Archive for October, 2011

The unbearable thinness of Denisovan

By Razib Khan | October 31, 2011 11:54 pm

A new paper in PNAS, Archaic human ancestry in East Asia: “These results suggest admixture between Denisovans or a Denisova-related population and the ancestors of East Asians, and that the history of anatomically modern and archaic humans might be more complex than previously proposed.” It’s open access, so do go read it. John Hawks has a long rumination. My main thought is that I’m starting to think that people are squeezing this orange too much. I wouldn’t be surprised if the broad conclusions here are correct, and in fact I’d lean in that direction. But is the discovery of relatively trace ancestry all that earthshaking? The reality is that a little over a year ago the interpretative framework of science in this area shifted. That was because of the concreteness of ancient DNA, which allowed for a direct comparison, instead of statistical sifting through the genomes of extant populations. Remember, before 2010 there were plenty of papers utilizing subtle statistics and computational muscle which “proved” and “confirmed” an Out-of-Africa with replacement model. The power and precision of these techniques tended to overshadow the reality of a margin of error, and uncertainty in their conclusions. We need to be cautious when the machinery turns itself in the opposite direction, gleaning glimpses of what we now know is likely there….

CATEGORIZED UNDER: Anthroplogy, Human Evolution
MORE ABOUT: denisovan

Sunday Stuff – October 30th, 2011

By Razib Khan | October 30, 2011 6:49 pm

FF3

Something different today. First, an elegant international cat:

Second, reading Madagascar: A Short History prompts me to repost a very long essay I wrote ~3 years ago. I have some new ideas in the area of the evolution of religious institutions, which I want to work out in a new essay. But that’s going to have to occur when I have a long period of time to focus on something like that, and that I do not have currently.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Blog

When genetics comes in handy in politics

By Razib Khan | October 30, 2011 1:21 pm

In Mother Jones Andrew Serwer has a long profile up of a Mitt Romney adviser who has associations with Lebanese Christian sectarian radicals. This section jumped out at me:

Régina Sneifer, who served in the Fifth Bureau in 1981 at the age of 18, remembers attending lectures where Phares told Christian militiamen that they were the vanguard of a war between the West and Islam. She says Phares believed that the civil war was the latest in a series of civilizational conflicts between Muslims and Christians. It was his view that because Christians were eternally the victims of Muslim persecution, the only solution was to create a national home for Christians in Lebanon modeled after Israel. Like many Maronites at that time, Phares believed that Lebanese Christians were ethnically distinct from Arabs. (This has since proven to be without scientific basis.)

The scientific issue is actually a little more complex than Serwer comprehends. It is true that Muslims and non-Muslims in any given region share a lot genetically, but non-Muslim minorities in the Middle East have gone through a long period of endogamy and demographic contraction, resulting in genetic differences (mostly obviously, they seem to have less Sub-Saharan African admixture than their Muslim neighbors). But the interesting point is how widespread genetic information is now becoming in trying to understand various issues. Serwer is broadly correct I’d say that the Maronite radicals who argue for a strong separation between the origins of their own people and the Muslim and Druze of Lebanon are not on solid basis, just as Muslim Arabs who believe that they are predominantly descended from Arabians are also not on solid ground.

CATEGORIZED UNDER: Culture, Human Genetics
MORE ABOUT: Ethnicity

Never seen such a candidate….

By Razib Khan | October 30, 2011 12:35 pm

In case you haven’t seen these….

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CATEGORIZED UNDER: Uncategorized

Evolution skeptical: not just fundamentalists

By Razib Khan | October 30, 2011 11:36 am

 

In the comments below Christopher Mims states:

But evolution? It seems as if denial of evolution comes from a place so basic — religious fundamentalism — that I wonder whether something like this could ever have even the slightest impact.

It’s hard to deny the relationship of religious fundamentalism and evolution denial and skepticism. But, I think it’s important to remember that in the United States the large critical mass of evolution-denying religious fundamentalists has resulted in a “bleed over” of the stance to people who aren’t religious fundamentalists. I know this anecdotally from friends who were of Roman Catholic and Mormon backgrounds who presumed that their religious orientation precluded an acceptance of evolution. In fact, my own first awareness that people might actually not believe in evolution came via a conversation with an evolution skeptic friend who was a nominal Roman Catholic. Nominal in that his family actually never went to church.

What Paul Bloom’s research suggests is that humans find the Creationist narrative intuitively plausible. But, the critical issue is that those who aren’t indoctrinated against the idea of evolution can be convinced of its plausibility.

Let’s look at how this distributes across society using the General Social Survey. The variable BIBLE asks if people think that the Bible is the actually word of god, the inspired word of god, or a book of fables, etc. This seems to be a reasonable approximation of whether one is a fundamentalist, a non-fundamentalist who still accepts the revealed nature of the Bible, or someone who denies the supernatural grounding of the Bible in totality. There are two evolution related questions I can cross with BIBLE. EVOLVED, which asks if humans developed from an earlier species of animal with a true/false response, and SCITEST4, which asks the same question but has a more graded set of responses. Please note that EVOLVED was asked in the mid-to-late 2000s, while SCITEST4 was asked in the 1990s.

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CATEGORIZED UNDER: Creationism, Evolution
MORE ABOUT: Creationism, Evolution

Evolutionary imperialism

By Razib Khan | October 30, 2011 3:16 am

So there’s a slick new webzine coming out, Evolution: this view of life. It’s another one of David Sloan Wilson’s projects. I don’t agree a lot with the specifics of David’s theories, but I admire his ambition. James Winters pointed me to the fact that they’re trying to raise money for this webzine via KickStarter. Their goal is $5,000. Having run much more bare bones websites for years this seems like a really modest amount in relation to their aims. I admire David’s attempts in this area enough that I gave some money. He tries a lot of things, many of which don’t succeed, but that’s science….

CATEGORIZED UNDER: Evolution
MORE ABOUT: Evolution

Notes on comments

By Razib Khan | October 30, 2011 2:59 am

I dislike cluttering this site with administrative notes, but I want to put this post up as a reference for the future. It’s not really aimed at regular readers/commenters, who know the explicit and implicit norms.

1) If you use quotation marks, make sure that you’re actually quoting something your interlocutor said, rather than adding them for effect (yes, believe it or not, people have quoted me, where the “quotes” were actually their own interpretation of what I intended)

2) It is generally not best to paraphrase someone else’s argument in your own words as a prologue to your own comment. Just quote the appropriate sections of text in your reply if you want it to frame your response. If you are engaging in paraphrasing to distill the argument of your interlocutor down to a pith, understand that subconscious tendencies are such that you’ll reshape that argument to better suit your response. In other words, you’re probably arguing with your own conception of their argument, not their argument as such. More maliciously some people just paraphrase because it makes setting up a straw man so much easier. That’s not nice. I have wasted a fair amount of time rereading posts to try and figure out how commenters came to a particular perception of my argument. I don’t take kindly to people telling me what I obviously really think, when I point out that their perception was wrong.

3) From that you can gather that inferring “between the lines” isn’t appropriate in most cases. It is part of normal human cognition, and you can’t help it to some extent. But being too liberal about the practice means that you’ll just distort the argument of the other person, who then has to waste their time correcting your misunderstandings. This gums up the exchanges because people have only a finite amount of time. Read as plainly as possible.

4) There’s no presumption here of symmetry. If the host asks you a direct question, answer and don’t evade. If the host tells you to drop a topic, don’t make the case for why you shouldn’t drop the topic. Wasting time trying to argue these issues is a banning offense.

5) I’m busy, and getting busier. I don’t respond well to people wasting my time. Some of the other commenters are busy too. It’s important to make exchanges “count.” Excessive posturing, and an obvious fixation on “winning” arguments with clever ripostes, are bannable offensives.

I’m not taking comments on this post, because as I said this post is more a placeholder so I don’t have to have the same stale argument over & over.

Note: See this companion post.

CATEGORIZED UNDER: Blog
MORE ABOUT: Admin, Blog

Unfrying the egg

By Razib Khan | October 29, 2011 4:17 pm

Dienekes has a long post, the pith of which is expressed in the following:

If I had to guess, I would propose that most extant Europeans will be discovered to be a 2-way West Asian/Ancestral European mix, just as most South Asians are a simple West Asian/Ancestral South Indian mix. In both cases, the indigenous component is no longer in existence and the South Asian/Atlantic_Baltic components that emerge in ADMIXTURE analyses represent a composite of the aboriginal component with the introduced West Asian one. And, like in India, some populations will be discovered to be “off-cline” by admixture with different elements: in Europe these will be Paleo-Mediterraneans like the Iceman, an element maximally preserved in modern Sardinians, as well as the East Eurasian-influenced populations at the North-Eastern side of the continent.

This does not seem to be totally implausible on the face of it. But it seems likely that any “West Asian” component is going to be much closer genetically to an “Ancestral European” mix than they were to “Ancestral South Indians,” because the two former elements are probably part of a broader West Eurasian diversification which post-dates the separation of those groups from Southern and Eastern Eurasians. In other words, pulling out the distinct elements in Europeans is likely a more difficult task because the constituents of the mixture resemble each other quite a bit when compared to “Ancestral North Indians” vs. “Ancestral South Indians.”

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CATEGORIZED UNDER: Agriculture, Anthroplogy

In it for the long run

By Razib Khan | October 29, 2011 1:59 pm

Over the past six months we’ve seen the “Libyan revolution” stall and then succeed. There’s no doubt that the late Libyan dictator was a marginally sane megalomaniac. That being said, he’d been on better behavior over the past 10 years, dismantling his nuclear program for example. I can see the logic in wanting to overthrow him though, there’s a lot of built up historical memory in relation to the various terrorist groups he’s funded in Europe, as well as actions like bombing of Pan Am 103. But is anyone really surprised when things like this occur:

It was just a passing reference to marriage in a leader’s soberly delivered speech, but all week it has unsettled women here as well as allies abroad.

In announcing the success of the Libyan revolution and calling for a new, more pious nation, the head of the interim government, Mustafa Abdel-Jalil, also seemed to clear the way for unrestricted polygamy in a Muslim country where it has been limited and rare for decades.

It looked like a sizable step backward for women at a moment when much here — institutions, laws, social relations — is still in play after the end of Col. Muammar el-Qaddafi’s 42 years of authoritarian rule.

In his speech, Mr. Abdel-Jalil declared that a Qaddafi-era law that placed restrictions on multiple marriages, which is a tenet of Islamic law, or Shariah, would be done away with. The law, which stated that a first wife had to give permission before others were added, for instance, had kept polygamy rare here.

“This law is contrary to Shariah and must be stopped,” Mr. Abdel-Jalil told the crowd, vowing that the new government would adhere more faithfully to Shariah. The next day he reiterated the point to reporters at a news conference: “Shariah allows polygamy,” he said. Mr. Abdel-Jalil is known for his piety.

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CATEGORIZED UNDER: International Affairs
MORE ABOUT: Libya

Ancient DNA in the near future

By Razib Khan | October 29, 2011 1:27 pm

I recently inquired if anyone was sequencing Cheddar Man. In case you don’t know, this individual died ~9,000 years ago in Britain, but the remains were well preserved enough that mtDNA was retrieved from him. He was of haplogroup U5, which is still present in the local region. Cheddar Man is also particularly interesting because he is definitely a Paleolithic hunter-gatherer, predating the Neolithic in Britain by thousands of years.

It turns out that no one is looking at Cheddar Man now. But that’s probably because money and time are finite. I was told that there are plenty of other specimens which would also probably be good candidates for sequencing in the Museum’s collection (this doesn’t seem to be a case where curators are being stingy and overprotecting of their specimens). That’s not too surprising. We’ll probably answer a lot of questions about the roles of demographic diffusion vs. cultural diffusion when it comes to agriculture soon enough (as in, over the next 10 years as techniques for getting signal out of old degraded and contaminated samples get better).

Prediction is very hard

By Razib Khan | October 28, 2011 1:17 am

Nate Silver has an important post, Herman Cain and the Hubris of Experts. It’s not really about Herman Cain. Rather, it’s about the reality that pundits tend to underestimate uncertainty and complexity. Saying you don’t know isn’t as satisfying as making a definitive categorical assertion. This manifests particularly in the domains of sports and politics because there are clear and distinct criteria to assess predictive power. Politicians win or lose elections, while teams win or lose games. And yet despite the long history of minimal value-add on the part of pundits they persist in both domains. Why? I think it’s pretty obviously a cognitive bias toward storytelling. Similarly, in the 1930s the Alfred Cowles concluded that financial newsletters didn’t help their readers “beat the market,” but he also assumed these newsletters would persist. There was a psychological need for them.

The key here is to change the attitude of the pundit class. The populace will always have a preference for stories with plausible and clean conclusions over radical uncertainty. Not surprisingly many professional pundits reacted with hostility to Silver’s observation that they’re quite often wrong. I don’t venture into political punditry often, but when the Democrats passed health care reform I predicted that Mitt Romney would have no shot to win the the Republican nomination. The facts in this case seemed so clear. Romney was going to be walloped over and over again over his record on health care reform when he was governor. I was wrong. Romney may not win, but obviously he’s a contender. My logic was simple and crisp, but the logic was wrong. That’s why you let reality play out. If what was “on paper” determined national elections, then we’d be talking about President Hillary Clinton.

Of course political journalists that engage in analysis still have a role to play. Don’t newspapers have horoscopes and style sections?

CATEGORIZED UNDER: Politics
MORE ABOUT: Epistemology

America has had 'non-Christian' presidents!

By Razib Khan | October 26, 2011 10:36 pm

A few weeks ago over at Slate Dave Weigel stated that “Electing Mitt Romney in 2012 would mean electing, for the first time, a president whose religion is not part of orthodox Christianity.” I tweeted to Weigel that this was just plain wrong. There have been plenty of presidents who rejected orthodox Christianity, the last one being William Howard Taft, a Unitarian who rejected the Trinity. And now Jeffrey Goldberg is saying the same thing in Bloomberg View:

But theological honesty demands that we recognize that. Romney would be the first president to be so far outside the Christian denominational mainstream.

There is much in Mormonism that stands in opposition to Christian doctrine, including the belief that the Book of Mormon completes the Christian Bible. Christianity had an established creed about 1,500 years before Joseph Smith appeared in upstate New York with a new truth, codified in the Book of Mormon, which he said was revealed to him by an angel named Moroni.

“The Nicene Creed and the Apostles’ Creed settled the basic ideas of Christianity,” said Michael Cromartie, an evangelical who is vice president of the Ethics and Public Policy Center in Washington. “The canon was closed, and then Joseph Smith comes along and says that there’s a new book, an extra-biblical addition to the agreed-upon canon.”

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CATEGORIZED UNDER: Religion
MORE ABOUT: Mormons, Religion, Romney

1000 Genomes Tutorial

By Razib Khan | October 26, 2011 8:05 pm

I don’t have time for this, but I’m sure some readers do. 1000 Genomes has put a tutorial up. Breakdown:

1. Description of the 1000 Genomes Data, Gabor Marth pdf|pptx

2. How to access the Data, Paul Flicek pdf|pptx

3. Lessons in variant calling and genotyping, Hyun Min Kang pdf|pptx

4. Structural Variants, Ryan Mills pdf|pptx

5. Imputation in GWAS studies, Bryan Howie pdf|pptx

 

All Slides in PDF

CATEGORIZED UNDER: Genomics, Human Genomics
MORE ABOUT: 1000 Genomes

In the year 2011….

By Razib Khan | October 25, 2011 6:45 pm

Follow up to the previous post, (Via Ed), Fetal gene screening comes to market:

Until last week, scrutinizing a fetus’s DNA for indications of genetic abnormalities meant tapping into the mother’s womb with a needle. Now there’s a test that can do it using a small sample of the mother’s blood. MaterniT21, a Down’s syndrome test that Sequenom of San Diego, California, launched in major centres across the United States on 17 October, is the first of several such tests expected on the market in the next year. It signals the arrival of a long-anticipated era of non-invasive prenatal genetic screening, with its attendant benefits and ethical complications….

In the “news your can use” section of their press release:

The out-of-pocket cost of the test for insured patients will be no more than $235. Sequenom CMM will initially operate as an out-of-network provider to ensure eligible patients will have coverage for the test. While negotiating to ensure coverage by most major private insurance programs, the reimbursement for the test is expected to be similar to that of current invasive procedures like amniocentesis or CVS.

CATEGORIZED UNDER: Personal Genomics

The perils of human genomics

By Razib Khan | October 25, 2011 1:45 pm

A friend pointed me to the heated comment section of this article in Nature, Rebuilding the genome of a hidden ethnicity. The issue is that Nature originally stated that the Taino, the native people of Puerto Rico, were extinct. That resulted in an avalanche of angry comments, which one of the researchers, Carlos Bustamante, felt he had to address. Eventually Nature updated their text:

CORRECTED: This article originally stated that the Taíno were extinct, which is incorrect. Nature apologizes for the offence caused, and has corrected the text to better explain the research project described.

Here’s Wikipedia on the Taino today:

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Admixture in Madagascar

By Razib Khan | October 25, 2011 2:49 am

In my spare time today I went through much of Madagascar: A Short History. After reading it I’m even more convinced that people need to stop talking authoritatively about this island and its people. There’s a lot of interesting material in it, but ultimately the years before European contact remain very shadowy. I don’t know much new about this period. This brings me to why I’m putting this post up: I am going to try and see if I can estimate an average age of admixture for my two Malagasy individuals. Hold me to it. I’ll make time.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Madagascar

John McCarthy, 1927-2011

By Razib Khan | October 24, 2011 10:20 pm

John McCarthy has died. Sadly I was expecting this, I was told that McCarthy was still teaching courses in 2008 by someone in Stanford’s computer science department, but he was in obvious bad health. One of the major downsides of the incredible information flow in the internet age is that you often hear through the grapevine that eminent so-and-so is ill, and have to prepare yourself years ahead for the inevitable. We all die, but it seems starker in the case of those individuals who have grasped upon a fragment of the sort of immortality given to Gilgamesh.

In the early to mid-2000s I had some conversations and arguments with McCarthy about the history of Islam and the politics of the Middle East (in hindsight I knew a lot more about the former than I did the latter). He followed Gene Expression now and then in the course of his meanderings around the web. Initially I did not make the connection that this was the John McCarthy, which was especially ironic in that I was playing at learning Lisp at that moment! Outside of his domains of almost godlike achievement I have to say that McCarthy was a relatively no-nonsense down to earth person from what little I could gather. He was curious about what he didn’t know, and if you weren’t aware that he was one of the most accomplished computer scientists in the world he didn’t seem too keen on cluing you in. My own overall impression was that he was a deep pragmatist and skeptic.

CATEGORIZED UNDER: Technology
MORE ABOUT: John McCarthy

Ötzi, the dead sea scrolls of genomics?

By Razib Khan | October 24, 2011 3:48 pm

Dienekes points me to the fact that Ewen Callaway has the dirt on what’s going on with Ötzi:

To get a better grip on his ancestry and predisposition to disease, Albert Zink, head of the Institute for Mummies and the Iceman in Bolzano, and his team sequenced Ötzi’s 3 billion base pair nuclear genome from a shard of hip bone. Their sequence covers more than 90 percent of the Iceman’s genome. Their team also analysed DNA preserved in Ötzi’s stomach in hopes of revealing the microbes that colonized his gut.

Zink says his team is keeping most of the results of these studies under wraps, pending publication. They had hoped to have the paper out in time for last week’s Mummy Congress and a television special called Iceman Murder Mystery.

His team plans to use the sequence to determine Ötzi’s status for genetic variations linked to diseases in modern humans, particularly arthrosclerosis. A full nuclear genome will also paint a more detailed picture of the Iceman’s ancestry and his relationship to present-day humans. Zink’s team will ask whether Ötzi is an ancestor of people living in Central Europe today, or whether he and his kin died out and were replaced by migrants from elsewhere, such as the Middle East. To buff up this analysis, they are analysing DNA preserved in the skeletons of other ancient inhabitants of central Europe.

~90 percent of a genome is way more than you’d need for some basic analysis and inference of relationships to contemporary populations. So what’s the big deal? No idea, but this tardiness makes me turn the needle up in terms of assuming that they found some interesting stuff. If it’s what you’d expect, why recheck and beef up your analysis with as much support as you can find? Of course, I hope that they found some interesting stuff, so I shouldn’t trust my own judgments in this area. My own suspicion is that they have found extensive genetic turnover over the past 6,000 years in Western Europe, and they are using modern and ancient samples to flesh-out their model. The two dominant paternal haplogroups in Europe today, R1a and R1b, are suspiciously scarce in the ancient DNA samples.

CATEGORIZED UNDER: Genomics, Human Genomics
MORE ABOUT: Ötzi, Ötzi the Iceman

Think right, not deep

By Razib Khan | October 24, 2011 2:19 am

Over the past few weeks I’ve been observing the response to Rick Scott’s suggestion that Florida public universities focus on STEM, rather than disciplines such as anthropology. You can start with John Hawks, and follow his links. More recently I notice a piece in Slate, America Needs Broadly Educated Citizens, Even Anthropologists. There several separate issues here. Superficial concerns of money going to your political antagonists, commonsense considerations of the best utilization of public educational resources, and broader reflections upon the nature of a ‘liberal’ education.

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CATEGORIZED UNDER: Science
MORE ABOUT: Science

The Ötzi embargo

By Razib Khan | October 23, 2011 4:57 pm

Dienekes has some harsh words for the way some science is produced, focusing on the genome of Ötzi the Iceman as a case in point:

Yesterday, I twitted in exasperation that Otzi’s genome, which must have been available in at least some sort of draft form since at least the beginning of this year, has been under lock and key, presumably because of the need to make a big splash with the simultaneous Bolzano conference, TV special, likely imminent journal publication, and all the media stories that will follow.

What I don’t understand: how come no one is editing the Wikipedia entry ahead of time? I wonder in hindsight if there’s no there, there, though I hope I’m wrong about this. Going by the lack of media mention of ahead of the NOVA documentary I do suspect we’re seeing the calm before the embargo explosion.

MORE ABOUT: Ötzi
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