Tuesday, May 27, 2014

More on 'racial' variation....

Holly's recent post on race, Wade's book, and HBDers identified some of the core issues that separate many anthropologists from their often openly or eagerly racist colleagues.  Some differences are scientific, but others really are emotional differences about sociopolitical views, whether or not that's actually stated or even understood.  This is so contentious, and indeed has been since Darwin himself if not, in pre-evolutionary terms, for the entire history of human societies, that measured discussion is rare. People take positions and, in their righteousness, suspect (or worse) anyone who might challenge their faith.  Even scientists are, after all, people.

Of course we know from clear, recent (as well as deep) history what can happen with explicit or covert racist views of human variation and evolution -- that was one motivation for our recent post on Mussolini, science and race.  Policy can use the scientific rationale to treat all members of a labeled race as if they were equally defective or superior, even if some weak caveats are added that this is only an approximation of average differences between groups.  Based on categorical thinking, policy decisions can allocate resources to enhance what is judged by the supposed experts to be superior so we can help Nature's own evolutionary path, or to deprive members of the inferior group.  Depriving need not be so draconian as some lethal episodes in race history, because we could simply deprive a group, as a whole, of resources such as investment in education.  Many, even some commenting on or about posts here, have made such statements.  This is part of the historical reality of these race-based ideas, and those making the assertions know this very well, or should.

One might agree that different categories of people, as s/he constructs them, inevitably have statistically different traits on average.  This is almost inevitably the case, and the differences will include genomic effects.  But why not make policy based on individual traits rather than on a group basis?  Many arguments-of-convenience are standard: it's a waste of money to invest in inner city schools because, even if some of the kids have above average IQ most won't, etc.; or don't give aid to Africa because they inherently cannot measure up to our standards.

Even accepting standard geographic categories as the definition of 'race', such as European, Asian, African, it is obvious that there is large overlap between the groups in most of the kinds of traits being discussed (like mate choice, sexual behavior, criminality, IQ, athletic ability....), which means, for example, that many members of the inferior group score higher or behave like members of the supposed superior group, and vice versa.  So from a social policy point of view, unless the one defining categories just wants reasons to keep resources in his/her category, individual based policy would seem to be far more equitable (if one believes in being equitable).  Even diseases with a genetic basis that may be group specific (until recent admixture) are far from present in every member of the affected group, and again, determining on an individual basis who's got the relevant allele is much more sensible than assuming it on the basis of membership in a group.

There are problems here even in legitimate disease-related contexts, and they merit quiet, measured attention which they don't usually get.  Many racist or commercial expedients seek to milk categories for drug sales, and others for sociopolitical reasons deny the levels of variation that we know exist.  For example, we can't just identify individuals with a given genetic risk variant without taking their geographic ancestry into account when making medical diagnoses or treatments.  The same genetic variant may be more common in one population, say, Europeans, than in another such as Africans.  But the variant often if not usually turns out to have different average effects on the individual that are origin-specific.  This can have to do with cultural differences in life-history exposures, which are often very hard to tease out, but can also have to do with polygenic background differences related to variants in the genome that are not measured but are different in different populations.

Such issues are real and important and have to do with whether medical practice should view people in terms of 'race'--even in a benign world where it was recognized by everyone that this is only a substitute for geographic origin (and takes admixture into account somehow).  If we could stop Pharmas from trying to use categories to cash in on putative 'race' differences in drug efficacy, and so on, and if we could disengage from the strident Darwinism that is prevalent in discussions of racial variation and its inherency and value, we might actually be able to address very important and scientifically legitimate issues.  But we can't really do that amidst the invective in today's arena.

The realities of human genomic variation, and the reasons
The obvious fact is that the presence and frequency of genetic variants, genomewide, vary over geographical space in ways related to population history: the flow of variation by mating patterns of many generations, geographic barriers affecting migration and mating patterns (mountains, rivers, seas), physical and ecological conditions, climate, and so on.  This is obvious and has been known long before we had any genetics to invoke.

Roughly speaking, the farther apart your ancestors the more different you'll be across the genome.  This means that if you sample from distant areas, you can easily conclude that the people are distinctly different--indeed, statistically, this is true even if based on variants that are shared among the groups but have different group-specific frequencies.  But this does not point to categorical differences, only to quantitative statistical ones.  Even within each group, there is about as much overall variation as between them, a point long known, current Lewontin-bashing notwithstanding.

Analyzing data from discrete, widely separated samples automatically treats, statistically,  the populations as categorical units.  This obviously can lead to what appears to be categorical variation among human populations (we talked about this a few days ago here).  But this is an  illusion of grouping decisions and statistical analysis of the geographic pattern of variation need not use such meat-axe approaches because there are statistical methods that more realistically depict the actual more continuously distributed pattern of variation (and this, of course, is rapidly being modified by large-scale, long-range migration---such as by anyone living in North America rather than in Asia, Africa or Europe as our ancestors did).

These considerations are neither racist nor politically correct, and relate directly to Holly's point about species designations, a subject typically of heated controversy when it has nothing to do with the emotionally loaded subject of modern humans.

Given this variation, across the genome, one has to expect some of it to reflect local adaptations, and some to have serious effects on the individual.  Much gene-specific disease susceptibility is found only, or more frequently, in one population compared to others.

The opposition to 'political correctness' that is manifest so typically if not in rabid self-satisfied proclamations by those advocating a strongly deterministic view of our species and its genomic evolution is, no matter if it's denied, essentially a confusion of two agendas.  One is the reality that some political-correctness denies or minimizes aspects of reality or the nature of causation in humans;  the other agenda is a very clear and cogent societal problem of class and other discriminatory distinctions in the quality of life in complex societies.  In fact, it is ironically the social politics, and not the technical science, that largely underlies much of the heat in the 'discussion' of this subject.

We could, of course, have an honest political discussion of whether it's OK for some groups to be allowed to have a disproportionate fraction of the material and cultural wealth and deprive other groups, or whether we should be more egalitarian.  If you agree on how to define the groups, this can be at least a fair discussion.  Arch capitalists argue that inequality is a good thing, though usually they don't couch this in racial terms.  Elitists have a right to view elitism as good, but this is a subjective value judgment and not something that can be justified on genomic or evolutionary grounds.  Why, for example, is depriving someone of his or her access to food or education justified just because the person isn't as good as the professor is, at calculus?   Even if that is based on a genetic difference, why does it suggest that one person can decide how many resources the other has?  We are, after all, here as human individuals, and our genomes are the result of a shared history of evolution.  How can one person declare the inherent worth of another, and on what kinds of legitimate scientific grounds--other than his/her personal, and hence subjective, opinion?  Or are you just defending power and privilege that you happen to enjoy?  Or are you denigrating differences because you want to gain power that you don't now have?

We'd be a lot better off, we think, if these distinct, scientific and societal, areas of discussion or disagreement were kept separate and treated on their own merits.  But that doesn't seem to be in the cards at present.


Holly Dunsworth said...

Thanks Ken. Yep, separating them feels impossible when any attempt at discussing whether some of these issues are even scientific is bombarded by so many who aren't willing to even consider that maybe their view of taxonomy and how/why it's done is not the only legitimate one or is incomplete/underinformed/mistaken. Too many enter these discussions assuming that Nature is on their side and that's pretty much always a thought-stopper and a discussion-ender isn't it?

Ken Weiss said...

Yes, like any religious, ethnic, or tribal conflict, it isn't usually about all the supposed facts, but is selective and motivated often by cultural or material self-interest. It can be called science as religion, perhaps.

Holly Dunsworth said...

Without Nature on their side, they'd be forced to explain their values and biases that shape their opinions and drive them to actively argue for them. They need Nature. Real bad.

Ken Weiss said...

Ideologies always need some ultimate truth to justify them and make their adherents feel OK about their views. Religion was ultimate 'Nature' (God's views), Marxism was the True course of history, and Evolutionary science a law of Nature.

Eric said...

I just recently stumbled upon this blog and I have to say: I'm really glad it exists.

I live in Germany and let me tell you: Not using the term "race" definately does not stop people from having racist tendencies. So having a bigger argumentative catalogue at my disposal to dismiss these kind of arguments, really helps.

Personally I don't think these tendencies will go away, people will always try find some kind of way to categorize others. However I think it's important to get evolutionary theory out the stranglehold those people seem to have over it in public.

Anne Buchanan said...

Thanks, Eric. I agree with you that these tendencies won't go away, even if science were to prove to everyone's satisfaction that there isn't a biological basis to the kind of classifying we still do. Which is why it's helpful to recognize that the social and scientific issues are distinct, but even that won't fix the conflation of evolutionary theory with politics, I don't think.

Anonymous said...

HBDers claim to be honest, brave tellers of objective truth while they label their critics 'cultural Marxists'. However, they're the ones whose views are evidence-free, unsound speculation and misinterpretation, while it's their opponents who have analytical rigor on their side.

Anne Buchanan said...

Well, yes, but they would say the same about the rest of us. So rather than a battle of words (that is, name calling) that goes nowhere, I think it's more useful to think about the sociology of what's going on here.

Science is never done in a vacuum. Scientists always make assumptions, explicitly and implicit, when they plan their experiments, write their statistical analysis programs, and interpret their data. Sometimes the assumptions influence the results as well as whether we choose to believe the results, and sometimes they don't, but we don't always remember that.

In the case of 'discussions' of race, we all come to the table fully loaded with preconceptions, prejudices, self-righteousness and so forth, and the fact that the subject is so close to the bone makes it pretty much impossible to discuss these assumptions at all dispassionately.

When HBDers see statistical analyses that prove that races exist, I see programs that were built with that assumption in mind. And when they accuse people who think that races are a social construct of being stupid and politically correct (ok, and more), I think about my nephew, whose mother has only European ancestry and whose father has some European and some African. My nephew is blonde and blue-eyed, but he identifies as black. I'm not sure what race is in this case other than a social construct.

And when they see genes for all kinds of behaviors, which somehow proves that race is a biological reality, I wonder how it could be so easy to find genes for traits that are even more complex than complex diseases, when we can't even find genes for those.

The problem, of course, is that we've been down this road before. I've had enough run-ins with HBDers to know that we can't discuss this, though. But if it weren't potentially dangerous, and if it didn't have deep implications about decisions about allocating society's resources, this disagreement would be unimportant. But it is and it does, and it matters.

Ken Weiss said...

It's the same reasoning by which I don't enter into 'discussion' with religious creationists. There's no discussion. There may be intentional ignoring of the actual evidence (on their part, I would say), but no real attempt to come to common ground. Committed postures, solidarity, tribalism, cults, and the like are hard to change.

Tom519 said...

If somebody would indulge me, sign off on or nix the following statements:

1-)Humans and chimp genomes differ in about 400-500 genes total out of 25,000 (2-3%)

2-)-Before the human genome was sequenced most scientists estimated it would contain 100,000 genes or so. We know now that the human genome contains 25,000 genes.

3-) Scientists overestimated the gene count and also overestimated the amount of the genome individual humans would scientist thought each human would differ at about .5% of their respective genomes.

4) The latest research indicates humans may differ genetically by as much as 12% (Redon R, Ishikawa S, Fitch K, Feuk L,2006) Scientists vastly understated the shared genome of humans, just as they overstated the total number of genes.

How can we change a genome 2-3% and get a chimp but change the genome as much as 12% and get another perfectly good human?
Is it a paradox, just plain wrong, or something else going on?

Ken Weiss said...

These questions are important, but can't easily be answered in a Reply to a Comment. The word ' gene' refers to protein code traditionally, but there are now countless other functional DNA regions, most of unknown function.

How we differ from each other, or from chimps, depends on what you count. The most important single fact is that the amount of difference is roughly correlated with the time since last common ancestor, unless we are very deeply wrong about the evolution process--and even this 'clock' calibration depends on various things like population size and so on.

The same process is always going on, so populations within species, such as in indigenous Americans compared to Polynesians, etc., will differ. Natural selection, sexual selection, chance and quirks of history can lead to some of the differences to yield systematic trait differences between distant (or even sometimes adjacent) groups. Skin color and facial appearance are examples that are largely genetic.

One nucleotide difference can kill you, and millions of variants can have essentially no effect. It depends on where in the genome they are. Every population has both, the lethal or 'disease' variants, and the benign (or functionless ones). Traits affected by hundreds of genes can vary between populations by a lot, or by a little, and even in the former case each person of a given height can have a different genotype.

Environments, especially cultural factors in the case of humans, affect many of our traits, even some that are present at birth, in ways we don't yet generally understand very well.

So the percent-change question isn't well-stated related to clear answers. It seems clear on the surface, but it isn't, and that's one reason there is so much work, and so much disagreement, about what genes do and how to understand that.

Holly Dunsworth said...

I am 99% the same as a chimp (according to present accepted fact) yet only about 85% the same as my mother (according to 23andMe) ... And on top of that shared problem with the above comment, there's another one: aren't I supposed to only be 50% the same as my mom? (Not if my parents have the same alleles!!)

Ken Weiss said...

This depends on what's being reported. Aligning single copy DNA (not counting various repeat elements like microsatellites), between a set of chromosomes from you (that is, one of each, chr 1, chr2, ...., X) with one from a chimp, the two will be 90-some percent alike (I'm not up to date on the most recent estimate).

Unless something strange happened (well, you may be strange enough!), you get exactly half your chromosome compliment from each parent. So, as you surmised at the end, the 85% seems likely to relate to variants that are carried identifiably by one or the other parent. If your mom is Aa and your father AA, and you have one 'a' allele you are 'like' your mother in a sense, but if not (you're AA) are you then 'like' your father or your mom, or both?

WIth a finite number of Mendelian draws examined, it's possible that deviation from Mendelian expectations by chance is what happened. So look more carefully at what they said about what they reported.

Holly Dunsworth said...

I'm sharing with over 50 people on 23andMe and also their stock people from various parts of the world and nobody's less than 60something% similar to me. Yet everyone, in terms of how we talk about chimps, should be greater than 99% similar to me.

Ken Weiss said...

Again I don't quite understand your description but I think the first refers to alleles at variable sites, while the chimp and any person's haploid sequence (one copy considered only) is 99% (I thought it was more like 95%, but that's a detail).

If one of your copies was aligned with a single copy from another human, it would be something like 99.9% identical. Again I think this ignores microsatellites and other sorts of repeats (e.g., near telomeres or centromeres). I think 23andMe is only reporting variable sites or something like that....but I've not seen exactly what you're referring to.

Holly Dunsworth said...

Sorry for confusing you. I was merely trying to help to illustrate the point that the earlier commenter made. We talk about these percentages of our "genes" or "DNA" or "genomes," but don't include what exactly it is that we're talking about. I'm glad that person pointed that out.

Ken Weiss said...

OK, good point, and sorry I over-analyzed what you had said. There is certainly a lot of loose talk about these subjects which deserve more serious consideration and are just as interesting, if not more so, than folk concepts.

Anonymous said...

The 12% divergence figure in that publication refers to CNVs (copy number variants of large hypervariable non-coding loci), not genes. Actual protein coding sequence and protein sequence itself is 99.9% identical between any two people on average. Citing the 12% figure, or any low estimate of sequence identity between humans based on non-coding sequence is, if context is not made absolutely clear, intended to mislead.

Anonymous said...

Important to remember the difference between coding sequence, which is 99.9% or so identical between any two humans, and the vast amount of much more variable non-coding sequence (LINE element, SINE elements, ALU elements, STRs microsats, pseudogenes. etc, etc) with our genome. 23andme essentially uses a forensic DNA methodology that analyses moderately to hypervariable variable regions of non-coding DNA to indirectly determine lineage or degree relatedness.

Anonymous said...

Sorry, senior moment, CNVs can comprise multiple genes (both non-coding and coding sequence) among other things but the actual coding nucleotide sequence is not divergent, there are just different numbers of big chunks of the chromosomes.

W. Benson said...

All things bright and beautiful,
All creatures great and small,
All things wise and wonderful,
The Lord God made them all.

The rich man in his castle,
The poor man at his gate,
God made them high and lowly,
And ordered their estate.

Ken Weiss said...

Unfortunately, if this represents a truth, then it doesn't put God in a very good light--rather nasty, one might think.

All things bright and beautiful,
The mass the few enthrall,
It's not so wise or wonderful,
How many take the fall.

The rich ease in their castle,
The poor gaze through the gate,
Luck made them high and lowly,
And God thought that was great?