Archive for September, 2007

Neandertals in Siberia & Central Asia

By Razib Khan | September 30, 2007 2:06 pm

I don’t know if we should believe Svante Pääbo anymore, but his lab has some new findings re: Neandertal mtDNA:

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Good in the name of God

By Razib Khan | September 30, 2007 10:28 am

Thich_Quang_Duc_-_Self_Immolation.jpgI have to say, this Ian Buruma op-ed, Religion as a force for good, read my mind in relation to the events of the past few days. Another rebellion civil society against an autocracy coalescing around the predominant religion of a society. What’s surprising? The Iranian revolution against the Shah, the Christian led protests against the dictatorship of Syngman Rhee (himself a Christian) in South Korea, Buddhist protests against the persecution of the government of Ngo Dinh Diem in South Vietnam, the role of liberation theology across Latin America. The list goes on. Of course, religion has also been implicated in horror, and given the imprimatur of godliness to abomination, whether the accusation was infidel, apostate, takfir or heathen.

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Carl Zimmer on

By Razib Khan | September 29, 2007 1:41 pm

Carl Zimmer is on


Atheists still more hated than Mormons & Muslims

By Razib Khan | September 29, 2007 11:44 am

Pew has a new survey out, Public Expresses Mixed Views of Islam, Mormonism. The table to the left summarizes the most important points in the survey: Americans dislike Islam somewhat more than Mormonism, and they think Mormonism is a pretty weird religion (and on the whole, barely Christian). And of course atheists are the gold-standard in terms of being disliked. There are a few points which I think are important to keep in mind. First, many Americans have vague understandings of their own religion, asking them about Mormonism or Islam is pretty humorous. What you’re gauging here are vague impressions and reflections of the Zeitgeist; not well thought out opinions. Second, as I’ve been saying for a while one of Mitt Romney’s major problems is that he is running as a Republican whose target constituency is the segment which has the most inbuilt hostility toward his religion. In other words, Mitt probably has more general election appeal than he does within the primaries. Third, asking about Pope Benedict seems really a stretch, I don’t think most Americans are keeping track of the goings on in the Vatican. I do keep track of these surveys; I’m a data fiend, what can I say? Yet despite that sometimes I look at the questions and imagine the average respondent, and wonder if the Memos at Pew are titled “So what are we going to ask stupid people this month?”


Important papers on recent human evolution

By Razib Khan | September 29, 2007 4:08 am

This post is more of a personal note…here are three papers that are really cool must reads:
Williamson SH, Hubisz MJ, Clark AG, Payseur BA, Bustamante CD, et al. (2007) Localizing Recent Adaptive Evolution in the Human Genome. PLoS Genet 3(6): e90 doi:10.1371/journal.pgen.0030090
Voight BF, Kudaravalli S, Wen X, Pritchard JK (2006) A Map of Recent Positive Selection in the Human Genome. PLoS Biol 4(3): e72 doi:10.1371/journal.pbio.0040072
Tang K, Thornton KR, Stoneking M (2007) A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome. PLoS Biol 5(7): e171 doi:10.1371/journal.pbio.0050171
E.T. Wang, G. Kodama, P. Baldi, R.K. Moyzis, Global landscape of recent inferred Darwinian selection for Homo sapiens, Proc. Natl. Acad. Sci. USA 103, 135-140 (2006). doi:10.1073/pnas.0509691102
All 4 papers are Open Access! The statistical & computational techniques can be hard to follow sometimes, but these HapMap datasets are the tip of the iceberg, so get comfy and start learning if you want to be able to follow the blow-by-blow over the next few years….
P.S.: If you dig flies, read Evolgen.



By Razib Khan | September 28, 2007 2:47 pm

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How the human species kept it together (?)

By Razib Khan | September 28, 2007 10:29 am

Yesterday I put up a post where I attempted to use a visual analogy for what I believe might be evolutionary forces operative over short periods of time that result in phenotypic diversification across populations with recent common ancestry. But what about the flip side? In the case yesterday the basic genetic substratum, the preponderance of the genome, was not subject to powerful diversifying forces because only drift was presumably operating over short periods of time. It was on selectively salient slices of the genome where differences came into sharp focus quickly. But there is an inverted process which may also occur: divergence on the neutral genome due to low migration which nonetheless is overlain by “species” wide selective sweeps of alleles of large phenotypic effect. In other words, where before the face was different but the flesh fundamentally the same, now we are considering a situation where the flesh is very different but the face remains invariant.

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How the human races got their stripes

By Razib Khan | September 27, 2007 5:53 pm

In my post The new races of man I tried to offer a verbal exposition of my current thinking as to how and why human physical variation shows the patterns we see around us. In short, I believe that powerful selective forces have reshaped a subset of the human genome in similar and different ways across a range of populations over the past 10,000 years. Empirically, I would predict that the physical appearance we denote as stereotypically “Chinese” or “Swedish” or “West African” might be rather recent ecotypes, adapted to new circumstances, both environmental and cultural. The types we see are simply a collection of correlations of salient phenotypic featuers (e.g., skin color, nasal form) which are the outcomes of selection driving evolutionary change on a small set of loci in the recent human past. But a great proportion of the genome might be relatively unaffected. And I believe this proportion is what we generally look toward to ascertain the phylogenetic characteristics of a population (generally you examine selectively neutral genes assuming that their evolution has proceeded via a constant molecular clock). Therefore, their may be a discordance between what a small number of recently selected alleles and their salient phenotypic outcomes may imply, and what the total genome content suggests.
Below the fold is my attempt to illustrate all that with a simple schematic representation.

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Bangladesh not most corrupt!

By Razib Khan | September 26, 2007 2:49 pm

cpi_2007_map.gifHere are the rankings for this year according to Transparency International.


A post-Christian America?

By Razib Khan | September 26, 2007 9:49 am

Regular readers know that I often check in on the results from The Barna Group, an evangelical Christian polling outfit. On the one hand I think The Barna Group tends to be a bit alarmist (they have a very narrow definition for a “Biblically based Christian,” e.g., Catholics don’t count), but on the other hand you can be sure that they aren’t going to be pushing atheist wishful thinking. So I was really interested when I saw that a new study had come out, A New Generation Expresses its Skepticism and Frustration with Christianity. In short, the authors find that a growing number of young adults are unaffiliated with Christianity, and many are downright hostile toward the religion. The authors are at pains to point that this is not “just a phase,” a far smaller proportion of Baby Boomers at the same age were religiously skeptical.

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Video of little "Michael Jackson"

By Razib Khan | September 25, 2007 4:16 pm

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Why care about species extinctions?

By Razib Khan | September 24, 2007 3:02 pm

The New Republic has a piece titled The Greatest Dying by Jerry Coyne & Hopi E. Hoekstra (see below the fold for how to read it for free if you don’t have a TNR subscription). The piece covers the a) general parameters of the mass extinction and b) the reasons why we should care. Coyne and Hoekstra immediately start out making the humanistic utilitarian case, i.e., “How does this help humanity be healthy, wealthy and secure?” But, they proceed to add near the end:

Our arguments so far have tacitly assumed that species are worth saving only in proportion to their economic value and their effects on our quality of life, an attitude that is strongly ingrained, especially in Americans. That is why conservationists always base their case on an economic calculus. But we biologists know in our hearts that there are deeper and equally compelling reasons to worry about the loss of biodiversity: namely, simple morality and intellectual values that transcend pecuniary interests. What, for example, gives us the right to destroy other creatures? And what could be more thrilling than looking around us, seeing that we are surrounded by our evolutionary cousins, and realizing that we all got here by the same simple process of natural selection? To biologists, and potentially everyone else, apprehending the genetic kinship and common origin of all species is a spiritual experience– not necessarily religious, but spiritual nonetheless, for it stirs the soul.

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One RNA to bind them all?

By Razib Khan | September 24, 2007 8:27 am

The Boston Globe has a long piece titled DNA unraveled. With the subtitle like “A ‘scientific revolution’ is taking place, as researchers explore the genomic jungle” you know what to except, lots of adjectives and a healthy dollop of hyperbole. I guess I lean toward the side of the conservatives in the article, but ultimately it doesn’t matter, nature always has the last laugh.
Update: Eye on DNA has a more thorough comment on this article and many others in the latest round up. Always worth checking out!


Liberals and low IQ believe in astrology more

By Razib Khan | September 22, 2007 5:17 pm

The Inducivist is always digging into the GSS and coming back with interesting stuff. For example, he reports:
Percent who believe astrology is very or sort of scientific
43.3% Extremely liberal
32.2% Liberal
31.4% Slightly liberal
25.9% Moderate
25.9% Slightly conservative
26.1% Conservative
25.0% Extremely conservative

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Why do you have blue eyes?

By Razib Khan | September 22, 2007 4:30 pm

Well, you may not have blue eyes, but many people do. The post below suggests that there is still a lot of confusion on how eye color is inherited, but now in 2007 we are coming close to clearing up many issues. A paper which came out early this year, A Three-Single-Nucleotide Polymorphism Haplotype in Intron 1 of OCA2 Explains Most Human Eye-Color Variation (Open Access), suggests that about 3/4 of the eye color variation in Europeans (from pale blue to dark brown) can be explained by polymorphism around the OCA2 gene. In other words, eye color comes close to being a monogenic Mendelian trait when it comes to inheritance, but not quite.

The diagram below is probably close to what you learned in high school:

Standard Model Brown heterozygote parent
Blue Brown
Brown heterozygote parent Blue Blue Blue
(Blue phenotype)
Blue Brown
(Brown phenotype)
Brown Blue Brown
(Brown phenotype)
Brown Brown
(Brown phenotype)

In this model the expression of blue eyes is recessive, you need two copies. Heterozygotes, those who carry one copy of each allele, express brown eyes but can have blue eyed offspring. Blue eyed people can only have blue eyed offspring because they have to be homozygotes, carry two copies. A physiological explanation also offers itself up in this case, the blue eye allele is simply a copy which has lost function and results in the lack of production of melanin in the iris. The brown eye allele on the other hand functions normally. Even if only one copy is functioning to produce melanin, that is enough in terms of dosage to produce a brown coloration. Only with two copies which are non-functioning is there a total loss of melanin in the iris.

Reality is more complex. The diagram below is adapted from the paper referenced above. I’ve limited the data to those where the number of individuals in their sample was greater than 10, and those combinations where a proportion of individuals expressed blue eyes. For ease of inspection I’ve continued to color code the genetic variation. Instead of a single clearly defined gene with two alleles, that is, two genetic variants on a well defined physical location, the diagram below illustrates the combinations of two haplotypes, termed diplotypes. This is important because there is possibly no one blue eye gene responsible for all the variation, rather, a host of tightly linked loci may operate as a sort of genetic network. In any case, I have colored the haplotypes so as to show their preponderant average effect.

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Correlation structure of traits

By Razib Khan | September 21, 2007 11:40 am

kathsheryl.jpgDo any readers know of work which tracks the correlation between characteristics such as blonde hair and blue eyes (within population where these are extant at high frequencies, but not fixed)? I am also interested in geographic distributions. In part I’m interested in exotic combinations, for example, look below the fold….

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One Belgium, two nations

By Razib Khan | September 21, 2007 2:49 am

Apropos of my post yesterday urging lack of sentimentality regarding the extinction of languages check out this article about Flemish separatism in Belgium. The salient bits:

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A tour of MHC

By Razib Khan | September 20, 2007 3:23 pm

I’ve talked about MHC a fair amount, mostly because of its evolutionary significance, so if you are interested in the topic Mystery Rays for Outer Space is starting a series ion the topic. Check out the first post. Also, PLOS Genetics has a new paper on MHC.


Flores Hobbits real deal with wrists

By Razib Khan | September 20, 2007 2:43 pm

Remember those funny little Flores Hobbits? Carl Zimmer has followed the story like a master tracker over the years. In any case, Wrist bones bolster hobbit status:

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Extinction of a language: cry or rejoice?

By Razib Khan | September 19, 2007 9:59 pm

There is an article in The New York Times which focuses on the fact that many languages are going extinct as native speakers die. Here is the critical issue:

In a teleconference with reporters yesterday, K. David Harrison, an associate professor of linguistics at Swarthmore, said that more than half the languages had no written form and were “vulnerable to loss and being forgotten.” Their loss leaves no dictionary, no text, no record of the accumulated knowledge and history of a vanished culture.

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Gene Expression

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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