Archive for July, 2008

Black and white twins & perils of Colored admixture

By Razib Khan | July 18, 2008 3:26 am

1_61_320_biracial_twins.jpgI was curious why an old Genetics and Health post, Twins with Different Skin Color Genes, was sending me many referrals today. Now I know, Two in a Million: Twins Born – One Black, One White:

The twin boys, named Ryan and Leo, are the offspring of a mixed-race couple.
The mother, Florence, hails from Ghana in western Africa, and dad, Stephan, is from Potsdam in Germany.
“Ryan came first, and everything was as usual,” said the hospital’s doctor, Birgit Weber. “But when Leo was born, I couldn’t believe my eyes.”
“Both kids have definitely the same father,” the doctor added.

These aren’t the first of these “amazing” of twins. I’ve posted on this sort of story before, Can you tell if you’re black or white?, “Black” & white twins again and Ivory & ebony, twins again…and again…. I touched on the major genetic points in depth in those posts, but this case is a bit different since you have two parents who are monoracial; this makes the odds in terms of genotypic combinations a bit confusing. I think that the easiest way to explain the outcomes are stochasticity of gene expression during development, and, possibly gene-gene interactions between these two parents which allow for deviations outside of the expected range. If what I’m saying is unintelligible to you, I recommend you read the posts I linked to above, it will make the context clearer.

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Down with Darwinism!

By Razib Khan | July 17, 2008 4:25 pm

I agree with all the other ScienceBlogs that Olivia Judson is right. Do we talk about Newtonism? Einsteinism? We do talk about Epicureanism, Platonism, Neo-Platonism, Aristotelianism, etc. I think that says it all….


Overplaying "AIDS genes"

By Razib Khan | July 17, 2008 1:32 pm

Brandom Keim at Wired says Genes Don’t Explain African AIDS Epidemic:

Seen in the wrong light, the numbers could present Africa’s AIDS tragedy as a biological inevitability. Several press accounts do exactly that. The New York Times credits the mutation for “explaining why the disease is more common there than expected.” Reuters says it could “help explain why AIDS has hit Africa harder than all other parts of the world,” as this can’t be fully rooted in “sexual behavior and other social factors.” The Guardian says it “may go some way” to explaining the African prevalence of AIDS. And the Gene Expression blog titles its coverage, “Evolution, a reason for the African HIV epidemic?”

My first reaction was, “who would be retarded enough to think that one genetic difference entails inevitability?” But on second thought, that’s just me being unreflective, many people are that stupid. In any case, I specifically titled my post “a reason” to highlight that the variation on the DARC locus might be able to account for some of the between population differences. It is true that most people aren’t used to thinking of a dependent variable which is the outcome of the joint effects of multiple independent variables; that’s why the genetic determinism straw-man is so easy to construct. Extrapolating from the study sample and the known nature of the polymorphism on the DARC locus, one could account for around 10% of the difference in HIV infection rates when it came to Duffy negative vs. Duffy positive populations. That’s a big impact. In height or IQ the quantitative trait loci, the genes which effect variation, are on the order of 1% or less in effect. Something similar to the polymorphism on the DARC locus would be the skin color genes, the largest few effects being on the order of 10-40%.

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Evolution, a reason for the African HIV epidemic?

By Razib Khan | July 16, 2008 11:20 pm

Please read: Follow up post.
Genetic Variation Increases HIV Risk In Africans:

A genetic variation which evolved to protect people of African descent against malaria has now been shown to increase their susceptibility to HIV infection by up to 40 per cent, according to new research. Conversely, the same variation also appears to prolong survival of those infected with HIV by approximately two years.

HIV affects 25 million people in sub-Saharan Africa today, an HIV burden greater than any other region of the world. Around 90 per cent of people in Africa carry the genetic variation, meaning that it may be responsible for an estimated 11 per cent of the HIV burden there. The authors observe that sexual behaviour and other social factors do not fully explain the large discrepancy in HIV prevalence in populations around the world, which is why genetic factors are a vital field of study.

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A request

By Razib Khan | July 15, 2008 11:14 pm

From Chris of Mixing Memory.


Global warming bad for civilization?

By Razib Khan | July 15, 2008 1:10 pm

climateIQ-720532.JPGThere’s a fair amount of evidence for greater social pathology among whites of Southern origin. One of the major issues that Blue State liberals like to point out that is that on metrics of moral turpitude Southern whites stand out; those who promote a narrow and strident conception of ethical behavior are the most likely to transgress those very norms. Logically one might contend that in a society where there is no murder there need be no laws against it. Similarly, in our society we don’t have specific laws against consumption of one’s own children for food because it is such a rare occurrence, in contrast to sexual abuse and what not. So the Southern promotion of an ethic of sobriety might very well be due to the fact that social disorder is generally far closer to the surface. But in any case, we might need to go beyond the proximate scale to understand these patterns.
In Albion’s Seed the historian David Hackett Fischer argues that there are “Four Folkways” which established themselves on these shores before American Independence. They are the Puritans of the New England, who are directly descended from Middle Class immigrants disproportionately from East Anglia who wished to practice a Calvinist form of English Protestantism (nobility and the poor were actually rejected as potential migrants!). In the highlands of the interior, what became Appalachia, settled the Scots-Irish, who hailed generally from the borders between England and Scotland and the Protestant colony in Ulster. In the lowlands of the South, starting in Virginia and on down toward Georgia you found settlements focused on aristocrats, often younger sons without title. Their estates were also characterized by a large underclass of poor. A symbiotic (exploitative) class relationship developed between this American gentry and their wards which recapitulated many of the cultural structures evident in southwest England, the stronghold of the Cavaliers. Finally, in the Mid-Atlantic between Maryland the Hudson river valley there was a melange of settlements of disparate origin. Fisher claims that the central organizing identity in this area was that of the religious non-conformists from the Midlands of England, such as Quakers, but he admits that the diversity of this region makes it harder to generalize, from the Dutch Patroons of New York to the Swedish settlement in Delaware. Ultimately the Mid-Atlantic Folkway is perhaps one defined by its pluralism and capitalist pragmatism, a lack of a coherent principled Folkway in some sense.

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Sizzle: not even bad?

By Razib Khan | July 15, 2008 5:00 am

sizzle.jpgWell, I never thought I’d watch a film with the title, Sizzle: A Global Warming Comedy. The “star” of the Sizzle is Randy Oslon, a contributor to Shifting Baselines here at ScienceBlogsTM. In fact, Randy is a major contemporary interpreter of the term shifting baselines. I assume that most readers of ScienceBlogsTM are more familiar with Randy’s oeuvre than I am, I haven’t watched Flock of Dodos, and in general I tend to not be familiar with mass-market documentary films. I haven’t watched either Al Gore or Michael Moore’s documentaries, and Expelled was an experiment on my part in plugging into the multimedia propaganda industries which seem to be determining the Zeitgeist at any given time. I suspect that I’ll keep on passing on documentaries; Expelled was mendacious. As for Randy’s newest work, I have to admit it left me kind of disoriented more than informed or entertained.
The mix of a serious topic with documentary intent interlaced with comedic set-ups didn’t really satisfy my appetite for either. I checked out some of the articles about this film and it seems Randy was aiming for a broad audience. I can’t believe any climate scientists would be very satisfied with the depth of scientific exposition, but I’m also not sure that the delivery was straightforward and focused enough to yield marginal returns for a broader audience which is only cursorily familiar with the science. To some extent I’m more in the latter camp as I don’t follow the politics and science of Global Warming with any depth; I know the general logic behind anthropogenic warming and the sketches of mitigating policies. But I defer to the experts on the details of both. My own personal politics are on the far Right edge of what you might find on ScienceBlogsTM, so I am more willing to listen to the arguments of individuals such as Jim Manzi at National Review than most around these parts. Nevertheless, in all honesty there’s a difference between will and implementation, and I’ve just not spent the marginal time boning up on this topic or the set of various responses proposed to feel very confident about any distinctive personal opinions I might have.
What someone like me needs is a thicker slice of the issues at hand, not a scattered attempt at reinforcing general insights and the expected ideological cut-outs. To appreciate some of the ironical, nuanced and meta aspects of the broader issue which Randy seems to want to shed light on I needed more detailed analysis and elucidation than I found in Sizzle. Perhaps I lack a sense of humor, I certainly didn’t laugh much, but then I’m no studied appreciator of the art of film. I also admit that a deeper exploration of the substantive scientific issues to the extent that I would have preferred might have made the film unmarketable, but I don’t think that the presentation schema that Randy selected is tight and fluid enough to hit home the few general points with enough force to compensate for the trade-off entailed by the space given to the wacky hijinks and silly situations.


E. O. Wilson, Neville Chamberlain controversialist?

By Razib Khan | July 15, 2008 1:05 am

A profile of E. O. Wilson in The New York Times, Taking a Cue From Ants on Evolution of Humans:

Dr. Wilson was not picking a fight when he published “Sociobiology” in 1975, a synthesis of ideas about the evolution of social behavior. He asserted that many human behaviors had a genetic basis, an idea then disputed by many social scientists and by Marxists intent on remaking humanity. Dr. Wilson was amazed at what ensued, which he describes as a long campaign of verbal assault and harassment with a distinctly Marxist flavor led by two Harvard colleagues, Richard C. Lewontin and Stephen Jay Gould.
The new fight is one Dr. Wilson has picked. It concerns a central feature of evolution, one with considerable bearing on human social behaviors. The issue is the level at which evolution operates. Many evolutionary biologists have been persuaded, by works like “The Selfish Gene” by Richard Dawkins, that the gene is the only level at which natural selection acts. Dr. Wilson, changing his mind because of new data about the genetics of ant colonies, now believes that natural selection operates at many levels, including at the level of a social group.

David Sloan Wilson in Evolution for Everyone, and Ullica Segerstale in Defenders of the Truth, both report that E. O. Wilson has always supported group selection. The recent broadside against the primacy of gene selectionism was only prompted by new empirical data from social insects enabled by DNA fingerprinting. Coefficients of relatedness below the threshold hypothesized by W. D. Hamilton confirmed to Wilson his intuitions that more than inclusive fitness was at work, and allowed him to make a renewed push toward an acceptance of multi-level selection in evolutionary theory.

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Why blogging sucks

By Razib Khan | July 11, 2008 2:15 pm

Dave Appell at Quark Soup has a jeremiad against blogging up. It’s fine, but I have to add that I was reading Dave’s original blog in early 2002 (the first science blog I ever read), and he would post his frustrations about how crappy it was being a writer and how blogging was unsatisfying. As it happens, it’s 2008, and he’s come back to blogging, and last I checked he’s still a writer. Dave also sent Rod Dreher an angry note for having supported the Iraq War (though Rod now opposes it).
So I’m just sayin’, keep the messenger in mind :-)


Old people scientifically illiterate?

By Razib Khan | July 10, 2008 10:32 pm

I’ve posted on general scientific literacy broken down by demographic groups in the GSS. I’ve also pointed to data which suggested that the lower scientific literacy of church goers vis-a-vis non-church goers is an due mostly to the influence of Young Earth Creationism. Finally, I put up a post which suggested that Americans aren’t that scientifically inept in the international context. So I thought I would repost the raw responses to various questions. Charts below the fold, but to explain the title, here’s the difference between the 18-24 demographic and the over 65 demographic in terms of correct responses to various questions:
The center of the Earth is very hot. (True) 14 point advantage to the young
All radioactivity is man-made. (False) 1 point advantage to the old
Lasers work by focusing sound waves. (False) 17 point advantage to the young
Electrons are smaller than atoms. (True) 24 point advantage to the young
The universe began with a huge explosion. (True) 2 point advantage to the old
The continents on which we live have been moving their location for millions of years and will continue to move in the future. (True) 22 point advantage to the young
Does the Earth go around the Sun, or does the Sun go around the Earth? (Earth around Sun) 20 point advantage to the young
How long does it take for the Earth to go around the Sun: one day, one month, or one year? (One year) 34 point advantage to the young
It is the father’s gene that decides whether the baby is a boy or a girl. (True) 3 point advantage to the young
Antibiotics kill viruses as well as bacteria. (False) 3 point advantage to the young
Human beings, as we know them today, developed from earlier species of animals. (True) 20 advantage to the young
Now, I know that Continental Drift was not the scientific consensus when the over 65 set were youth, but I think evolutionary theory predates any of the seniors in the survey. I suspect part of the issue here is just confusion, and I think it goes to show the importance of reflective acuity in scientific response, since many scientific truths, such as heliocentrism, do not reflexively follow form intuition.

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Americans are scientific geniuses (relatively)

By Razib Khan | July 10, 2008 4:54 pm

I’ve already posted on GSS results on science knowledge. But what about the international context? Th working paper Civic Scientific Literacy in Europe and the United States has some interesting data which has international comparisons. Here’s an interesting fact regarding “scientific literacy”:

This confirmatory factor analysis demonstrates that all 32 of these items reflect a common factor. The uniformly high factor loadings suggest that many of these items are interchangeable and that would be possible to use a subset of these items if one needed a measure of civic scientific literacy and could not collect a set of 32 items.

In short, the data here suggests to me that the stupid within a population are less scientifically literate. That’s probably the single factor which explains most of the variation. But note the factor loadings on specific questions:

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Fundamentalism is bad for your science knowledge

By Razib Khan | July 10, 2008 12:02 pm

This is a follow to the previous post focusing on which demographics know scientific facts. One of the major differences was between those who were very religious and those who were not, with more scientific literacy among the latter. Inductivist looks into the question that many have asked:

I eliminated the three questions that touched on the question of creation or the age of the earth (i.e., the Big Bang, continental drift, and human evolution) and re-calculated scores with the remaining eight questions. Here are the results:

The Protestant mean goes up a few points when…when the 3 questions are removed. And, compared to the very religious, the folks who never go to church no longer have higher scIQs. In fact, the churchgoers’ means are higher for whites and all races together.
I mentioned in the last post that there is practically no correlation between IQ and church attendance, and after removing the 3 questions from the scIQ quiz, there is now no correlation between it and going to church–it is .01.
So it’s not that people who are informed about science at a basic level are staying away from church; they just reject what science says if it conflicts with their religious beliefs.


Jesse Jackson goes nuts over personal morality

By Razib Khan | July 10, 2008 1:21 am

I don’t post much about “politics in the news” because I almost never (OK, never) have anything value-added to say. That being said, I do want add something to the Jesse Jackson comment about wanting to cut off Barack Obama’s testicles. Many people are framing this at Jackson’s irritation at Obama talking down to black people and putting a specific focus on their social pathologies as opposed to broader societal dynamics. I think it is important to remember that Jesse Jackson isn’t an exemplar of bourgeois probity himself (unlike Obama, at least what we know of him). He had an extramarital affair which produced a child. No one’s perfect, but it wouldn’t surprise me if Obama suggesting that black men should take some responsibility might irk an individual whose failings were exposed in public in such a manner.


The Structure of Evolutionary Theory blogging, chapter 8

By Razib Khan | July 10, 2008 12:20 am

GOUSTR.jpgChapters read:1, 2, 3, 4, 5, 6 and 7.
It’s been a while since I blogged Stephen Jay Gould’s The Structure of Evolutionary Theory. I haven’t forgotten it, but once I finished the historical preamble, nearly 600 pages, I was in the mood for a breather. My hunch was that despite Gould’s emphasis on contingency in his theory in terms of his narrative there would be only a broad contextual relationship between Part I and Part II, the intellectual history of evolution by Stephen Jay Gould, and the scientific theory of evolution by Stephen Jay Gould. I’ve finished the 8th chapter, which is ostensibly the first science chapter, though since Gould promiscuously mixed science & history it is more a notional than substantive distinction. Though a long section, at 150 pages this is nothing compared to the next chapter I’ll hit (and probably won’t blog for a while), which was spun off into a separate book, Punctuated Equilibrium.
In any case, the general complaints about Gould’s prose style holds; despite his shift from narrative history toward a more scientifically inclined exposition the first portion of the chapter is larded with so much florid arcana as to put one to sleep. There are flashes of expository clarity and brilliance embedded within the mush, but there is an interesting caveat to this: my general sense is that Gould is at his best when he is polemically tearing down Richard Dawkin’s gene-centered paradigm. I find this ironic, because whatever you might think of Dawkins’ science his prose is generally a good balance between sober economy and flourishing engagement at the appropriate points. Gould rises to the challenge specifically when he has to meet Dawkins’ prose head-on after a quotation from the latter’s body of work. In the The Structure of Evolutionary Theory there are some general arguments about the level at which selection operates, the power of selection vis-a-vis other evolutionary forces, and the scale independence of evolutionary process (i.e., the extrapolation of microevolutionary dynamics to the macroevolutioanry level). The previous chapters have prefigured Gould’s arguments copiously, so the introduction of these three points was no surprise. Like a ponderous oil tanker which operates more as a force of nature then an active agent against a physical background the prose rolls on evermore, page after page, example after example. But when confronted by the simplicity of Dawkins’ and George Williams’ arguments the tenor of the narrative shifts radically as each paragraph is dense with articulation and elucidation, as if Gould was shocked out of a torpor.
Of course, these pools of activity in the deep waters reemerge multiple times and the arguments are only very subtle twists on the general objections. Gould feels that the gene-centered view of Dawkins and the Oxford tradition of evolutionary biology which goes back to R. A. Fisher is exceedingly simple; he objects to the assumption that evolutionary can properly be modeled as the additive substitution of alleles on single loci against a genetic background. The Fisherian tradition assumes that nature works by the “least-squares principle,” and Fisher himself aspired to a model of evolutionary genetics which mimicked the deterministic inevitability of thermodynamics. Gould will have none of this, and denies flat out that the assumption of additivity is often not appropriate or valid. He contends that emergence of properties among the network of genetic effects are critical, non-linear responses to genetic variation which are only extracted in particular contexts. These arguments ultimately lead back to the disputes between R. A. Fisher and Sewall Wright as the power of selection to optimize fitness in populations. While Fisher had a rather elegant but simple model in mind of large populations scaling single peaks in a landscape of spare topography, Wright contended that nature was truly characterized by rugged adaptive landscapes where gene-gene interaction and drift operated as essential parameters within and across subpopulations. Gould agrees with Wright, and in fact he suggests that Wright deemphasized the role of stochasticity in his model as the Modern Neo-Darwinian Synthesis crystallized to conform to the orthodoxy as promoted by Ernst Mayr.

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America's mixed-race Vice President

By Razib Khan | July 9, 2008 6:38 pm

charlescurtis.jpgMost Americans are not aware that Herbert Hoover’s Vice President, Charles Curtis, was 3/8 Native American and spent time on the Kaw reservation as a youth. He was also a Kansan. NPR has a piece up which looks back at this historical footnote.


Which demographics know science?

By Razib Khan | July 9, 2008 2:15 am

The always fascinating Inductivist takes a look at science comprehension of Americans via the GSS. Here’s his methodology:

In 2006 the General Social Survey asked 437 respondents eleven basic science questions. The first one, for example, was whether the earth’s center is hot. I gave each person one point for answering a question correctly, and then summed the scores. My next step was to convert these totals so they resemble IQ scores. I set the white mean at 100, and the standard deviation at 15. Here are some averages:

Since we know the standard deviation I decided that it might be interesting to take the numbers he generated and convert them into standard deviation units, and display them on one single chart in a comparative manner.

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By Razib Khan | July 8, 2008 12:17 am

merc_span_600.jpgFlyby of Mercury Answers Some Old Questions:

Mercury, the smallest planet, bakes in the heat of the Sun, but it has water in some form. It has volcanoes. It appears to have an active magnetic field generated by a molten iron core. And it has shrunk more than scientists thought.


Timelessness of the classics

By Razib Khan | July 7, 2008 5:20 pm

Most of you who read this weblog know that one of my primary preoccupations is how to invest my marginal time in terms of reading to optimize whatever it is I want to optimize (i.e., to “know stuff”). Life is short. So I recently began reflecting on the choices I make in terms of reading “classics,” and how great thinkers of the past are remembered. Euclid’s Elements for example is still relevant today. Arguably the most successful textbook in the history of the world its usage is obviated by the integration of many of its insights into mathematics as a whole. I know many people who go to the Dover Books website and stock up on a host of out of date texts on math…but the reality is that with math nothing is every really “out of date” unless you’re a mathematician or mathematical physicist. Most modern biologists have little fluency with math beyond calculus, a technique deriving from the period of the late 17th century. A given field of math may not be useful to you, but it is not wrong as such because of the passage of time.

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Who doesn't like Genetically Modified Organisms?

By Razib Khan | July 6, 2008 4:10 pm

I was looking at poll results for Genetically Modified Organisms (GMO). Internationally the results are all over the place, but within nations the data suggest a pretty strong notional resistance to “playing God,” with a rank order of aversion spanning plants (least averse) to humans (most averse). There is some mild positive correlation between education and trust/acceptance of GMOs, and also some between irreligion and attitudes towards cloning and such for animals. The The Pew Initiative On Food And Biotechnology has some good data. For example:

Religious attendance also has a significant effect on comfort with animal cloning, with less religious Americans expressing greater comfort and more religious Americans harboring greater reservations. Nearly one third (30%) of those who attend religious services a few times a year or less are comfortable with animal cloning and just 54% are uncomfortable; those who attend once a month exhibit somewhat less comfort, at 21%, and great discomfort, at 64%; among somewhat frequent churchgoers, just 12% are comfortable while 76% are uncomfortable; and among weekly church attendees, 17% are comfortable with cloning and 70% are uncomfortable.

Note that though the less religious are more comfortable they are mostly still uncomfortable. Additionally, there seems to be a consistent pattern where women are more suspicious of GMOs than men:
But it gets far more interesting when you look at international data. Check out this figure from Public Attitudes towards Agricultural Biotechnology:

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Fundamentalism is bad for your health?

By Razib Khan | July 5, 2008 7:13 pm

This is a follow up to the post yesterday, Religion is good for your health? Conservative Christianity bad?. I finished reading the paper. It’s not a bad one really, but its plausibility will be strongly conditioned by theoretical priors. It is a work in the tradition of Emile Durkheim, and attempts to resurrect a functionalist conception of religious denominations, David Sloan Wilson is smiling somewhere…. The authors posit that the other-worldly orientation of Fundamentalist and Pentecostal denominations results in a host of social dynamics which increase mortality rates. In contrast, they contend that the this-worldly orientation of Mainline and Catholic denominations results in a more communitarian public spirit which generates positive externalities within a society. They don’t use the the term externality. In the paper they seem intent on carving out a non-economical space for their analysis, but that’s basically what they’re talking about. Mainline Protestantism and Catholicism focus on public social justice in a manner which injects capital into the community as a whole irrespective of sect. Fundamentalist and Pentecostal churches on the other hand are focused on their own narrow church-life and rather disengaged from collective public action which might produce communal capital (this shows up in the nature of mission-work, while Mainline and Catholic activities being more strongly geared toward education and health as opposed to just converting). An individual illustration of this might be James G. Watt, Reagan’s Secretary of the Interior, and a Pentecostal, who reputedly had little interest in being a steward of the land due to his belief that the End Times were approaching and environmentalism was ultimately in vain.

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