Ta-Nehisi Coates

Last week there was some debate across the blogosphere about race and IQ (again), much of it springing from the controversy of Jason Richwine's dissertation, "IQ and Immigration Policy." You can read my thoughts here, here, and here. One helpful critique made of these posts by Razib Khan held that they could use more science. Razib added some of that in his own post which was rooted in this paper:"Characterizing the Admixed African Ancestry of African Americans."

I read the paper, understood most of it, but was basically lost trying to understand the graphs. (It's true that my math and science foundation is fairly weak.) So I read it again. Still not quite getting it, I reached out to one of the authors -- geneticist Neil Risch, who directs the Institute for Human Genetics at University of California San Francisco. Professor Risch agreed to chat with me via e-mail. He also sent me these two papers ("The Importance of Race and Ethnic Background in Biomedical Research" and "Assessing Genetic Contributions to Phenotypic Differences Among 'Racial' and 'Ethnic' Groups"), which I found enlightening and would urge everyone to read.

I want to thank Professor Risch for his time. Our conversation is below.

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Thanks for agreeing to talk with me, Professor Risch. I've been involved in a good number of conversation around race lately -- specifically regarding race and IQ. I was referred to a paper you wrote with some co-authors on the African ancestry of African Americans. My science background is not particularly strong, and I'd like to bring more science (and less humanities) to my readers on this topic.

Let's start with the dumb and simple questions first. In your paper "Characterizing the admixed African ancestry of African Americans," we see a chart (Figure 1) depicting a "Principal components analysis of Africans, U.S. Caucasians and African Americans." For the less mathematically literate among us, can you explain what we're seeing?

In reference to Figure 1, there are primarily 2 different types of analysis we used.  Both are based on genetic information.  As you have probably read, everyone has 23 pairs of chromosomes, 22 of which are autosomes and one pair is the sex chromosomes (X and Y).  Most of that sequence (about 3 billion nucleotides) is identical among individuals, but there are millions of locations where people can differ.  In our analysis, we focused on about 450,000 of them.  Modern technology now allows us to get a pretty good look at DNA sequence variation among individuals.

The two analyses we used were admixture analysis  and principal components analysis (PCA).  The first figure shows results of both.  What we attempted to do in the bar chart (the admixture analysis) was to estimate for each African American in our study, what proportion of their genome derived from different population groups.  In this case, we were focusing on potentially different African subgroups, but did not focus on possible European subgroups.  In theory, we possibly could also have done the latter, but because the proportion of ancestry in this sample that was from Europe was not large, that would be more challenging.  Our ability to do this analysis depends on how much genetic differentiation there has been between the possible ancestral groups included in the analysis (e.g. the Mandenka, Yoruba, San, Mbuti and Biaka, as well as Europeans).  I should be clear that these represent current day populations, and are only possible surrogates for the actual ancestral groups.

That differentiation is depicted in the rest of that figure (the dots with population labels) - which was the result of the PCA.  In PCA, you define a few variables that explain the most variation in the data (in this case it is the genetic information).  It is a data reduction procedure - in other words, to reduce the information in 450,000 genetic markers to just a few variables.  Here we present the first two such reduced variables that explain most of the variation.  As you can see, the Europeans and Africans are very well separated on the X axis while the African subgroups are well separated on the Y axis.  This separation is what allows us to estimate the proportion of ancestry in the African Americans from each of these groups.  You will notice that the African Americans (purple triangles) fall on a line between the Yoruba/Mandenka and the Europeans.  This indicates that they have mixed ancestry that is both African and European.  The broad spread of the purple triangles along the X axis indicates that individual African Americans in this study vary quite a bit in terms of how much of their ancestry is African and how much is European. You can also see that the majority of the African ancestry is Central-West African because of the approach on the X axis towards the Yoruba/Mandenka.  If there were a substantial amount of ancestry from the other groups, you would see the line going more horizontally and less to the upper right.   

The actual proportions of ancestry are then given in the bar chart.  Here again, you can see the varying amount of European ancestry.  It is also confirmed in the bar chart that most of the African ancestry is Central-West African.

You can also see in the bar chart that compared to the European ancestry component, there is much less variation in the different African subgroup components of ancestry -- in other words, there aren't some individuals who have much more Yoruban ancestry and others that have much more Bantu ancestry.  This is why we concluded that it is likely that mating patterns in African Americans probably did not strongly reflect actual origins in Africa.  And that is also the reason we concluded that because most African Americans appear to have admixed African ancestry, looking only at a single genetic location (e.g. the Y chromosome or mtDNA, as often done by ancestry companies) gives only a  narrow picture of the entire ancestry.

Subsequent figures in the paper pretty much reinforce these conclusions.

OK, so that helps. A lot. Here is another question. I want to know what someone with your background thinks about the notion of "race." As a writer, I approach this through the lens of history. I imagine, because of that, I might be missing some things. I want to know, as a geneticist, whether you think of African Americans as a "race?"

I believe it is inaccurate to refer to African Americans as a race or racial group (much as it is similarly inappropriate to refer to Latinos that way) -- unless you move away from the more classical definitions of race. We try to use the term race/ethnicity. There has been a lot of debate about whether genetic variation in the human population is continuous or discrete.  From my view, it is both. This is what makes it challenging to create categories.

One question pops out at me. You indicate some suspicion to referring to African-Americans as a "race" but (in some of your research) you support using "race" in terms of collecting med data and disease studies. Is this a case of a definition -- though it may be imperfect, clunky and at times even misleading -- still telling us something? From what I gathered from those articles "race" can be a proxy not just for genetic stuff, but for social phenomenon too (such as access to health care.) Am I seeing that right? Is it correct to say, for instance, "Yes, race is a social construct, but this does not make it meaningless." It still useful to look at "race," for instance, when studying sickle-cell. Perhaps some day, when we have more refined technique, it won't be. 

Definitions can indeed be "clunky." I would use the phrase race/ethnicity rather than just race because in common parlance it is a better description.   I tend to think that race has been used more in terms of continental origins (Africa, East Asia, Europe, Americas).  On that basis, one would not characterize African Americans as a racial group, but rather as an ethnic group.  We sort of implied this in the Genome Biology paper.  The reason is that African Americans typically have European as well as African ancestry (and possibly other ancestries as well) and are also culturally distinct from Africans.  Sort of similar to Latinos - who from a genetic ancestry standpoint can be nearly anything.  Hence our use of race/ethnicity.

Just to opine a bit, I think part of the problem is the notion of a causal relationship -- i.e. "dark-skin" or "blackness" causing sickle-cell -- as opposed to a more geographic definition that might encompass people regardless of skin color.

Yes, exactly. Groups living in isolation from each other for long periods of time have acquired many genetic differences. The large majority of those are due to "genetic drift" -- i.e. random fluctuations in gene frequencies. That also includes many genetic variants that code for traits and diseases.  But then there are some genetic variants that differ in frequency due to differential selection pressure in different environments. The best examples are for genes that confer resistance to malaria. One of those causes sickle cell disease in those who carry two mutations; those who carry one copy have sickle cell trait, which is generally benign but confers greater resistance to severe malaria infection. Mutations for sickle cell disease are found at pretty high frequency in some African populations, but also found in parts of the middle east and India. Beta thalassemia is another disease where carriers are offered greater protection from malaria. This disease is more common around the Mediterranean (e.g. Greeks).  

Then there is G6PD deficiency.  Mutations for that are found at increased frequency in parts of Africa, but also in the Middle East. The mutations underlying these disorders generally differ geographically, which is another indication that while the mutations are different ancestrally, they achieved high frequency in different populations for similar reasons (i.e. resistance to malaria). Another more recent example is a gene called ApoL1. There are a couple of genetic variants found in West Africans (and African Americans); when carrying two of these, there is an increased risk for kidney disease if hypertensive.  It was shown that these variants likely provide some immunity from African Sleeping Sickness (tsetse fly disease) which may have led to them becoming more common where the disease is prevalent. 

Various populations have an increased frequency of genetic diseases, which are often unique.  Probably a lot or most of it is just chance, but perhaps not all of it. Proving historical selective advantages can be pretty challenging. So, as I mentioned above, groups living in isolation developed their own genetic (and cultural) profiles. Generally, there is no cause and effect between the traits that differentiate groups. East Asians have dark hair and eat with chopsticks.  But there is no causal relationship. You can use a whole variety of different traits to place individuals into the same categories, but those traits may have nothing to do with each other etiologically.

I often hear people say that Africa has the highest genetic diversity in the world. What does that practically mean?

If you sequence the genome of an African individual (pretty much from anywhere except North Africa), you will generally find more locations in their DNA that are variable than for any non-African individual. Why is this the case? Population geneticists believe that the world outside of Africa was initially populated by humans who migrated out of Africa. The presumption is that if the number of such individuals migrating was small, then some of the genetic variation was lost in the process. As I described before, genetic drift (fluctuation in allele frequencies) can happen when a population is small. The random fluctuation means that some alleles increase in frequency and others decrease. The ones that decrease may be lost altogether. You tend to find that the amount of genetic variation decreases along the migration routes out of Africa (more or less by distance from Africa, but of course population bottlenecks can also happen anywhere along the way).

What is the impact of this?  As I mentioned before (and above), random fluctuations in allele frequencies can mean that rare alleles that create risk for a disease may increase in frequency, by chance.  So some diseases may become more common.  But the flip side is that some diseases may also become less common.

One last question. Your paper on assessing genetic contributions to phenotype, seemed skeptical that we would ever tease out a group-wide genetic component when looking at things like cognitive skills or personality disposition. Am I reading that right? Are "intelligence" and "disposition" just too complicated?

Joanna Mountain and I tried to explain this in our Nature Genetics paper on group differences.  It is very challenging to assign causes to group differences. As far as genetics goes, if you have identified a particular gene which clearly influences a trait, and the frequency of that gene differs between populations, that would be pretty good evidence. But traits like "intelligence" or other behaviors (at least in the normal range), to the extent they are genetic, are "polygenic." That means no single genes have large effects -- there are many genes involved, each with a very small effect. Such gene effects are difficult if not impossible to find. The problem in assessing group differences is the confounding between genetic and social/cultural factors. If you had individuals who are genetically one thing but socially another, you might be able to tease it apart, but that is generally not the case. 

In our paper, we tried to show that a trait can appear to have high "genetic heritability" in any particular population, but the explanation for a group difference for that trait could be either entirely genetic or entirely environmental or some combination in between.

So, in my view, at this point, any comment about the etiology of group differences, for "intelligence" or anything else, in the absence of specific identified genes (or environmental factors, for that matter), is speculation.

Pardon my French

I have more to say on race and IQ and the president's speech at Morehouse. But my head is swimming right now. You can read Fallows and Andrew on Morehouse here and here. You should also read Jonathan Capehart's piece which points to Obama's inclusion of gay man, at the all male HBCU.

Here is a great video on the effects of the "Crack Baby" hysteria of the early 1980s. One thing I did not know was that pregnant women who used crack were actually being prosecuted in response to the madness. 

The first lady went to Bowie State and addressed the graduating class. Her speech was a mix of black history and a salute to the graduates. There was also this:

But today, more than 150 years after the Emancipation Proclamation, more than 50 years after the end of "separate but equal," when it comes to getting an education, too many of our young people just can't be bothered. Today, instead of walking miles every day to school, they're sitting on couches for hours playing video games, watching TV. Instead of dreaming of being a teacher or a lawyer or a business leader, they're fantasizing about being a baller or a rapper.

And then this:

If the school in your neighborhood isn't any good, don't just accept it. Get in there, fix it. Talk to the parents. Talk to the teachers. Get business and community leaders involved as well, because we all have a stake in building schools worthy of our children's promise. ...

And as my husband has said often, please stand up and reject the slander that says a black child with a book is trying to act white. Reject that.

There's a lot wrong here.

At the most basic level, there's nothing any more wrong with aspiring to be a rapper than there is with aspiring to be a painter, or an actor, or a sculptor. Hip-hop has produced some of the most penetrating art of our time, and inspired much more. My path to this space began with me aspiring to be rapper. Hip-hop taught me to love literature. I am not alone. Perhaps you should not aspire to be a rapper because it generally does not provide a stable income. By that standard you should not aspire to be a writer, either.

At a higher level, there is the time-honored pattern of looking at the rather normal behaviors of black children and pathologizing them. My son wants to play for Bayern Munich. Failing that, he has assured me he will be Kendrick Lamar. When I was kid I wanted to be Tony Dorsett -- or Rakim, whichever came first. Perhaps there is some corner of the world where white kids desire to be Timothy Geithner instead of Tom Brady. But I doubt it. What is specific to black kids is that their dreams often don't extend past entertainment and athletics  That is a direct result of the kind of limited cultural exposure you find in impoverished, segregated neighborhoods. Those neighborhoods are the direst result of American policy.

Enacting and enforcing policy is the job of the Obama White House. When asked about policy for African Americans, the president has said, "I'm not the president of black America. I'm the president of all America." An examination of the Obama administration's policy record toward black people clearly bears this out. An examination of the Obama administration's rhetoric, as directed at black people, tells us something different.

Yesterday, the president addressed Morehouse College's graduating class, and said this:

We know that too many young men in our community continue to make bad choices. Growing up, I made a few myself. And I have to confess, sometimes I wrote off my own failings as just another example of the world trying to keep a black man down. But one of the things you've learned over the last four years is that there's no longer any room for excuses. I understand that there's a common fraternity creed here at Morehouse: "excuses are tools of the incompetent, used to build bridges to nowhere and monuments of nothingness."

We've got no time for excuses -- not because the bitter legacies of slavery and segregation have vanished entirely; they haven't. Not because racism and discrimination no longer exist; that's still out there. It's just that in today's hyper-connected, hyper-competitive world, with a billion young people from China and India and Brazil entering the global workforce alongside you, nobody is going to give you anything you haven't earned. And whatever hardships you may experience because of your race, they pale in comparison to the hardships previous generations endured -- and overcame.

This clearly is a message that only a particular president can offer. Perhaps not the "president of black America," but certainly a president who sees holding African Americans to a standard of individual responsibility as part of his job. This is not a role Barack Obama undertakes with other communities.

Taking the full measure of the Obama presidency thus far, it is hard to avoid the conclusion that this White House has one way of addressing the social ills that afflict black people -- and particularly black youth -- and another way of addressing everyone else. I would have a hard time imagining the president telling the women of Barnard that "there's no longer room for any excuses" -- as though they were in the business of making them. Barack Obama is, indeed, the president of "all America," but he also is singularly the scold of "black America." 

It's worth revisiting the president's comments over the past year in reference to gun violence. Visting his grieving adopted hometown of Chicago, in the wake of the murder of Hadiya Pendleton, the president said this:

For a lot of young boys and young men in particular, they don't see an example of fathers or grandfathers, uncles, who are in a position to support families and be held up in respect. And so that means that this is not just a gun issue; it's also an issue of the kinds of communities that we're building. When a child opens fire on another child, there is a hole in that child's heart that government can't fill. Only community and parents and teachers and clergy can fill that hole.

Two months earlier Obama visited Newtown. The killer, Adam Lanza, was estranged from his father and reportedly devastated by his parents divorce. But Obama did not speak to Newtown about the kind of community they were building, or speculate on the hole in Adam Lanza's heart.

When Barack Obama says that he is "the president of all America," he is exactly right. When he visits black communities, he visits as the American president, bearing with him all our history, all our good works, and all our sins. Among recent sins, the creation of the ghettos of Chicago -- accomplished by 20th-century American social policy -- rank relatively high. Leaving aside the vague connection between fatherhood and the murder of Hadiya Pendleton. Certainly the South Side could use more responsible fathers. Why aren't there more? Do those communities simply lack men of ambition or will? Are the men there genetically inferior?

No president has ever been better read on the intersection of racism and American history than our current one. I strongly suspect that he would point to policy. As the president of "all America," Barack Obama inherited that policy. I would not suggest that it is in his power to singlehandedly repair history. But I would say that, in his role as American president, it is wrong for him to handwave at history, to speak as though the government he represents is somehow only partly to blame. Moreover, I would say that to tout your ties to your community when it is convenient, and downplay them when it isn't, runs counter to any notion of individual responsibility.

I think the stature of the Obama family -- the most visible black family in American history -- is a great blow in the war against racism. I am filled with pride whenever I see them: there is simply no other way to say that. I think Barack Obama, specifically, is a remarkable human being -- wise, self-aware, genuinely curious and patient. It takes a man of particular vision to know, as Obama did, that the country really was ready to send an African American to the White House.

But I also think that some day historians will pore over his many speeches to black audiences. They will see a president who sought to hold black people accountable for their communities, but was disdainful of those who looked at him and sought the same. They will match his rhetoric of individual responsibility, with the aggression the administration showed to bail out the banks, and the timidity they showed  in addressing a foreclosure crisis which devastated black America (again.)They wil weigh the rhetoric against an administration whose efforts against housing segregation have been run of the mill. And they will match the talk of the importance of black fathers with the paradox of a president who smoked marijuana in his youth but continued a drug-war which daily wrecks the lives of black men and their families. In all of this, those historians will see a discomfiting pattern of convenient race-talk.

I think the president owes black people more than this. In the 2012 election, the black community voted at a higher rate than any other ethnic community in the country. Their vote went almost entirely to Barack Obama. They did this despite a concerted effort to keep them from voting, and they deserve more than a sermon. Perhaps they cannot  practically receive targeted policy. But surely they have earned something more than targeted scorn.

My sense is that there is a need for an open thread today. I don't think I should say much more.