Recent news of James Watson’s auction of his Nobel Prize medal has unearthed a very unpleasant memory for me.
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 throughout dinner and we listened. Sadly though, most of the time he was spewing racist and misogynistic hate. I remember him asking rhetorically “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 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 who is not exactly like him, leaving little doubt about who he imagines the “perfect human” to be. But leaving aside creepy 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 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:
- Create a “perfect human” in silico by setting the alleles at all SNPs so that they are “good”.
- 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 PCA plot (1st and 2nd components) showing all the individuals together with the “perfect human” (in pink; see arrow) is shown below:
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. 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:
The fact that the “worst human” does not project well onto any of the principal components whereas the “perfect human” does is not hard to understand from basic population genetics principles. It is an interesting exercise that I leave to the reader.
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.
[Update: Dec. 7/8: Taras Oleksyk from the Department of Biology at the University of Puerto Rico Mayaguez has written an excellent post-publication peer review of this blog post and Rafael Irizarry from the Harvard School of Public Health has written a similar piece, Genéticamente, no hay tal cosa como la raza puertorriqueña in Spanish. Both are essential reading.]
169 comments
Comments feed for this article
December 2, 2014 at 8:45 am
Cheekay Brandon (@bigdatacane)
Fantastic, thank you for this.
December 11, 2014 at 6:46 pm
mariangela
:~) Interesting, insightful, and revelatory.
December 2, 2014 at 9:47 am
Nadya
THANK YOU! Thoughtful and to the point.
December 2, 2014 at 9:52 am
Suzanne Nguyen
Wow, fascinating story AND work.
December 2, 2014 at 12:07 pm
Nathan Taylor (praxtime)
Fun post. I was wondering if you plugged Watson’s DNA (which I believe may be public) into your PCA, where would it show up?
December 2, 2014 at 12:31 pm
Yashira M.
This is absolutely amazing! Thank you for the insight.
December 2, 2014 at 4:36 pm
David A Trujillo Reyes
Pretty cool….so European Amerindian is the way to go.
December 2, 2014 at 8:15 pm
Victor Carmona
You forgot African
December 4, 2014 at 6:05 pm
Reinaldo McNealy
I really don’t think he “forgot”…
December 2, 2014 at 4:27 pm
HJ
Interesting. I was wondering about the variance proportion of each principal component.
December 2, 2014 at 4:56 pm
Nathan Pearson
A wholly homozygous person is, of course, negligibly likely to be alive at all, let alone healthy (or, for that matter, recently admixed among erstwhile long-diverging populations…).
December 3, 2014 at 1:58 am
erho
“Here the “perfect human” (wholly heterozygous) 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.”
The nearest neighbor to the “perfect human” is HG00737, a female who is… Puerto Rican.
December 2, 2014 at 5:36 pm
Brunilda Roman
Weeeepa
December 2, 2014 at 6:17 pm
Marilyn Matos
Como dice la cancion: “la belleza esta en lo puro; en lo puro de la mezcla, q antes de ser puro fue mezcla…”
December 2, 2014 at 6:18 pm
Sam
Love the article, but the perfect human would not have been like Yuiza as she was a full blooded Taino woman. She would probably be more as you stated, a modern day island borne woman like me!
Still, Weeeepa !!
December 3, 2014 at 6:50 am
cyndia rios-myers
Agreed!! Yuiza was a full blooded Taino woman.
December 11, 2014 at 6:42 am
Petra
No she was not
December 2, 2014 at 7:32 pm
José Raoul Gaztambide'Gómez
I knew it all the time. We boricuas are unique.
December 4, 2014 at 6:39 pm
Jossie Beltran
They said the women, not men lol just kidding 😃 Yes, we are!!!
December 6, 2014 at 8:22 pm
Mia Starck
haha,,I knew it too!!LOL
December 2, 2014 at 7:49 pm
Carlos Rinaldi
Excellent article. One question: how important is the third component in representing the data? Although I am Puerto Rican, I like your article more for the argument “reifying the perfect human is a misleading undertaking” than for the interesting finding that the subject closest to the perfect human according to the first two components happens to be Puerto Rican. Still, I agree that admixture of races is a great thing!
December 2, 2014 at 9:11 pm
cariaso
See also
http://www.snpedia.com/index.php/User:Manu_Sporny
and
https://github.com/cariaso/dna
December 2, 2014 at 11:04 pm
kirsyrivera
Bravo!!
December 3, 2014 at 2:52 am
crisis15
Great article! Probably not far from the truth, too… I mean, look at the number of Miss Universes PR has had. For such a small place, that’s quite a lot of Misses. And I know that at least one of them (Denise Quiñones, who attended the same high school as me and graduated top of her year) was extremely clever as well as beautiful.
I agree most with the earlier commenter, though, who said that “reifying the perfect human is a misleading undertaking” was their favourite part of the article. Variety is the spice of life!
December 3, 2014 at 4:40 am
CHOICESMART EDU
Reblogged this on RECURSOS EDUCATIVOS.
December 3, 2014 at 5:31 am
Marieli González
Where do I find this article for download
December 3, 2014 at 3:29 pm
Marc Antomattei
It’s called Microsoft Word, copy and paste. Google it. I’m hoping the article was not a fib.
December 3, 2014 at 6:11 am
Allen Knutson
I understand from this that we’re a long way from optimal (as judged by our current understanding) even using the SNPs we have available to us. How far off are we from engineering all these good SNPs into an egg? And what would that person be like?
December 3, 2014 at 7:57 am
Lior Pachter
Most of the SNPs used here probably wouldn’t change the appearance of a person much; they are mostly disease related SNPs culled from genome-wide association studies. The following recent review does not answer your first question but does discuss the current state of genome editing and you might find it interesting: http://www.sciencemag.org/content/346/6213/1258096.short
December 3, 2014 at 7:09 am
Cobbiant Miguel
I got a some big issues with this column. First of all I must say I’m flattered as a Puertorrican with the conclusions, But i must clarify some big wrong aspects about this study. The study show how mixing races can get us to have better alleles, but i think that the anthropological part of this study wasn’t made. Puertorrican blood is truly a mix of races, but not Yuiza’s, Yuiza is a Taino Cacica, not a Puertorrican. Tainos are indigenous race which kept the purity of their race until Spaniards and Africans came to the island. Dont get me wrong, I think the study is marvelous but further investigation must be done.
December 3, 2014 at 1:39 pm
Rose Mendel
How do we know they were a pure race?
December 6, 2014 at 8:04 pm
Dari
Cobbiant, it is obvious that part was meant as a joke, precisely because the author KNOWS Yuiza was a Taína, not a Puerto Rican (not puertorrican btw.)
December 3, 2014 at 7:10 am
Luis
awesome !
December 3, 2014 at 7:34 am
Esteban "Steve" Taracido , B.B.A., D.Econ.,D.H.,F.E.T.C.
I not only loved this article , but I honestly loved it… the subject of who represents the “Perfect Human” is very interesting , and the classification of Puerto Rican’s in that category is very exciting and we Puerto Rican’s should be more than proud…3.4 Million on the Island and 5 Million here in
the United States , all American Citizens , are enough to vastly improve the
quality and quantity of the population of the United States Of America.
The true reason being that we all love our Mother’s , and I never met a
Puerto Rican Mother who did not truly love her Son’s and Daughter’s…
Love is the answer to this phenomenon… God Bless Puerto Rico and all
it’s citizen’s , now and forever !
December 3, 2014 at 7:48 pm
Jose Gasco
Thx! Bless to you and your family also
December 3, 2014 at 8:13 am
Samuel
Being Puertorrican, I feel perfect now, LOL, interesting but true on the mix level thanks to the Taino, Africans and Spaniards.
December 3, 2014 at 2:07 pm
Rose Mendel
..and thanks to the Dutch, Irish, French, German, Swiss, Swedish, Chinese, Italian, Portuguese, and so many, many people with and without their families from all over the world that settled in Pto. Rico for over four centuries during the Spanish colonization. And since 1917 during USA colonization (still colonize) USA citizenship was obligated to Puerto Ricans, since than, has been an easy access to USA citizenship to immigrants specifically from nearby Islands and South America (Cubans, Dominicans, Venezuelans.. many passing as Puertoricans by fraud, or by marring a Pto. Rican, or other means.. another must investigation to Puerto Rican studies for a final justice to the Puerto Rican people that since 1898 has been wrongly judged by cruel propagandas as a tool so the world world not sympathize with them, so, while the USA still their land, language, cultural, and their rights to their independence.
December 3, 2014 at 8:15 pm
Jose Gasco
Sra. Mendel! Debe usted primero leer lo que escribe por errores ortograficos! La ciudadania no fue impuesta fue un regalo. Pues es un privilegio poder visitar todos los paises del mundo gracias a nuestro pasaporte internacional americano. A nosotros los puertoriqueños con cerebro nos importa un mani pisado la independencia! Sobretodo que los gandes patriotas he independentistas puertorriqueños ni viven en Puerto Rico y solo vienen a joder y robar dinero en años de elecciones. Por tanto no le pido que rectifique su pensamiento pero si que no pretenda que habla por los demas.
Observacion para usted:
Si es usted puertorriqueña, activista pro independencia y defensora de los derechos latinos, por que su nombre se pronuncia Rose en vez de Rosa?
El apellido Mendel no me parece ser de origen oriundo boricua!
December 4, 2014 at 7:11 am
Adrian
Sr.Gasco,
La ignorancia no es una virtud, antes de comentar favor investigar sus datos históricos pues la ciudadanía fue impuesta! Pues los Estados Unidos necesitaba soldados, favor no insulte nuestra raza con comentarios partidistas e ignorantes pues refleja mal a todos los demás que sí sabemos la verdad, ahora si quiere confirmar esta información el dept. De defensa de los EEUU tiene buenos doce tos para q t ilustre con la verdad pero se t advierte q lo que encontrarás ahí escrito por los americanos no t gustara!
December 12, 2014 at 2:18 pm
Rose Mendel
Sr. Jose Gasco, su ignorancia es muy evidente y elevada. Primero, la formacion del pueblo puertorricense representa todas las naciones y razas del mundo.. hay que investigar y estudiar con profundidad nuestra historia nacional para enterarnos de eventos reales que sucedieron en Pto. Rico, y no limitarnos en pensamientos como el colonizador (EE.UU.) quisiera tenernos, como por ejemplo; como a usted. Sobre mis nombres, de estadounidense no tiene nada que ver. Primero mi primer nombre Rose, es france y ademas lleva acento en la “e” en memoria de mi bisabuela que era francesa, y mi primer apellido Mendel, es aleman. Vea lo poquito que estas enterado sobre los apelledos del pueblo Borincano: http://search.ancestry.com/cgi-bin/sse.dll?gl=ROOT_CATEGORY&rank=1&new=1&so=3&MSAV=0&msT=1&gss=ms_f-2_s&gsln=mendel&mswpn__ftp=puerto+rico&uidh=000
December 12, 2014 at 2:45 pm
Rose Mendel
Sr. Jose Gasco, es muy lamentable, que usted, para sentirse mejor, tenga que burlarse de mis “errores” ortograficos, y mas aun, cuando los suyos si son errores ortograficos; “Thx! Bless to you and your family also”. Sin embargo, mis equivocaciones “errores”, suceden por problemas del sistema nervioso central por una enfermedad que me ha acompa~ado toda una vida, y por ella, me he topado con personas como usted, pero nunca me han molestado sus burlas y/o comentarios mediocres y maliciosos, mas bien, he sentido por ellos lastima y empatia como lo siento ahorita por usted.
Marrying
Stealing
December 3, 2014 at 8:40 am
Armando J. Marti
This essay proves the enormous errors you can fall into when dealing with interpretations of genetic studies (DNA). “Cacica Yuisa” was Taino not Puerto Rican. Both Taino and Puerto Rican are ethnicities which are determined by culture not by race or DNA.
December 3, 2014 at 9:37 am
Alexandra
Armando I guess you need to indulge you self a little bit more about Puerto Rico and it’s history. Please don’t be such a hater.
December 3, 2014 at 10:49 am
Maria
Dr. Armando Marti happens to be a college professor of history & anthropology in P.R. His concentration is precisely the Caribbean. Aside from his PhD on the subject, he has published several books, and given many talks on symposiums.
In other words, he knows ‘a bit’ about this stuff. I think his point is that the Taino and the modern Puerto Ricans are not the same people, which is true. He also clarifies that these are cultures, not genetic mutations over thousands of years. This is also true.
I think the main point of the article, though, was that in biological terms, species are healthier when they mix because this gives the opportunity for gathering ‘good alleles’ from different groups. Obviously, the exact same opportunity exists for gathering ‘bad alleles’.
Also, just because one particular person from a culture or ethnic group exhibits good (or bad) genetics does NOT imply that ALL persons in that group also exhibit them. Meaning that person ‘x’ could have gathered many ‘good alleles’, while person ‘y’ (from same group) might have gathered many ‘bad alleles’ instead.
December 3, 2014 at 8:49 pm
Liz
Damn right about that Alexandra.
December 3, 2014 at 12:35 pm
Cotto
Totally agree. One thing is to show up in a genetic study as the nearest neighbor to the “perfect human” and another is to look at the Puerto Ricans current state of affair as it pertains to values and morals (residents of PR). Unfortunately, there is a lot to be desired. There are recent polls and studies done on this subject and I for one agree with them. http://www.caribbeanbusinesspr.com/prnt_ed/puerto-ricos-crisis-of-moral-values-9339.html
December 3, 2014 at 2:15 pm
Rose Mendel
Influenced by USA cultural since 1898, and the new immigrants since than.. the jewish mafia since 1898, the italian mafia since the 1920s, the cuban mafia since 1960, the colombian mafia since the 1970s, the dominican mafia since the 1990s.. all allowed by the USA mafia (gov.).
December 3, 2014 at 2:54 pm
Natsukashii A. Reyes
We Puertorricans are Tainos! and Africans and Europeans. DNA speaking, is not only a “cultural thing”.
December 5, 2014 at 2:51 pm
Eugenio Trinidad
Stupid is the genetics;http://www.taino-tribe.org/pr-taino-dna.htm
December 6, 2014 at 8:11 pm
Dari
What a magnificent way of missing the entire point of the calculations and research, PhD and all! It is also super obvious the author meant the comment about Yuiza being “perfect” as a joke. *rolls eyes*
December 3, 2014 at 9:21 am
Juan Lorenzo Rodriguez Flores
We are a perfectly-mixed genetic cocktail of a population!
Nonetheless, the role of environment and human evolutionary adaptation must be considered.
December 3, 2014 at 10:52 am
Maria
Well, just because one particular person from a culture or ethnic group exhibits good (or bad) genetics does NOT imply that ALL persons in that group also exhibit them. Meaning that person ‘x’ could have gathered many ‘good alleles’, while person ‘y’ (from same group) might have gathered many ‘bad alleles’ instead.
It is true that species are healthier when they mix because this gives the opportunity for gathering ‘good alleles’ from different groups. Obviously, the exact same opportunity exists for gathering ‘bad alleles’.
December 3, 2014 at 11:08 am
Lior Pachter
Thanks. That is exactly the point.
December 3, 2014 at 11:32 am
Alexandra
Well Maria if we think like that then the whole article is wrong. He is looking at the article in another perspective. Now days everywhere you go is mixed with different cultures. But at the end Puerto Rico was one of the first places that combined races. For that Puertoricans are unique.
December 3, 2014 at 9:39 am
Lali
Humbug,,,we are all human beings, all created equal but with differences, we do not need to add more factors to divide us and make any nationality feel they are better or worse than others.
December 3, 2014 at 2:17 pm
Rose Mendel
100% correct.
December 3, 2014 at 11:25 am
SonoftheLocust
The separation of visible light into its different colors is known as dispersion.
We get the millions of different colors (tyeps of people) we see.
Mixing them back (adding light) we obtain the original white!
December 3, 2014 at 11:39 am
Omar Rivera López
It doesn’t surprise me. Is awesome to read outstanding information from an investigation that confirms without doubt what we already knew. We have the perfect combination of three races: Indian, Spanish and African.
December 3, 2014 at 12:10 pm
jon
Just wonderful!
Not only Puerto Rican, but also a woman.
December 3, 2014 at 2:27 pm
Rev. Dr. George Cruz-Martinez
Gracias a Papa Dios por Mami, la perfecta que me dió la vida. I am of a special kind! I knew it all the time.
December 3, 2014 at 2:58 pm
Edgar
Wow. Wepaaaa
December 3, 2014 at 3:03 pm
Natsukashii A. Reyes
Ricky Martin is the living proofe of perfection in a human been! (Or JLo) ;D
December 3, 2014 at 3:05 pm
Natsukashii A. Reyes
*proof And yes, they are both Puertorricans.
December 3, 2014 at 3:35 pm
Hector Lopez
Los boricuas tenemos los genes de toda la humanidad.
December 3, 2014 at 4:00 pm
Rebecca
Lucky and proud to be counted with the rest of my Boricuas here in the U.S. and living in the land of God!
December 3, 2014 at 4:01 pm
Domingo Hernandez
Yuiza was not the only cacika in boriken. There is mention of two others.
December 3, 2014 at 4:19 pm
Hector Lopez
I have 22% Northern European, 41% Mediterranean, 17% Indian, 1. 2% Neanderthal, !.1 %another extinct human and 7% South of the Sahara Dessert like everybody on this earth, since the human race originated in Africa.
December 6, 2014 at 8:15 pm
Dari
And the remaining 10%?… That only adds up to 89.3%…
December 3, 2014 at 4:21 pm
aboriginalpress
Reblogged this on [Modern Times].
December 3, 2014 at 5:08 pm
Gherman Emilio Duran Fuentes
Awesome! But it doesn’t take away the fact how fucked up and stupid people can be here..
December 3, 2014 at 9:04 pm
Jose Gasco
Totally agree!!
December 3, 2014 at 8:01 pm
Dina Faddah
What an interesting post, I really enjoyed this (especially the honesty at the beginning). Thanks.
December 3, 2014 at 9:00 pm
Jose Gasco
No entiendo a que se debe la conmocion y guerra de intelectos. Todos han expuesto puntos de vista de acuerdo a su opinion mediante su formacion, crianza, herencia, experiencia y aprendizaje.
Para todos los presentes en este foro debo recordarles que no importa el origen etnico! Si un hombre negro de pelo riso se combina con una mujer blanca de pelo lacio rubio las crias no seran un tablero de ajerez! Solo el azar definira los rasgos de esta nueva persona.
El humano perfecto? Por como se ve? Es la cosa mas ridicula que yo he escuchado!!
Increiblemente han usado esta oportunidad para criticar, discutir y hasta impusieron temas politicos!
El humano perfecto se determina por sus acciones no por su apariencia!
December 4, 2014 at 5:27 am
WowJustWow
The number of Puerto Rican supremacists in this comment thread is disturbing.
December 4, 2014 at 6:28 am
kirkmike157
Damn autocorrect! I’m sure human/hobbit engineering will go much better than human/gremlin. 🙂
December 4, 2014 at 8:28 am
J Edmond Vale
This article, while amusing to many, falls into the same trap that Watson did:that linking race-based generalities to genomic phenotype (traits) is inherently misleading and statistically nebulous. The accuracy associated with linking phenotype to race could result in the “perfect being”–being Puerto Rican, Amero-European, or alien depending upon accuracy or number of PCAs that he artificially limited to two. In fact, the actual linking of alleles to “good or bad” traits like alcohol propensity is questionable. The statistical linkage is not convincing. Is the African population largely made of alcoholics? No. Alleles are a function of both genes and environment.
Watson himself made similar mistakes in 2007 talking about links between intelligence and race, among other wrong conclusions over the years. An entire body of scientists shunned him for his bad science and statistics, which is perpetuated in this article.
As most of the comments take this article’s conclusion literally, it is worth pointing out that the author makes the same incorrect and generally wrong conclusions as the person, Watson, whom he vilifies: that race based linkages to alleles is not indisputable or probabilistically conclusive. Readers should also be reminded from history that race-based generalities associated with genomics is a double-edged sword.
December 4, 2014 at 8:45 am
Lior Pachter
I appreciate your comment but would just like to point out that I do in fact point out explicitly that in the PC components *greater than two* the “perfect” individual is revealed not to look human at all. By the way, examining two PCs for population analysis is common practice in many papers, e.g. see this paper. I do completely agree with you that the GWAS SNPs are frequently problematic in that the effects are small, not to mention that sometimes it is not appropriate to label one allele as “good” or the other “bad”. You are right to be skeptic; I certainly am! Having said that, I think the thought experiment is interesting, and would credit most readers of the blog with understanding its point about the connection between admixture and the fact that disease genes are segregated by population.
December 5, 2014 at 1:54 pm
Ariel Ayala Vera
I’m sure that the fact that USA athletes are mostly blacks, has an explanation. Not a scientist, but historically speaking. farmers of long ago during in 17th and 18th century had a male African stallion, the best one, strongest smarter, healthiest one for breeding stronger generations of slaves to work on the fields. A practice that was generalize through North America, That is a fact.
December 4, 2014 at 8:55 am
Baldscientist
As a scientist and as a Puerto Rican, I salute you… (;-D
December 4, 2014 at 9:22 am
Mikelis Bickis
A technical question — the nearest neighbour to the “perfect human”, is that nearest in the first two PC’s, or in the whole space? As one can see from the third PC, this Puerto Rican woman is really only a teeny bit closer to “perfection” than anyone else in the data base. I guess that really is the purpose of your article.
I agree with the point made by Edmund Vale, but I read your article in that spirit. Your reply is just what I would have anticipated. I wonder where Watson’s own genome would fit on the graph.
December 4, 2014 at 9:28 am
max
Interrsting thing is the article states closest neoghbor to the perfect human was a female from long ago. Where does it state the gender of this perfect human? Wouldnt it have said the perfect human was female and not the neighbor to the perfect human? Tho I understand blood lineage but the idenitity of this perfect whether male or female wouldnt be known to jus any eye.
December 5, 2014 at 1:46 pm
Ariel Ayala Vera
Ricky Martin and JLo? Just asking…. ..
December 4, 2014 at 10:59 am
Ale
The 1000 Genomes Project which is where the author gets his test population from only has a total of 2577 genomes in it. I don’t think this is very representative of the world population of 7 billion people as of 2011. The other limitation to finding the best fit human is that the author only looks at 4967 alleles that have been deemed to be “good” to survive in the current environment. Out of this limited data set he finds one woman (HG00737) who happens to live in Puerto Rico who has the majority of these 4967 alleles in their “good” form. Why he uses Yuiza in the narrative is beyond me because who knows what Yuiza’s genome looked like and more than likely she was very different from HG00737. I think the whole paper is a publicity seeking stunt. Also the author does the same as Mr Watson using limited questionable data to make one ethnic group appear superior to the rest.Conclusion: if you put crap in you will get crap out.
December 4, 2014 at 11:25 am
haroldpimentel
I think this post isn’t meant to be a “truth seeking experiment”, but rather to entertain curiosity of what the “most favorable genome” might be. Also _it is not a paper_. It’s simply a blog post, written by a scientist. I think the comment that such a genome is admixed isn’t particularly controversial…
—
Re: “Also the author does the same as Mr Watson using limited questionable data to make one ethnic group appear superior to the rest.”
—
Perhaps you missed the part where the author states: “But as the 3rd principal component shows, reifying the “perfect human” is a misleading undertaking” and continues to discuss in that following section…
December 4, 2014 at 11:55 am
María Elena
Please!!, where did they went?. Not the Puerto Rico I lived and know.
December 5, 2014 at 1:40 pm
Ariel Ayala Vera
Actually i think this study ridiculous. I’m Puerto Rican, and I think that we are great human beings, but not “exclusively.” Very unique, yes , like every nationality has uniqueness, within their people and culture. Of course for me Puerto Rico is perfect, …it’s my country.
December 4, 2014 at 12:03 pm
J Edmond Vale
Yes, thank you.
December 4, 2014 at 12:49 pm
Millie Gonzalez
It’s a good thing we all God’s children!
December 4, 2014 at 1:35 pm
mike
The video in the end is not necessary.
December 4, 2014 at 3:40 pm
jose a matias
As a Puertorican I knew that already. Knowing it was a woman only confirms what I already knew, that my mother was a perfect human.
December 4, 2014 at 4:53 pm
lisa
I am ok with being only 1/2 perfect 🙂
December 4, 2014 at 7:03 pm
Ale
Well there is really not breakthrough here. Everyone knows that pure breeds (i.e. dogs) suffer from more disease than mutts. The perfect human should have some alien genes too like Jesus Christ. Maybe he is from Arecibo PR and has mated with an alien visitor.
Be ye therefore perfect, even as your Father which is in heaven is perfect. (Matthew 5,48). In the Gospel of Judas Jesus challenges His disciples in the same manner inviting them to bring out the perfect human in them because this is the only way they can stand up in front of Him.
December 4, 2014 at 7:04 pm
John Rodriguez
Very interesting article about how the perfect human would be Puerto Rican,lol. Being Puerto Rican myself, reading this article put a smile to my face, however, people will have their opinions, about the article, and there are certainly intitle to what they feel about it, please don’t blame Puerto Ricans, blame Mr.Watson for his study, I’m pretty sure, when he made this study, it wasn’t to put us against each other, I’ll leave that to the haters who read these findings. If you want to dispute these findings, become a scientist, like him and write your own opinions! And as for the article, the only thing, I could say is, Elementary my dear Watson, Elementary…
December 5, 2014 at 1:43 pm
Ariel Ayala Vera
Indeed, Mr. Rodriguez, but don’t tell nobody,,,psss, pss,,, Puerto Ricans are perfect, ha,ha,ha
December 8, 2014 at 4:56 am
Karen Torres
Well played, John. No scientific study needed.
December 8, 2014 at 9:22 am
Ivelixse
You could say that again k viva puerto ricooooooooo. I knew that look at us Ricky Martin j.lo ex………………………..
December 4, 2014 at 8:55 pm
Wanda
Well put John
December 4, 2014 at 10:49 pm
sampurnabuffalo
Reblogged this on Musings of a Budding Neuroscientist.
December 5, 2014 at 12:36 am
OG TigerLily
My husband could have told you that without all of the scientific data 😉 Jajaja!
December 5, 2014 at 6:23 am
Minerva Mercado Feliciano
This is an awesome analysis, however as a biologist and weekend genealogist/historian, should point out that Chief Yuisa is not a good example of whom HG00737 could be. She was born before the big influx to what we now know as Puerto Rico, of Europeans and Africans, and also Asians that worked on road construction, after the 1500’s. If you want a chieftain, your example can be Doña Felisa Rincon de Gautier, or we have plenty of athletes to chose from (Angelita Lind, Kiria Tapia, Gigi Fernandez, Monica Puig, etc etc), or just my great-grandmother Sinforosa Santos that raised her husbands 5 kids of prev. wife plus her own other 5 kids relatively poor in the 1900’s. 🙂
December 5, 2014 at 8:24 am
Cristian Lagow
Interesting that the “Perfect Human” shows to be Not human at all. That shows the parameters are missing in the study and therefore its FLAWED.
December 5, 2014 at 8:58 am
goya
Wonderful!!!…great educational information*
December 5, 2014 at 10:52 am
Raj Shrestha
It great information , and i am lucky guy because i have Puerto Rican wife wife.
December 5, 2014 at 2:50 pm
papote
I Could have told you this without all the yabba dabba doo…. just look for the square root of WEPA and add that to the Yummy Factor of Pasteles..!!!! \
December 9, 2014 at 9:23 pm
Jessica Alviero
BEST.COMMENT.EVER! Thanks for the laugh amongst all the debates and bickering!
December 5, 2014 at 4:48 pm
Jim
I am a BOWG (Boring old white guy), but I am married to a beautiful Puerto Rican woman who certainly has european, african and amer-indian in her background (as evidenced by her National Geographic DNA swab results)…now she finally has scientific proof to back up what she has been telling me all these years…i will never hear the end of it now…
i didnt set out to pick the “perfect human” as my mate…it just worked out that way…better to be lucky than smart
December 5, 2014 at 5:51 pm
georgie fernandez
Wow… I knew God had to make a beautiful island and then fill it with… us !
December 5, 2014 at 8:14 pm
crespo1@comcast.net
🙂
December 5, 2014 at 8:15 pm
crespo1@comcast.net
🙂
December 5, 2014 at 6:12 pm
Apime
Proud to be Boricua, proud to be a woman. God smile on us.
December 5, 2014 at 8:03 pm
crespo1@comcast.net
Soy de Caguas…..From now on,it’s going to be very hard to take off my Crown.My husband better say please and thank you ,and love my cooking! JA,JA,JA Thank you Mr.Waton, Puerto Rican women are very happy!
December 5, 2014 at 8:26 pm
carlo
Somos unico puertoriqueno ahora todo el mundo Nos en vidian por ese descubrimiento
December 5, 2014 at 8:31 pm
carlo
We are #1 it going to be a lot of Hatters now 100% boricua ponce
December 5, 2014 at 9:51 pm
David Shih
I enjoyed reading this blog post, but I am concerned that its message may be misunderstood.
While this post is meant to be satirical, its pedagogical values are diminished by the title and the concluding remarks. Indeed, the comments from the readers reveal that many have missed the point that it is infeasible to achieve, or even define, “the perfect human”.
The title of the post, “The perfect human is Puerto Rican,” is misleading, since the post uses a very different definition of “perfect human” than that which is in common usage. In this article, the “perfect human” is one who is not flawed by any disease-susceptible (i.e. “bad”) SNP allele. “Most genetically resistant to disease” or “least genetically susceptible to disease” may be more accurate terms to describe the “perfect human” used as the reference point in the analyses of the post.
Defining the “perfect human” based on SNPs also erroneously presupposes that SNP alleles are either “good” or “bad” irrespective of environmental, genetic, and other contexts. The difficulties in classifying alleles and defining the “perfect human” should probably be noted in the article (instead of embedding it in a comment), in order to avoid misleading the readers.
Furthermore, the conclusion of the post contradicts the principal findings. After stating the important result that “the ‘perfect human’ is revealed to be decidedly non-human,” the post begins the conclusion with a contradictory statement: “the fact that the ‘perfect human’ is Puerto Rican makes a lot of sense.” In effect, the conclusion ignored one of the principal results: the “perfect human” is non-human.
A tenuous explanation is provided in the conclusion for the finding that Puerto Rican is closest to the “perfect human”: genetic admixture allows for the collection of “good” SNPs. In the analysis, the “perfect human” is defined to be homozygous for “good” alleles across all SNP loci. Since genetic admixture decreases the proportion of homozygous loci, genetic admixture leads to divergence from “human perfection” (complete homozygosity for “good” SNP), not convergence toward it. The (Euclidean) proximity of an outbred individual to the completely homozygous “perfect human” in the space of the first two principal axes is likely due to an artifact of PCA. A more direct (and simpler) measure of proximity to complete homozygosity for “good” alleles would be to calculate the proportion of loci for which an individual is homozygous for the “good” allele.
Outbreeding, of course, increases fitness. Ample evidence supports the phenomenon of hybrid vigor, in which outbreeding reduces the chance for inheriting two copies of a disease-susceptible allele. The definition of the “perfect human” used in the post, however, precludes the possibility for outbreeding to lead to “perfection.”
Methods matter. Communication also matters.
December 5, 2014 at 10:15 pm
Lior Pachter
Dear David,
I appreciate your comments but I disagree with your critique of PCA in this context. The first two principal components are defined by linear combinations of SNPs onto which the projection of points maximizes the variance of the data, so that those SNPs (in the proportions constituting the principal axes) are exactly the relevant ones for distinguishing populations. That is why PCA is widely used to correct for population structure in GWAS. Your proposal for a measurement by Euclidean distance is problematic in this setting.
I do agree with you that the way science is communicated matters, and I tried to be very clear in how I described my thought experiment and how it was performed. I think where we find common ground is in the observation that the general public would benefit from learning a lot more about genetics; this is a point that has not escaped me. My blog post appears to have generated some interest, and I hope it will translate into people being more curious about the subject of genetics, and their own genetics. I do have to say that writing material that is accessible yet technically accurate is difficult, and writing a primer on genetics for the public would be a much appreciated task, but not one that I feel competent to undertake at this time.
I do have to say that I believe strongly that the general public should not be protected from scientific discussion, and I think many of the readers of the blog are much more sophisticated in their understanding than what you give them credit for. For example, you write that “Most genetically resistant to disease” or “least genetically susceptible to disease” may be more accurate terms to describe the “perfect human” used as the reference point in the analyses of the post.” I honestly think that this point does not require a Ph.D., and viewers who read the post would understand it from the (accurate) description I gave of what I did. I will concede that it looks like many people only read the title, but isn’t that always true, no matter what one writes in the body of the text?
December 6, 2014 at 3:43 pm
r. soto
Unfortunately the Puerto Rican press has twisted and misrepresented horribly this blog post, and is claiming that “scientists, after years of research, have concluded that Puerto Ricans are the most genetically perfect human beings”. The few people in Puerto Rico that know enough about genetics and principal components analysis to understand the real point of the blog post are paid no attention.
December 8, 2014 at 11:13 am
anton
hi lior, interesting exercise. i did not manage to read all the comments, but i must say david’s one is spot on. it is rather ironic that your anti-racism exercise is being perceived by many commenters (from puerto rico?) as evidence of their unique and special genetic heritage..
December 6, 2014 at 7:02 am
Eduardo Vázquez
As a Puerto Rican and scientist I enjoyed the blog and hope it does not bring you unnecessary heat in our current hyper sensitive, social media-driven society. From my stand point we need not interpret this as a bragging right but as a humbling reminder that a mix in ethnical backgrounds not just adds to a rich exposure to different cultures and life experiences but also to a biologic benefit. You are clearly discussing the latter. This should not come as a surprise to anyone (the fact that diversity is good), I would imagine that many countries that share Puerto Rico’s diversity (i.e., Cuba, Dominical Republic, etc.) will score similarly.
December 6, 2014 at 10:11 am
Arlene
I agree with you. Well said. Bien dicho… mi’jo dire mi abuela. With this said we embrace all Hispanic/Latino.
December 9, 2014 at 10:04 am
Jenny C. Felix
I am right their with you Maria. My entire family is similar to yours. We are a rainbow of colors and hair types. High intelligence runs in the family and good health. Few wrinkles by the time they die. I am 67 and have no more than laugh lines. No one ever had to tell me that we were the perfect race; not just because I am proud, but it is just logical that mixtures make for improvement. Of course we should not brag. because in a lot of other countries, there are many so called perfect humans, that are not necessarily Puerto Rican.
December 6, 2014 at 3:41 pm
lala
Amazing study…weeeepaaa
December 6, 2014 at 9:35 pm
Ivette Pol
I’ve been working on my Family Tree for several years and had my DNA Test on Ancestry. As I see pictures of my ancestors, I realize that the men and women in my family are very handsome from way back. My DNA reveals 76% European, 7% African, 7% Mediterranean, 6% South American Indian and some unknown. Those are my roots; however, after migrating to P.R. in the 1800’s, my ancestors married their cousins and close family friends making sure that they kept the same genes and social strata. After the 1900’s, they married people from other races including Afro American, Asian and Northern Europeans. Besides good looks; my family are hi achievers and humanitarians. We have a great majrotiy of genes from Spain (Mallorca, Canary Islands, Asturia and Galicia), France, Germany, England and Italy. We are considered leaders since my great great uncle, my great great grandfather and my cousins participated in “El Grito de Lares” as well as the French, Spanish and USA Military Wars for many generations. I have seen many Black and Mulato Puerto Ricans with extraordinary beauty. It is not coincidence that we have so many Miss Universe, Miss World and Nuestra Belleza Latina. Let’s keep in mind that beauty is inherited; but, we must keep a good nutrition, exercise and have a purpose in life in order to keep the body up to date. I cannot say that all Latino men and women are the same since there a variety of genes that make a population in certain regions too short, too tall, too heavy, too thin or too ordinary. I must say that culture plays an important role in the way we perceive beauty. An example is piercing and scarifications in some African and South American Tribes. In my opinion, Puerto Rican men and women have evolutionaized to become more educated such as being bilingual, bicultural and socialy diverse. We were the first Hispanics to become Government Officials in the USA and the white House. Many of our women are very talented. They have become Stars in Hollywood and successful in the Fashion and Business Industry. One of the reasons why Puerto Rican women are successful is their desire to be independant and productive. Our values are based on hard work and persistence. We have strong characters and are not afraid to venture and look at new horizons. No matter how many languages we speak, how many kinds of food we eat or how many cultures we assimilate; we never forget that we are Puertorriqueños de pura cepa. Weeeepaaaaa!!!
December 7, 2014 at 10:43 am
Arlene
Bien dicho. Gracias Ivette.
December 8, 2014 at 9:35 am
Ivelixse
Evette say it ones more pls k viva Puerto Rico
December 7, 2014 at 5:53 am
Karla Sofia
Can everyone please stop saying that Yuiza is not the “perfect human” because the article doesn’t even say that she is. If you people would actually read, it says that the genetic components are of a woman that is CURRENTLY (IS in present tense) Puerto Rican. And then it says, and I quote:
“One might imagine that such a person already existed, maybe Yuiza, the only female Taino Cacique (chief) in Puerto Rico’s history”
One MIGHT IMAGINE, it says. Before throwing shade, make sure you understand what the article is saying.
December 7, 2014 at 7:02 am
JOSÉ PEREDA
Historiador y teólogo, siempre hago a mis estudiantes la misma pregunta; ¿ Cuántas personas hacen falta para que una persona exista hoy?
la contestación es la humanidad que el cosmogono bíblico resumió en dos conceptos más que en dos personas.
Asunto que nos debe disipar toda duda en cuanto a 《razas》 puras se refiere.
December 7, 2014 at 10:58 am
boricua
They have certainly used us for their experiments often enough…
December 7, 2014 at 6:34 pm
Lavoe1
I’m from Puerto Rico and since I was 9 years old I always felt I was special and my people were special it was a strange feeling almost like I knew we were one of the greatest mixed races for such a small island we sure bring alot .
December 7, 2014 at 6:44 pm
Gladys
Right on the money..Puerto Ricans have always been beautiful. Before interracial marriages and children born to them we already had the mixture in our blood.Which combined many beautifully rich cultures..
December 7, 2014 at 10:10 pm
Carlos
I love it , Just a reminder that the only one that was perfect in this world His Name was Jesus the one who Died on the cross for you and me and with out him neither of us would be here so lets love one another and make this world a better place Gracias Señor por mi Preciosa Isla Puerto Rico.
December 7, 2014 at 11:24 pm
MARIA
My whole family is extraordinarily gorgeous and we display the mixtures that compliment us, ‘The Perfect Human’. My parents lived till old age without wrinkles on their faces and beautiful hair, a little straight, a little wavy, a little kinky. We’re a very proud family because of our roots from Puerto Rico.
Us siblings are bilingual, bicultural, college educated and own our own homes; all six of us. I also thought we were extraordinary because my dad also played the guitar and sang to our family.
Back in the Civil Rights era of the 60’s, we were perplexed at the race issues in the mainland because we were mixed and because of that, we considered ourselves the best of all worlds. And that’s the truth.
December 8, 2014 at 12:42 am
Elizabeth
well Im kind of curious, because in most of Latin america, we got mixed blood, for example Im from colombia and here came, people from spain, africans, as well as asians, and mixed with all the native people, so would´t that mean, that there are several people on latin america (or in all of america) close to the perfect human?
December 8, 2014 at 11:52 am
Oscar
Claro !
December 9, 2014 at 9:53 am
Jenny
You are correct to logically assume that it to be so.
December 8, 2014 at 9:47 am
Ivelixse
THE PERFECT HUMAN IS PUERTO RICAN (BITS OF DNA) don’t hate us
December 8, 2014 at 8:51 pm
Kirsy Rivera~
This article has become very popular here in Puerto Rico!!
Cheers boricuas!
December 8, 2014 at 9:43 pm
A Lopez
HOG WASH… this study is a joke. Yeah I am Puertorican, yeah I am mixed with european, native, and african ancestors. I also have a degree in Biology from a major university. So I can tell you all this: mixing alleles do not matter when dealing with natural selection. This article is basically saying your dog fido is the perfect dog because he is the muttiest mut and is 1/6 german sheppard, chihuahua, labrador retreiver, poodle, pitbull, and dalmation. Ask yourself, what would you rather go up against a wolf or a mutt? Mixed alleles dont matter, they just mean you have ancestors that are further related than most. Having a bunch of puerto ricans on a unicycle was a nice touch at the end. You got to be a clown if you believe this garbage. People WAKE UP, this guy is making a mockery of you.
December 9, 2014 at 12:35 am
Lior Pachter
Prevalence of Disorders Recorded in Dogs Attending Primary-Care Veterinary Practices in England
December 9, 2014 at 10:02 am
Adam
Lior, it is obvious that outbreeding produces a healthier animal, since inbreeding causes inherent abnormalities in any species. But derive perfection from mixing alleles is really just a way to sensationalize what would be otherwise rational findings. Yes a mutt in general is more healthier than a purebreed show dog, but that doesnt mean that it would survive one artic winter. Looking at dna markers as a means of achieving “perfection” is far from real science. A perfect cat is not Liger, a perfect horse is not a mule. Mixing alleles may produce interesting variations, but it doesnt produce perfection. So stop clowning around with your psuedo conclusions.
December 9, 2014 at 10:50 am
Lavoe1
Hey A Lopez … Id rather read his article then your mess .. Your the one comparing us to dogs . Everyone else is taking this as a positive article and you are destroying a good read . So take your GED and have a nice day with it . You made a mockery of your self.
December 9, 2014 at 9:19 pm
A Lopez
People with low self esteem like Lavoe1 have to grasp on pseudo science to believe that they are greater and more perfect. Eugenics has been proven to be a falsehood. Take into consideration one of the greatest scientific minds today, Steven Hawkings, he would be deemed absolutely inperfect because of his alleles, yet his theories, and writings will survive all the ages of mankind, but this article will fall into the annals of scientific sensationalism. It is a shame that some puerto rican people have to grasp on to so little when they have so much in them. Be real with yourself, Lavoe1 and pick up a genetics book. Sorry that you can not see truth and deception. Your the type of person that rather spend money on a scratch off than on a legitimate education. Be well in your delusion Lavoe1, my kid still believes in Santa too.
December 8, 2014 at 10:37 pm
francisco sotomayor
nuestra mezcla de raza taina negra espa~ol…nos ha convertido en una raza fuerte luchadora
December 8, 2014 at 11:18 pm
joanne
As a puerto rican I have to say this put a smile on my face. My father in law would have loved this but as previous post and Elizabeth from Columbia points out, it is all about the mixture of the races allowing for the best of each race to be combined. I think if more south american dna had been available to compare there maybe more nationalities that came close to “perfect”. I also think the alien theroist should be happy to have “proof” that the perfect human doesn’t even look human. Lol. Most importantly I applaud the author of this study who felt compelled to show a racist, using his own science, that “perfection” comes with diversity.
December 9, 2014 at 10:14 am
Flavio Acareon-Ortiz, PhD
Si se sumaran todos los individuos de cada país que han sobresalido en todas las áreas de la actividad humana, como la intelectual, atlética, artística, deportiva, científica, etc. y se dividiera por la cantidad de población de cada país, ello nos podría dar un índice por población.
Este índice se podría usar para comparar, por región o por país, como andan las cosas desde un punto de vista globalizado y no pormenorizado. Este método serviría para tener una idea de como andan las cosas por región y entonces se utilizaría para generalizar las cosas que hayan resultado positivas y tratar de eliminar las que producen negativismos.
Creo que la perfección no existe porque después de ella no hay crecimiento ni mejoramiento, solo estancamiento y hastío, así que siempre será relativa.
Nota: Escribo en este idioma porque es el segundo más hablado en el mundo y porque el multi-lingüismo debe abundar mucho a la perfección.
December 9, 2014 at 10:40 am
Michael Auld
Don’t get too excited about the article, for human mixing is an ancient phenomenon. The historical evidence of ancient hybrid vigor (the result of a mixture of two different “races” where the offspring is superior to the parents) was missing. Ancient cultures (the Egyptians, Hindu, Chinese, etc.) have already shown remarkable world achievements that we greatly value as human beings. “Africans” (many ethnic groups), the “Spanish” (Moor who were already mixed with Berber and Arab, also Celt, Hebrew) as well as the “Taino” (Arawakan people who were already possibly mixed before 1492 with the pre-Taino from Florida, Yucatan, South America) are already found in most of the Caribbean. If “racial purity” ever existed, to some experts, it came out of Africa thousands of years ago. So, until another “expert” comes up with another THEORY, we have to be content with the motherland as Africa. (Spoken by a “tri-racial” person with ancient and new mixtures).
December 9, 2014 at 10:58 am
Sam Diaz-Munoz
Dear Lior,
Interesting and thought-provoking post. Immediately brought me back to Juan C. Martinez-Cruzado’s research. I first learned to do PCR and run gels in his lab. I knew Puerto Ricans would have a field day with it, as we tend to be a very proud people 🙂 I think your comment above (in response to David) is spot on, even if the title was a bit too provocative. Reminds me that Martinez Cruzado’s research has been incorrectly interpreted a number of times even though he is very careful in his communication.
I think the *really* interesting point here is the importance of diversity in science. Do I remember correctly that Martinez-Cruzado, Oleksyk, and CD Bustamante had to fight pretty hard for including some admixed populations in the 1000 genomes project? I think Taras alluded to this in his post. If not for that the exercise you conducted above wouldn’t have been possible. And if there were more samples in there you would probably get equally “perfect” individuals from other populations as mentioned by Rafa Irizarry in his post.
Seems that increasing the breadth of sampling is going to be critical so we aren’t doing science with “one eye closed” as Eric Lander said.
http://www.forbes.com/sites/erincarlyle/2013/10/30/carlos-slim-gives-another-74-million-to-make-genomic-research-less-ethnically-biased/
What is your read of the direction that this is heading? Is using the growing sequencing capacity for increasing breadth of sampling a priority?
Thanks,
sam
December 9, 2014 at 11:20 am
Lior Pachter
Thanks for your comment Sam. To answer your question I personally think it is *really* important that we not only sequence more diversely from around the world, but also greatly expand medical databases and the collection of phenotypic data from diverse populations so that “precision medicine” does not end up being a privilege of Caucasians. As you have noted, Bustamante, Oleksyk, Cruzado and others have been advocates for obtaining the data, but unfortunately there is a lot of catch up work to do. I have not played a role on the data collection side but I am focusing in my group on the development of methods for properly accounting for population structure when performing studies across diverse groups of (possibly admixed) individuals. There are many difficult and interesting problems to solve.
March 2, 2015 at 6:03 pm
Sam Diaz-Munoz
Dear Lior,
Thanks for your reply. Very interesting about the phenotypes. The phenotyping and “metadata” issues are also a big deal in the microbial world, where there is a lot of sequence data, but not a lot of systematic environmental data associated and certainly not much (if anything) in the way of a phenotype.
Aside from that belated comment, wanted to share with you Martinez Cruzado and Oleksyk’s reply to your post; written at that time but only recently translated and posted to the Scientific American blog Voices.
http://blogs.scientificamerican.com/voices/2015/02/05/why-there-is-no-perfect-human-in-puerto-rico-or-anywhere-else/
Hope all is well in Berkeley!
sam
December 9, 2014 at 1:43 pm
Dr. Rex
Thanks so much for this post!! I am from Puerto Rico …. reblog!! Paz …. 😎
December 9, 2014 at 1:45 pm
Dr. Rex
Reblogged this on It Is What It Is and commented:
“The nearest neighbor to the “perfect human” is HG00737, a female who is… Puerto Rican. ” ……. Yuiza!
December 9, 2014 at 9:39 pm
Jessica A
Lior, I am of Puerto Rican heritage and I was wondering what you thought about DNA services like 23andMe and AncestryDNA to trace family roots just for fun. Gracias!
December 9, 2014 at 9:49 pm
Lior Pachter
Hi Jessica,
Thanks for asking. There is a lot to say about direct-to-consumer genetics and a comment here is not the place to say it all. I will say this: genetic testing and genetics technology is about to become much closer to the lives of the general public than it currently is, and it’s important for people to educate themselves about the biology and technology, and also the ethical issues concerning both. I think that signing up for services like 23andme is educational, and users should approach it as a learning experience. There is much to learn! Personally speaking I’ve used 23andme and found out all sorts of interesting things about myself, but I also felt that it was good that I knew something about genetics because it helped me interpret much of the information they were offering.
Lior
December 11, 2014 at 8:35 am
Jessica A
Ethical issues? uh oh doesn’t sound very comforting. Are these ethical issues related to privacy? Thanks again for your input.
December 11, 2014 at 8:40 am
Lior Pachter
Mostly privacy but there are also other unforeseen issues that can arise, e.g. see this article on how 23andme gave someones parents the gift of divorce.
December 9, 2014 at 10:38 pm
parrillaturi
I had always suspected that there was something unique about my mom. Now I know why. She was part Portuguese, and Taino. Thank you.
December 13, 2014 at 9:43 am
mimiluz
LOVE THE ARTICLE. THANK YOU FOR SHARING! ❤ WEEEEPPAAAA!!!!
December 17, 2014 at 10:24 am
sparrow
Makes sense – enjoyed your post, but it’s disappointing to hear about Watson ‘s views.
December 17, 2014 at 2:10 pm
Lueny Morell
Reblogged this on Lueny Morell and commented:
Why am I not surprised? And it is a PUERTORRICAN WOMAN!
January 3, 2015 at 9:54 am
curious one
I am curious. What is the criteria for determining a good or bad alelle? Are there any neutral or inert alleles?
January 18, 2015 at 3:28 pm
Lior Pachter
I am no longer approving comments on this post.
March 23, 2015 at 1:59 pm
Susanne Green
Hello there, just became alert to your blog through Google,and found that it’s really informative. I’ll appreciate if you continue this in future. Many people will be benefited from your writing. Cheers!
Thanks
Susanne Green
medical assistant
May 22, 2015 at 7:13 pm
AimeeCandelaPhoto
Very interesting! I can see where parts of this article can ring true.
I’m part Dominican and Russian.. yeah, I know born in NY.
October 24, 2015 at 7:51 am
Lior Pachter
The comments section for this post is closed.
April 14, 2016 at 1:03 pm
MC
I used to work at CSHL. Everyone used to worship the ground this man (watson) walked on. Not me. I never held in him high regard after hearing about his hate filled spews. Makes you question ‘intelligent’. And what about all the (seemingly intelligent) people (CSHL employees) who regard this man as someone great?
February 4, 2017 at 8:39 pm
Jer
” …i attended an invitation only genomics meeting”. So one could read this as intended, ‘a genomics meeting one can attend by invitation only’, or, ‘attended a invitation meeting where only genomics would be discussed’. Ok, ok, being a bit silly. Just making the point that it should be invitation-only, not invitation only. Great article quite lucidly explained.
February 4, 2017 at 8:53 pm
Lior Pachter
Thanks! Typo fixed.
June 15, 2019 at 1:11 pm
orlando jimenez
Yes, we are indeed a mixture of races.I took a dna test.Much to my surprise, i have 12% jewish ancestry.Also some British.I read that we puerto ricans have jewish ancestry because of the spanish inquisition
July 4, 2022 at 10:47 pm
let's find out
Reblogged this on yazım'yazgısı (typography).