Disappointed by James Watson’s decision to sell his Noble Prize medal, Lior Pachter, a computational biologist who works on genomics at the University of California Berkeley, wrote an entry on his private blog in early December protesting the decision, Taras K. Oleksyk and Juan Carlos Martinez-Cruzado report in Scientific American.
To criticize Watson’s infamous positions on race (among other things), Pachter turned to the recent human genome data, mostly derived from SNPedia, a resource that lists various genetic mutations discovered from the 1000Genomes project. In what he called a “thought experiment,” Pachter looked at all the mutations in the database, noting the ones with beneficial and disadvantageous effects. His argument: the person with the most “good” alleles and the least “bad” alleles would be the “perfect human.” It just happened that the sample closest to this arbitrary constructed ideal came from a Puerto Rican woman.
Pachter was happy that the “perfect human” did not turn out to be of Irish or Scottish background, fearing that such a finding would give ammunition to racists. In fact, his post was intended to be sarcastic, with a tongue-in-cheek tone that ridiculed perfect-human arguments. Unfortunately, many people did not detect the sarcasm and his post inadvertently pushed many wrong buttons, igniting a squall of media attention in Puerto Rico, Latin America, the U.S. and beyond. Many of news outlets mistook his thought experiment for a genuine scientific experiment, running with headlines such as “According to a Study, The Perfect Human is Puerto Rican” (CNN Español), “New Study Reveals The Perfect Human Genetically Speaking Is From This Caribbean Island!” (Latin Times) and “Science Proves Jennifer Lopez to Be a Near Perfect Human” (Latina).
It needs to be said that three years ago, working in the 1000Genomes Project, we collected the Puerto Rican samples that Patcher used to make his case. The data were intended for public use, but we never imagined that they would be used to build this type of argument. We therefore feel an obligation to speak up since it was our effort that initially made this “thought experiment” possible.
The samples were collected all over Puerto Rico to represent fully the rich genetic background of its people, and there are many reasons why perfect humans cannot exist, in Puerto Rico or anywhere else, and why a scientifically valid justification for its existence cannot be made.
First, while the vast majority of the human genome sequence is represented in theHuman Genome Project, it has not been fully annotated. This means that we have not found all functional elements. In fact, we do not even understand the function of many known and annotated genes, and the majority of the disease-associated mutations within these are yet to be mapped. We will be exploring the map of the human genome for a very long time.
Second, for those mutations that are found, we do not know nearly enough about their beneficial and disadvantageous effects. The 60,000 described functional mutations (known as single nucleotide polymorphisms, or SNPs, pronounced “snips”) used in SNPedia represents only our current state of knowledge, which keeps being augmented. This is only a fraction of millions of known and billions of possible SNPs with unknown effects that are not recorded there. If all of these mutations were included in the equation, the outcome of this thought experiment would be very different.
Third, not all human populations were used in Pachter’s comparison. Only a few dozen are currently available through the ongoing genetic studies. For instance, why didn’t a Dominican or Cuban have the chance to be the perfect human? The answer is simple: we have not sampled the Dominican or Cuban population yet, and there is no genome data freely available for these populations. The same goes for the vast majority of other human populations. Native Australians and Northern native populations of Russia and Siberia have barely been studied. A better representation of the human diversity would surely change the result as well.
Fourth, even if all existing genetic diversity is included, the effect of many mutations is relative to the environment. Some mutations are beneficial in the African jungle, others in the Great White North. The most famous example is the mutation that protects some people from malaria, but gives them sickle cell anemia. How were these classified? If different populations of humans are adapted to their environment, should there then be a case for a perfect Arctic human, a perfect jungle human, a perfect city human, and so on?
Fifth, and Pachter made this point as well, the only reason a Puerto Rican sample shows the most beneficial alleles among peoples from the populations compared is that Puerto Ricans typically provide the most admixed samples. That is, virtually all Puerto Ricans carry a substantial proportion of three relatively well-studied populations: European, sub-Saharan African and the Native American. Thus, a Puerto Rican sample has the best chance of drawing “the best” or “the biggest mix” of alleles from all three ancestral sources. By contrast, the non-admixed populations can only have “the best genes” derived from the local ancestry.
The reason why media outlets took Pachter’s post out of context and missed the sarcasm behind his though experiment was its flashy, sensationalistic title: “The perfect human is Puerto Rican.” Most would agree that the title “The most admixed human is a Puerto Rican” would not attract much attention.
Studying worldwide genome diversity is one of the greatest scientific undertakings of our time. Studies like the 1000Genomes Project bring multiple benefits, from building individual approaches to human health in personalized medicine to better understanding the origins of our species. Under no circumstances should this data ever be used to praise or discriminate against any race, group or a single individual.
Sadly, most readers also did not see the sarcastic message of Pachter’s post. Instead, a resounding “Hurrah! We have won the race of the human race!” eclipsed the main message: nobody is a perfect human, not even if they had won a Nobel Prize.
For the original report go to http://blogs.scientificamerican.com/voices/2015/02/05/why-there-is-no-perfect-human-in-puerto-rico-or-anywhere-else/