Newsweek has an entertaining story which highlights the recent penetration of science into the venerable enterprise of genealogy. The good:

…Adopted at birth, Royer knew nothing about her biological parents. But certain physical traits-wide nose, dark skin-led people to guess that she was Iranian or even Cambodian. “I always wondered,” she says. Two hundred dollars and a swab of her cheek gave her an answer: Royer’s maternal ancestors were most likely Native American. The knowledge, she says, “makes you feel more of a person.”

The dumb:

DNA testing is forcing some people to rethink their identities. Phil Goff, 42, of Naperville, Ill., thought his heritage was pure English, but a Y chromosome test matched him at least partially to Scandinavia. Now he wonders if he has any Viking blood in him.

Note the contrast here. In the first case, we have an extreme and unfortunate situation where an adoptee doesn’t know the identity of her biological parents and whose appearence bespeaks an “exotic” lineage. The conditional probabilities, that is, take the lack of knowledge about antecedants and physical clues into account, work out so that an mtDNA test can be very illuminating. In the second case we have a situation where you are attempting to make inferences far back into the past and resolve distinctions that are relatively minor in comparison to the first scenario. Not only are Scandinavians and the English relatively affinal populations in comparison to Native Americans and Europeans, but there is plenty of evidence of gene flow between Scandinavia, northern German and England. Additionally, the historical literature (as well as linguistic clues) tells us that the “Danelaw” of the north and east of England was actually settled by a fair number of Danes ~1000. Drawing too many inferences from a uniparental lineage can be very misleading, all you are gleaning is the coalescent for that one gene. Oxford geneticist Bryan Sykes actually found that half the people with his surname share the same Y chromosomal lineage. That doesn’t mean they are particularly closely related at all, they simply have a patriline in common. Similarly mtDNA lineages are tracing a sequence of mothers and daughters.These tests don’t speaking to the overwhelming majority of your ancestral paths which are “broken” by mother-son or father-daughter steps.¹ Another problem is that many of the haplotypes might be misclassified. Or consider an individual who hails from southern India but was told by Spencer Wells (pretaped video) about “ancestors who left Central Asia for Europe” after his DNA was sequenced by the Genographic Project. The article also highlights autosomal methods bandied by DNAprint Genomics which give you a measure of your various ancestries. And they also have problems.² When friends ask me if they should shell out a few hundred dollars I usually say no, because I don’t think that these tests tell you anything you don’t know (there are exceptional cases, such as the one above).

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I’ve been cruising through the feminist blogosphere of late and in the past few weeks there have been three stories on the Crisis in Boy’s Education that have captured their interest, the first from The New Republic, the second in Newsweek, and the last in The Boston Globe. The tone has ranged from outright hostile mocking of the Boston story, which involves a boy suing his school for discriminatory bias against boys, to outright denial that the problem even exists. Tied closely to both poles of this spectrum of criticism are the outright dismissals of the sociological shifts which are likely to follow, such as the often quoted prediction of the shortage of marriageable men. The odd thing about these commentaries is that they are simply dismissals rather than refutations. I haven’t read one blogger tackle the “marriage issue” head-on and argue why it is nonsense, it’s simply laughed off as naifish attempt by social conservatives to put woman back into the kitchen.

Now, because none of the commentary took on the issue in a serious fashion, I have no idea how feminists are framing the issue. I imagine that any thought they’ve actually given to the demographic issues probably centers on an outlandish framing which sees a generation of professional women actively out there scouring their community for suitable mates and this is clearly dismissed as ridiculous. If this is the vision that they’re dismissing, then I’ll join them in their mocking of the supporters of this vision.

These women will have their choices constrained by a few factors. The first, is obviously, the lack of men in their generation who share their educational achievements. The second is whether these women are going to be able to reorient their mate selection preferences towards men who are great at playing videogames but not so great at pursuing a professional career. The third constraint would be their willingness to remain single, and possibly childless. And the last constraint is whether they’re willing to engage in subtle poaching of suitable and desireable men who just happen to be married.

Of the constraints facing them, I think the obstacle of the man being married to another woman will be the easiest to surmount for this surge of educated women will prove to be an incentive for older, successful men to take the opportunity to remarry. Afterall, if the woman is successful in choosing this strategy, she benefits and so does the man. The main loser, in this game of musical chairs, is the older married woman who just had her family torn apart.

Discuss.

I’ve talked about MHC before. 1 It is important because it has a key role in the adaptive immune system and is illustrative of an important dynamic in evolutionary genetics, balancing selection, which perpetuations extreme polymoprhism within populations. Over time a functionally constrained locus which has an important fitness effect should fix toward the most advantageous allele. Polymorphism, where the modal allele is exhibited at lower than 95% frequency, suggests a population in transition. One can imagine such a scenario in a newly admixed population which has not had time to fix in populations. But MHC is different, many of the alleles on this locus persistent across species and have extremely deep evolutionary roots. There are two standard reasons given for this, a) heterozygote advantage or b) frequency dependent selection. No matter the details of the case, the importance of MHC and the persistence of polymorphism across many lineages and deep back into time is one of those truisms that thankfully takes a little of the territorial sloppiness that is habitual in much of biology. But assumptions need to be tested, so I pointed you to this paper, MHC class I genes in the tuatara (Sphenodon spp.): Evolution of the MHC in an ancient reptilian order). Here is the interesting part:

Preliminary analysis of variation among individuals from an island population of tuatara indicates these loci are highly polymorphic….

The Tuatara is an extremely ancient reptilian species on a lonely branch of that class of animals.

1 – MHC also might play a role in inbreeding and outbreeding avoidance.

Today’s London Sunday Times (January 29) has an article in the Education section on new research which claims that British children’s ‘intelligence’ has declined dramatically in the last 30 years. If the link works, the article is here.

The research is by Profs. Adey and Shayer of King’s College London. Adey claims, based on a sample of 25,000 children, that ‘the intelligence of 11-year-olds has fallen by three years’ worth in the past two decades’.

Naturally this is of interest in the context of the Flynn Effect – the long term trend of rising IQ scores. Several recent reports suggest that the Flynn Effect has halted or gone into reverse.

I haven’t been able to find any further details of the research than those in the ST article, and I suggest a need for caution. The tests used do not appear to be standard IQ tests but rather tests of ‘scientific reasoning’, which combine general intelligence (g) and more specific mathematical and physical concepts. In IQ terms, a fall of 3 years in average mental age at chronological age 11 would be massive: if we suppose the baseline 30 years ago is IQ = MA/CA = 11/11 x 100 = 100, the new IQ would be MA/CA = 8/11 x 100 = approx. 73. I don’t think mean IQ can possibly have fallen by 27 points in 30 years! The school at King’s College is also known for unorthodox views on the nature of intelligence, including the belief that ‘thinking skills’ can be radically improved by fairly small amounts of direct ‘thinking’ teaching.

I also note that there is no mention of the ethnic composition of the samples, which must certainly have changed in the last 30 years. However, in IQ terms the fall is far too large to be explained by compositional changes of this kind.

[Added: The last point should be sufficiently self-evident, but let me expand on it for the benefit of the innumerate. In 1975 the proportion of non-whites at age 11 in Britain was around 5%. In 2005 it was around 15%. (These are very rough figures, but good enough for the present purpose.) Let us suppose that in 1975 the mean ‘intelligence’ of white 11-year-olds, by standard IQ tests or any other valid instrument, was 100, while that of non-whites was 85. This is about the size of the black-white differential in the US, or the difference between whites and the offspring of recent non-white immigrants in European countries. It probably overstates the differential between whites and non-whites in Britain, since non-whites in Britain include large numbers of Indians and other high-achieving groups. Assume that white and non-white IQ is unchanged between 1975 and 2005. These assumptions gives us mean population IQ of 99.25 in 1975 and 97.75 in 2005 – a fall of less than 2 percentage points. This is far too small to account for the kind of decline reported by Adey and Shayer. To explain such a large decline by changes in the composition of the population, either the magnitude of the compositional change, or the differential between the different components, or both, must be much larger than is at all credible.]

Despite these reservations, this is clearly interesting research, and I will try to follow it up.

Added: I found a more informative account of the research in the Guardian here. The full report will be published in the British Journal of Educational Psychology next year.

Since very few of you have likely read Fair Women, Dark Men: the Forgotten Roots of Racial Prejudice by Peter Frost, I’d like to you point you to his website, where he introduces many of his ideas in a series of essays. Steve also has an essay on based on Frost’s ideas, and you might find this paper by Frost, European hair and eye color A case of frequency-dependent sexual selection?, of interest.

Science isn’t perfect, it often misses obvious truths. Consider the 2005 Nobel in medicine, awarded for the work of Barry Marshall and J. Robin Warren in establishing the connection between Helicobacter pylori and ulcers. After the fact you hear many stories of doctors who had stumbled onto the solution, antibiotics, long before the scientific consensus. Many others now understood why they always saw these pathogens in samples taken from patients with ulcers. Now it all makes sense, but these sort of screw ups make you wonder how far we’ve gone past Galen! Falsification is a decent formalization of the scientific process if you distill it down to its bare essentials, but it ignores the reality that science is executed by people, not computers. Thomas Kuhn’s work in The Structure of Scientific Revolutions speaks to that sociological reality, instead of a gleaming geometrical crystal city, natural science is filled with booming unplanned towns, citadels being swarmed by unexepected squatters, and castles in the hinterlands striving in vain to maintain their relevance. Even mathematics, that most rational of disciplines, is driven by an engine of intuitive insight and gestalt understanding, no matter the clean final product carved from axioms. Alas, science has a low signal to noise ratio, but paraphrasing Winston Churchill, it’s the best system we’ve got.
Of course, because of the socially contextual nature of much of science there is a niche for historians and sociologists to study it as a subculture. It is on the great mound of noise in which the signal swims that Will Provine has established his career as the historian of evolutionary genetics. His biography of the American population geneticist Sewall Wright displayed not only an encyclopedic knowledge of the personalities who touched Wright’s life, but the technical details of the theoretical biology which served as his legacy. It was with an understanding of this background that I came to Provine’s The Origins of Theoretical Population Genetics.
Basically a slim elaboration on his Ph.D. thesis at the University of Chicago this text explores the social and scientific dynamics between the initial high tide of the Darwinian phase in evolutionary theory and the reemergence of its primacy during the 1920s as population genetics fused the Mendelian framework with the wealth of statistical tools that were found in the biometrical school. In the interregnum Darwin’s original ideas which emphasized the importance of natural selection on continuous variation as the primary motive force for evolutionary change were relegated to the margins. A thorough survey of this period can be found in Peter J. Bowler’s The Eclipse of Darwinism, but Provine’s work is more narrowly focused, and tends to put the spotlight upon individuals rather than grand social movements. The importance of personality in inflating semantic confusions and mediating sociological dynamics shows exactly where much of the noise in the scientific system comes from.
In short Provine’s thesis centers around the conflict between the Mendelians, led by William Bateson, and the biometricians, headed by Karl Pearson (the Pearson’s correlation coefficient), and the subsequent fusion which culminated in R.A. Fisher’s 1918 paper, The Correlation between relatives on the Supposition of Mendelian Inheritance. The conflict between these two groups was in part on genuine scientific grounds, but Provine makes it clear that personal animosity, turf wars and inability to master the methodologies of the other side perpetuated a discord which was really much ado about nothing (and resulted in far less getting done).
The dispute had its seeds in the somewhat confused ideas of Francis Galton in the field of evolution. Unlike his cousin Charles Darwin and Alfred Russel Wallace Galton did not believe that natural selection upon continuous variation within populations was sufficient to explain evolutionary change. Like many scientists, including Thomas Huxley, Galton contended that evolution was due to the emergence of unique mutant forms, “sports,” which were at sharp discontinuity with the normal variation within a population. Galton did not accept that selection upon continuous variation would induce evolutionary change because he had some peculiar ideas in regards to regression toward the population mean. He seemed to posit some sort of innate stabilizing factor within a population which kept it around a species typical mean, bounded by its range and characterized by a particular variance. So individuals at the extremes would give rise to offspring who would regress back toward the mean of the population. Mutant varieties on the other hand might offer the opportunity to break out of this tendency by generating de novo a new central tendency. Pearson, Galton’s protege, pointed out that he neglected to consider that repeated generations of assortative, or selective, mating of exceptional individuals would avoid the problem of regression back toward the ancestral mean as “mediocrity” (that is, random mating of exceptional individuals with less than exceptional ones) would not dilute the offspring and successive population means would be established.¹

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In the news…Parkinson’s gene of large effect found in Jews and North African Arabs and group differences in lung cancer rates controlling for variables (or are they?). I am more intrigued by the Parkinson’s result because my understanding is that North African “Arabs” are Arabicized Berbers by and large. There is some implication that the Parkinson’s Disease gene might be found in common because of phylogeny, that is, both derive from common Middle Eastern stock. But if most North Africans are simply Arabicized Berbers their Middle Eastern origin should be pushed rather far back in history, probably at least greater than 6,000 years before the present (some evidence suggests that post-Neolithic Demic diffusion occurred). Some of the interpretations are based on founder effect being the culprit, but we can’t ignore selection, can we? (though if you do a search on PubMed note that there are papers out there that do assert that North Africans seem to be highly substructured and it is difficult to establish a rhyme or reason,)

All of the other science bloggers are talking about the finding that the British might be more Creation-friendly than we’d have thought. My first thought is that we need to be careful about the survey. But my second thought is to remind myself that a 1988 survey (page 8 of the PDF) found that “…one-third of British adults understood that the Earth rotates around the Sun once a year….” vs. “…half of US adults know that the Earth rotates around the Sun once a year….” (year 2000 for the American survey). The difference in anti-evolutionary activism in the two nations is, I suspect, a function of British class structure and popular deference to elites.

Anyway, I’m going to snag some data from religious tolerance on evolution internationally:

Q: “In your opinion, how true is this? …Human beings developed from earlier species of animals..”

Nation & percentage answering affirmative

United States < 35.4
N. Ireland 51.5
Philippines 60.9
Ireland 60.1
Poland 35.4
Italy 65.2
New Zealand 66.3
Israel 56.9
Norway 65
Great Britain 76.7
Netherlands 58.6
W. Germany 72.7
Russia 41.4
Slovenia 60.7
Hungary 62.8
E. Germany 81.6

Update: Thanks to Dan for the correlation matrix for the data above below the fold….

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Over the past 5 years Matthew Harris has been doing some interesting research into feather morphogenesis, and he has produced some must watch videos. His work on quantitative modeling of development via the activator-inhibitor system is, I believe, a necessary precursor in fruitfully talking about the evolutionary context of feathers. To my mind the videos are essential for anyone who isn’t fluent in molecular developmental biology (like me), so we can have the big picture in mind when digging through the essential details.