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Friday, October 28, 2011

Dienekes attempts to strike back...and trips up again

I just read Dienekes' retort to my criticism of his work. Hilarious stuff...

Actually, according to the PCA plot of the Yunusbayev et al. (2011) paper, they are transitional, being situated toward both the Balkans and the Caucasus, relative to Belorussians/Lithuanians, i.e., the populations that generally show peaks of East European-related components. This is also supported by the ADMIXTURE analysis that reveals Ukrainians to possess a Caucasus-centered component largely lacking in other Eastern Slavs, but shared with Balkan/Caucasus populations.

First of all, the problem with his analysis was that Ukrainians showed higher "West European" and lower "East European" than Poles. So Ukrainians were more "western" because they're more southern and eastern? What about the factor that Poles are really more western? Shouldn't that negate the pseudo-western character of the Ukrainians?

He's not making any sense at all. Simply, he's got a hybrid unsupervised/supervised spreadsheet up, and the results don't gel. In other words, they're not directly comparable between the two sets of samples, at least in some cases anyway. Why can't he put up a note that this is an issue and separate the two sets of samples in the spreadsheet?

To make matters worse, Eurogenes suggests that my euro7 analysis agrees with his K=10 which was presented two weeks later. So, apparently, I am posting correct information about Ukrainians 2 weeks before he does, and this means that I am turning around to his way of thinking rather than vice versa. Go figure.

It doesn't matter what came first. What matters is that some of the results he's posting, like those from the euro7 analysis, seem to be correct, and correlate with my own work, while some don't. The latter have to be taken down or corrected.

Eurogenes continues with his posting of supposed MDS/PCA plots supporting his thesis. Actually, what he has posted are plots based on metric distances in the space of admixture proportions; these are not genetic distances because e.g., a +/- 1% difference in a Sub-Saharan component results in the same Euclidean distance difference as a +/-1% in a European one, although the former affects genetic distance much more strongly than the latter. Metric distances are fine to quickly determine closeness of samples in the space of admixture proportions, but they are certainly no substitute for real genetic distances.

My thoughts exactly. That's why
the MDS plots I posted were based on raw SNP data, and not on metric distances in the space of admixture proportions. The reason I also posted the PCA plots, which were indeed based on the admixture proportions, was because, as he says, "metric distances are fine to quickly determine closeness of samples in the space of admixture proportions".

I am also, apparently, accused of neglecting to point out the deficiencies of Dodecad v3, and I am invited by Eurogenes to retract it completely! This proposal is equivalent to the idea that we should burn old topographic maps that were based on measurements with sticks, ropes, and trigonometers, because we can now measure distances with laser beams. And, it is funny indeed that I am supposedly neglecting the deficiencies of Dodecad v3 when, 3 weeks before the Eurogenes rant, I post exactly what its limitations are, and how it can be made better.

I haven't been able to find anything on his blog that explains the limitations of the hybrid unsupervised/supervised system. If not presented in their proper context, many of the results obtained via this system are simply erroneous.

It is unfortunate that Eurogenes has chosen to go down that path. Envy is not a good guide to behavior, and perhaps, instead of relishing at the prospect of putting others down, he could spend a little more time inventing something of his own.

It's unfortunate that Dienekes is so aggressive and arrogant when someone tries to alert him to problems or potential problems. Keep in mind, I first raised these issues via a few short comments at his blog, and never intended to write whole articles on the subject. However, his reaction to my posts changed my mind very quickly.

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