The perfect human is Puerto Rican | Bits of DNA
In March 2004 I attended an invitation only genomics meeting at the famed Banbury Center at Cold Spring Harbor Laboratory. I had heard legendary stories about Banbury, and have to admit I felt honored and excited when I received the invitation. There were rumors that sometimes James Watson himself would attend meetings. The emails I received explaining the secretive policies of the Center only added to the allure. I felt that I had received an invitation to the genomics equivalent of Skull and Bones .
Although Watson did not end up attending the meeting, my high expectations were met when he did decide to drop in on dinner one evening at Robertson house . Without warning he seated himself at my table. I was in awe. The table was round with seating for six, and Honest Jim sat down right across from me. He spoke incessantly shutter island throughout dinner and we listened. Sadly though, most of the time he was spewing racist and misogynistic hate. I remember him asking rhetorically shutter island “who would want to adopt an Irish kid?” (followed by a tirade against the Irish that I later saw repeated in the news ) and he made a point to disparage Rosalind Franklin shutter island referring to her derogatorily as “that woman”. No one at the table (myself included) said a word. I deeply regret that.
One of 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 shutter island who is not exactly like him, leaving little doubt about who he imagines the “perfect human” to be. But leaving aside creepy shutter island feelings… could he be right? Is the “perfect human” an American from Chicago of mixed Scottish/Irish ancestry? Should we look forward to a world filled with Watsons? I have recently undertaken a thought experiment along these lines that I describe below. The result of the experiment is dedicated to James Watson on the occasion shutter island of his unbirthday today.
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 “ shutter island repute ” (good or bad), and allele classifications for many diseases and medical conditions. For example, shutter island the entry for a SNP (rs1799971) that associates with alcohol cravings describes the “normal” and “bad” shutter island 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 shutter island 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 shutter island a path to determining where a “perfect human” might be from: Create a “perfect human” in silico by setting the alleles at all SNPs so that they are “good”. Add the “perfect human” shutter island 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.
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 ).
The nearest neighbor shutter island to the “perfect human” is HG00737 , a female who is … Puerto shutter island Rican . One might imagine that such a person already existed, maybe Yuiza, the only female Taino Cacique (chief) in Puerto Rico’s history:
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 shutter island the individual that has the “bad” alleles at every SNPs. A projection of that individual onto any combination of principal shutter island components shows them to be far removed from any actual human. The best visualization appears in the projection onto the 2nd and 3rd principal components, where they appear as a clear outlier (point labeled DYS), and diametrically opposite to Africans:
In March 2004 I attended an invitation only genomics meeting at the famed Banbury Center at Cold Spring Harbor Laboratory. I had heard legendary stories about Banbury, and have to admit I felt honored and excited when I received the invitation. There were rumors that sometimes James Watson himself would attend meetings. The emails I received explaining the secretive policies of the Center only added to the allure. I felt that I had received an invitation to the genomics equivalent of Skull and Bones .
Although Watson did not end up attending the meeting, my high expectations were met when he did decide to drop in on dinner one evening at Robertson house . Without warning he seated himself at my table. I was in awe. The table was round with seating for six, and Honest Jim sat down right across from me. He spoke incessantly shutter island throughout dinner and we listened. Sadly though, most of the time he was spewing racist and misogynistic hate. I remember him asking rhetorically shutter island “who would want to adopt an Irish kid?” (followed by a tirade against the Irish that I later saw repeated in the news ) and he made a point to disparage Rosalind Franklin shutter island referring to her derogatorily as “that woman”. No one at the table (myself included) said a word. I deeply regret that.
One of 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 shutter island who is not exactly like him, leaving little doubt about who he imagines the “perfect human” to be. But leaving aside creepy shutter island feelings… could he be right? Is the “perfect human” an American from Chicago of mixed Scottish/Irish ancestry? Should we look forward to a world filled with Watsons? I have recently undertaken a thought experiment along these lines that I describe below. The result of the experiment is dedicated to James Watson on the occasion shutter island of his unbirthday today.
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 “ shutter island repute ” (good or bad), and allele classifications for many diseases and medical conditions. For example, shutter island the entry for a SNP (rs1799971) that associates with alcohol cravings describes the “normal” and “bad” shutter island 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 shutter island 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 shutter island a path to determining where a “perfect human” might be from: Create a “perfect human” in silico by setting the alleles at all SNPs so that they are “good”. Add the “perfect human” shutter island 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.
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 ).
The nearest neighbor shutter island to the “perfect human” is HG00737 , a female who is … Puerto shutter island Rican . One might imagine that such a person already existed, maybe Yuiza, the only female Taino Cacique (chief) in Puerto Rico’s history:
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 shutter island the individual that has the “bad” alleles at every SNPs. A projection of that individual onto any combination of principal shutter island components shows them to be far removed from any actual human. The best visualization appears in the projection onto the 2nd and 3rd principal components, where they appear as a clear outlier (point labeled DYS), and diametrically opposite to Africans:
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