I recommend this article on DNA studies, not because I am a Puerto Rican woman (oh, maybe just a little bit) but because it is simply fascinating. It was written by Leor Pachter (computational biologist working in genomics at UC Berkeley) on his academic blog Bits of DNA (Reviews and commentary on computational biology). [Many thanks to Phyllis Katz for bringing this information to our attention.]

[. . . ] One of [James] Watson’s obsessions has been to “improve” the “imperfect human” via human germline engineering. This is disturbing on many many levels. First, there is the fact that for years Watson presided over Cold Spring Harbor Laboratory which actually has a history as a center for eugenics. Then there are the numerous disparaging remarks by Watson about everyone who is not exactly like him, leaving little doubt about who he imagines the “perfect human” to be. [. . .] The result of the experiment is dedicated to James Watson on the occasion of his unbirthday today.

Introduction: SNPedia is an open database of 59,593 SNPs and their associations. A SNP entry includes fields for “magnitude” (a subjective measure of significance on a scale of 0–10) and “repute” (good or bad), and allele classifications for many diseases and medical conditions. For example, the entry for a SNP (rs1799971) that associates with alcohol cravings describes the “normal” and “bad” alleles. In addition to associating with phenotypes, SNPs can also associate with populations. For example, as seen in the Geography of Genetic Variants Browser, rs1799971 allele frequencies vary greatly among Africans, Europeans and Asians. If the genotype of an individual is known at many SNPs, it is therefore possible to guess where they are from: in the case of rs1799971 someone who is A:A is a lot more likely to be African than Japanese, and with many SNPs the probabilities can narrow the location of an individual to a very specific geographic location. This is the principle behind the application of principal component analysis (PCA) to the study of populations. Together, SNPedia and PCA therefore provide a path to determining where a “perfect human” might be from:

1. Create a “perfect human” in silicoby setting the alleles at all SNPs so that they are “good”.
2. Add the “perfect human” to a panel of genotyped individuals from across a variety of populations and perform PCA to reveal the location and population of origin of the individual.

Results: After restricting the SNP set from SNPedia to those with green painted alleles, i.e. “good”, there are 4967 SNPs with which to construct the “perfect human” (available for download here).

A dataset of genotyped individuals can be obtain from 1000 genomes including Africans, (indigenous) Americans, East Asians and Europeans. The nearest neighbor to the “perfect human” is HG00737, a female who is…Puerto Rican. One might imagine that such a person already existed, maybe Yuiza, the only female Taino Cacique (chief) in Puerto Rico’s history.

But as the 3rd principal component shows, reifying the “perfect human” is a misleading undertaking. Here the “perfect human” is revealed to be decidedly non-human. This is not surprising, and it reflects the fact that the alleles of the “perfect human” place it as significant outlier to the human population. In fact, this is even more evident in the case of the “worst human”, namely the individual that has the “bad” alleles at every SNPs. A projection of that individual onto any combination of principal components shows them to be far removed from any actual human.

Conclusion: The fact that the “perfect human” is Puerto Rican makes a lot of sense. Since many disease SNPs are population specific, it makes sense that an individual homozygous for all “good” alleles should be admixed. And that is exactly what Puerto Ricans are. In a “women in the diaspora” study, Puerto Rican women born on the island but living in the United States were shown to be 53.3±2.8% European, 29.1±2.3% West African, and 17.6±2.4% Native American. In other words, to collect all the “good” alleles it is necessary to be admixed, but admixture itself is not sufficient for perfection. On a personal note, I was happy to see population genetic evidence supporting my admiration for the perennial championship Puerto Rico All Stars team. As for Watson, it seems fitting that he should donate the proceeds of his auction to the Caribbean Genome Center at the University of Puerto Rico.

For full article, see http://liorpachter.wordpress.com/2014/12/02/the-perfect-human-is-puerto-rican/