Category: genetic structure

Sallis Agrees With the Alt Right on Something

Some good sense.

I essentially agree with and endorse this article, with some caveats, and it should be read together with this piece I wrote several years ago.

The article is reasonably sound, although one caveat is that if one approaches these tests with a sense of realism with respect to their limitations – limitations spelled out in my Counter-Currents piece – then getting tested may not be a bad idea.  Having the raw data could be useful if you can find someone who can do a genetic kinship analysis with it. But taking the details of the data literally – thinking that there’s a real difference between 100% A, 0% B vs. 99.3% A, 0.7% B, for example – is ludicrous. I would take even the 90% confidence readings with a large grain of salt, and the 50% confidence readings are so absurd that the salt grain needs to be the size of the iceberg that sunk the Titanic.

The other caveat to the article is that the comments section is mixed; some comments are useful, some are asinine, so caveat emptor.

There are two basic questions here.

1. Is 23andMe a good test?

2. Assuming an ancestry test is good, is it worthwhile?

To which I answer: 1) No and 2) Maybe, depending on context.

In an absolute sense, 23andMe is superior to DNAPrint’s tests from ~15 years ago; in a relative sense – comparing each test to the “state of  the art” available at the time – it really isn’t better at all.  With the level of understanding and methodology we have today, coupled with a prudent interpretation of the data, one could do much better.

What if a test was sound?  Well, sure, it can be interesting, but I’ll repeat something I’ve been hammering home here over the past few years – the only biopolitically relevant genetic metric is genetic kinship (at all levels of genetic integration).  If one can measure that, then it is useful. All else can be interesting, but not directly important from an EGI standpoint.

And if people are going to hysterically obsess over sub-fractional admixture percentages then this is missing the forest for the trees.

HBD in the News, 9/16/16

HBD is the enemy, White man.

Raving retard “Razib” Khan:

if you had the money and resources it wouldn’t be hard to pull out northern europeans in totality from a few thousand african americans.

Sure, it happens every day. Is this guy a raving brown turd of a lunatic, or what? That’s also the “genetic expert” who doesn’t understand the difference between sister chromatids and homologous chromosomes.

Now, it may be possible at some future date (not now) to computationally fully recreate a native racial genome from the fragments thereof scattered within the genomes of the racially mixed. But, if so – so what? To go from that to recreating even one single actual living human being, much less an entire race – who is going to do that? How? The ranting of this ignorant Desi, and his fake appeal to (his own) authority, may fool the rubes, but not anyone who has a real science background. Sorry “Razib,” your sci/fi fantasies do not make it “alright” that low-rent Ganges-spawn like yourself mates with White women.
And moronic commentary about how “genes don’t mix” is irrelevant. Racial genotypes and phenotypes are characterized by (spectrums of) combinations of genes, not atomized genes working alone, and these gene complexes are effectively destroyed by miscegenation (the hybrid phenotype being a proxy for, and a result of, the scrambled genome). Indeed, for all practical purposes, racial integrity is (permanently) lost upon mixing across wide racial lines. Speculation even less realistic than Jurassic Park does not alter these facts.
Taylor, interviewed by Derbyshire:

I’m not sure quite what an “AR-style” forum would be, since our conferences are unique, but we don’t screen people, because we don’t have to. AR‘s position on Jews is well-known: Jews have always been full participants in the work of race realism and have taken prominent roles in almost all of our events.

The Alt-Wrong goes marching, marching, marching on. And the Alt-Right had better decide what it is they stand for, or they’ll have others do it for them.

More on the Ethnotype

More thoughts.

A correspondent has shown interest in my ethnotype idea and has made two major suggestions, one I mostly agree with and the other I have some reservations about but partially agree with.
First, the suggestion was made that the ethnotype is best conceived as a normal distribution. Thus, while all the possible (and, of course, existing) genotypes of an ethny contribute to the ethnotype, some are more possible, or more frequent, than others.  Therefore, one will observe a cluster of more common genotypes defining the central or median part of the normal distribution curve, with outliers (the y axis is of course frequency, the x axis may be defined in various ways; perhaps a 3-D rather than 2-D distribution is best; in any case the genotypes making up the ethnotype can be distributed both relative to each other and relative to those of other ethnies).
This has certain advantages.  One can observe how the central tendency varies with time.  If one wanted, one could break up the genotypes to look at various traits (see second point below, but this in my opinion deviates from what I’m considering here, which is the entire genotype as an integrated genetic unit.  Another important advantage is how it handles the question of miscegenation and assimilation, including the assimilation of hybrids (this assumes that hybrids would be assimilated and not ejected from the population, which could be favored).  Consider mixing across wide racial lines.  Assume small-scale mixing that affects only a small fraction of the population.  This would increase the range of possible, and actual, genotypes, but would not really alter the mass of more central genotypes that make up the median ethnotype.
On the other hand, more massive miscegenation, assimilation, etc., particularly with widely divergent populations, would indeed shift the entire normal distribution and alter the central/median types, indicative of more serious effects on genetic interests.
In general, this may not be a bad idea.
The second idea, of which I am less enthusiastic, is to tie the ethnotypes to phenotypes, stressing functional genes (and, as above, possibly dividing the ethnotypes, if desired, into more specific traits).  Now, this confuses my use of the ethnotype concept – that is genetic – with the more anthropological phenotypic view.  I’m not defining ethnotype to describe a racial phenotype or set of phenotypes.  I’m using it to express the reality that while individual phenotypes are ephemeral, the range of possible genotypes of an ethny can be reasonably stable over long periods of evolutionary time.  And by genotype, I consider the entire genetic integration of individuals of a population, not individual alleles in isolation.  Further, while I am willing to grant (true) functional genes a higher per-allele value than (true) non-functional genes (since the functional ones influence their own replication, I do not – for reasons I have discussed many times – relegate non-functional genes to irrelevance.  It is the entire distinctive genome that contributes to genetic interests.  One must be careful that a sole focus on form, function, and phenotype does not lead to a John Ray-like memetic attitude that large scale miscegenation and genetic replacement is acceptable as long as certain phenotypic traits are maintained (e.g., “White-looking” heavily admixed mestizos of Latin America).
Again, a focus on form, function, and phenotype (while it has its relevance in particular contexts) deviates from the objective of my ethnotype definition: to capture the reality of a relatively stable set of (genetically integrated) genotypes (genetic structures) that define an ethny and its genetic interests, and to distinguish the ethnotype from an individual and unique “one-shot” genotype.

The Ethnotype

Introducing a new genetic concept.

The following I see as extremely important.
This paper discusses the “beanbag” approach to population genetics.

In a sexual population, each genotype is unique, never to recur. The life expectancy of a genotype is a single generation. In contrast, the population of genes endures. The quantities that are followed, in mathematical theories or in observations, are allele frequencies. The geneticist knows that at any desired time, the genotype frequencies can be obtained by the simple binomial rule.

Now, herein lies a problem I see with mainstream population geneticists (and other, related scientists) blinded perhaps by anti-racist political correctness.  It’s true than an exact, specific genotype is unique (except for identical twins) and does not recur.  The error – the fundamentalerror – these people make is not admitting that some genotypes are more similar than to others.  It’s not just a comparison between a genepool and a genotype, at opposite ends of the genetic integration scales.  There are levels in between the general population of genes at one end and the unique, never-to-be-reproduced genotype at the other end.
I therefore name one such level, which is of importance to the preservationist viewpoint: the ethnotype. 
An ethnotype is a range of possible genotypes that characterizes populations that have specific genepools.  An ethnotype is not as specific as a genotype, and ethnotype can be found in the many millions, and is stable across evolutionary time.  Otzi the Iceman and contemporary Europeans can be said to belong to the same broad ethnotype.  Ethnotypes can be considered to total set of possible genotypes produced by a genepool, the total set of possible allele combinations, and that will be different from that produced by another genepool.
Ethnotypes can be broader or narrower.  Europeans vs. East Asians are examples of two ethnotypes, each consisting of specific combinations of alleles from their respective genepools (ethnotypes, like genotypes, are emergent properties of genepools, and the frequencies of ethnotypes should be calculable from genepool allele frequencies as are genotypes).  One can go narrower: different types of Europeans (North, South, East, West, Central, etc.) can be thought of as being represented by a specific ethnotype or set of ethnotypes, the same for East Asians or any other population group.
Thus, while the forces of independent assortment and recombination at meiosis, combined with genetic drift and various forms of selection, insure that exact genotypes will never again be reproduced, ethnotypes will continue to be reproduced.  The European genepool may produce Isaac Newton or Michelangelo or Tesla only once, but can produce allele combinations reasonably similar to those individuals and similar to Europeans worldwide over and over again, as long as the genepool says intact.  Of course, over time, with drift and selection, the genepool changes, so that the possible ranges of ethnotypes and genotypes produced from the genepool will be altered, but these ranges will be more similar than to alien peoples. 
Therefore, the European genepool of 1016 AD had the potential to produce a different set of ethnotypes and genotypes than the European genepool of 2016; nevertheless, both are much more similar to each other than to, say, East Asian genepools of any date picked.  Again, genotypes are one-shot affairs, while ethnotypes are more stable over time, since they are a less specific, and more generalized, arrangement of genepool alleles.
The advantages of considering comparisons at the ethnotype level are that (a) this is the level that has the most practical significance (including selection) at the population level, as populations are collections of genotypes, not a soup of randomized alleles floating around; (b) given that genetic distance increases with increasing genetic integration and that the ethnotype is at a higher level than at the genepool, then considering the genetic structure inherent in the ethnotype will increase the level of genetic interests; and (c) while not as unique as the genotype, the ethnotype is unique in cross-population comparisons AND has the advantage of being preservable.  Thus, while genotype can be preserved only by cloning, ethnotypes can be preserved, to a reasonable degree over time, by following the precepts of Salterian Universal Nationalism.  Preserving the ethnotype can be done today, via acts of political will and social convention, no new technology needs be implemented.  Further, while “beanbag” genetics will tell you that miscegenation in some cases (at least at the parental level) can be compensated by increased reproduction and replication of the individual alleles, ethnotypes are specific to particular ethny genepool – no number of hybrids could reproduce the genetic structure of ethnotypes; hence, the ethnotype concept better represents the preservationist imperative.  I may add that ethnotypes better represent an ethny’s phenotypes as well, since phenotype is produced not by individual alleles working alone, but by the interaction of the whole genome with the environment.

Further, the ethnotype concept is compatible with eugenics, since, unlike the genotype, we are not talking about a fixed, perfectly unique set of genetics, but a more flexible range of genetic types that can still exhibit similarity over time even with some degree of substitution if alleles (again, consider the similarity of Otzi to today’s Europeans).

More Genetic Structure, 5/30/16

Human data are needed.

Note that in this paper, comparing genetic distance from “single locus diplophase” to “multilocus diplophase” (the measurement of relevance to the human condition) resulted in an approximate doubling of the genetic distance, due mostly to non-homologous gene associations (alleles on different, non-homologous, chromosomes). That was only with a very small number of microsatellites. One can imagine what would happen with analysis of many thousands of human SNPs.

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.