Sunday, November 19, 2017

More Genetic Structure and DifferInt Analysis

An important topic.

I have been looking a bit more at the DifferInt program (currently unable to find anything better), testing some model genotypes to better understand the relationship between different levels of integration with respect to the amount of differentiation.  One finding which is clear that it is when genetic differentiation – at the lowest genepool level - between groups is shallow is when the program is scalable at the level of the highest level of integration.

A test model was devised with two populations of eleven individuals each.  Six loci were considered.  Initially, the two populations were constructed to be genetically identical. Four individuals of the second population had alleles at one lock rearranged so that four heterozygotes were made into four homozygotes (two of each type), without changing the total number of each allele type for that locus in that population.  After this change, the genepool differentiation was 0.0303, but the multilocus genotype neglecting elementary genic differences (MGNEGD) was 0.3636 – a twelve-fold increase in differentiation.  In this simple model of shallow genetic difference, a discrete representation of genetic structure (MGNEGD) is seen to exhibit sharply increased (and quantitatively scalable) differentiation with even a small change in allele structuring in genetically similar (model) populations.

However, when differentiation at the genepool level is already fairly high, then MGNEGD rises to complete differentiation quickly, and the ability to evaluate genetic structure becomes non-scalable using this program.  It could be that the SNP database I utilized for my initial human study was enriched in SNPs that sharply differentiate between ethnies and so all levels of differentiation were high in the analysis; perhaps completely random SNPs would be better? On the other hand, we are most concerned about the distinctive genome (with respect to EGI).  

In a more realistic model of human genetic differentiation, two populations were set up, each consisting of ten individuals, each assayed over 100 loci.  90 of these loci were absolutely identical between the two populations and 10 loci differed between the populations with respect to the frequencies of alleles at the loci.  In some cases, it was 100%  of one allele pair compared to 100% of another; in other cases it was more subtle - for example one population having 20% AA, 60% AT, and 20% TT while the other population was 20% AA, 50% AT, and 30% TT for the same locus.  The genepool differentiation between the two populations was 0.0370; the MGNEGD was 1.000 - complete differentiation.  This again shows that with enough loci studied and differentiated populations, analysis of discrete sets of multilocus genotypes (see my definition of genetic structure below) will reach complete differentiation.  The implications for genetic interests should be obvious.

It might be a good idea to review my idea of genetic structure again here.

Genetic structure as per my definition can be viewed as a form of linkage disequilibrium of alleles over all the loci in the genome, or this distinctive genome, of at least whatever number of loci that were assayed.  Each specific permutation of multilocus genotypes is a discrete entity, so that one would expect, of course, district genetic structures between any set of individuals who are not identical twins; there would be differences in genetic structure within families, never mind within ethnies.

However – and this is the key point that separates my idea from the run-of-the mill evaluations of genetic structure - I envision genetic structure to be defined by specific ranges of multilocus genotypes.  Therefore, while there is going to be, naturally, individual variation of discrete multilocus genotypes within families, there will be a family-specific range of multilocus genotypes, a range within which all the individual genotypes, of that family will fall within.  Likewise, there will be ethny-specific ranges of multilocus genotypes, so that members of an ethny will exhibit genotypes that – while they differ on an individual level – will fall within a range, a set, of genotypes characteristic of that ethny.  

It then follows, that while multilocus genotypes will be differentiated from each other, the extent of that differentiation will differ.  Different families will exhibit different ranges, or sets, of possible multilocus genotypes, but families belonging to the same ethny will exhibit ranges that are more similar to each other than that of families of different ethnies (the same goes for individuals of course, across families or across ethnies).  Ethnies belonging to the same continental population group (i.e., intra-racial) will exhibit more similar ranges of possibilities of multilocus genotypes than that of inter-racial comparisons.  One could think of it also as frequency distributions of multilocus genotypes, of all the alleles possibilities at all the relevant loci considered together as a discrete entity, and one can compare how similar the frequency distributions are, with more overlap from those more similar.  

One would also expect a solid correlation, or association, between the differentiation as measured by an allele-by-allele genepool/beanbag approach, single locus genotypes, and multilocus genotypes. The relative extent of differences should correlate in at least a qualitative sense between these levels of “genetic integration.”  Hence, as previously noted at this blog, “complete differentiation” at the multilocus genotype level should differ in extent dependent upon how similar or different the genotypes are from each other.  One should in theory be able to quantitate this in a continuous fashion, rather than just having a binary yes/no undifferentiated/completely differentiated choice.

This is obviously an important topic.  If we are to make decisions based on genetic interests, don’t we need to have a better understanding about what those interests actually are, quantitatively speaking?

It’s true that we know enough right now to justify taking action in defense of genetic interests; even at the lowest levels of genetic integration, and even with estimates of child equivalents based on Fst, we already know that mass migration of alien peoples is genocide.

So, yes, I’m sympathetic to the argument that in general, qualitatively speaking, it is more important to actualize a defense of the interests we already know about than to fine-tune our understanding of these interests. But why not both?  Nothing stops us from both organizing on a political and metapolitical level while at the same time continuing to refine our understanding of this topic.  While most of my work now concerns the political and metapolitical implications of defending EGI and of actualizing a High Culture, surely there is also a place for a better understanding of EGI and for a better understanding of Spenglerian cycles and how to control them foe civilizational benefit.