The day has come! Dr. Daniel MacArthur has finally gotten the stamp of approval from Tobias MacArthur, and Genetic Future is over at Wired, with all their other great science blogs. Since it can sometimes be a bit difficult to figure out where these diamonds-in-the-rough are in the bramble that is the Wired website, I recommend everyone switch to the new new RSS pronto. Oh, and lest anyone wonder about Wired‘s beefing up of their predominantly white male lineup, Dr. MacArthur and I are distant paternal kin. I’m sure you can connect the dots on the appropriate syllogisms.
Month: January 2011
Introducing the Harappa Ancestry Project
A few weeks ago I hinted at a South Asian equivalent to Dodecad & Eurogenes BGA. It is now public and in the data collection phase. You can read the whole thing here:
http://www.zackvision.com/weblog/2011/01/harappa-ancestry-project
This is the feed:
http://www.zackvision.com/feed/
If your ancestry is from these nations:
- Afghanistan
- Bangladesh
- Bhutan
- Burma
- India
- Iran
- Maldives
- Nepal
- Pakistan
- Sri Lanka
- Tibet
Read on! If not, “for entertainment purposes only”….
Synthetic associations and all that
PLoS Biology has four items of great interest out today:
– Synthetic Associations Created by Rare Variants Do Not Explain Most GWAS Results
– Synthetic Associations Are Unlikely to Account for Many Common Disease Genome-Wide Association Signals
– The Importance of Synthetic Associations Will Only Be Resolved Empirically
– Common Disease: Are Causative Alleles Common or Rare?
These are a response to last year’s paper on synthetic associations from the Goldstein lab. Here’s a critique of that that paper. I plan on reviewing the first in the list above soon. #3 is a response to #1 and #2 from David Goldstein, while #4 is a summation more aimed at the general audience.
ADMIXTURE vs. MDS, visualization is just visualization
Dienekes did another run of his data with K = 64. He posted a huge plot with the two largest dimensions of variation. He also posted an accompanying spreadsheet with the coordinates of where the Dodecad samples were. So I found my own position pretty quickly. Before going to that, I thought I’d repost a comparison between myself, the HapMap Gujaratis, the North Kannadi sample, and the HGDP Uygurs. This is at K = 10 in ADMIXTURE from Dodecad.
OK, with that in mind, here’s the full MDS with the two largest components of genetic variation. I’ve added large labels. Also, click the image for a larger file so you can read the small labels.
Knowing without knowing: what tune deafness and face blindness have in common
I have a new post over on the Scientific American Mind Matters website. It describes new research which suggests that tune deafness and face blindness – two examples of conditions known as agnosias, both of which can be genetic – are caused not by a failure of the brain to recognise previously seen faces or detect incongruous musical notes, but a failure to communicate these events to frontal brain regions where conscious awareness is triggered. In essence, your brain knows something but can’t tell you. Read more…
The "science diet"
Cell has an interesting piece, profiling four diets, Cell Culture: New Year’s Diets. I know many of the readers of this weblog take an interest in this area. In particular, many subscribe to the Paleo diet or are avid fans of Gary Taubes’ Good Calories, Bad Calories, as well as Art Devany’s ideas. Personally I think one issue which we need to acknowledge more are individual differences. The returns on the margin for a given diet may differ from person to person. The morbidity cost to someone with a family history of type 2 diabetes who has a weakness for dessert is likely much higher than someone without such a family history.
The Cell article gives a scientific overview of the diets in question, and then has pointers to the scientific literature.
Around the Web – January 18th, 2011
Yes, The Singularity is the Biggest Threat to Humanity.
Imitation and Social Cognition in Humans and Chimpanzees (I): Imitation, Overimitation, and Conformity. Doesn’t fall into the trap of either/or, where chimpanzees are qualitatively different from humans in too stark of a manner, or simply quantitatively different in an implausible fashion.
Emulation, Simulation, and the Human Brain. Tim B Lee is skeptical of whole brain emulation.
Borderless Economy, Jobless Prosperity. The real issue is whether the nation-state matters in any deep way as anything more than an organizational convenience and semantic convention. I would say it does. Many globalists would disagree.
Introducing the Harappa Ancestry Project
A few weeks ago I hinted at a South Asian equivalent to Dodecad & Eurogenes BGA. It is now public and in the data collection phase. You can read the whole thing here:
http://www.zackvision.com/weblog/2011/01/harappa-ancestry-project
This is the feed:
http://www.zackvision.com/feed/
If your ancestry is from these nations:
- Afghanistan
- Bangladesh
- Bhutan
- Burma
- India
- Iran
- Maldives
- Nepal
- Pakistan
- Sri Lanka
- Tibet
Read on! If not, “for entertainment purposes only”….
The Assyrians and Jews: 3,000 years of common history
[5] Then the king of Assyria came up throughout all the land, and went up to Samaria, and besieged it three years.
[6] In the ninth year of Hoshea the king of Assyria took Samaria, and carried Israel away into Assyria, and placed them in Halah and in Habor by the river of Gozan, and in the cities of the Medes.
…
[18] Therefore the LORD was very angry with Israel, and removed them out of his sight: there was none left but the tribe of Judah only.
Most Americans are aware of the term “Assyria,” if they are, through the Bible. The above quotation is of some interest because it alludes to the scattering of the ten northern tribes of Israel during their conquest and assimilation into the Neo-Assyrian Empire. Neo because the Assyrian polity, based around a cluster of cities in the upper Tigris valley in northern Mesopotamia, pre-dates what is described in the Hebrew Bible by nearly 1,000 years. During the first half of the first millennium before Christ they were arguably the most antique society with a coherent self-conception still flourishing aside from their Babylonian cousins to the south and the Egyptians (other groups like the Hittites who may have been rivals in antiquity had disappeared in the late Bronze Age). The period of the Neo-Assyrian Empire, in particular under Ashurbanipal, was arguably the apogee of the tradition of statecraft which matured during the long simmer of civilization after the invention of literacy and the end of the Bronze Age. The Neo-Assyrian Empire marked the transition from cuneiform to the alphabet, from chariots to cavalry. Assyria’s political evisceration by its vassals and enemies was inevitable, as a agricultural society on the Malthusian margin can squeeze only so much marginal product out of so many for so long. Once social and cultural capital is gone, there’s a “run on the bank,” so to speak.
But the Assyrians are still with us! Baghdad Raids on Alcohol Sellers Stir Fears:
Eight men carrying handguns and steel pipes raided a Christian nongovernmental organization here on Thursday night, grabbing computers, cellphones and documents, and threatening the people inside, according to members of the group.
“They came in and said, ‘You are criminals. This is not your country. Leave immediately,’ ” said Sharif Aso, a board member of the organization, the Ashurbanipal Cultural Association. “They said, ‘This is an Islamic state.’ ”
The intruders wore civilian clothes, said Mr. Aso and others at the organization, but their arrival was preceded by three police vehicles that blocked off the street. He said the men stole his ring and bashed him on the leg with a pistol.
Which nation is the most pro-natalist?
Poking around Google Data Explorer I reacquainted myself with an interesting fact: though the teen birth rate in Bangladesh is greater than that in Pakistan, the total fertility rate is far lower. The disjunction has emerged over the last generation, as Bangladesh’s TFR has dropped much faster than Pakistan’s. To the left you see a scatter plot, which shows teen fertility rates (age 15-19) as a function of total fertility rates. I’ve labeled a few nations, and also added the color coding by region. It is notable that the nations above the trend line seem to be Latin American, while those below are disproportionately Middle Eastern. That means that Latin American nations have higher teen fertility in relation to their total fertility, while Middle Eastern nations have lower teen fertility in relation to their total fertility. Sweden actually has a rather high fertility rate in relation to its teen birth rate. The expectation is generated by world wide patterns, so I thought I’d look more closely at the original data sets from the The World Bank. All the data is from 2008. The teen birth rates are per 1,000 of teens in the age range, with TFR’s are per woman.
My contention is this: those nations with high overall fertility despite low teen fertility rates indicate an ideological or operational pro-natalist cultural stance. That means that mature adult women in marriages are presumably having many children. The high teen fertility rates in Bangladesh vis-a-vis Pakistan is probably simply due to lower aggregate development (Pakistan is still higher up on the HDI ranking, though the gap is closing).
Below are some charts. First, a plot with lines of best fit (as generated by R’s loess function). Then, absolute deviations from the line of best fit as a function of fertility. Also, percentage deviations from the line of best fit as a function of fertility. I provide the weighted trend line, but rely on the unweighted fit for the rest of the charts.