Archive for August, 2010

How August Should Have Ended

By Razib Khan | August 31, 2010 8:02 pm
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Daily Data Dump – Tuesday

By Razib Khan | August 31, 2010 11:05 am

The Democrats’ New Normal. It’s looking real bad. On the other hand, the Dems passed Health Care Reform. What’s the point of being in power if nothing is achieved? I’m sure the Republicans would have lost bigger if they’d passed Social Security Reform, but they would have achieved a big goal of their party.

Guardian science blogs: We aim to entertain, enrage and inform. They don’t have many science blogs. Yet. But I’m sure they’ll add more, and other “big media” outfits will be adding/expanding in the near future.

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The New World in three easy steps

By Razib Khan | August 31, 2010 10:28 am

One aspect of human demographic expansions seems to be the fact that we often model them as a constant diffusion process, when in reality there were likely pulses (economic historians can conceive of this as the periodic gaps between land and labor factor inputs). I don’t know much about the human movements prior to H. sapiens sapiens, and from what I can gather the fossil remains are too sparse to be too wedded to a specific model, but it seems clear that anatomically modern human expansion occurred through a series of rapid outward sweeps which would periodically reach a “natural barrier.” Modern humans reached the Solomon Islands ~30,000 years ago, after which there was stasis for ~25,000 years. Only with the Austronesian expansion did humanity push past the Solomons. And this was no baby-step, ultimately the Austronesians went as far as the Hawaiian islands and Easter Island.

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Science with soul sells

By Razib Khan | August 31, 2010 1:51 am

Vivienne Raper who analyzed the Wikio Top 100 Science Blogs left a comment below:

I’m now curious to find out why there are no ‘popular’ blogs in certain subjects. Do working condensed matter physicists who want to engage with the public write about astrophysics? Or are astrophysicists the only physicists who want to blog for the public? Or does the public only read astrophysics blogs?

675px-CrabNebulaHubbleThe contrast between astrophysics and solid state physics is a clue to what’s going on I think. Solid-state physics is very important work. Like agricultural science solid-state physics may not have all the public glamor, but it puts bread on the table of our civilization. So why all the love for astrophysics? I think part of the issue is real straightforward. Astrophysics lends itself easily to a visual “hook,” such as the false-color image of the Crab Nebulae to the left. This isn’t necessarily the heart of astrophysics of course, but it’s a way to connect with the broader public in a literally eye-catching manner. Compare the image search results for “solid state physics” vs. “astrophysics. Not a good sign if the first page is overloaded with head-shots of old nerdy white, Middle Eastern, and brown guys. But that’s not the only issue here. I think there’s a “soul factor” at work. To understand what I’m getting at, let’s look at Vivienne’s breakdown by the umbrella categories:

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Open Thread – August 30th, 2010

By Razib Khan | August 30, 2010 1:46 pm

I always forget about open threads! Anyone read any good books over the summer? Bad ones to avoid? I’ll have a review of The Tenth Parallel up soon, but after reading it, and several other books…I’m beginning to think that for most Americans they should stick to American history if they want to read history. Unless they read high school level books. Shorter works are really hard to get much out of unless you have a thicker interpretative framework. So many times I catch myself thinking, “Ah, makes sense, I read in X the context behind this fact.” Or, “That’s a biased reading, I know that it doesn’t comport with the field’s consensus orthodoxy, which the author isn’t noting for readers….” Next in my list is The Invisible Gorilla: And Other Ways Our Intuitions Deceive Us, but first I need to finally finish The Troubled Empire: China in the Yuan and Ming Dynasties. Also looking forward to Eureka Man: The Life and Legacy of Archimedes.

MORE ABOUT: Open Thread

Daily Data Dump – Monday

By Razib Khan | August 30, 2010 12:55 pm

Hope you had a good weekend! Winter is not quite coming…but summer is ending.

Phoneme Inventory Size and Demography. Some original data analysis in this post! Turns out that phoneme segment length is positively correlated with population density. Too often culture is viewed as something we can only have a qualitative understanding of, but these sorts of analyses show that there are ways to get a quantitative grasp of the sea of memes (if this post was of interest, see the blog Replicated Typo).

Why Isn’t the Missing Heritability Nearly Neutral and Tightly Networked?. Interesting idea that we’re missing causal variants because of selection bias on the set of SNPs which current gene chips detect. The past 10 years have been awesome in genomics, but what’s going to happen when whole genome sequencing becomes the norm?

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10 Questions for Hugh Pope

By Razib Khan | August 30, 2010 10:02 am

popehughHugh Pope is the author of Dining with al-Qaeda: Three Decades Exploring the Many Worlds of the Middle East, Sons of the Conquerors: The Rise of the Turkic World, and Turkey Unveiled. He was a foreign correspondent in the Middle East for 25 years, most recently with The Wall Street Journal, and has a degree in Oriental Studies from Oxford. He currently works for the International Crisis Group, focusing on issues of Turkey and Cyprus. Despite similarities of physiognomy and Oxford educations Hugh Pope is not Hugh Grant.

Below are 10 questions.

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When the ancients were wise

By Razib Khan | August 30, 2010 4:46 am

2009-02-02-HouseofWisdomcovI picked up The House of Wisdom: How the Arabs Transformed Western Civilization on the run, as I was about go traveling somewhere. I didn’t look at the contents or even the jacket summary very closely. My interest specifically was to get to know a little more about the Abbassid House of Wisdom, which like the Academy of Athens was more defined by a bustle of intellectual activity rather than a physical space. In particular I wanted to know more about Thābit ibn Qurra, arguably the most renowned translator of ancient works for the House of Wisdom, and the last pagan intellectual of note in western Eurasia before Plethon. Thābit ibn Qurra was a Sabian, a religious sect in Haran which had convinced the Islamic authorities that they were a People of the Book, but who clearly descended from the pagan tradition of that city which persisted down to late antiquity thanks to the protection given by the nearby Persian rulers (during the period when Justinian was eliminating all traces of institutional paganism from the Byzantine Empire, from the Academy in Athens, the Sun Temple in Balbek, to the Temple in Philae, Haran was spared because the proximity of the Persian Empire meant that the Byzantines did not have a free hand in disrupting the local social equilibrium without cost to their domination of the region). But The House of Wisdom is not that book at all, only a few pages are given over to the Abbassid House of Wisdom. Rather, the title refers to the interaction between the civilization of Islam and Western Christendom between late antiquity to the high medieval period, and is a metaphor for Arab Islamic civilization. If you want to know about Adelard of Bath, Roger of Sicily, and Frederick II, this is the book for you! These are some of the novel bit players in the rather well worn story of “How X Saved Western Civilization,” with X being the Arabs in this narration (the other figures, such as Averroes, are well known to you from other works).

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MORE ABOUT: Arabs, History, Islam

What do science bloggers blog about

By Razib Khan | August 30, 2010 12:51 am

What do science bloggers blog about? My study of the Wikio Top 100:

As a former scientist, I like evidence-based blogging so I needed a dataset to test my theory that ‘all top bloggers are biologists’. To get a randomish sample of big science bloggers, I did a dodgy analysis of the blogs in the Wikio Top 100 science bloggers ranking.

Here’s the breakdown of bio bloggers topicality:

The large number of neuroscience bloggers has always perplexed me. Any idea what’s going on there?

A minor note: could someone at Wikio update my blog’s address? I tried to do it let myself but it wouldn’t let me. Would be nice to get that before I drop off the list of top 20 science blogs.


God's trade

By Razib Khan | August 29, 2010 6:32 pm

One of the issues with pre-modern trade is that international banking and communication as we understand it did not exist, and trust was a major problem across distance and time. This is why dispersed ethno-religious groups could be the vectors by which private trade occurred between civilizations, because there was a circle of trust which existed between these groups despite their particular residence. Jews are the most famous cases of this, but the pre-Islamic Silk Road saw a similar phenomenon with the Sogdians. In the modern world various ethno-religious groups from Gujarat whose traditional occupation is trade also maintain this link to the past of international commerce, which was embedded in kin and religious networks, not transnational corporate institutions.

A major way to establish fellow feeling and trust is religion. The Islamic scholar and traveler Ibn Battuta trekked from his native Morocco across the world of Islam, all the way to China. Notably throughout his travels he remained within the confines of a predominantly Muslim subculture. This made sense in regions where Islam was the religion of the majority, or of the minority which was in power (India), but even in China he found refuge among that region’s Islamic community (the presence of Muslims was important, because he could always offer up his services as an Islamic legal expert, though in some cases he was obviously drafted into the role). Ibn Battuta flourished in the 14th century, when Islam may have been ceding ground to Western Christendom (e.g., in Spain), but was waxing in the east, and in particular the Indian ocean basin. Already regions of maritime Southeast Asia such as Aceh were Muslim, and within the next three centuries all of what is today Indonesia would come under sway of rulers who were professing Muslims (with the minor exception of Bali).

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MORE ABOUT: commerce, Islam, shafi'i, trade

Marc Hauser's consequences

By Razib Khan | August 29, 2010 12:14 pm

Update: Results so far….

Too harsh – 3.0%
About right – 15.0%
Not harsh enough, though he shouldn’t be ostracized – 26.0%
He should be ostracized from science – 56.0%

The editor of Cognition believes that Marc Hauser was guilty of fabrication in light of what he’s seen in the Harvard report on Hauser’s misconduct. Marc Hauser is on on leave, and will be supervised in his research in the future. But, he continues to teach extension courses. It doesn’t seem as if his work on human moral cognition is under a cloud. There are other researchers working in the same area who have been able to replicate his general findings. Rather, it seems that it was the work on cotton-top tamarins which is under scrutiny, in large part because Marc Hauser was the only one who was doing that sort of research on that organism.

In the end this is about a violation of trust. Alison Gopnik told Nicholas Wade that “It’s always a problem in science when we have to depend on one person.” Science is a famously a self-regulating culture. The system works because science is about something real, and scientists are constrained by the data. But, science is also a human enterprise so conscious and unconscious bias enters into the system. The question is whether the system works well enough that scientists trust their colleagues to report truthful results. If every scientist had to check in on every other scientist I suspect that the system would collapse because there aren’t enough labor hours to go around. Science is very competitive, and many people work many hours for only modest renumeration. Careers hang in the balance, and many are weeded out. People accept this because there is at least a perception of a minimal level of fairness. Finally, on a social scale the economic growth which our society depends on is driven in large part by scientific innovation. The culture of science is the engine upon whom billions depend.

My first thought about what has happened with Hauser is that he is “too big to fail.” He’s at Harvard, and, he has powerful friends. It reminds me of what a friend of mine told me about what occurred at a major tech corporation he had worked at. Apparently there had been an incompetent hire who lasted for years because no one wanted to take responsibility and fire him, because the very fact that managers actually hired him was a negative reflection on their discernment if someone eventually passed judgement on this individual. So there wasn’t an incentive to bite the bullet, and the incompetent employee was moved from department to department for years.

But I’m curious what readers think. Below is a survey asking what you think of the magnitude of Marc Hauser’s punishment in relation to his infractions. I’ll update the results at the top of this post every day for a week.
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People, not pots, in Africa

By Razib Khan | August 29, 2010 1:40 am

324_1035_F5Last weekend I mentioned a paper, The Genetic Structure and History of Africans and African Americans, which had the best coverage of disparate African populations we’ve seen so far. The map to the left shows the various ancestral population clusters inferred from the samples they had. Really the only failing is that they didn’t have samples from Angola, Zambia, Zimbabwe and Mozambique. Unfortunately, that’s not totally trivial. These are regions which were effected by the Bantu Expansion, with southern Angola in particular still having remnants of Khoisan language speakers which likely attest to the pre-Bantu populations. Luckily for us innovation and scientific ingenuity are such that minor questions can quickly be answered because of how cheap the basic methods have become. A new paper in The European Journal of Human Genetics tackles Mozambique in particular, and discerns a heretofore unknown possible population cluster. A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations:

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CATEGORIZED UNDER: Genetics, Genomics

Nigerians agree despite religious differences

By Razib Khan | August 28, 2010 12:13 pm

I am currently reading Eliza Griswold’s The Tenth Parallel: Dispatches from the Fault Line Between Christianity and Islam. The first half of the book is about Africa, and much of that is given to religious conflict in Nigeria. Africa’s most populous nation happens to be split down the middle religiously, with a Muslim north and a Christian south, meeting in the “Middle Belt” to contest. Griswold describes a very competitive religious marketplace.

One thing I was curious about though: are the religious conflicts in Nigeria simply due to coalitional fissures, or deep substantive divergences which track the religious differences? To illustrate, if Muslims and Christians share a village, then Christians who slaughter pigs in public places because pork is their primary protein source will likely have tensions with Muslims, who as a matter of substance object to pig slaughter which might pollute the landscape (this is a problem in parts of Southeast Asia where Muslims live downstream from Christians). In contrast, if you have economic difficulties in a region, and it is fractured ethnically or religiously, trivial tensions may quickly exploded into violence. In other words, in the second case religion is just a “quick & dirty” coalitional marker around which inevitable conflicts are going to swirl (in Mauritius Muslim Indo-Mauritians play a “wild card” role between Christian Creoles and Hindu Indo-Mauritians, despite greater substantive religious affinity with the Christians and greater cultural and racial affinity with the Hindus).

To answer this question I looked at the World Values Survey. For Nigeria there was data from 1995 and 2000, so I combined them to increase my sample size. Additionally, I wanted to focus on the Yoruba ethnic group, which is religiously divided between Muslims and Christians. In the WVS the religious categories actually break down further among the Christians, and I selected Pentecostals and Protestants for the Yoruba because of the large N for these groups, along with Muslims. Additionally, I selected Hausa Muslims as a comparison. The Hausa are an overwhelmingly Muslim northern ethnic group, while the Yoruba are a religiously pluralistic southern group (the Igbo of the southeast are as Christian as the Hausa are Muslim).

Please note that the survey was taken during a period of military rule by Hausa strongmen. I included only a subset of questions. You can follow to link to do your own queries.

Mus = Muslim, Pent = Pentecostal, Prot = Protestant. Some cells for Pentecostals are missing because for some questions all Protestants were aggregated together.

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Daily Data Dump – Friday

By Razib Khan | August 27, 2010 1:00 pm

Have a good weekend.

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes. This is in my RSS, but not on the Nature site, so here’s the snip I have: “The ratio of X-linked to autosomal diversity was estimated from an analysis of six human genome sequences and found to deviate from the expected value of 0.75. However, the direction of this deviation depends on whether a particular sequence is close to or far from the nearest gene. This pattern may be explained by stronger locally acting selection on X-linked genes compared with autosomal genes, combined with larger effective population sizes for females than for males.” Looks interesting.

Journal: Hauser fabricated data. Scientists can be “too big fail” it seems.

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Not the origin of genome complexity

By Razib Khan | August 27, 2010 12:50 pm

ResearchBlogging.orgOver the past decade evolutionary geneticist Mike Lynch has been articulating a model of genome complexity which relies on stochastic factors as the primary motive force by which genome size increases. The argument is articulated in a 2003 paper, and further elaborated in his book The Origins of Genome Architecture. There are several moving parts in the thesis, some of which require a rather fine-grained understanding of the biophysical structural complexity of the genome, the nature of Mendelian inheritance as a process, and finally, population genetics. But the core of the model is simple: there is an inverse relationship between long term effective population size and genome complexity. Low individual numbers ~ large values in terms of base pairs and counts of genetic elements such as introns.

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CATEGORIZED UNDER: Evolution, Genetics, Genomics

Katz, 8-27-2010

By Razib Khan | August 27, 2010 10:48 am


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Chosen genes of the Chosen People

By Razib Khan | August 27, 2010 1:48 am

ashjewheadshotLast spring two very thorough papers came out which surveyed the genetic landscape of the Jewish people (my posts, Genetics & the Jews it’s still complicated, Genetics & the Jews). The novelty of the results was due to the fact that the research groups actually looked across the very diverse populations of the Diaspora, from Morocco, Eastern Europe, Ethiopia, to Iran. They constructed a broader framework in which we can understand how these populations came to be, and how they relate to each other. Additionally, they allow us to have more perspective as to the generalizability of medical genetics findings in the area of “Jewish diseases,” which for various reasons usually are actually findings for Ashkenazi Jews (the overwhelming majority of Jews outside of Israel, but only about half of Israeli Jews).

Just as the two aforementioned papers were deep explorations of the genetic history of the Jewish people, and allowed for a systematic understanding of their current relationships, a new paper in PNAS takes a slightly different tack. First, it zooms in on Ashkenazi Jews. The Jews whose ancestors are from the broad swath of Central Europe, and later expanded into Poland-Lithuania and Russia. The descendants of Litvaks, Galicians, and the assimilated Jewish minorities such as the Germans Jews. Second, though constrained to a narrower population set, the researchers put more of an emphasis on the evolutionary parameter of natural selection. Like any population Jews have been impacted by drift, selection, migration (and its variant admixture), and mutation. Teasing apart these disparate parameters may aid in understanding the origin of Jewish diseases.

ResearchBlogging.orgThe paper is open access, so you don’t have to take my interpretation as the last word. Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population:

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CATEGORIZED UNDER: Anthroplogy, Genetics

Size doesn't always matter

By Razib Khan | August 26, 2010 11:56 am

The autosomal genome of Ötzi the Austrian “Iceman” is apparently in the pipeline (from what I can tell they’re doing the analysis right now). What can we learn from one sample? Ann Stone, who was a graduate student on the original team which recovered his body, says:

A specialist in anthropological genetics, Stone is excited by the recent news but also cautious. “It is a sample of one. For us to really say something about that period, you need a sample of 25 to 50 individuals,” she explained during an interview with Deutsche Welle, Germany’s international broadcaster.

This is fine as it goes. Worries about sample size are pretty generic and if the practicalities permitted who wouldn’t want a bigger N? But whether you should worry about sample size is partly conditional on how much the findings deviate from what you’d expect. Imagine for example that ~25% of Ötzi’s genome was of Neandertal origin. Obviously it would be great to have 25 to 50 representative individuals from this region to know whether Ötzi was atypical…but the very finding itself would be of such large effect that an N = 1 would tell us quite a bit. Similarly, one genome of a Sub-Saharan African would be very informative if you had several hundred non-African genomes as a point of comparison (because Sub-Saharan Africans have so much genetic variation which is outside of the distribution found among non-Africans).

MORE ABOUT: Ötzi, Sample Size

Daily Data Dump – Thursday

By Razib Khan | August 26, 2010 11:29 am

Essential Science Fiction Movies. People always put Metropolis on the list, or bemoan the fact that they haven’t seen it. What do you think of it? I quite enjoyed, but much of the greatness of the film seems to be that it prefigured so much of what was to come.

The Real Estate Collapse. Jonah Lehrer suggests that the problem with prices not declining (or at least listed prices) has a lot to do with loss aversion/sunk cost fallacy. I agree. On the other hand, many Americans who are older bought into the idea that real estate was the “safe” place to put their savings, and now are looking at taking a big loss. If you have 15-30 good years left it might be really hard to simply “move on” when you don’t have the time left to rebuild equity.

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Hitler's "Jewish genes"

By Razib Khan | August 26, 2010 2:16 am

A reader asked about the bizarre story of Adolf Hitler having “non-Aryan” ancestry. Specifically, The Daily Mail title is: “DNA tests reveal ‘Hitler was descended from the Jews and Africans he hated.'” Since it’s a British newspaper I frankly wouldn’t put it past them to simply pass along a hoax…but I think if they were going to do that they would have said it was the Cohen Modal Haplotype. The article claims that Hitler’s Y lineage was haplogroup E1b1b (all biological descendants of the same common male ancestor through the direct patriline will carry this set of Y chromosomal markers). This is really vague, as the haplogroup has many subclades. Obviously if you pull the lens far back enough you’ll find a phylogeny where Hitler and Jews and/or Africans are within the same clade. Dienekes notes that this is not a rare haplogroup. It is correct that if one is an Ashkenazi Jew the odds of one carrying this haplogroup are much higher. But, it is not necessarily entailed from this that one is likely to be an Ashkenazi Jew if one carries this haplogroup (or is of Ashkenazi Jewish descent).

This is clear from the map of the distribution of E1b1b’s two major subclades:

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MORE ABOUT: Hitler, Trash Genetics

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