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

August 31, 2010

How August Should Have Ended

Filed under: Blog,Comedy,Video — Razib Khan @ 7:02 pm

Daily Data Dump – Tuesday

Filed under: Blog,Daily Data Dump — Razib Khan @ 10:05 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.

Wolves Are Smart, but Dogs Look Back. Makes me think of the empathizing–systemizing theory. Dogs empathize, wolves systemize.

Scientists Square Off on Evolutionary Value of Helping Relatives. Carl Zimmer has a good overview of the controversy which emerged out of the Nowak et al. paper, which seems to take a maximalist position against the utility of kin selection in explaining euosociality. Apparently some “big names” are going to be writing a response, so I’ll be curious. I haven’t bothered going through Nowak et al.’s supplements, so I really can’t say much more than that.

Outlines Emerge of Future State in the West Bank. The thing that stood out was the relative quiescence engendered by economic growth. Idle hands and all.

The New World in three easy steps

Filed under: Anthroplogy,Archaeology,Human Expansion,New World,Paleoanthropology — Razib Khan @ 9:28 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.

The New World is similar. The initial migration out of Africa by modern humans resulted in the range expansion of the human lineage into a region which had been untouched by earlier hominins, Australasia. But after that point tens of thousands of years passed before our species pushed into virgin territory, in this case North America. The when and the how of this though is still up for debate. A new paper PLoS One attempts to construct a plausible scenario by taking archaeological data points and inputing them into a diffusion model. Archaeological Support for the Three-Stage Expansion of Modern Humans across Northeastern Eurasia and into the Americas:

We use diffusion models…to quantify these dynamics. Our results show the expansion originated in the Altai region of southern Siberia ~46kBP , and from there expanded across northern Eurasia at an average velocity of 0.16 km per year. However, the movement of the colonizing wave was not continuous but underwent three distinct phases: 1) an initial expansion from 47-32k calBP; 2) a hiatus from ~32-16k calBP, and 3) a second expansion after the LGM ~16k calBP. These results provide archaeological support for the recently proposed three-stage model of the colonization of the Americas….Our results falsify the hypothesis of a pre-LGM terrestrial colonization of the Americas and we discuss the importance of these empirical results in the light of alternative models.

It’s an interesting paper because it seems to have been triggered in part by inferences made from the genetic data. I don’t know how confident archaeologists are about their radiometric dates, but I think some of the molecular clock results from the genetics of Amerindians need to be taken with a grain of salt (I don’t see many people repeating some of the really ancient coalescence dates for Amerindian Y lineages at this point).

These data seem to indicate that modern humans made it no further than previous hominin groups for several tens of thousands of years. But something happened within the last 20,000 years, and our species made the leap across Beringia. The bottleneck here is certainly not the Bering Strait, which was spanned by land much of the time in any case. Rather, our species didn’t have the biological or cultural capacity to survive in extremely frigid environments. I’ve read modern humans pushed the boundaries of their range in northern Europe further than Neandertals ever did, indicating our flexibility and plasticity. Since the human lineage had been resident in Eurasia for at least one million years that suggests to me that it was behavioral modernity that was key. In particular, how quickly our cultures evolve and shift. Though that flexibility itself may be a function of our biological competencies.

Science with soul sells

Filed under: Blog,Blogs — Razib Khan @ 12:51 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:


Neuroscience, evolution, and astrophysics speak to normative concerns of our species. That is, they grapple with values. The brain is the seat of our self in a material sense, and neuroscience emerges out of a deep tradition of philosophy of mind which goes back 2,500 years. Evolution has had a fraught relationship with teleology, and some philosophers of biology have quipped that their field to a first approximation can be reduced to philosophy of evolution. Molecular biology is more fundamental in a concrete proximate sense, but evolutionary biology is more fundamental in the ultimate abstract sense. And finally, astrophysics when it bleeds into cosmology rather obviously treads on the ground which was once the domain of mythology, of cosmogony. In a very broad sense these disciplines push against our conceptions of ontology. Astrophysics in the most general sense, neuroscience in a very anthropocentric sense, and evolutionary biology spanning the two extremes.

I think the anti-alternative medicine category also emerges from the same dynamic, but mainly not to appeal to it, but to battle it. Modern scientific medicine does not jive with the deep intuitions of many people of how bodily processes work, They wish for a more “holistic” and “natural” model. I use the quotations because these sorts of terms are more figures of speech in this context than anything substantive. If there was a “holistic” and “natural” alternative engineering discipline then engineering weblogs would no doubt sprout up to battle intuitive pseudo-science.

Mathematics is a strange discipline because I think it too falls into the category of a soulful science. But as Keith Devlin observed in The Millennium Problems translating deep cutting edge mathematics to the general public can be very difficult, because there is less room to use metaphor and analogy than in the natural sciences. Technical hurdles are not barrier if analogy and visuals can substitute, but this does not seem so easy for many deep mathematical questions.

I believe therefore the issue here is to a large extent demand side. People get worked up over controversy, and emotionally invested in topics which cross the threshold of deep emotional commitment. Whether we are simply another primate, or sui generis and a Special Creation, fits that bill. More practical, and very important in an economic sense, endeavors may not fit the bill.

Note: I think other factors are at work as well. Climate science is popular because of its high profile in public policy right now and the potential existential implications. There are probably other hidden factors too. Why is neuroscience blogging more well developed than psychology blogging (or at least so a psych blogger has complained to me)? Neuroscience is a young field which is maturing right now, and perhaps it simply has the right demographic profile which allowed it to bloom very quickly in the next technological context. And I also think fMRI images are preferable to another stock photo of rats in a maze!

Image Credit: NASA

August 30, 2010

Open Thread – August 30th, 2010

Filed under: Uncategorized — Razib Khan @ 12:46 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.

Daily Data Dump – Monday

Filed under: Blog,Daily Data Dump — Razib Khan @ 11:55 am

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?

Bring Your Genes to Your Life Insurance Sales Representative. Brad DeLong makes the argument for single-payer as a way to obviate the conundrums which will emerge when genetic profiling of disease becomes more efficacious. This is an area where I think the marketing of personal genomics companies have given people the wrong impression of how powerful the techniques are currently. But the time will probably come when there’s a lot more juice to squeeze out of the prediction algorithms. And yet one issue that DeLong assumes is that your genetic endowment is a lottery. That it’s something we can’t control in generation t + 1. That’s false. Parents will be able to screen. If health care is totally socialized, should we also socialize some aspects of the decision making process in relation to procreation? Rights without responsibilities?

Iranian Jews in America: Torn Between Homelands. In the 2004 movie Crash both of the Persian leads were played by Iranian Americans who also happen to be Jewish, Shaun Toub and Bahar Soomekh. Here’s Bahar Soomekh, “Just because I’m in Hollywood doesn’t mean that I forget that I’m Persian or that I’m Jewish. Judaism is not only my religion—it’s my identity.” Remember that only a minority of Iranian Americans are self-identified Muslims.

In Search of Time. A cognitive trick to stretch out your perception of time? Perhaps.

10 Questions for Hugh Pope

Filed under: Uncategorized — Razib Khan @ 9:04 am

I have posted a Q & A with author Hugh Pope over at Discover. Other 10 Questions can be found here.

10 Questions for Hugh Pope

Filed under: 10 questions,Culture,Hugh Pope,Islam,Middle East — Razib Khan @ 9:02 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.

1 – In Sons of the Conquerors I recall you being able to communicate with people from all over the Turkic world in Turkish. My impression from that is that from Xinjiang to Anatolia the differences between Turkic languages are relatively marginal. Am I misremembering something here? Can you give an analogy as to the distance between Turkic languages in terms of intelligibility? (e.g., Spanish:Italian::Turkish:Uzbek)

Turkic languages are in three main groups: roughly the more westerly group of Turkish, Azeri, Balkan Turkish and Turkmen; a central group including Uzbek and Uygur; and an eastern group that includes Kazakh and Kyrgyz. The westerly is the most developed, and you could say share the same inter-intelligibility of Spanish, French and Italian. A Kazakh and a Turk will however take longer to learn each other’s languages. However, since the structure is similar, and there is quite a good overlap of words (although they can be pronounced very differently), they learn them much quicker than learning a tongue in another language group. Because Japanese shares many grammatical similarities with the group, many Turks and Japanese can also learn their languages much quicker than others.

2 – One of the first nations in the Middle East in which you lived was Syria. As you observe in Dining with al-Qaeda Syria preserves a great deal of religious diversity, a variety draining out of many of the other nations in the region. In particular, I am curious as to your assessment of the attitudes of Alawis to the Muslim world as a whole. From my reading I am to understand that they have been “mainstreaming” their identity over the past few generations so that they are now a sect of Twelver Shia Muslims, whereas in the early 20th century their own self-perception was much grayer, with an identity more distinct from Islam as a whole like the Druze or Yezidis.

Interestingly, Alawis in Syria are different from the Alevis in Turkey, but both have hesitated to describe themselves completely outside mainstream Islam. Clearly they come from rural groups who share a common point of a different, Shia-style tradition, distinct from the main (Ottoman) Sunni power of the Middle Ages. In Turkey, many Alevi communities appear to have been converted by missionaries from Safavid/Shia Iran, and because there was so little communication between different parts of the empire, it gave rise to many different Alevi traditions. The picture in the two main post-Ottoman countries with Alevis/Alawis, Syria and Turkey, has diverged somewhat since then. The minority Alawism of the Assad family, in power since the 1970s, has had more impact on their efforts to keep Syria ’secular’ rather than promoting any Alawi orthodoxy. In Turkey, where Western style rights and freedoms have been spreading, various Alevi factions compete to be known as mainstream or even official. There are some Turkish Alevis, apparently a minority, who want to be considered as a distinct religion. One feature shared with Syria is a love of secularism — some Turkish Alevis even treat republican founder Kemal Ataturk as a kind of saint, probably because his secularism defended them from oppression by the Sunni majority. A difference with Syria is that even though the Alevis in Turkey can’t agree on a common dogma, Alevism is now very much established as an alternative to Sunni Islam.

3 – I’ve never been to the Middle East so what I know is mostly from books, papers, and various data sources. The World Values Survey in 2005-2008 had he following results for selected nations in regards to those who were convinced atheists:

Great Britain – 10.4%, 105 out of 1041
USA – 3.6%, 42 out of 1249
Turkey – 0.5% 7 out of 1346
Egypt – 0% 0 out of 3051
Iran – 0.1% 3 out of 2156
Jordan – 0.1% 1 out of 1106

I’ve provided percentages and counts. As someone more intimately familiar with Middle Eastern people, do these numbers tell us anything real? (I know in the USA the percentage who don’t believe in God is higher than those who say they’re atheists, because the label atheist has some stigma)

It’s true that religion, and respect for religion, is very deep-rooted in Middle Eastern societies. I think it is partly because they have had a very rough time in the past couple of centuries, making people distrustful of human efforts and outside powers. You should also take into account the very vivid and influential stigma attached by the Koran and Muslim societies to anyone leaving the faith or not believing in God.

4 – The term nation has a relatively broad meaning in English today, and informally denotes a particular land mass enclosed by political boundaries. But a narrower older meaning is that a nation consists of a particular people with an identity as a nation on a particular territory. The nation-state if you will. By the second definition it seems that Turks and Iranians (despite the ethnic and religious diversity in both these nation-states) have a sense of nationality. Most Americans at this point would probably agree with the assertion that Iraqis do not have such a viewpoint, while it seems that many of the Persian Gulf monarchies are more coalitions of clans brought together by personal rule. Of the Arab nations Egypt in particular seems to stand out to me as analogous to Turkey or Iran. What would say of this assertion?

I think your assertion is broadly correct, and I’d also note that the sense of Iraqi nationality may be in eclipse but that it is still there. Most Iraqi Kurds might dream of an independent Kurdistan, but I’m not sure they really want to merge their advanced society of three million people with, say, the 12-15 million poorer, less educated Kurds of Turkey. Turkey, Iran and Egypt all have long and well-established state traditions, which also tends to nurture a sense of nationhood. Arab states, many of which were previously part of the Ottoman Empire, have a much harder time making their statehood seem like nationhood. Saudi Arabia may come the closest to this – the Saudi family has been running things in that part of the world off and on for 300 years – but Saudi Arabia is a rather unusual place so hard to make generalisations about it!

5 – Let’s play at “alternate history.” What if the world’s largest concentration of oil reserves were not in the Arab Middle East and Iran. Would these Middle Eastern nations be more well off, like Turkey, or would they be ignored and destitute like much of Africa and Afghanistan?

With all the caveats of alternative history, I suspect that a country like Iraq, with a state tradition and a long history would have done better, and that it would have been very hard without oil to make something of the Persian Gulf states. I agree however with the underlying idea behind your question, that lack of oil has forced a country like Turkey to work harder and have a more tolerant and pluralist culture.

6 – I’m curious about your interactions with the Yezidi’s. Did you discuss the details of their religion at all with them? If so, were you simply stonewalled, or did they give you consistent or inconsistent descriptions of their beliefs?

I did discuss aspects of their religion with some Yezidis, and they seemed to have as coherent a world view as any other in terms of theology (try explaining the Trinity to an outsider). In terms of religious culture, however, they had almost nothing to talk about since they have been so marginalized and oppressed. Certainly they feel a lot freer in U.S.-backed Iraq than they did under Saddam Hussein, but the attacks on them by extremists show that things could go badly for them too.

7 – I have an Iranian American friend. He is an ethnic Persian, and I inquired of him as to the existence of an independent Azeri Iranian community, and he did not know if such a group existed. Of course he knew that many Iranians were Azeris, but the distinction seemed of minimal interest to him. More a matter of curiosity than any importance. I’m curious as to ethnic relations in Iran, which seem relatively amicable. One model I have proposed for why Azeris and other Turks are so well integrated into the Iranian state is that to a great extent modern Iran as a Shia nation is a product of the Turkic Safavids and their successors. What do you think of this thesis?

That’s possible, but I’m not sure the Safavids took their ‘Turkicness’ very seriously (the Ottomans, their big rivals, didn’t make a big deal of it either). Iranian Azeris are well-integrated because they share Shia faith, they fought side by side with the others in the Iran-Iraq war, and because there is no limit to how high they can rise in Iranian society (despite all the Iranian snobbery against Turks and the Turkish language, and the occasional ethnic frictions there are in Persian/Azeri border towns). Supreme Leader Ali Khamenei comes from an Azeri family, as does Hossein Mousavi. The merchants of the Tehran bazaar are mostly Azeris.

8 – In Dining with al-Qaeda I was struck by the fact that Iranians you questioned about their militant rhetoric dismissed those who took their slogans literally. There seems to have been a gap in how people perceived language from culture to culture (this is true even within the United States). Perhaps a specialist in semiotics would have been handy. Your task as a journalist was to transmit information to the Western public, and so serve as an intermediary. And yet sometimes you encountered difficulties because your editors were less than familiar with the different way language is used in other cultures. Are the diplomats and politicians who deal with Middle Eastern issues versed in these nuances? After the Iraq War debacle I am not so sure that complacent confidence in the “commanding heights” of American civil service and politics should be a default.

The American civil service was well-versed in the nuances of Iraq before the war, but the political power chose to disregard their wisdom almost completely. (Same goes for the UK). American civil servants could not be expected to rebel against an unwise policy – in fact, only a handful resigned – but applied their can-do optimism to what (to me) seems like a completely impossible proposition. In Dining with al-Qaeda I was trying to tell people that they should trust no one with complacent confidence, especially not the media, and that they should develop a sceptical approach to information.

9 – A personal question. Your “divided loyalties,” so to speak, are highlighted in Dining with al-Qaeda. You’re British by national origin, have lived in the Middle East for much of your life, and worked for American journalistic outfits. If someone asks you “where are you from?, what do you answer? Is it very important who is asking the question?

I find this a very difficult question to answer. I was born in South Africa and raised there until I was nine, by English parents; I went to school in Britain; my university studies were of the Arab and Iranian worlds; I lived nearly half of my life in Turkey; I first married a Swiss national and now a Dutch national; my children have been educated in French and German schools. Generally I say, “I’m from Istanbul”, but even that seems less part of my loyalties now, since my favorite place to live is my house in the mountains in the south of Turkey.

10 – There exists the category “Middle East,” which includes the Arab nations (or perhaps the Arab nations of the Mashriq + Egypt + Arabia), Turkey and Iran. And yet there is also quite a bit of prejudice between Arabs, Turks, and Persians (as a South Asian I have experienced members of each group taking pains to distinguish itself from the others). But walking through Istanbul, Tehran, and an Arab city such as Damascus or Cairo, are the cultural differences that stark? Can the casual observer tell simply from styles of architecture what is Turk and Persian and Arab? Is it simply narcissism of small differences?

There are real differences between Turks, Persians, Arabs, Kurds and Jews, who are all main Middle Eastern peoples. But each national category has many sub-categories, some of which seem closer to the other main categories than they are to each other! It’s the same with Islam – people keep claiming it’s ‘one’, but in fact, Turkish, Persian and Saudi Islam, despite their shared theological reference points, could be entirely different religious cultures. The important thing in the Middle East is to recognize these differences, but also to see where they overlap, along with equally important overlaps with Western culture and commerce.

Image Credit: Thomas Foley

When the ancients were wise

Filed under: Arabs,History,Islam — Razib Khan @ 3:46 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).

I was disappointed with the framework of The House of Wisdom. Because I misunderstood the title I thought it was going to be a narrowly focused work with a scholarly bent. Instead it was meandering, broad brush, and most definitely aimed toward an ignorant lay audience. This sort of work isn’t all bad. Colin Wells’ Sailing from Byzantium: How a Lost Empire Shaped the World is of similar bent, though more focused and scholarly. The intent of the publishers in these sorts of works are clear. Here another book in the same vein, Lost to the West: The Forgotten Byzantine Empire That Rescued Western Civilization (I can not recommend this as much as Wells’ attempt). Jonathan Lyons tries to do the same for the Arabs as Colin Wells did for the Byzantines, but there are differences which I think are instructive. Lyons turns the Byzantines into bit-players on the margins of his story, which is really about the dance of the West, those societies which were heirs to the Western Roman Empire, and the Muslims of Araby (there is sentence where he refers to “Christians” and then to “Byzantines,” with it being obvious that he’s distinguishing the two. This is obviously a minor error, but it points to the fact that the Byzantines have been pushed so far to the margin Lyons’ story that they aren’t even included in Christendom!). Wells used the Muslims as a contrast with the Byzantines, showing how these two streams of preservation of ancient wisdom differed in the details, and how they complemented each other. So Byzantine influence was more powerful in Italy, while works derived from Al-Andalus were more prominent in what became France. The historical reasons for this moderate disjunction are straightforward and need not concern us here. But of more interest is that while the Muslims tended to focus on the abstract philosophical and technical wisdom of the Greeks, it was from the Byzantines that we derive the preservation of the Hellenic humanistic tradition. Euripides, Sophocles and Aristophanes. This is a substantive distinction, and one that is not often highlighted.

Instead the author of The House of Wisdom spends an inordinate amount of time contrasting the civilized and the barbaric. The civilized in this case being the Arab Muslim, and the barbaric being the Latin Frank. We’ve been around this block many times, and I don’t understand why we need to revisit this normative inversion again. Perhaps I’m not part of the intended audience, I’m the type of person who reads thousand page books on the Crusades, so I’m not really interested in rehashes of the conflict over a few paragraphs. The corrective bias which I believe Lyons is operating under because of the presumption of an Islamophobic ignorant audience is why there are counter-polemics such as Rodney Stark’s God’s Battalions: The Case for the Crusades. The Crusades were of course balanced by the Arab conquests, which was a veritable rollback of Christendom. One could write another book about “how the Greeks and Persians civilized the Arabs.” The contempt with which the older cultures viewed the Arab Muslims is evident in the Shahnameh or John of Damascus’ writings, and the transformation of Araby into a font of literate sophistication which the Franks encountered in the 4th Muslim century is an important story in and of itself. But instead we’re treated to these black & white morality plays which satisfy the Middle Eastern urge to remind the West who was savage and backward once. This isn’t serious scholarship. Positivism may not be possible in a pure form, but there’s a spectrum between the objective and polemical.

But there are gems of interest in The House of Wisdom. With only 200 pages at his disposal the author really didn’t have time to delve into the literature which he cites and alludes to (which makes the standard West-is-bad framework annoying as it wastes space). In particular, though not explicitly fleshed out I think one can see how Arab Muslim civilization benefited from its geopolitical position and economies of scale. The Arabs reunited many parts of Alexander the Great’s Empire, bringing Alexandria under the same political and social order as the Persian heartland. With the Arab conquest of Sindh, and the defeat of the Tang at Talas, we see that they had interface with other great civilizational traditions. At its height the Umayyad Caliphate was bounded on the West by Latin Christian civilization and on the east by the outposts of the Chinese cultural penumbra. In India the Umayyad’s seem to have come to an understanding with both the Buddhists and Brahmins of Sindh (in particular, the tax exemptions of Buddhist monks and Brahmin priests were maintained as a holdover from the pre-Islamic order). Greek, Chinese, Indian, and Persian wisdom all came together during the Abbassid period in the House of Wisdom (as well as extinct civilizations, such as that of Persian Christianity and Central Asian Buddhism). If there is one fact which I found to be noteworthy in The House of Wisdom it is that Lyons connects the spread of paper from China to the Arab world in the 8th century with the explosion in translation in the 9th century under the aegis of Al-Ma’mun. So like the printing press paper may have triggered an intellectual revolution. It is very interesting that almost all the earliest preserved works of the ancients can be traced to the Carolingian Renaissance, the Abbassids in the 9th century, and the Byzantines under Constantine VII. This occurred over ~150 years or so, and it is to this expenditure of capital on the part of these potentates to which we can give thanks for our remembrance of secular Western antiquity.

So what wisdom did the the Arabs transmit to the Franks? If you’re deeply interested in that, I recommend Aristotle’s Children: How Christians, Muslims, and Jews Rediscovered Ancient Wisdom and Illuminated the Middle Ages and more especially The Beginnings of Western Science: The European Scientific Tradition in Philosophical, Religious, and Institutional Context, Prehistory to A.D. 1450. Remember that a disproportionate contribution by the Arabs was in the domain of natural philosophy, the precursor to science. The Byzantine advantage lay in works in the original Greek, but the Arabs transmitted the works through the intermediation of several languages, from Greek to Syriac to Arabic to Latin. Science’s beauty is that such translation shouldn’t garble the meaning so much, it is a clear and distinct enterprise with little need for semantic nuance. The introduction to most of Aristotle’s thinking in the West was famously through Averroes, the “Commentator” cited by Aquinas. Averroes did not know Greek, and himself relied on Arabic versions of Aristotle’s work.

ESBdioceses0811The aforementioned Adelard of Bath looms large in The House of Wisdom because he brought back works from the Arab world on astrology and philosophy of immediate technical utility. Prior to the modern era astrology and other pseudo-sciences were part of the body of natural philosophy. Star charts and models of celestial mechanics were critical to a proper astrological enterprise. The ancient societies had developed excellent techniques over time, culminating in the work of Ptolemy. Additionally, the Islamic world had an infusion of complementary knowledge from Indian astrologers. The combination of the wealth of the Arab world, the fact that it had access to ancient works, and its cross-cultural connections, meant that in the domain of astrology it was far superior to anything found in the Latin West. Because of the belief in the power of the stars the Arab wisdom in this case had immediate yield and quickly spread after Adelard’s translation effort. Something similar occurred in the realm of geography, where Arabs had a natural advantage over the isolated and parochial Franks. Jonathan Lyons does not explore the economic basis of these differences in cultural capital much, but if you are curious I recommend Christopher Wickham’s Framing the Early Middle Ages: Europe and the Mediterranean, 400-800. Of the successor polities to the Roman Empire that of the Arab Muslim world was clearly the wealthiest to start out with. Much of the subsequent advancement in various technical arts can be attributed to the ability of the Arabs to marshal their surplus capital, and the consequent positive feedback loops which might emerge even in a Malthusian world.

In the big picture though The House of Wisdom has less impact on the modern mind because I believe we do not comprehend the power of the ancients over those who lived before 1800. Lyons himself observes that Western Europeans on occasion selected inferior techniques and truths from the Greeks over Arab derivations and extensions because of the presumption that the Greeks were superior in all way to later peoples. The idea that ancient peoples were wiser, and lived in a better age, is not one that most of us in a post-Malthusian consumer world of technological obsolescence can grasp, but it is a cultural universal. The Chinese, Indians, Greeks and Romans all looked to golden ages, when morals were superior, and wealth and health were the way of the world. Part of this may be that in the Malthusian world there were recollections of periods in their culture when the demographic parameters were expansionary. That is, land was in surplus, labor in a deficit, and necessities a surfeit. But whatever the origin, this model persisted down to the 18th century and the Enlightenment. The Renaissance had been an efflorescence of learning, but it had been retarded in its progress in some ways because of the reverence for ancient precedents. This is most evident in medicine and physics, where Galen and Aristotle led scientists astray.

There are some domains where the ancients still hold sway today. Religion is one. To some extent the literary humanities as well. Among non-scientific, and even some scientifically minded, there is still the idea that “ancient wisdom” can unlock secrets which we moderns have forgotten. To understand psychology I know of individuals who go seeking wisdom in the Sufis or Bhagavad Gita. I suppose that says something about the state of modern psychology. But it is also testament to the fact that despite our modern reliance on technological and scientific advancement the mind still craves ancient wisdom which can be gotten for free. Many believe that just by digging in musty archives one can find magics which unlock the secret of the universe. Magics which the ancients had stumbled upon, and which we have forgotten. To me that is the real polemical lesson that books such as The House of Wisdom should be teaching us, that pre-modern man thought that wisdom could be excavated and borrowed, and not created de novo. Instead, these sorts of popularizations are aimed toward an ignorant and dull modern audience caught up in Glenn Beck and Keith Olbermann’s latest hobby-horses.

Image Credit: Howard Wiseman

August 29, 2010

What do science bloggers blog about

Filed under: Blog — Razib Khan @ 11:51 pm

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

Filed under: commerce,Culture,Islam,shafi'i,trade — Razib Khan @ 5:32 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).

How did this happen? This became the subject of discussion below. There aren’t any hard & fast answers here. Much of what I know is from a few books, After Tamerlane: The Rise and Fall of Global Empires, 1400-2000, Power and Plenty: Trade, War, and the World Economy in the Second Millennium, and A Splendid Exchange: How Trade Shaped the World. In none of these books is the Indian ocean trade network the center of the narrative, but all of them focus on its evolution. In particular, with the rise of the Portuguese in the 16th century we get a sense that in that period the Indian ocean was for all practical purposes a Muslim sea! Granted, the peoples who inhabited the shores were not necessarily Muslim, but from the European (and also earlier Chinese) perspective the trade seems to have been captured by peoples who professed Islam. In this lay the possible answer for why maritime Southeast Asia became Muslim, while mainland Southeast Asia did not. The main exception in the latter case are the Chams, a people who happen to be Malay, and so were intimately connected with maritime Southeast Asia.

madhabTo me the striking evidence of this happens to be a map of the distribution of schools of Islamic jurisprudence. The details are not relevant, but it is interesting to note that the Hanafi school is found in regions where Turkic or Persian culture was dominant. The Muslims of most of South Asia and China proper are generally assumed to have come from these two cultural stems, and so they are by and large Hanafi, despite the fact that they are neither Persian nor Turkic (the Sunnis of the Balkans are Hanafi as well, whether they’re Turkish or not). But look at the distribution of the Shafi’i school. The map does not show it, but the Muslims of Sri Lanka, Kerala, and the Maldives are Shafi’i as well. It seems then to me that the Indian ocean trade network which was dominated by Muslims between 1000 and 1500 A.D. resulted in the spread of the Shafi’i school of Islam, in particular from the Hadhramaut region of Arabia. If we didn’t know anything else about the history of the Indian ocean except for this map, I think we’d have a sense that the Shafi’i school was spread by people who had some involvement in trade and seaborne traffic.

Image credit: Wikimedia

Marc Hauser’s consequences

Filed under: Blog,Culture,Marc Hauser,Marc Hauser Survey — Razib Khan @ 11:14 am

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.

Create your free online surveys with SurveyMonkey, the world’s leading questionnaire tool.

People, not pots, in Africa

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:

Studies of large sets of single nucleotide polymorphism (SNP) data have proven to be a powerful tool in the analysis of the genetic structure of human populations. In this work, we analyze genotyping data for 2841 SNPs in 12 sub-Saharan African populations, including a previously unsampled region of southeastern Africa (Mozambique). We show that robust results in a world-wide perspective can be obtained when analyzing only 1000 SNPs. Our main results both confirm the results of previous studies, and show new and interesting features in sub-Saharan African genetic complexity. There is a strong differentiation of Nilo-Saharans, much beyond what would be expected by geography. Hunter-gatherer populations (Khoisan and Pygmies) show a clear distinctiveness with very intrinsic Pygmy (and not only Khoisan) genetic features. Populations of the West Africa present an unexpected similarity among them, possibly the result of a population expansion. Finally, we find a strong differentiation of the southeastern Bantu population from Mozambique, which suggests an assimilation of a pre-Bantu substrate by Bantu speakers in the region.

The main value-add of the research were the 279 individuals from Mozambique, who they plugged into previous data sets (e.g., HGDP, HapMap3). It must also be noted that they limited their genetic survey to ~2800 SNPs.This is sufficient for their purposes. Below are the figures of interest from the paper. Note immediately how Mozambique separates out at K = 4 in the first image. The subsequent figures are from PCA. The axes represent components of variation. The last panel shows a PCA plot transposed onto a map. In this case, PC 1 & PC3.t

The first figure is important because it suggests population structure we hadn’t known of in the Bantu Expansion. This doesn’t mean that it should be surprising. With Africa’s current level of genetic variation it seems implausible that the carriers of the Bantu culture would not have assimilated other groups along the wave of advance. In fact, as a cultural movement gains steam through positive feedback loops different societies may become co-opted into them, and spread the culture in their own turn. As an American example, I will give the Irish American Catholic hierarchy’s campaigns against German language parochial school instruction in the 19th century. Old English aside the language of the Irish was originally not English, but by the early 19th century apparently English had already become dominant among the Roman Catholic peasantry of Ireland. So they brought English, not Gaelic, to the United States. Similarly, the spread of Islam in India occurred predominantly under the ageis of Turks and Afghans, not Arabs, while the spread of Islam in Southeast Asia was promoted by South Asian Muslim merchants in their turn. So you have Arab cultural forms in eastern Indonesia thanks to cultural expansions at two removes from the original Arab source (in fact, it could be argued that the Turks and Afghans were Islamicized through a Persian intermediate as well).

But it is the PCA plots which are of more curiosity for me. They note that it is the third component of variation which maps well onto geographic distance. In the paper they say:

This is the PC that is mostly correlated with geography…and the fact that it is the third rather than the first component, as would be expected if isolation by distance was the predominant force shaping genetic diversity…implies that directional population movements (such as the Bantu expansion) and barriers to gene flow (such as that between food producers and hunter gatherers) are more relevant than geographic distance to understand the genetic landscape of sub-Saharan Africa….

There were folk migrations in Africa. They might simply not have been the ones we are aware of, at least in our sparest conceptions. Those folk migrations were very recent, within the last ~2,000 years or so. Which is why the distinctive correlations between language and genes persist, especially on the outer edge of the wave of advance in southern Africa (in contrast, the Pygmies of the Congo have lost their native language, and the western Pygmies are highly admixed with their neighbors).

Citation: A genomic analysis identifies a novel component in the genetic structure of sub-Saharan African populations

Addendum: The life of Shaka may give us a clue as the disturbances which pushed the Bantu ever outward.

August 28, 2010

Nigerians agree despite religious differences

Filed under: Data Analysis,The Tenth Parallel,World Values Survey — Razib Khan @ 11:13 am

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.

Question Hausa Mus Yoruba Mus Yoruba Pent Yoruba Prot
% Lower Class 51 34 22 23
% Completed University 6.5 12 36 23
% No Children 35 38 40 47
% Married 59 55 63 48
% Male 54 54 45 50
% Politics Very Important 39 20 12 21
% Work Very Important 89 94 96 91
% Religion Very Important 97 90 90 90
% Would not like people of difference race as neighbors 28 25 13 30
% Would not like immigrants as neighbors 28 20 12 15
% Would not like Muslims as neighbors 5.2 4 10 15
% Would not like homosexuals as neighbors 81 90 90 84
% Would not like people of a different religion as neighbors 36 14 20
% Totally satisfied with life (1-10 scale) 22 8 14 8
% Totally satisfied with financial situation (1-10 scale) 16 6 6 5
%Men should have more right to job than women 74 60 47 54
% Natives should have more right to job than immigrants 87 87 87 84
Mean, Ideal # of children 5.8 4.5 4 4
% A woman needs children to be fulfilled 81 93 96 93
% Disapprove of woman has single parent 89 76 92 77
% One should enjoy sexual freedom 23 16 9 11
% Marriage is outdated 18 19 11 13
% Agree strongly that men make better political leaders 63 56 44 51
% Agree strongly that university is more important for boy 46 22 12 21
% Very important that a woman is educated 80 76 82
% We need radical change in society 27 32 28 38
% Need larger income differences as incentives (1-10 scale) 21 25 41 15
% Gov. ownership of business should be increased (1-10 scale) 31 21 21 9
% The gov. should take more responsible (1-10 scale) 31 40 44 27
% Competition is harmful (1-10 scale) 7.2 8.2 1.8 14
% success is matter of luck and connections (1-10 scale) 12 13 4 13
% Wealth grows so there’s enough for everyone (1-10 scale) 28 17 29 28
% A great deal of confidence in armed forces 47 14 8 12
% A great deal of confidence in police 40 10 4 10
% A great deal of confidence in government 41 6 2 12
% A great deal of confidence in justice system 36 11 10 8
% A great deal of confidence in women’s movement 30 17 18 18
Mean, self position Left-Right (1-10) 6 4.9 5.5 4.7
Mean, rating of political system (1-10) 3.8 2.8 2.3 2.3
% Very satisfied with how democracy develops 28 13 15
% Favors open borders for immigrants 19 33 14 32
% Willing to fight for country 83 60 55 38
% There is a lot of respect for individual human rights 25 14 12
% Scientific advances will help 84 85 79 88
% A religious person 97 97 98 95
% God is very important in life (1-10) 88 92 93 86
% Get comfort and strength from religion 99 99 98
% Attend religious services more than once a week 72 85 58 60
% Raised religiously 97 97 93 90
% Believe in God 100 99 100 100
% Believe in Life After Death 87 80 86 86
% Believe in Hell 91 93 98 95
% Believe in Sin 85 97 98 95
% Believe in Devil 96 98 99 100
% Religious institutions give moral answers 85 69 71
% Agree strongly people atheists are unfit for public office 65 63 58
% Homosexuality never justifiable (1-10) 81 84 91 81
% Cheating on taxes never justifiable (1-10) 66 69 79 60
% Prostitution never justifiable (1-10) 77 85 90 79
% Abortion never justifiable (1-10) 78 83 82 72
% Divorce never justifiable (1-10) 55 64 74 56
% Very proud of nationality 78 66 57 60

And here’s a correlation matrix:

Hausa Mus Yoruba Mus Yoruba Pent Yoruba Prot
Hausa Mus * 0.94 0.9 0.93
Yoruba Mus * * 0.97 0.98
Yoruba Pent * * * 0.97

The Yoruba and Hausa have a high degree of agreement irrespective of religion, but there does seem to be a tendency for the Yoruba to agree across the religious divide. On the political questions I think the historical context is important. Additionally, it seems that the Pentecostals are the most religiously conservative and enthusiastic of these groups. Because the Hausa tend to be culturally Muslim (though there are a large minority of Hausa Christians in the sample) as a matter of course I was not totally surprised that they were not as zealous as one presumes Muslims to be.

August 27, 2010

Daily Data Dump – Friday

Filed under: Blog,Daily Data Dump — Razib Khan @ 12:00 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.

Epistasis: Obstacle or Advantage for Mapping Complex Traits? They argue that it’s an advantage, and you can squeeze more juice by taking into account gene-gene interactions.

Genome-wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. There’s a model that unexpected deaths from infections which should be benign or asymptomatic are actually due to genetic variation. Specifically, these deaths run in families. Was there a time when everyone was symptomatic? It seems that this is a case where looking at indigenous populations who haven’t been as exposed to pathogens would be of interest.

Does Your Language Shape How You Think? It seems more a matter of degree if so.

Not the origin of genome complexity

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.

A quick reminder: effective population size denotes the proportion of the population which contributes genes to the next generation. So, in the case of insects with extremely high mortality in the larval stage the effective population size may be orders of magnitude smaller than the census size at any given generation evaluating over all stages of life history. In contrast, with humans a much larger proportion of children end up contributing to the genetic makeup of the subsequent generation. With large organisms I’ve heard you can sometimes use a rule of thumb that effective population size is ~1/3 of census size, though this probably overestimates the effective population size. One reason that reproductive variation reduces the effective population, because many individuals contribute far less to the next generation than other individuals. The greater the variance, the more evolutionary genetic variation is impacted by a few individuals within the population at a given generation, reducing effective population which contributes to the next (the reproductive variance is often assumed to be poisson, but that is likely an underestimate). Additionally, there is the issue of variation over time. Long term effective population is much more sensitive to low bound values than high bound values, so it is liable to be much smaller than the census size at any given period for a species which goes through cycles. Humans for example have a relatively small long term effective population size evaluated over the past 100,000 years because we seem to have expanded from a small initial population. Mathematically since long term effective population size is given by the harmonic mean it stands to reason that low bound values would be critical. If that doesn’t make sense to you, remember the outsized impact which population bottlenecks may have on the long term trajectory of a species, in particular by removing genetic variation.

How does this influence genome complexity? Basically Lynch’s thesis is that when you reduce effective population you dampen the power of natural selection, specifically purifying selection, from preventing the addition of non-adaptive complexity through random processes. It isn’t that selection is rendered moot, rather, its signal is overwhelmed by the noise. Here’s the abstract of his 2003 paper:

Complete genomic sequences from diverse phylogenetic lineages reveal notable increases in genome complexity from prokaryotes to multicellular eukaryotes. The changes include gradual increases in gene number, resulting from the retention of duplicate genes, and more abrupt increases in the abundance of spliceosomal introns and mobile genetic elements. We argue that many of these modifications emerged passively in response to the long-term population-size reductions that accompanied increases in organism size. According to this model, much of the restructuring of eukaryotic genomes was initiated by nonadaptive processes, and this in turn provided novel substrates for the secondary evolution of phenotypic complexity by natural selection. The enormous long-term effective population sizes of prokaryotes may impose a substantial barrier to the evolution of complex genomes and morphologies.

The implication here is that prokaryotes with massive population sizes are biased toward smaller genomes by the more efficacious application natural selection. In contrast, more complex organisms which have smaller population sizes, and so are more impacted by the random fluctuations generation to generation due to sample variance, are less streamlined genomically because selection can do only so much against the swelling sea of noise. One intriguing argument of Lynch is that the genomic complexity is then later useful downstream as the building block of phenotypic complexity, but let’s set that aside for now.

A new paper in PLoS Genetics challenges the statistical analysis of the original data which Lynch et al. used to make their case. Technically the argue was that there was an inverse relationship between Neu and genome size. Ne is effective population size, and u is nucleotide mutation rate. Though argument is technical, and the basic objection should be easy to understand: there are other variables which may actually be responsible for the correlation which Lynch et al. discerned. To the paper, Did Genetic Drift Drive Increases in Genome Complexity?:

Genome size (the amount of nuclear DNA) varies tremendously across organisms but is not necessarily correlated with organismal complexity. For example, genome sizes just within the grasses vary nearly 20-fold, but large-genomed grass species are not obviously more complex in terms of morphology or physiology than are the small-genomed species. Recent explanations for genome size variation have instead been dominated by the idea that population size determines genome size: mutations that increase genome size are expected to drift to fixation in species with small populations, but such mutations would be eliminated in species with large populations where natural selection operates at higher efficiency. However, inferences from previous analyses are limited because they fail to recognize that species share evolutionary histories and thus are not necessarily statistically independent. Our analysis takes a phylogenetic perspective and, contrary to previous studies, finds no evidence that genome size or any of its components (e.g., transposon number, intron number) are related to population size. We suggest that genome size evolution is unlikely to be neatly explained by a single factor such as population size.

lynchfig2In the original analysis by Lynch et al. ~66% of the variation in genome size was explained by Neu! That’s a pretty large effect. Figure 1 illustrates how phylogeny could be a confound in adducing a relationship. Here’s some of the text which explains the figure:

In this hypothetical example, eight species have been measured for two traits, x and y, as indicated by pairs of values at the tips of the phylogenetic tree (A). Ordinary least-squares linear regression (OLS) indicates a statistically significant positive relationship (B; r-squared = 0.62, P = 0.02), potentially leading to an inference of a positive evolutionary association between x and y. However, inspection of the scatterplot (B) in relation to the phylogenetic relationships of the species (A) indicates that the association between x and y is negative for the four species within each of the two major lineages. Regression through the origin with phylogenetically independent contrasts…which is equivalent to phylogenetic generalized least squares (PGLS) analysis, accounts for the nonindependence of species and indicates no overall evolutionary relationship between the traits…The apparent pattern across species was driven by positively correlated trait change only at the basal split of the phylogeny; throughout the rest of the phylogeny, the traits mostly changed in opposite directions (A; basal contrast in red)….

The argument then seems to be that the relationship in the original work by Lynch was an artifact due to the evolutionary history of the species which he surveyed to infer the relationship. Instead of a general principle or law then what you have is an outcome of contingent historical processes. Not very neat and clean. You can see the taxa-clustered nature of the relationship in figure 1 from the 2003 paper in Science:


OK, now let’s look at the visualization of the same data set from this paper, as a tree to illustrate the correlations:


lynchfig5The last figure shows the difference between a scatterplot using conventional OLS regression, and the phylogenetic least squares model (PGLS). You go from an obvious linear relationship, which translated into the high r-squared noted above, to basically nothing (r-squared near zero, no statistical significance).

The paper itself isn’t that long, the objection is pretty straightforward. They’re simply claiming that Lynch didn’t correct for an obvious alternative explanation/confound, and that we don’t know what we thought we knew. Additionally, there is the assertion that the idea that effective population size predicts genome size robustly is becoming conventional wisdom within the scientific community. I don’t know about that, this seems like such a young field in flux that I think they oversold how widespread this assumption is to make the force of their rebuttal more critical. Certainly the patterns in genome size can be quite perplexing, but my intuition is that an r-squared on the order of 2/3 of the variation in genome size being explained by one predictor variable is rather astounding. Obviously genome size is pretty easy to get in the “post-genomic era,” but Ne and u are harder to come by for many taxa, or even within a given taxon for a set of species of interest. It looks to me an opportunity for experimental evolutionalists, who can control the confounds, and observe changes within a lineage. And yet even if Neu is predictive as an independent variable all things controlled, what if all things are not usually controlled, and random acts of phylogenetic history are more important? Mike Lynch is credited in the acknowledgements, so I assume we’ll be seeing a response from him in the near future.

Citation: Whitney KD, & Garland T Jr (2010). Did Genetic Drift Drive Increases in Genome Complexity? PLoS Genetics : 10.1371/journal.pgen.1001080

Katz, 8-27-2010

Filed under: Blog,Katz — Razib Khan @ 9:48 am





Chosen genes of the Chosen People

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:

The Ashkenazi Jewish (AJ) population has long been viewed as a genetic isolate, yet it is still unclear how population bottlenecks, admixture, or positive selection contribute to its genetic structure. Here we analyzed a large AJ cohort and found higher linkage disequilibrium (LD) and identity-by-descent relative to Europeans, as expected for an isolate. However, paradoxically we also found higher genetic diversity, a sign of an older or more admixed population but not of a long-term isolate. Recent reports have reaffirmed that the AJ population has a common Middle Eastern origin with other Jewish Diaspora populations, but also suggest that the AJ population, compared with other Jews, has had the most European admixture. Our analysis indeed revealed higher European admixture than predicted from previous Y-chromosome analyses. Moreover, we also show that admixture directly correlates with high LD, suggesting that admixture has increased both genetic diversity and LD in the AJ population. Additionally, we applied extended haplotype tests to determine whether positive selection can account for the level of AJ-prevalent diseases. We identified genomic regions under selection that account for lactose and alcohol tolerance, and although we found evidence for positive selection at some AJ-prevalent disease loci, the higher incidence of the majority of these diseases is likely the result of genetic drift following a bottleneck. Thus, the AJ population shows evidence of past founding events; however, admixture and selection have also strongly influenced its current genetic makeup.

The sample size of Ashkenazi Jews was ~400, and they looked at ~700,000 SNPs. As I said, how Jews relate to other populations really isn’t at the core of this paper as it was in the earlier ones from the spring, but there were the PCA plots (sorry Mike), a frappe bar plot, and a phylogenetic tree derived from Fst statistic. Again, remember that PCA is showing you the largest independent components of genetic variation within the data. The bar plot has a set of ancestral populations of which individuals are composites of. And finally, Fst measures between population component of genetic variation. The larger the Fst across two populations the bigger the genetic distance.

Using the Druze & Palestinians as the ancestral Middle Eastern reference the authors estimated that the European admixture into Ashkenazi Jews is on the order of 30-55%. This is in the same ballpark as the previous studies, so no great surprise. As I stated in earlier posts the authors can spin the same results in very different ways. From what I can tell these authors are inclined to emphasize the strong possibility that in terms of genetic distance Ashkenazi Jews are somewhat closer to Europeans than they are to Levantine Arabs. Of course these sorts of assertions need to be handled with care. The genetic distance between Ashkenazi Jews and Tuscans is less than half that between Ashenazi Jews and Russians, while the Jewish-Russian value is about 50% larger than the Jewish-Palestinian one. Remember that there’s a fair amount of circumstantial evidence that Tuscans may themselves be a relatively recent hybrid population between indigenous residents of the Italian peninsula and Near Easterners.

ashjtab1One thing that this paper does do is rebut any strong assertion that Ashkenazi Jews are a genetically homogeneous population which went through a powerful bottleneck. Basically, the idea that Jewish diseases are just an outcome of the operational inbreeding that occurs when genetic variation is expunged from a population through low effective population size. The clincher seems to be comparison of heterozygosity of Ashkenazi Jews and gentile Europeans. The former are actually somewhat more heterozygous than the latter. There’s been a bit of evidence from previous research that the long term effective population size of Ashkenazi Jews was not necessarily very small, so this isn’t a total surprise. Remember that heterozygosity simply means the fraction of individuals heterozygous at a locus.

One way you can become heterozygous is naturally admixture. Remember that populations differ across many genes. As an example, there’s a pigmentation gene, SLC24A5, where all Europeans are at one state, and all West Africans in another. Naturally African Americans exhibit much more heterozygosity on this locus than the ancestral populations. The Ashkenazi Jewish case is less extreme because the two parental populations are genetically closer, but the principle still holds.

A consequence of recent admixture between genetically different populations are high levels of linkage disequilibrium, non-random associations of alleles at different loci across the genome. Why? There are many genes where two populations may be very different. Offspring inherit half their genome from one parent, and half from the other, and the parents pass along to their offspring particular associations of alleles. There may be a set of European distinctive alleles on a chromosome, and an African distinctive set of alleles, so that in a hybrid individual the alleles are strongly correlated across loci. These associations are broken down over time by recombination. The regularity of this process can serve as a clock with which to measure the period since admixture. African Americans were used to calibrate the time since admixture for the Uyghur people of western China, who are mixed from West and East Eurasian populations. The authors did not do this in this paper, I assume because the ancestral populations were genetically rather close in comparison to the two above examples, so there’d be less linkage disequilibrium to break down in the first place.

In the Ashkenazi Jewish population they found more linkage disequilibrium than in Europeans as well as longer haplotypes. This could be the result of a population bottleneck where drift could drive up the frequency of blocks of the genome, but as they note in the paper that should probably reduce heterozygosity. The natural inference then is that admixture between distinct populations can explain both data points.

ashslselectBut let’s cut to the chase. What genes exhibit signatures of natural selection in Ashkenazi Jews? More precisely, what distinctive regions of the genome exhibit signatures of natural selection? They used the standard haplotype type based methods. Basically you’re looking for regions of the genome where there are long blocks of correlated alleles, signs of a selective sweep due to a favored variant which dragged along flanking genomic regions as it rose rapidly in frequency, more rapidly than recombination could break apart the associations. Because recombination does breaks up associations over time, you need the selective sweeps to be relatively recent to detect them with these methods. Since the Jewish people, and Ashkenazi Jews more particularly, are relatively recent historically timing shouldn’t be an issue for Jewish specific sweeps. But another factor is that the two primary tests they used, EHH and iHS, are not good at picking up sweeps which are just starting. EHH is geared toward sweeps which are almost complete, so the frequency of the selected allele is near 100%. iHS is better are mid-range values. Using a combination of these two techniques they found that six genes which are implicated in diseases characteristic of Ashkenazi Jews have the hallmarks of natural selection. Natural selection is self-evident, so what seems to have been going here is that the disease was simply a side effect or byproduct of adaptation.

The strongest signal they found was in ALDH2. The strongest signal in Europeans, LCT, was not found in Ashkenazi Jews. But is LCT a strong signal in Europeans? Many Southern European populations have low frequencies of the derived LCT allele, indicating that they haven’t been subject to strong selection for lactase persistence. These are the same populations genetically close to the Ashkenazi Jews. The authors suggest that the Jewish-European admixture occurred before the sweep of the derived LCT allele, but it seems more plausible that the Ashkenazim simply admixed with a European population, such as Italians, which do not exhibit much lactase persistence. As for ALDH2, the association between genetic variation on this locus and alcoholism is well known, and has been used to explain the low Jewish rates of the disease. In this case, the authors posit that protection from alcoholism is a positive side effect of natural selection:

The mechanism driving selection of the ALDH2 locus is unknown, but a plausible target of selection also within this selected region is the TRAFD1/FLN29 gene, which is a negative regulator of the innate immune system, important for controlling the response to bacterial and viral infection (49). TRAFD1/FLN29 may have conferred a selective advantage in the immune response to a pathogen, perhaps near the time that the Jews returned to Israel from their Babylonian captivity. Despite the unclear selective mechanism, this remains a remarkable example of a putatively selected region accounting for a known population phenotype.

Many of the other loci naturally did not show signatures of natural selection. But this sort of work is exploratory, and there are limits to the power of their techniques. As it is, it seems that we’re very far along on understanding the phylogenetic tree of the Jewish people, and we’re finally getting a grip on the exogenous parameters which might prune the branches.

Citation: Steven M. Bray, Jennifer G. Mulle, Anne F. Dodd, Ann E. Pulver, Stephen Wooding, & Stephen T. Warren (2010). Signatures of founder effects, admixture, and selection in the Ashkenazi Jewish population PNAS : 10.1073/pnas.1004381107

Related: John Hawks, New data on Ashkenazi population history.

Image Credit: Wikimedia

August 26, 2010

Size doesn’t always matter

Filed under: Anthroplogy,Ötzi,Sample Size — Razib Khan @ 10:56 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).

Daily Data Dump – Thursday

Filed under: Blog,Daily Data Dump — Razib Khan @ 10:29 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.

Our advice re: donations for Pakistan flood. The idea is to get the most bang-for-your-buck. From what I have heard ~20 million people have been impacted by the floods. I guess it gives you a sense of what a Pakistani peasant’s life is worth to the world.

Generation X More Loyal to Religion. This looks more likely to just be the law of diminishing returns. The disaffection of the Baby Boomers from organized religion correlates with a relaxation of social norms. The distribution of religiosity among Gen-X probably more accurately reflects their individual preferences.

This Hauser thing is getting hard to watch. David Dobbs reviews some of the issues with l’affaire Hauser. Basically everyone who is a blogger of note seems to be getting emails from people who wish to remain anonymous. Draw whatever conclusions you want to from that.

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