Archive for August, 2010

The past in color

By Razib Khan | August 26, 2010 1:11 am

I don’t know about you, but I have a weird mental problem whereby my visual model of the past is strongly shaped by the constraints on the various representational modes which preserve images from a particular era. For example, the paintings of the 18th century shape how I imagine the 18th century, while the black and white photos of the early 20th century tend to drain color out of that period from my mind’s eye. So it’s always of interest to me when extremely old color photographs are discovered. A reminder to my subconscious that the past looked just like the present in many ways. But this set from The Boston Globe are so good that it’s mind blowing. All the images are from between 1909 and 1912, and within the boundaries of the Russian Empire.

Here’s a sample:

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Inbreeding in the Persian Gulf

By Razib Khan | August 25, 2010 5:01 pm

On the heels of my post on cousin marriage, I thought readers might find this article on genetic screening in the United Arab Emirates of interest. One way to tackle the problem of genetic diseases which emerge out of consanguineous unions apparently isn’t to discourage the unions themselves, but dodge the outcomes. So pre-implantation screening of eggs as well as selective abortion of fetuses both seem to be options being evaluated. Aside from the costs, especially in the former case (though abortions are not without risk, and the initial stages of pregnancy are an investment of time as well), I still think there are long term problems with this. But first, Alan Bittles (who produced the map in the previous post) points to a major shortfall of a simple do-not-marry-cousins heuristic in this case:

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CATEGORIZED UNDER: Culture, Genetics
MORE ABOUT: Culture, Inbreeding

E. O. Wilson against Hamiltonian inclusive fitness

By Razib Khan | August 25, 2010 3:27 pm

There is a new paper in Nature which is a full frontal attack on the utility of William D. Hamilton’s inclusive fitness framework in explaining eusociality. Martin A. Nowak, Corina E. Tarnita, & Edward O. Wilson are the authors. Wilson is famous in large part for his authorship of Sociobiology: The New Synthesis, and is arguably the doyen of American organismic biology. He is both an active scientist, and, a premier public intellectual. So with that in mind, I notice that Dienekes Pontikos alludes to “E.O. Wilson’s change of mind about group selection.” This is conventional wisdom, but it is I think wrong (though from what I can tell Wilson has not done much to disabuse the press of the notion). In Defenders of the Truth Ullica Segerstrale notes that Wilson did not expunge group selection thinking even in Sociobiology. In Evolution for Everyone David Sloan Wilson recounts that it was in fact E. O. Wilson who pointed out a group selective interpretation of data he was presenting at a conference, helping to push him early on in a rather unfashionable direction. From what I have heard Wilson always believed that the empirical data was not adequately explained by a pure inclusive fitness model, and simply waited until things shook out before pushing back with more theoretically trained colleagues who had the same skepticism.

From page 30 of Sociobiology:

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CATEGORIZED UNDER: Biology, Evolution, Genetics

Daily Data Dump – Wednesday

By Razib Khan | August 25, 2010 10:44 am

Welcome (and Welcome Back) to FiveThirtyEight. Nate Silver moves to The New York Times. Now if only we could get rid of those stupid made up “trend stories.”

Image of inflation adjusted home prices 1890-2006. Crazy! Classic case of a bubble, but it really hasn’t popped. And the government will try and make sure it doesn’t.

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Across North American borders

By Razib Khan | August 25, 2010 10:11 am

There is a border across which fertility drops by a factor of two in North America (defined as from Canada to Panama). Specifically, one nation has a TFR of ~4, and the other ~2. Can you guess the two nations? You can find the answer in the charts below.

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CATEGORIZED UNDER: Culture, Data Analysis

The individual & social risks of cousin marriage

By Razib Khan | August 25, 2010 4:04 am


The map above shows the distribution of consanguineous marriages. As you can see there’s a fair amount of cross-cultural variation. In the United States there’s a stereotype of cousin marriage being the practice of backward hillbillies or royalty. For typical middle class folk it’s relatively taboo, with different legal regimes by state. The history of cousin marriage in the West has been one of ups & downs. Marriage between close relatives was not unknown in antiquity. The pagan emperor Claudius married his niece Agrippina the Younger, while the Christian emperor Heraclius married his niece Martina. Marriage between cousins were presumably more common. With the rise in the West of the Roman Catholic Church marriages between cousins were officially more constrained. Adam Bellow argues in In Praise of Nepotism: A Natural History that there’s a material explanation for this: the Roman church used its power over the sacrament of marriage to control the aristocracy. Though the church required dispensations for marriages between cousins of even distant degrees of separation, they were routinely given, as was obviously the case among Roman Catholic royal families like the Hapsburgs. But once given the dispensation could be revoked, rendering the marriage null and void. A highly convenient power politically.

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CATEGORIZED UNDER: Culture, Genetics

Decline in forest cover

By Razib Khan | August 24, 2010 12:29 pm

I’ve spent most of my life in relatively forested areas, and took forestry courses in secondary school (which is why I can still distinguish doug fir from spruce by looking at the needles). In my youth I even had friends who were loggers during the summer. But I haven’t taken a deep scientific interest in forests for a long time. So I decided to look at the Google public data set to get a sense of long term trends.

As you can see, there hasn’t been much of an aggregate decline in forests. How about the nations with a lot of forest cover?

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MORE ABOUT: Environment, Forests

Daily Data Dump – Tuesday

By Razib Khan | August 24, 2010 11:20 am

Glenn Beck Wrong on Darwin: How Evolution Affirms the Oneness of Humankind. I can see where the individual is coming from, but I think more people should just come out say that evolution is just science, and has no deeper moral implications besides those which humans impute to it. No one cares about the ethical implications of physics, and fundamentally biology is no different. I realize that since it’s closer to the phenomenon of humanity than physics it won’t play out that way, and philosophers and theologians can do with it what they will. But really, if you look at a specific question like cross-racial mating among humans in 1910 and 2010 you learn a lot more about human values of scientists than about the science of human evolution and genetics.

Did Ancient Coffee Houses Lay the Groundwork for Modern Consumerism? ‘Coffee house discourse often challenged the authority of the state and religion and led to changes in the society. “Simultaneously, a new Ottoman consumer, resisting the prescriptions of the state and religion, actively constructing self ethics, and taking part in the formation of the coffeehouse culture, was forming as well.’ OK.

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The non-superstars you don't see

By Razib Khan | August 24, 2010 10:52 am

Jonah Lehrer has a post up on why it might be that top-level athletes seem to come from smaller urban areas rather than larger ones. The possible reason is interesting. But I was reminded of the “10,000 hour rule” made famous by Malcolm Gladwell. You know, how Tiger Woods’ dad “turned him” into a world class athlete from scratch? Even setting aside the elementary question of necessary and sufficient conditions, what about all those kids who invest thousands of hours and don’t “make it” big? I once knew a girl from a large Mormon family, and noticed offhand that she was far shorter than any of her siblings. I inquired as to this fact, wondering if perhaps she was adopted. Her explanation for her small stature (~2 standard deviations below the female norm) was that she was involved in competitive gymnastics up to early adolescence, and that stunted her growth.

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The oldest science blog of all?

By Razib Khan | August 24, 2010 3:16 am

800px-Bristlecone_CAI began blogging in April 2002 (I once had a graduate student approach me and tell me that she was a big fan of my blog back in high school!). Derek Lowe is the only science blogger I can think of off the top of my head who was around before I was, is still around, and has been around continuously across all those years. The mildly unbalanced Dave Appell left the scene to clear his head for a few years. In those early days a term like ‘science blogger’ would have seemed kind of quaint and strange, but I do recall being approached by others to rebut the naive Creationism of some parts of the blogosphere. It was early days, and the big division was between the older cohort of techbloggers who had emerged organically before 9/11, and the political blogosphere which rapidly crystallized in the months after that event.

But in any case, Chad Orzel’s asking straight up, who’s the oldest science blogger? My money is on Derek, but I’m no Bora Zivkovic, so I could be wrong.

Image Credit: Wikimedia

MORE ABOUT: Blogging

Just pushing buttons

By Razib Khan | August 24, 2010 12:05 am

Mike the Mad Biologist, whose bailiwick is the domain of the small, asks in the comments:

I don’t mean to bring up a tangential point to the post, but why does the field of human genetics use PCA to visualize relationships? When I see plots like those shown here that have a ‘geometric pattern’ to them (the sharp right angles; another common pattern is a Y-shape), that tells me that there are lots of samples with zeros for many of the Y-variables (i.e., alleles that are unique to certain populations). Thus, the spatial arrangement of the points is largely an artifact of an inappropriate method: how does one calculate a correlation matrix when many of things one is correlating have values of zero?

If one really was keen on using PCA, one could calculate a pairwise distance matrix and then use that instead of the correlation matrix (Principal Coordinates Analysis).

Since I know some human geneticists do read this weblog, I thought it was worth throwing the question out there.

MORE ABOUT: Analysis, PCA, Tools

Daily Data Dump – Monday

By Razib Khan | August 23, 2010 10:07 am

I hope you had a good weekend.

Why is Israel So Poor? Israel is a nation with a high level of human capital and moderate wealth. The author points out that Israel is a “low trust” society. It is not often remembered that Israel is arguably the most ethnically diverse developed society in the world, because “Jews” get lumped together into one category by outsiders. Additionally, I think Israel’s geopolitical situation is probably an economic drain. Long term uncertainty is probably does not encourage investment. Why not put your capital to use somewhere safer?

Genes May Overpower Diet in Battle of the Bulge. The title is kind of deceptive, the article is much more nuanced, and puts the focus on gene-environment interaction. Precisely, not everyone has the same effect from the same change in diet. This is why I’ve started to get annoyed by my “paleo fundamentalist” friends (I lean paleo myself, but I’m not a purist). Humans vary, including in their response to diets, and what may work for most may not work for all.

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A thousand little adaptive platoons

By Razib Khan | August 23, 2010 4:40 am

adaptive_landscape_labelledLast week I took an intellectual road trip back nearly a century and explored the historical context and scientific logic by which R. A. Fisher definitively fused Mendelian genetics with quantitative evolutionary biology. In the process he helped birth the field of population genetics. While the genetics which we today are more familiar with begins at the biophysical substrate, the DNA molecule, and the phenomena which emerge from its concrete structure, population genetics starts with the abstract concept of the gene. This abstraction and its variants are construed as algebraic quantities from which one can infer a host of dynamics. These are the processes which are the foundations of evolutionary change, as population genetics flows into evolutionary genetics, and ultimately the raw material of natural history.

ResearchBlogging.orgFisher’s accomplishments were a function of both his abilities and his passions. He was a mathematical prodigy, with the ability to distill natural processes down to highly general abstractions. And like many English gentlemen of his age he had a passion for evolutionary biology, and cherished his copy of The Origin Of Species. His ultimate aim was to transform evolutionary biology into a discipline with the same analytical rigor as physical chemistry. But he wasn’t the only major figure on the scene in his era.

Sewall_WrightSewall Wright was an American physiological geneticist with a background in animal breeding. While Fisher was a mathematician who sought to apply his skills to evolutionary biology, Wright was a biologist who taught himself mathematics to further his own understanding of evolutionary processes. The two were in many ways the Yin and the Yang of early population genetics, with their conflicts and disagreements being termed the Wright-Fisher controversies, and the common formal framework which they converged upon becoming the ubiquitous Wright-Fisher model. Wright’s life spanned 99 years, from 1889 to 1988. His biography, both personal and scientific, are explored in rich detail in Will Provine’s Sewall Wright and Evolutionary Biology. Because of the length and breadth of his influence in evolution it’s worth reading just to get a sense of how Wright shaped the Modern Neo-Darwinian Synthesis behind the scenes. Provine seems to indicate that Wright was the primary theoretical influence on Theodosius Dobzhansky,* who mentored a whole generation of evolutionary biologists to come (e.g., Dobzhansky → Lewontin → Coyne).

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CATEGORIZED UNDER: Evolution, Genetics

Genetic variation within Africa (and the world)

By Razib Khan | August 22, 2010 1:16 pm

Last year a paper came out in Science which made a rather large splash, The Genetic Structure and History of Africans and African Americans by Tishkoff et al. Since it’s more than a year old I recommend that those of you curious about the details of the paper and don’t have academic access go through the free registration, as you can then read it in full. Unlike Reich et al. the Science paper didn’t unveil a new method of analysis. It was the standard bread & butter, with PCA’s & STRUCTURE plots & phylogenetic trees. But the coverage of populations within Africa was massive. They had a lot of results and relationships to cover, and ended up with a 100 page supplement.

I commend the whole paper to you. But there are two elements I want to highlight. First, a three dimensional PCA plot. It has the first, second and third principal components of variation. In other words, the three largest independent dimensions in terms of explanatory power of genetic variation. Panel A includes all world populations, and panel B just Africans.

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CATEGORIZED UNDER: Genetics, Genomics

Open thread – August 22, 2010

By Razib Khan | August 22, 2010 12:04 am

I found out this week that the idea of the “Noble Savage” is erroneously attributed to Jean Jacques Rosseau. I haven’t read much Rosseau myself, so I’m familiar with the general shape of his ideas through the filters of later interpreters. But even if I’d consumed the great man’s oeuvre in totality I wonder if the urban myth is so powerful that I’d impute to him the concept anyhow?

Which got me thinking, quite often people in the sciences are unfamiliar with the great works of the past in their primary form. I haven’t read a word of Isaac Newton, but that’s not very important to me because I’ve taken courses which cover mechanics. I only recently read The Origin of Species with any level of understanding, but ultimately much of Charles Darwin’s thinking has become seamlessly interleaved into the body of modern evolutionary biology. In contrast in the humanities the past seems very fresh, and the “readings” of original authors can give one a very distorted impression of the primary source.

MORE ABOUT: Open Thread

"India's" population bomb isn't rocket science

By Razib Khan | August 21, 2010 7:59 pm

The New York Times has a piece up, Defusing India’s Population Time Bomb, which reiterates what I was trying to get at yesterday, India’s demographic problems are localized to particular regions, not the nation as a whole. First, let’s review the world’s population growth & fertility rates:

Now let’s focus on a few nations:

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CATEGORIZED UNDER: Culture, Data Analysis

Desmond Tutu, Spaniards, and genetic distance

By Razib Khan | August 21, 2010 12:35 pm

Since we’ve been talking about Fst a fair amount, I thought it might be nice to put it in some concrete graphical perspective. First, to review Fst in the genetic context measures the proportion of genetic variation which can be attributed to between population differences. To give a “toy” example if you randomly divided the population of a large Swedish village into two groups, and calculated their Fst, it should be ~ 0, because if you randomly select from an unstructured population by definition there shouldn’t be noticeable between population differences. In contrast, if you compare a Swedish village to a Japanese village, a large fraction of the genetic variation is going to be distinct to each population. Around ~10% of the genetic variation in fact will be between the two groups. Many of the genes will be extremely informative, so that if you know the allelic state from a given individual you can predict with a high degree of certitude which population that individual was from (e.g., SLC24A5 and EDAR). A small set of ancestrally informative alleles would produce a sequence of conditional probabilities of extremely high certitude (on the order of 10 genes for these two populations should suffice, perhaps three for “government work”).

But to put this in perspective, and show how genetic variation differs from locale to locale, I though I would compare continental-scale Fst values with that in a small region, southern Africa. The Fst values for the first I obtained from Investigation of the fine structure of European populations with applications to disease association studies, and the second, Complete Khoisan and Bantu genomes from southern Africa. The Bantu in this case is Desmond Tutu, who is from the Xhosa tribe, and has substantial admixture from the non-Bantu populations which were resident in South Africa prior to the arrival of the Bantus.

First, in tabular format:

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CATEGORIZED UNDER: Genetics, Genomics

Star Hustler passes away

By Razib Khan | August 20, 2010 8:18 pm

A little “off topic” for this blog’s core content, but Jack Horkheimer, the “Star Hustler/Star Gazer” passed away today. Here’s vintage 1985:


Daily Data Dump – Friday

By Razib Khan | August 20, 2010 5:26 pm

Have a good weekend.

More Evidence for Hauser’s Scientific Misconduct. Stuff like this keeps bubbling up from anonymous “sources.”

Excessive regulation of DTC genomics will come at a cost. Sometimes the cost is tangible in terms of slower innovation, but sometimes it is straightforward in monetary terms as increased prices to jump through regulatory hurdles. Not that costs aren’t always justified, though in this case I lean toward looser regulation.

Male Menopause Affects More Than Five Million Men.

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MORE ABOUT: Daily Data Dump

India's Deep North

By Razib Khan | August 20, 2010 5:11 pm

In my post Pakistan ~10 years on I alluded to the fact that despite India’s robust economic growth of the past ~15 years or so in the aggregate there is a wide range of state-by-state variation. It is conventional in the media to point out the massive caste/class divisions in India, but because of the lack of familiarity with the geography of that nation there’s less reference to the regional gulfs. But if you look at the state-level data they’re rather large. The total fertility in the northern gangetic states of Uttar Pradesh and Bihar is ~4, while that in the southern states of Kerala and Tamil Nadu is ~2. Uttar Pradesh and Bihar are not trivial states, rather, they’re the two most populous! Additionally, they’re a meaty portion of the South Asian “Cow Belt”, the cultural heart of the subcontinent. The first great historic polities of South Asia, that of the Maurya and Gupta, had their focus in what is today Bihar, while later on the Muslim dynasts famously operated from a base around the region of Delhi in Uttar Pradesh. In the Indian cultural geography these states are the heart of Āryāvarta.

Wikipedia has a set of pages which rank the states of India by various metrics. The tables themselves are illuminating, but for non-Indian readers I thought a series of thematic maps would be better. Additionally, I added one scatterplot.

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CATEGORIZED UNDER: Anthroplogy, Culture, Data Analysis

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This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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