseudo-philosophical blather that Majority Rights has degenerated into over the past several years does the opposite: obscures the fundamental necessitates of racial activism with abstract nonsense that is more “tree” than “forest.”  Der Movement is lost, completely adrift.

Getting back to Shoup: he asserts that difference is the ultimate foundation of reality; at their most fundamental level, objects (or any other entity) are defined by difference.

We can note the relevance to the concept of genetic interests, which is based on distinctive genetic information.  Hence, the greater the (genetic) difference, the greater are the (genetic) interests.  The greater the genetic difference (distance) between two biological entities, the greater the interest each entity has in its genetic continuity as contrasted to the other entity. Just as time and space emerges from the differences between objects, genetic interests emerge from the differences that exist between the information encoded in the DNA of biological entities.

Race in the News, 8/6/16

Or should that read Der News?

“…the storm has only begun to gather,” indeed.
Der Movement’s favorite genetics company continues its long decline, emphasis added:

Some outdated or underused features have been discontinued in the new 23andMe experience.

These features include:
DNA Melody
Haplogroup Tree Mutation Mapper
Inheritance Calculator
ABO Blood Lab

Global Similarity

Profile SmartSearch
Family Inheritance Genome View
Reynold’s Risk Score Lab

Sure, I mean why would anyone care to know what groups they are more or less genetically similar to at the global level? After all, dat be rayciss and all.

White Worthlessness in the News, 6/10/16

Several items.

Of course those brown cows have contempt for Whites.  Wouldn’t you?  I mean, you invade someone else’s country and they not only allow you to stay, but they heap benefits on you (full tuition to a Ivy League school), give you advantages their own children do not have, and then they sit back, cuckily blushing like useless pansies, as you publicly insult them and rub their faces in it.

Whites are infinitely contemptible, infinitely useless, infinitely worthless.  As I have said before: a maggot eating its way through a festering lump of dog feces on a sweltering August sidewalk is infinitely superior from the standpoint of adaptive biological fitness than is the entire White race.

Yes indeed, the Germans who, along with the peoples of Britain, have contributed more to human progress over the last few centuries than any other ethny, require to mix with racially alien, stupid, and violent third world immigrants to avoid becoming “inbred.”  

Note the majestic hypocrisy on race I’ve written about before.  Putting aside that its these immigrants who are truly inbred (but this kraut would never say that), these anti-racists are the same scum who tell us: “more genetic variation between groups than between.”  Very good! Thus, not only do the German people constitute sufficient genetic variation among themselves to avoid any inbreeding, but, according to the anti-racist left, Germans and Arabs/Turks are more genetically similar than Germans are to each other – by this “logic” Germans can only avoid inbreeding by only mating with other Germans, no?  I mean, if the Left really believes that members of the same ethny are more different than they are to complete aliens, then only strict ethnic endogamy can ensure sufficient genetic variation. On the other hand, if the Left now says that Germans are really more similar to each other, then their genetic interests demand they oppose the alien influx so as to prevent genetic displacement (and with their large population, there is no threat of “inbreeding” in any case).

Genetic Structure Redux

Genetic structure, from Western Biopolitics.

Something (slightly edited) from my old Western Biopolitics site about genetic structure, based on this paper, with a few new comments at the end.

Although this is highly preliminary, this is all completely consistent with what I (and James Bowery and Ben Tillman) have been saying for years: simple Fst measurements of genetic distance, while crucially important and necessary, are not sufficient to give the complete picture for EGI. Genetic distance based on structure is likely greater than that estimated from Fst for humans as well as for oak. Further, the genetic structure estimates can be viewed, as I’ve been saying, as an extra, independent measure of genetic distinctiveness superimposed on top of the foundation of Fst distance. Therefore, a complete estimation of EGI must include consideration of genetic structure, and this paper is an initial, preliminary attempt at quantifying that structure. More to come, we hope. This research groups compares analyses of combinations of coinherited alleles compared to the “one-by-one” Fst method. This paper is free online, take a close look at Table 1 – as the level of genetic structural complexity increases, genetic distance between the oak groups also increases. Note in all cases, emphasis added.

…is characterized by special combinations of genes. (To emphasize this aspect, genic integration might be the more appropriate term.) The main motivation for this paper was the realization that impacts of particular forces, selective or not, on population differentiation may not be observable at every level of genetic integration. Measurements of differentiation among populations based on gene frequencies, for example, provide no specific insights into the effects of mating systems nor of epistatic interaction on population differentiation. This is due to the fact that gene frequencies refer to the lowest level of genetic integration, namely its absence. This level, which is commonly addressed as a population’s gene-pool, is conceived to consist of the set of all individual genes present in the population members for a specified set of genetic traits. Genetic studies of population differentiation are almost always based on this “beanbag” (critically reflected by Mayr [2] and defended by Haldane [3]; for concise reasoning of the persistence of the gene-pool concept see e.g. [4] or [5]). Studies of differentiation at multiple loci are no exception, since they commonly report averages over single-locus differentiation indices. Also disregarded in studies of gene-pool differentiation are gene associations that deviate from Hardy-Weinberg proportions (homologous, or intralocus, association) or gametic equilibria (non-homologous, or interlocus, association). 

Considering that forms and degrees of gene association may differ at different levels of genetic integration, it thus appears that previous studies on patterns of population differentiation have provided very little information on levels of genetic integration above the gene-pool. One important reason for the usual focus on gene-pool differentiation is probably the lack of a method for measuring population differentiation consistently at all levels of genetic integration. Consistency means that comparison of the amount of differentiation among a set of populations between levels of integration provides information about the complexity of the gene associations that distinguish them. 

Since gene associations do not decrease as level of integration increase, neither should differentiation. Moreover, the extent of an increase in differentiation between subsequent levels should in some way reflect the degree of complexity of the additional gene associations, with equality as an indication of lack of additional complexity by some standard. Such a differentiation measure must thus be based on a conceptual characterization of the complexity of gene associations. The existence of such a measure would not only facilitate experimental studies… 

It turned out that the large increases in differentiation between levels that were observed in the real data were not producible in numerous simulations of simple selection models, indicating that these models cannot explain the complexity of the real data. 

Proceeding from lower to higher levels of integration, one expects an increase in differentiation among populations simply because of the larger varietal potential inherent in more complex structures. 

Table 1 lists the distance matrix of pairwise distances…between stands and their mean as well as the symmetric population differentiation…SD and its components…j, both based on the elementary genic difference between genetic types, for each of three levels of integration: the gene-pool distance is the average of the six single-locus allelic distances; the single-locus diplophase distance is also the average over the loci; the multilocus diplophase distance. It is seen that for each pair of stands, all pairwise distances…increase considerably with the level of integration. 

Thus it appears that differentiation among populations with respect to their forms of gene association may be a normal occurrence. This insight questions the common practice of restricting the measurement of population differentiation to the allelic level (e.g. FST), thereby ignoring the considerable effects of gene association on population differentiation.

The authors then try to end the paper on a conservative, hedging note, perhaps to please reviewers:

This analysis is the first of its kind. Therefore, we cannot venture a prediction about whether the above findings on covariation between levels of integration constitute a general trend. It is conceivable, for example, that these findings are mainly determined by the conspicuously large polymorphism characteristic of the microsatellite markers used in this study. Other genetic markers may tell different stories.

Actually, there really is no logical reason to suppose that their findings are not generally applicable. It in fact makes perfect sense, as I (and others) have been arguing for years, that the correlation structure inherent in the genome is a general form of heritable genetic information above and beyond Fst, and that, therefore, this structure is an important part of genetic interests. There is no reason it must be limited to microsatellites; it is almost certainly an inherent, “emergent” characteristic of genetic information in all organisms. And, certainly, within and between human populations.

Therefore, it can be expected that genetic differentiation between human populations will be greater when overall structure (e.g., the combinations of coinherited alleles/genetic sequences) is considered, compared to Fst, and, that both Fst and genetic structure constitute genetic interests, both are important and both must be measured.

Genetic interests = Fst + Genetic Structure
And this paper is the initial step in the necessary quantification of genetic structure.
Yet more excerpts:

Conclusions: This new approach to the analysis of genetic differentiation among populations demonstrates that the consideration of gene associations within populations adds a new quality to studies on population differentiation that is overlooked when viewing only gene-pools. 

In general, traits are genetic only if they are inheritable, and the goal of inheritance analysis is to identify genes as the basic units of inheritance. The term genetic integration is used here to designate the combination or arrangement of these elementary objects “gene” into the haplotypes of gametes, into the genotypes at diploid (or polyploid) nuclei of diplophase individuals, or into the cytotypes of mitochondria or plastids, for example. 

At higher levels of genetic integration, where the objects of interest represent compositions of several individual genes together with their gene-types, association among gene-types becomes relevant for differentiation studies.

…neither the gene association within single loci (homologous association nor the gene association among loci (non-homologous association) is of the same form in any two stands, and in particular that association is present. Both the distances and the snail components show a much larger increase between the single-locus diplophase and the multilocus diplophase than between the gene-pool and the single-locus diplophase. 

Hence the non-homologous gene associations make a distinctly greater contribution to the differentiation than the homologous gene associations.

“Non-homologous gene associations” being a predominant component of what I refer to as “genetic structure.”

And consider the implications with respect for both EGI and parental kinship with intermarriage.

Genetic structure…here to stay.

New comments:

One question is whether the increase in genetic interests inherent between population (or individual) comparisons when taking genetic structure into account will be proportionately the same with increasing general genetic distance, or will the genetic structure differences increase proportionately with increasing genetic distance. For example, let’s hypothesize that genetic structure increases the genetic interest a Dane has with another Dane compared to a Greek by 50%, compared to allele-by-allele considerations. Will the increase in genetic interest of Dane vs. Nigerian also be 50%, or greater (it almost certainly could not be less). I hypothesize it would be greater, because the increase in allele-by-allele differences with greater genetic distance would lead to a proportionate increase in the genetic structure combination differences possible. Image ways of shuffling decks of cards where it is possible for the individual cards to differ between decks – the more individual card difference, the greater the number of novel card combinations between decks. This would of course need to be shown with the data (not that population geneticists would touch such a politically incorrect subject – they won’t even do genetic kinship studies). 
On a functional basis, one needs to consider epistasis. Certainly, there are cases where individual genes can influence phenotype; however, in the vast majority of cases, important phenotypic traits (the HBDers vaunted “form and function”) are affected by numbers of genes working together. This by the way is an important riposte to some of Dawkins’ more stupid extensions of his “selfish gene” meme, more properly, that should be plural, as in “selfish genes.” Or, perhaps, the “selfish genome.” In the end, selection acts upon the entire organism that is the product of all its (functional) genes. A given individual gene can of course affect the phenotype and influence that gene’s own selection, but even in that case, it does so in the context of the entire functional genome.
As I’ve written before, one cannot base genetic interests solely on “functional genes.” Putting aside that the distinction between functional and non-functional is becoming increasingly blurred due to findings that show that much of the “non-functional” genome actually does have function, the point is that even truly non-functional genes, if they vary in frequency between peoples, carry information on kinship and, even more to the point, as part of the distinctive genome, constitute a fraction of kinship, and thus have inherent value in this manner. After all, if genetic interests are based on genetic kinship, therefore all genes that constitute that kinship, as well as carry information that helps quantitate that kinship, have value. One can of course argue that functional genes that influence their own selection are of greater value on a “per gene” basis, but one cannot simply dismiss non-functional genes are being irrelevant to genetic interests.