Razib Khan One-stop-shopping for all of my content

August 31, 2011

Don’t count old stock Anglo-America out

Filed under: Data Analysis,Demographics — Razib Khan @ 2:54 pm
One of the things I really hate are unqualified linear projections. They’re so useless most of the time. A science fiction magazine will give you more insight about the future than the United Nations population projection for the year 2100. This is just as much of an issue when it comes to American Census demographic [...]

An attempt at “open science”

Filed under: Open science,Personal genomics — Razib Khan @ 2:09 pm
I was asked by the person who provided me the Tutsi genotype for detailed results. Of course I would do so! So I uploaded the raw csv files to Google Docs. The format and explanation isn’t totally clear, though if you follow my posts you’ll get it. This is for people who want more than [...]

Why Melanesians are blonde resolved?

Filed under: Blonde Melanesians,Human Genetics,Human Genomics,Pigmentation — Razib Khan @ 11:08 am
Sort of and possible. I’ve been talking about this for years, and Greg Cochran points me to an abstract at the human genetics conference referenced earlier. Novel coding variation at TYRP1 explains a large proportion of variance in the hair colour of Solomon Islanders: The Solomon archipelago comprises over 1,000 islands located east of Papua [...]

Survey on personal genomics

Filed under: Genetics,Genomics,Personal genomics,Survey — Razib Khan @ 10:25 am
Just got this email, and I thought I would share with my readers: I’m a biologist from Germany and together with 2 fellow biologists I’m currently working on a project that evaluates the sharing of raw data from DTC-genetic-testing companies like 23andme. I was genotyped myself and have already published the data set on GitHub [...]

Human genetics presentations of interest

Filed under: Human Genetics,Human Genomics,ICHG — Razib Khan @ 10:16 am
Dienekes alerts me to the fact that the International Congress of Human Genetics abstracts are online. I spent an hour using only a few keywords, and came up with a lot. 1) If you have a presentation and think it might interest the readers here, feel free to drop a link in (I will look [...]

“Aryan invasion”

Filed under: Genetics,Indo-Aryans — Razib Khan @ 9:15 am

Estimating a date of mixture of ancestral South Asian populations:

Linguistic and genetic studies have shown that most Indian groups have ancestry from two genetically divergent populations, Ancestral North Indians (ANI) and Ancestral South Indians (ASI). However, the date of mixture still remains unknown. We analyze genome-wide data from about 60 South Asian groups using a newly developed method that utilizes information related to admixture linkage disequilibrium to estimate mixture dates. Our analyses suggest that major ANI-ASI mixture occurred in the ancestors of both northern and southern Indians 1,200-3,500 years ago, overlapping the time when Indo-European languages first began to be spoken in the subcontinent. These results suggest that this formative period of Indian history was accompanied by mixtures between two highly diverged populations, although our results do not rule other, older ANI-ASI admixture events. A cultural shift subsequently led to widespread endogamy, which decreased the rate of additional population mixtures.

I will put a modest amount of money on the proposition that there were at least two admixture events, and that their LD based methods are picking up the second Indo-European one. If it was just one admixture event, then you have to accept the proposition that South Indian tribals are at least ~30% Indo-European in ancestry. Not impossible, but seems unlikely.

India vs. China

Filed under: Economics,India vs. China — Razib Khan @ 8:56 am

India Measures Itself Against a China That Doesn’t Notice:

“Indians are obsessed with China, but the Chinese are paying too little attention to India,” said Minxin Pei, an economist who was born in China and who writes a monthly column for The Indian Express, a national daily newspaper. (No Indian economists are known to have a regular column in mainland Chinese publications.)

Most Chinese are unconcerned with how India is growing and changing, because they prefer to compare their country with the United States and Europe, said Mr. Pei, a professor at Claremont McKenna College near Los Angeles. He says he has tried to organize conferences about India in China but has struggled to find enough Chinese India experts.

Liu Yi, a clothing store owner in Beijing, echoed the sentiments of a dozen Chinese people interviewed in Beijing and Shanghai, in dismissing the idea that the two countries could be compared. Yes, he said India was a “world leader” in information technology but it also had many “backward, undeveloped places.”

“China’s economy is special,” Mr. Liu said. “If China’s development has a model, you could say it’s the U.S. or England.”

The sentiments are real. But the Indian assumption that the difference is the governance style of China is false. It’s the aggregate difference in human capital.

The Indian elites have presided over a situation where their nation is the world capital of cretinism.

August 30, 2011

Tutsi genetics, ii

In my post below, Tutsi probably differ genetically from the Hutu, there were many comments. Some I did not post because they were rude, though they did ask valid questions. I will address those issues, but let me quote one comment:

That’s an interesting possibility, but this admixture run didn’t split the non-hunter-gatherer Africans that well. In one of your previous analyses on East Africa you managed to get a pretty accurate ‘Afro-Asiatic/Cushitic’ and ‘Nilotic’ cluster. Is it possible that you could run this Tutsi sample using the same admixture settings as in the ‘Flavors of Afro-Asiatic’ blog post to see if he carries a significant Nilotic component or is mainly Bantu & Cushitic derived?

So I replicated ADMIXTURE runs for many of the same populations as I did in my post, Flavors of Afro-Asiatic. I also pared down the population set and generated a PCA with EIGENSOFT. Before I get to those results, let me tackle the questions.

1) “Are the Luhya suitable proxies for the Hutus?”

Probably. The reason is that Bantu-speaking populations, from the Congo to South Africa, are surprisingly similar. Not only that, but these populations are very distinctive from groups which are close them ...

Where is the ArXiv for X?

Filed under: ArXiv,Open science,science — Razib Khan @ 12:36 pm

Derek Lowe asks “Why Isn’t There an ArXiv For Chemistry?” Where indeed. A few years ago I went to a talk given by Michael Eisen and asked him about why the biological sciences didn’t have an ArXiv, and one of his explanations was that intellectual property was more of a concern in this area (e.g., pharmaceutical funded research). That sounds plausible enough to me. But the existence of ArXiv still should serve as a starting point for people outside of the physical and mathematical sciences in terms of the possibilities. Much of the discussion around Joe Pickrell’s post ‘Why publish science in peer-reviewed journals?’ seemed to operate in a world where ArXiv didn’t exist. And it’s not just ArXiv, SSRN makes it easy to get papers in social science. We have the technology, and we see the possibilities. There are obstacles, but let’s not pretend as if we don’t have a model for some success.

August 29, 2011

They’re called “peer reviewers”

Filed under: science,South Park — Razib Khan @ 11:06 pm

George Monbiot’s piece, Academic publishers make Murdoch look like a socialist, is making the rounds. This paragraph jumped out at me:

Murdoch pays his journalists and editors, and his companies generate much of the content they use. But the academic publishers get their articles, their peer reviewing (vetting by other researchers) and even much of their editing for free. The material they publish was commissioned and funded not by them but by us, through government research grants and academic stipends. But to see it, we must pay again, and through the nose

It reminded me of this scene from the South Park episode Crack Baby Athletic Association (click):

Crack Baby Athletic AssociationTags: SOUTHPARKEric Cartman,Kyle Broflovski,more…

Analysis of a Tutsi genotype

Filed under: Genetics — Razib Khan @ 10:14 pm

With this post, Tutsi probably differ genetically from the Hutu, I hope to tamp down all the talk about how the Belgians invented the Tutsi-Hutu division. After putting the call out it took 2 months for me to get my hands on a genotype, and less than 24 hours to post some results.

Tutsi probably differ genetically from the Hutu

Paul Kagame with Barack and Michelle Obama

I first heard about Rwanda in the 1980s in relation to Dian Fossey’s work with mountain gorillas. The details around this were tragic enough, but obviously what happened in 1994 washed away the events dramatized in Gorillas in the Mist in terms of their scale and magnitude. That period was a time when the idea of “ancient hatreds” leading to internecine conflict was in the air. It was highlighted by the series of wars in the former Yugoslavia, and the Tutsi-Hutu civil wars in Rwanda, Burundi, and Congo. Of the latter the events in 1994 in Rwanda were only the most prominent and well known.

After having read Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa I am relatively conscious of the broader canvas of what occurred in Central and East Africa in the 1990s. Not only was there a conflict between Tutsi and Hutu in Rwanda, but a similar dynamic also flared up in Burundi. The tensions are more complex in Congo and Uganda, in large ...

Around the Web – August 29th, 2011

Filed under: Blog,Links — Razib Khan @ 1:16 am

Thoughts on the BGI IQ study.

Language Evolves in R, not Python: An apology. Open science is good.

Are Twin Studies “Pretty Much Useless”? One interesting, but unsurprising, aspect of the response to execrable Brian Palmer piece is that several of us in the blogosphere pointed out pretty much the same set of well known findings to refute his weird charges. This isn’t rocket science.

Romney vs. Perry: It’s personal. ‘“I think he had a few exasperating experiences with Perry, and he’s not alone in that,” said one source close to Romney. “I think Mitt thinks Perry is not that bright.”’

Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci. Probably a good idea to study diabetes in the most numerous hper-diabetic population in the world.

North Korea: The Long Coma. I have said many a time that North Korea is the best modern representation of a pre-modern divine monarchy.

Men Are From Mars, Women Like Kindles. I think we need vouchers for males to close the “Kindle gap.”

Working for GiveWell. Holden is a very cool guy, for what it’s worth.

Phylogenetic rate shifts in feeding time ...

August 27, 2011

The liberal religious and astrology

Filed under: Astrology,Data Analysis,GSS — Razib Khan @ 11:51 pm

In the comments below a weird fact came to light: it does not seem that liberal/Democrat reduced skepticism toward astrology vs. conservatives/Republicans can be explained just by a secularization, and therefore diminished Christian orthodoxy. There are two reasons for this. First, on a priori grounds most people are religious, liberals and conservatives. The difference between the religious and irreligious on this issue would have to be rather large, and the different apportionment across ideology to be striking, for it to drive the division which seems so robust. Second, within the results it seems rather clear that the gap between liberals and conservatives is most evident amongst the religious of both! In other words, secular liberals and conservatives tend to agree (and be skeptical) in relation to astrology. While religious conservatives are skeptical of astrology, as one would expect from orthodox conservative Christians, religious liberals are not. The table below shows some results.

Astrology is…. Very scientific Sort of scientific Not at all scientific Protestant Liberal 5 31 64 Conservative 5 18 77 Catholic Liberal 3 35 62 Conservative 6 25 69 No religion Liberal 6 22 72 Conservative 9 31 60 Atheist & agnostic Liberal 7 19 74 Conservative 3 22 75 Believe in higher power Liberal 3 26 71 Conservative 3 31 66 Believe in god sometimes Liberal 1 28 71 Conservative 19 18 63 Believe in god with doubts Liberal 3 29 68 Conservative 3 20 77 Know god exists Liberal 6 35 59 Conservative 6 21 73 Southern Baptist Liberal 11 33 56 Conservative 7 16 77 United Methodist Liberal 4 13 83 Conservative 4 23 73 Episcopal Liberal 4 23 72 Conservative 5 16 80 Bible is Word of God Liberal 8 41 51 Conservative 6 22 72 Bible is Inspired Word of God Liberal 5 28 67 Conservative 5 21 74 Bible is Book of Fables Liberal 3 23 73 Conservative 8 21 71 Humans developed from animals Liberal 4 25 71 Conservative 8 25 67 Humans did not develop from animals Liberal 7 37 56 Conservative 5 16 79

Observe the huge ...

Beware of scientific revolutions!

Filed under: Behavior Genetics,twin studies — Razib Khan @ 11:15 pm

Above is the Ngram result for paradigm shift, a ubiquitous descriptive concept which can be quite slippery when applied to contemporary science. For example, every few years there is always a new “revolution” which is going to overturn “Darwinism.” Be it punctuated equilibrium, symbiogenesis, or epigenetics. But over time revolutionary fervor abates, and the orthodoxy remains standing, albeit with modifications and alterations, making it all the more robust.

I thought of this when I saw Andrea Cantor’s comment below in relation to twin studies:

Twin studies underestimate heritability only if you subscribe to the crude notion that the effect of genes is additive, i.e., keeping “environments” the same, the more similar two people are genetically the more alike they will be. This ignores everything we now know about the way genes work.

Genes are not self-activating: they do not turn themselves on and produce traits. Genes do not, in fact, produce anything. Genes are turned on and off by the epigenome in response to environmental inputs. If you are inclined to doubt this, then consider: If all the cells in our body are supposed to contain identical ...

August 26, 2011

Republicans more skeptical of astrology than Democrats

Filed under: Astrology,Data Analysis,GSS — Razib Khan @ 9:30 pm

Someone on twitter was curious about GOP attitudes toward astrology. I left the party breakdown out of the previous post because ideology accounts for most party differences. In other words, conservatives are more skeptical of astrology than liberals, and Republicans more than Democrats, but the second result just seems to emerge from the Republican’s greater conservatism.

Astrology very scientific Astrology somewhat scientific Astrology not scientific Strong Democrat 6 31 63 Democrat 7 30 63 Lean Democrat 4 28 67 Independent 7 37 57 Lean Republican 3 26 71 Republican 4 21 75 Strong Republican 4 20 76

Why are independents so gullible? It probably has to do with their lower average intelligence (this goes for moderates too). So I simply limited the sample to those with at least bachelor’s degrees to control for intelligence:

Limited to those with college degrees or more Astrology very scientific Astrology somewhat scientific Astrology not scientific Strong Democrat 3 21 76 Democrat 4 17 79 Lean Democrat 2 21 78 Independent 4 22 75 Lean Republican 1 9 90 Republican 0 11 88 Strong Republican 1 10 89

The distinctiveness of independents diminishes somewhat, but Democrats with college degrees or more remain more gullible than Republicans with the same (the difference remains if you control for sex by the way).

Slate, science, and Brian Palmer

I’m still scratching my head over the rather atrocious Brian Palmer piece in Slate, Double Inanity: Twin studies are pretty much useless. It’s of a quality which would make it appropriate for WorldNetDaily. Here are the responses of Jason Collins, Daniel MacArthur, and Alex Tabarrok. The comments at Slate were rather scathing too. I observed over at Genomes Unzipped that many of the assertions in the piece were in the “not even wrong/what does that even mean?” class. Palmer is apparently a freelancer at Slate, and they’re doing a bunch of stories on twins this week. I wonder if they just sent him the assignment with instructions on the slant, and he took it a little too far. Even if it was a polemic it was a shoddy and embarrassing one. My main concern is that many people perceive Slate to be an organ which publishes “smart” and well researched pieces, and they’ll take Palmer’s screed at face value.

The scientific problems with the article are legion. But still: how does something like this get published in a relatively high-end publication? Brian Palmer has editors presumably. If the copy was an undergraduate paper the prose would be ...

The less intelligent more likely to accept astrology as scientific

Filed under: Astrology,GSS,Social Science — Razib Khan @ 12:00 am

Over at Culture of Science Sheril Kirshenbaum posts a figure from the NSF displaying what proportion of those without high school educations and those with college educations accept the scientific status of astrology. It’s pretty clear to me that this is the ASTROSCI variable from the General Social Survey. It asks:

Would you say that astrology is very scientific, sort of scientific, or not at all scientific?

It’s also nice that this question was only asked in the latter half of the 2000s. So it’s timely in terms of demographic breakdowns. Speaking of which, here are a whole host of classes and their attitudes toward astrology’s scientific status:

Very scientific Sort of scientific Not at all scientific Male 5 26 69 Female 5 30 65 Age 18-34 8 34 58 Age 35-64 4 26 70 Age 65- 4 24 72 White 4 25 72 Black 11 38 51 Hispanic 8 40 51 Extreme liberal 7 31 62 Liberal 5 30 65 Slightly iberal 4 28 68 Moderate 5 34 61 Slightly conservative 5 25 70 Conservative 6 19 75 Extreme conservative 6 18 76 No high school diploma 9 41 50 High school diploma 7 32 62 Junior college 4 28 68 Bachelor 2 17 80 Graduate degree 1 13 85 Atheist and agnostic 6 23 71 Higher power 4 28 68 Believes in god sometimes 7 24 70 Believe in god, but with doubts 4 27 69 Know god exists 6 30 65 Protestant 5 27 68 Catholic 5 31 64 Jewish 6 16 78 No religion 7 28 65 Bible word of god 6 31 64 Bible inspired word of god 5 28 67 Bible book of fables 6 25 70 Human beings developed from animals 6 28 66 Human beings don’t develop from animals 5 26 69

But what about intelligence? To look at that I used the WORDSUM variable, which is a 10-question vocabulary test which has a 0.70 correlation with IQ. Below are the attitudes toward astrology by WORDSUM score (0 = 0 ...

August 25, 2011

Friday Fluff – August 26th, 2011

Filed under: Blog,Friday Fluff — Razib Khan @ 11:20 pm


1) Post from the past: Men at work: hoes, ploughs, and steel.

2) Weird search query of the week: “neanderthal human hybrid.” Do they have someone in mind?

3) Comment of the week, in response to Twin studies are not useless:

Brian Palmer’s identical twin … is a moron.

4) And finally, your weekly fluff fix:

Deleterious drag as a side effect of adaptation

The Pith: Evolution is a sloppy artist. Upon the focal zone of creative energy adaptation can sculpt with precision, but on the margins of the genetic landscape frightening phenomena may erupt due to inattention. In other words, there are often downsides to adaptation.

A few weeks ago I reviewed a paper which suggests that Crohn’s disease may be a side effect of a selective sweep. The sweep itself was possibly driven by adaptation to nutrient deficiencies incurred by European farmers switching to a grain based diet. The reason for this is a contingent genomic reality: the positively selected genetic variant was flanked by a Crohn’s disease risk allele. The increment of fitness gain of the former happens to have been greater than the decrement entailed by the latter, resulting in the simultaneous increase in the frequency of both the fit and unfit variants. You can’t always have one without the other.

But that’s just focusing on one gene, though the authors did indicate that this may be a genome-wide feature. A new paper in PLoS Genetics argues that that is the case, at least to some extent. Evidence for Hitchhiking of Deleterious Mutations within the Human Genome:

Deleterious mutations reduce ...

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