Tuesday, September 16, 2008

Genetics and Race

 
John Hawks has some interesting things to say about genetics and race based on a New York Times article about David Goldstein. The article can be found at: A Dissenting Voice as the Genome Is Sifted to Fight Disease, and the Hawks' posting is at: David Goldstein profile.

Scientists are discovering more and more genetic differences between human races and this is starting to cause some problems as described in the New York Times article ...
Another pursuit that interests him, one of high promise for reconstructing human evolutionary history, is that of discovering which genes bear the mark of recent natural selection. When a new version of a gene becomes more common, it leaves a pattern of changes that geneticists can detect with various statistical tests. Many of these selected genes reflect new diets or defenses against disease or adaptations to new climates. But they tend to differ from one race to another because each human population, after the dispersal from Africa some 50,000 years ago, has had to adapt to different circumstances.

This newish finding has raised fears that other, more significant differences might emerge among races, spurring a resurrection of racist doctrines. “There is a part of the scientific community which is trying to make this work off limits, and that I think is hugely counterproductive,” Dr. Goldstein said.
John Hawks is an expert in these kinds of studies so it's interesting to read his comments. Note that there's no disagreement over the facts; races are genetically different. I disagree with Hawks and Goldstein on the cause of some of this variation. In my opinion they are placing too much emphasis on selection as the cause of variation between species and not enough emphasis on chance. Differences in ABO blood type frequencies, for example, are probably not due to selection.

At the end of his posting Hawks mentions a quotation from Theodosius Dobzhansky. This is a quotation that everyone should keep in mind as they enter the debate. You can find out more by reading a 2006 posting about Dobzhansky on continuing human evolution. Here's the actual Dobzhansky quotation from that posting ...
The chief reasons why so many people are loath to admit the genetic variability of socially and culturally significant traits are two. First, human equality is stubbornly confused with identity, and diversity with inequality, as though to be entitled to an equality of opportunity, people would have to be identical twins. Human diversity is not incompatible with equality. Secondly, it is futile to look for one-to-one correspondence between cultural forms and genetic traits. Cultural forms are not determined by genes, but their emergence and maintenance are made possible by the genetically conditioned human diversity
Let me sound a note of caution to those who wish to comment. The fact that humans races might be genetically different says absolutely nothing at all about equality and racism. For this thread only, I will delete any comments where the author is confused about this distinction. This is a discussion about science and whether some scientific investigations should be censored because they might be misinterpreted.

Hawks doesn't allow comments on his blog. This is such an interesting topic that I thought I'd mention it here to get some feedback.


[Image Credit: The image is obviously the cover of Scientific American from December 2003. This is one of the most blatant examples of political correctness ever published in a prestigious journal and it's one more example of the decline of Scientific American. It doesn't take much to recognize that the faces on the cover are identical except for skin color. As if that's all there is to human populations.]

38 comments :

  1. "The fact that humans races might be genetically different says absolutely nothing at all about equality and racism. For this thread only, I will delete any comments where the author is confused about this distinction"

    Funny how you get on the topic of race.
    I don't even know if I understand you. I myself think that the differences must all be researched, whatever they may be. If racism says some traits (iq tests, etc) are genticlaly different among races, when this is scientifically put to test, it does not hold water.

    You attitude, instead, seems like simply trying to "define" problems away of an equality that is a perfectly clear ideal, yet completely inexistent in reality; in many parts of the world, people with darker skin color are basically treated like second-class citizens.

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  2. I fully appreciate the reasons some might fear this line of research. But not moving forward with science has never yielded anything positive.

    As far as there being genetic differences: how could there not be? Would anyone think that it is a good idea to test a Swede for sickle-cell?

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  3. Of course science shouldn't be censored due to a real or perceived threat of misinterpretation, despite what Dennet thinks about dangerous ideas.

    It's an awfully dim and cynical view of humanity to predict that there is a type of knowledge out there that will always be horribly misinterpreted or incapable of human understanding.

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  4. From what I've read, there are real genetic differences between the "races", but that there is greater genetic diversity within a race than between different races. The issue is that the difference between races align and cluster, where differences within a race are more random or uniformly distributed.

    Can anyone confirm this or help me put the genetic differences between races in some sort of context?

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  5. It seems you believe without a doubt that human races are biologically real entities...

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  6. We as scientists have let things jump the shark from `we have naturally occurring populations` to `our preconceived notion of race is a) very correct and b) functionally significant.` A lot of that gets lost in the translation between the scientists (of whom I believe, or at least hope, know that there's a long distance between what we've shown, and showing that race is relevant) and the science media/consumer of information (who doesn't know that). Given the nature of how we openly conduct science, censorship won't work - reporters will pick up on articles, and run with them.

    So instead of censoring our work, I think there's an ethical obligation for researchers in this field to devote a large portion of their time putting their research in the exact context. They, and other people who engage in research that has the potential to really muck up people's lives, need to make the significance and the non-signifigance of their research exactly clear.

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  7. "It seems you believe without a doubt that human races are biologically real entities..."
    Isn't that a bit like saying we believe that the Irish and the Japanese are biologically real entities?
    I hardly think this is a surprising attitude. I think both the racists and the left wing luddites (Im a lefty myself, just not so ludditian!) make the same mistake of assuming that to say races are real is akin to saying they are different species, that there is some essentialism underling the differences between races.There is so much genetic variation within races (and genetic admixture between races) that its incorrect to make assumptions about someone of a particular race on an individual basis. In other words you should not single out or exclude someone on the basis of race - even though the factor in question - say sickle cell, for instance - may be closely associated with that race, since the variability question means that the person could easily be negative for that trait.
    The same thing goes for more contentious issues such as IQ - hypothetically even if Belgians are slighly lower in IQ on average than Chinese the variability factor means that a random belgian may have a higher IQ than a chinese counterpart.

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  8. No, I don't think "human race" equals "human subspecies". I think human races are traditional divisions that dont match any modern biological concept. Of course you can redefine them as equal to populations, but then you'll probably provoke too much misunderstanding and unnecessary distraction.

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  9. "Biological races" are sure to exist in any species with broad geographic distributions. I think a problem in the science to popular culture translation is the simply what we mean by race. Most non-scientists that you talk to will identify 3-6 ethnicity-derived races. But looking at the so-called "African" race, if you look the mtDNA tree in figure 1 in http://www.ajhg.org/AJHG/fulltext/S0002-9297(08)00255-3 "African" is clearly divided into two clades. Everything except “African” derives from a single divergence within the L2/3 mitochondrial haplogroup. Is "African" then truly a meaningful description? It seems like most human diversity would then be covered by this single “race”.

    There were some interesting examples cited in a et al and Venter paper at http://www.nature.com/clpt/journal/v84/n3/full/clpt2008114a.html. “One's ethnicity/race is, at best, a probabilistic guess at one's true genetic makeup.”

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  10. I always have to laugh at the response of so many people when this topic comes up - of course there is genetic variability between races; otherwise we wouldn't look different from each other.

    That there may be bigger differences than physical appearance isn't that much of a stretch; if our genetics can define differences in physical traits, then why would we not expect there to be potential differences in other traits.

    That said, I wonder just how "race-specific" some of these traits will really be; races are hardly genetically homogeneous (or even easy to define), so while we may find that some races are "enriched" in genes that make them smarter (or whatever) its unlikely to be a trait found in ever member of a race.

    Conversely, there is gene flow between races, meaning that there shouldn't be hard "edged" in where those types of genes will be found.

    As for the social end of things, I think its PC gone wild. We may be legal before the law; we are not equal biologically. If we were I wouldn't be short-sighted, balding, and white...

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  11. Can anyone inform me of the definition of race being used here? Clearly race definitions of "black" or "white" will not do.
    Jim51

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  12. Re IQ, I find http://www.cscs.umich.edu/~crshalizi/weblog/520.html and the related posts to be good stuff.

    Dr. Moran, you mention that you "disagree with Hawks and Goldstein on the cause of some of this variation. In my opinion they are placing too much emphasis on selection as the cause of variation between species and not enough emphasis on chance." But I thought selection left evidence. As John Hawks quotes from the NY Times article:

    When a new version of a gene becomes more common, it leaves a pattern of changes that geneticists can detect with various statistical tests.

    So on what basis do you disagree re the causes of variation (or more specifically, the relative contributions of selection and chance/drift)?

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  13. You mean "palau man" John Hawks? hehehe

    About signatures of selection at sequence level, I'd recommend you read this:

    Hughes, AL (2007)Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    Heredity 99, 364–373

    When selection is inferred from a supposedly higher than normal population frequency, this usually implies making several assumptions about the history and current structure of a population.

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  14. From the very interesting (about stuff you might be surprised to find there's so far no demonstrable genetic component of) http://www.fims.org/default.asp?pageID=782860264 , here's a relevant snippet:

    "Recent data from the HapMap study, which aims to characterise human genetic variation by genotyping African, Asian and European individuals, show values between 7 and 12% of total genetic variation attributable to between-population differences. Similarly, the data shows that haplotypes (linked segments of genetic variation, rarely subject to reassortment by recombination) are shared across populations 28. Indeed, the level of genetic diversity between human populations is not large enough to justify the use of the term ‘race’ (see Jobling et al. 29 for a review). Consequently, any differences in physiology, biochemistry and/or anatomy between groups defined solely by skin colour (e.g. comparing ‘black’ with ‘white’) are not directly applicable to their source populations, even if the differences found are indeed genetically determined."

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  15. "so while we may find that some races are "enriched" in genes that make them smarter (or whatever), its unlikely to be a trait found in ever member of a race"

    The point that not every member of a race will be the same is obvious; the only point of discussion is whether there are any such "enriched" races or not.

    There aren't. If there is any hard evidence for such a thing, I haven't seen it. Of course, there is tons of phony articles based on weak evidences; it's not like no one is trying. It's just they seem unable to ever progress beyond the "hypothesis" phase.

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  16. Do most of the races of the world have black skin and remain in Africa? How many black African races are there?

    Would the Caucasian, Mongolian, and Autralian Aboriginal races (for example) have diverged from one particular (black skinned) race in Africa, and spread out over the world, while many other black skinned races remained in Africa?

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  17. Also from the NYT profile:

    "He says he thinks that no significant genetic differences will be found between races because of his belief in the efficiency of natural selection. Just as selection turns out to have pruned away most disease-causing variants, it has also maximized human cognitive capacities because these are so critical to survival. “My best guess is that human intelligence was always a helpful thing in most places and times and we have all been under strong selection to be as bright as we can be,” he said.

    This is more than just a guess, however. As part of a project on schizophrenia, Dr. Goldstein has done a genomewide association study on 2,000 volunteers of all races who were put through cognitive tests. “We have looked at the effect of common variation on cognition, and there is nothing,” Dr. Goldstein said, meaning that he can find no common genetic variants that affect intelligence. His view is that intelligence was developed early in human evolutionary history and was then standardized."

    That makes sense to me. Anyone disagree?

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  18. In this paper:

    Nei, M. (2007) The new mutation theory of phenotypic evolution. PNAS, 104, 12235-12242.

    Nei says:

    Most molecular evolutionists are well aware of the importance of mutation in protein evolution. Yet, many investigators are trying to identify even the slightest trace of natural selection using various statistical methods (99–102). Using these methods, a number of authors have reported that a substantial proportion of amino acid substitutions are caused by positive Darwinian selection (103–106). However, the statistical methods used are based on many assumptions, which are not necessarily satisfied with actual data (18, 107, 108). Furthermore, their estimates of selection coefficients are often of the order of 10–6 (100, 106) and are unlikely to affect gene function (18). Note also that although these authors emphasized natural selection, they are actually estimating the proportion of mutations that are adaptive.

    I wonder what John and other positive selection folks think of this critique?

    The paper can be read here:

    http://www.pnas.org/content/104/30/12235.full

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  19. I have a question about the statistical methods used to measure selection.

    Lets say there are two genes - gene A and gene B - that become enriched in a population. A through natural selection, B through drift. Both end up enriched to a similar extent.

    Would the statistical methods be able to differentiate between the mechanisms that lead to A being enriched verses B?

    If so, how?

    Just curious; I took population genetics in the pre-genomics era, so I don't think this stuff was part of the curricula...

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  20. "How many black African races are there?"

    Good question :-D
    Let's count. There are the the Bushman Blacks, the Pigmy Blacks, the Tall Blacks, the Jungle Blacks, the Thick Bearded Blacks, the Dessert Blacks, the Blacks that Can Run A Lot, the Brownish Blacks of the North (like me), the Very Black Blacks, and of course the Common Blacks.

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  21. But they tend to differ from one race to another because each human population, after the dispersal from Africa some 50,000 years ago, has had to adapt to different circumstances.

    While the word "adapt" raises the obvious red flag about strict adaptationism, I read that sentence and thought "But what about gene flow?"

    Allelic differences between human geographic populations (using a pretty fuzzy definition of "population", here) must surely be influenced by a past history of gene flow between populations, as well as drift, mutation, and selection.

    ---

    As for censorship, self- or otherwise, it seems both extremely difficult and extremely unlikely for any branch of science to be effectively suppressed, barring massive financial barriers to entry into the field. Genetic analysis technology is now advanced to the point that human population surveys are probably limited more by airline prices accessing remote regions and isolated populations than by lab equipment. And there are so many journals and publishers that should any one publisher institute some kind of not-publish-that-topic policy, any interesting research will probably show up pretty quickly elsewhere.

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  22. "There aren't. If there is any hard evidence for such a thing, I haven't seen it."

    Absence of proof is not proof of absence.

    We do see some alleles enriched in some races/populations - CFTR ΔF508, G542X, G551D, N1303K & W1282X in Caucasians, HLA-A*6802 and HLA-B18 in sub-Saharan Africans, etc.

    There is no underlying reason why enrichment of alleles that would give enhanced intelligence (or whatever) could not occur in a racial group. We haven't done a good job of looking for it; that doesn't mean it cannot and has not happened.

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  23. "There is no underlying reason why enrichment of alleles that would give enhanced intelligence (or whatever) could not occur in a racial group"

    The absence of evidence is actually quite understadable when you abandon the world of mere statistic correlations and consider some hard brain plasticity data from experimental and developmental psychology. Genes are necessary to develop intelligence, but they are also insufficient to attain even normal intelligence levels. This is a complex trait. Single mutations of great effect always, lower, but never enhance, intelligence. Ever wondered why, and what are the implications?

    "We haven't done a good job of looking for it"

    Are you sure? Truly significant genetic effects don't need all that tech to be detected.
    Take into account, this was considered to be a fact "plain and simple" for a veeery long time. Even after WW II made it decidedly wrong to be racist, only in the 70's do we start unmasking the shameful frauds and crappy science that was behind the supposed "established facts" of racial differences of intelligence.

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  24. In Response to anonymous. To paraphrase Stephen Jay Gould: The definition of black is someone with skin dark enough that we can call them black.

    In response to Bryan: There must be races because we look different. What is your point? How does that in any way validate the concept of genetic difference? There may be differences that you think that you can "see" that don't really have any meaningful application in genetics. You could say that a Canadian (of english descent) looks different from a northern European, does that mean they are different races?

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  25. || PaleoFreak said...

    "How many black African races are there?"

    Good question :-D
    Let's count. There are the the Bushman Blacks, the Pigmy Blacks, the Tall Blacks, the Jungle Blacks, the Thick Bearded Blacks, the Dessert Blacks, the Blacks that Can Run A Lot, the Brownish Blacks of the North (like me), the Very Black Blacks, and of course the Common Blacks.

    Tuesday, September 16, 2008 6:33:00 PM ||

    And, PaleoFreak, I think the Monty Python team wants to hear from you :^)

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  26. Sanders wrote: "Are you sure? Truly significant genetic effects don't need all that tech to be detected."

    I am sure - traits such as intelligence will most likely be multi-genic, and the tools for identifying those are rather new. We're still finding new risk genes involved in "obvious" processes like diabetes and other autoimmune disorders. A pubmed search shows no such attempt at finding intelligence genes.

    "Single mutations of great effect always, lower, but never enhance, intelligence."

    That we know of - genes which cause medically identifiable disorders are always much more obvious than genes with neutral, or slightly advantageous effects. And, as I pointed out before, I could not find any evidence in pubmed that such a search has taken place.

    Besides, who said anything about single genes? Intelligence is most likely a combination of multiple genes and our environment. And until we look (and a pubmed search revealed no evidence that we've looked) we have no way of knowing if certain genes that lead to intelligence are concentrated in one race verses another.

    And even if all neuronal-based mutations lead to less intelligence, there is no reason why those detrimental genes could be enriched in a race/population.

    Keep in mind that we're talking about racial-associated traits here. It doesn't have to be more intelligence to occur; it can be less intelligence, something immune, or something else all together.

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  27. Before we look if there's genetic differences in IQ, it would be a good idea to be able to identify IQ genes first, nope? Pubmed that!

    The results are disappointing; and this particular search has been going on with sufficiently modern tools for quite some while now

    Maybe this can explain why taking it to the race level with such flimsy data is not such an attractive quest

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  28. This comment has been removed by the author.

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  29. IQ does not associate significantly with race when people are raised in the same educational institutions and similar socio-economic condition.

    What do you think that tells you about genetic differences of IQ between races?

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  30. Lets say there are two genes - gene A and gene B - that become enriched in a population. A through natural selection, B through drift. Both end up enriched to a similar extent.

    Would the statistical methods be able to differentiate between the mechanisms that lead to A being enriched verses B?

    If so, how?


    Assuming that in both A and B originated from single mutations, positive natural selection will cause A to become common vastly faster than drift can cause B to become equally common. So if A and B are the same current frequency, the selected allele A should be much younger than B.

    Methods for detecting positive natural selection depend on identifying allele age, mostly by linkage decay. Recombination breaks up linkage over time; an allele that has a high current frequency and has maintained linkage over a very wide region is very young.

    These methods do not distinguish other kinds of selection, such as balancing selection, and they are ineffective on rare alleles (for which we have insufficient data to estimate linkage decay).

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  31. Sanders wrote: "IQ does not associate significantly...What do you think that tells you about genetic differences of IQ between races?"

    Based on a brief look at what's in pubmed, I'd have to stand by my original statement - we really haven't looked.

    That said, my pubmed search did find several studies that claimed genetic-based differences in IQ among racial groups - see the work of JP Rushton, AR Jensen, and L He for some examples.

    On example, from a joint paper between Rushton & Jenson:

    The preponderance of evidence demonstrates that in intelligence, brain size, and other life-history variables, East Asians average a higher IQ and larger brain than Europeans who average a higher IQ and larger brain than Africans. Further, these group differences are 50-80% heritable

    PMID: 18656315

    My (granted brief) look at the issue makes me think that they are overstating the case, but regardless, at least three experts in the area think there is evidence to support a claim of differential IQ's between races.

    If IQ truly represents our intelligence is another issue all together...

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  32. This comment has been removed by the author.

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  33. John, thanks for that informative reply. It answered my question perfectly.

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  34. Bryan, you either whine we are not looking, or bonk the table and say we already have the evidence... make up your mind, dudrness.

    I doubt those papers are good evidence. I may have alook into them, ut it's bound to be more of the same of this speculativ-crappy brand of "evolutionary psychology" science.

    Have a nice day

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  35. "Bryan, you either whine we are not looking, or bonk the table and say we already have the evidence... make up your mind, dudrness."

    Maybe try reading what I wrote before you reply next time; you'll look a little less dumb that way.

    Its blatantly clear from my reply that I don't think we've looked into the issue to any extent. Its also very clear from my reply that there are researchers in the area (i.e. their opinion, not mine) who think the evidence says there is a strong genetic link.

    I even provided a citation to an article where the authors (who once again, are not me) make that very claim.

    I've been perfectly consistent in my statements. I'm sorry for confounding the issue by introducing the statements of others; apparently that was too much for you to follow.

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  36. Sorry that I could not help you.
    I might read the papers...

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  37. There is no such thing as "genes that lead to intelligence". Genes are necessary but without the adequate nutrition and cultural-learning environment, they don't lead to even normal levels of intelligence.

    Genes are involved in basic, "physiological" scaffolding; their variation only causes large decreases, never increases, of intelligence. For variation within the "normal", upper range of IQ, the effect of genetic variation is negligible.

    It is also interesting to point out here that some of the "degenerative" mutants can be rescued by nutrition, conversely, some non-mutants can have severely abnormal phenotypes (e.g.autism), all of which indicate the environment is involved in the very basic scaffolding, too.

    Say we find that some ethnic-racial group have higher frequencies of genes that produce severe mental problems (for instance, a deletion leading to prader-willi). Or that they have higher incidence of microcephaly. Sure, they contribute to the variation of the IQ of that population. You are going to find things like that. Would you then argue that the race is genetically of a lower IQ? Nobody will be jumping to that conclusion since it is misleading about the variation in the upper, normal range of IQ in that group.

    Some have brought up the possibility of variation of neural-brain genes causing small, hard-to-detect effects (increases or decreases), using statistics to detect correlations. Of course the best low tech thing thing would be to acccumulate these effects by artificial selection for high IQ; some historical attempts suggest it doesn't work.

    Looking for statistical correlations is fine but we have to understand the level to which the entire question has been removed. We are asking ourselves about the existence of hard-to-detect genes with "small" effects on intelligence and the answer is almost always stuck in "maybe".

    The other thing we may find is a higher frequency ina given group of a gene that has been argued to have a small, hard-to-detect effect (positive or negative). That may be so, but again, notice how far removed this question is from the terms of discussion of misinformed people who are wondering, for instance, whether it is a waste to educate blacks!

    Some think that a given race may have an accumulation of several small-effect genes. If so, outbreeding from one race into another "non-enriched" race should "dilute" the genetic IQ of progeny, much like when you outbreed an artificially selected "race"; if several small-effect genes are accumulated, the trait will be significantly diluted. Nothing like that happens with IQ, of course.

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