Archive for September, 2011

Saturday Stuff – September 17th, 2011

By Razib Khan | September 17, 2011 12:32 pm

FF3

Very busy week. I don’t have time to look for past posts and I haven’t been reading the comments closely, so I’m skipping those.

1) Weird search query of the week: “why, according to christian, did foragers become farmers?.”

2) And finally, your weekly fluff fix:

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CATEGORIZED UNDER: Blog
MORE ABOUT: Friday Fluff

Not the great stagnation

By Razib Khan | September 16, 2011 1:13 am

Dan MacArthur points me to this story on the sequencing of the West family. You can read the full paper in PLoS Genetics. When the price point for a full genome comes down to $1,000 or so I plan on getting the code for everyone in my immediate family, just like I got everyone genotyped (the latter was cheaper, but a full genome is a much richer data set for intra-familial comparison).

I generated the chart from the figures quoted in the article about the cost of full genome sequencing. I’m moderately familiar with this trend, but it still boggles my mind that we’ve shifted two orders of magnitude in four years! Nice to know that in some domains progress continues.

CATEGORIZED UNDER: Genetics, Genomics, Personal Genomics

Shades of 2050

By Razib Khan | September 16, 2011 12:49 am

I have long had a problem with projections of the racial makeup of the USA which implicitly neglect the complexities inherent in the identity of someone of mixed origin. A new study analyzing Census data on interracial marriages between 1980 and 2008 highlights some of the subtleties:

The study also examined trends in biracial and cohabiting Americans.

The study found that people who classified themselves as white-Asian or white-American Indian were more likely to marry whites than Asians or American Indians.

“The rise in America’s multiracial population blurs racial boundaries,” Lichter said.

However, black-white biracial people are still more likely to marry blacks than whites.

First, the simplest way to state the implications of these data is that whites are becoming more Asian and American Indian, while blacks are becoming whiter. At least in terms of ancestry if not identity.

Consider the case of the actor Dean Cain, born Dean Tanaka. His paternal grandfather was of Japanese ancestry. He has a son with ex-girlfriend Samantha Torres. She happens to be a blonde and blue-eyed Spanish model. By the cultural norms of hypodescent Christopher Dean Cain is not a non-Hispanic white. If you have too many people who “look white” but have non-European ancestry hypodescent is not feasible. That was not the case for the United States of America for most of its history. But by 2050 the situation may be very different, and the cultural landscape of race and ethnicity may be very different.* I suspect that many of the assumptions we make about the world of 2050 by naively projecting out growth rates and the cultural mores of 2010 are going to fall into the “not even wrong” category.

* In many Latin American nations it is obviously not the case that mestizos make common cause with indigenous people against white elites as “people of color.”

CATEGORIZED UNDER: Anthroplogy, Culture

Google+, very different from Facebook

By Razib Khan | September 15, 2011 12:35 pm

TechCrunch has a post up on the declining public usage of Google+. It’s been several months since I’ve been “using” Google+. I put usage in quotes because I am not a big active poster on twitter, Facebook, or Google+. But I do participate passively a fair amount. At this point for me I can say that Google+ is turning into a very different beast from Facebook. I have 70 people in a circle labeled “Friends,” but well over 700 in another labeled “Internet.” The latter category are those individuals who I basically don’t know, but usually know of me. Recall that I purposely limited the number of individual who I invited to Google+. So I’ve been passive the whole time. At this point I suspect that within ~3-4 months, at current rates, I will have more people in my Google+ circles than who follow me on twitter.

And remember, I raised the funds to defray the cost of a genotyping kit via Google+. That’s worth something. I didn’t get any response on twitter or Facebook. Why? I think because Facebook is strongly biased toward people who I know in real life, not all of whom share my obsession with personal genomics. My twitter followers exhibit a stronger concordance of interests, but still far less than those people who sought me out on Google+.

CATEGORIZED UNDER: Technology
MORE ABOUT: Google

Poll on personal genomics

By Razib Khan | September 14, 2011 10:08 pm

Genomes Unzipped points me to a Nature survey on personal genomics for scientific researchers. With price points down to $200 or so many scientists have been at least genotyped. Though it varies by domain. Many molecular biologists seem intrigued by the novelty of personal genotyping services. In contrast, in a room of a dozen or so population geneticists and the like nearly half are liable to have already gone through some service.

All that being said, I haven’t heard from people who want to make their genotype public in a long, long, time. Has the steam run out of that project? You might hear from me again with a subtle twist on this in the near future.

CATEGORIZED UNDER: Personal Genomics

Ötzi, first, but not last, farmer?

By Razib Khan | September 14, 2011 9:59 pm

Dienekes relays that Ötzi the Iceman carried the G2a4 male haplogroup. He goes on to observe:

We now have G2a3 from Neolithic Linearbandkeramik in Derenburg and G2a in Treilles in addition to Ötzi from the Alps. G2a folk got around. He joins Stalin and Louis XVI as a famous G2a.

It was already clear with the discovery of G2a in France and Central Europe, that this otherwise uncommon present-day haplogroup in Europe was more prominent during the Neolithic, and Ötzi’s data point seals the case.

In a sense, the triple G2a finds in Neolithic Europe confirm the origins of the European Neolithic population in West Asia, but renew the mystery as to how all the rest of the “players” of the European Y-DNA scene appeared on the scene, with everything except G and I first appearing in the ancient DNA record after the end of the Neolithic.

Yes, I believe that the Paleolithic-Neolithic dichotomy is more hindrance than help in understanding the European past (the Paleolithic itself may have exhibited more population turnover than we can appreciate). I suspect that the two most common European Y haplogroups, R1a and R1b, underwent rapid increase in frequency over the past ~5,000 years. I do not believe that this is necessarily representative of the rest of the genome. The spread of male lineages can be rather unrepresentative.

In other news, Ötzi’s genome is going to drop any day now. My prediction that it’s more West Asian than we might have expected seems more plausible, though less surprising and risky, at this point.

Image credit: 23andMe

CATEGORIZED UNDER: Anthroplogy, Human Genetics
MORE ABOUT: Ancient DNA, Iceman, Ötzi

When all probable things can not be right

By Razib Khan | September 14, 2011 8:35 pm

I’ve been chewing on the modern human range expansion into Neandertal territory paper for a few days now. But I haven’t been able to bring myself to say much. There are two reasons. First, it’s a simulation paper, and I don’t exactly know what I can say besides being skeptical of the plausibility of some of their results and their assumptions, unless I bother to replicate their simulations. There’s something of a “black-box” aspect from the outside operationally in the case of these sorts of research. Second, Ed Yong has boiled down the paper to its essence rather well, while John Hawks and Dienekes have offered their critiques. Dienekes and John get at one of my gnawing worries about all these sorts of models about deep history. Here’s John:

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Rick Perry and his transcript

By Razib Khan | September 14, 2011 3:05 pm

This piece in The New York Times goes through the A’s, B’s, C’s, D’s, and F’s, of Rick Perry’s transcript. Two questions which come to mind:

1) If we know this about Perry, why shouldn’t we know this about all the candidates? I don’t know what getting a B in business law and a D in principles of economics means, but it’s kind of interesting, with the latter being alarming. My liberal friends are generally in awe of Barack Obama’s intellect, so there shouldn’t be any objection from that quarter.

2) If Perry is so dull & lazy, how was it that they let him fly a plane as a pilot? Perhaps he wasn’t academically motivated? Or perhaps in the 1970s the standards in the military were low enough that a marginal college graduate sufficed.

CATEGORIZED UNDER: Politics
MORE ABOUT: Rick Perry

Personal genomics & rare populations notes

By Razib Khan | September 14, 2011 12:32 pm

I’m going to address two points in this post. The next possible target for getting an undersampled population, and the Malagasy results.

First, lots of great submissions in regards to populations which are undersampled. Some of them are actually already in the data sets. For example, the Burusho and Kalash are in the HGDP. There has been a major dump of data from the Americans recently as well. Zack Ajmal at HAP has the most systematic description online about where to find these that I know of. Additionally, I’m looking for stuff which is interesting where N = 1 would make a difference. I think that was the case for the Tutsi sample, as well as the Malagasy. When you have no prior information, adding one data point is notable. Obviously I can’t afford the money, time, and energy, required to get a good representative sample from a given region. Though I hope researchers who have a gusher of grant money might look at the above thread for ideas.

I think the next population to look for is someone with Ainu ancestry. This is easier said that done, so I need to think about it (both because of dilution and the language barrier). But then again, the Tutsi and Malagasy requests had a much more positive and faster turnaround than I had expected. So I’m not going to get all down about the likelihood.

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Neandertal introgression and admixture

By Razib Khan | September 12, 2011 3:11 pm

Ed Yong has a good good review of a new Neandertal introgression/admixture paper in PNAS. It’s not live on the web yet, so let me quote Ed:

Even if the odds of successful interbreeding were just 5 percent, Neanderthal genes would make up the majority of the human genome today. As it is, a lack of viable sex explains why none of the Neanderthals’ mitochondrial DNA made its way into modern humans, and why so little of their main genome did.

Currat and Excoffier suggest that either modern humans and Neanderthals didn’t have sex very often, or their hybrids weren’t very fit. They favour the first idea. According to their model, it would only have taken between 197 and 430 liaisons between ancient humans and Neanderthals to fill 1-3 percent of modern Eurasian genomes with Neanderthal DNA. Considering that they two groups probably interacted for 10,000 years or so, it would have been enough for one human to sleep with one Neanderthal every 23 to 50 years.

From what I gather in the comments this is due to the fact that if there was a wave of advance very small levels of admixture per unit of advance can build up rather rapidly. I think this is easy to express in temporal rather than spatial terms.

For example, let’s imagine a population of modern humans expanding into a population of Neandertals. The original source population doesn’t receive any more contributions after the initial push, so you have a series of admixture events over time. Assuming 5% admixture per generation, this is the dilution of the “original ancestry” which would occur over 30 generations, or 750 years:

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Which undersampled groups would you like to see?

By Razib Khan | September 9, 2011 10:22 pm

To my excitement I got the Tutsi (almost) and Malagasy genotypes. These are cases where N = 1 is a big deal, as opposed to N = 0. What other groups might be informative? Most of the world’s population is obviously not sampled, but they’re not always of equal interest. What would be equivalent to the Tutsi (politically relevant) or Malagasy (demographically very unique)? If I solicit funds to pay from someone’s genotyping it won’t be a successful solicitation if the interest is very narrow.

CATEGORIZED UNDER: Blog
MORE ABOUT: Blog

The Merina of Madagascar are Malay and Bantu

By Razib Khan | September 9, 2011 12:46 pm

A month ago I asked for a Malagasy genotype. Almost immediately I received a response from someone that was 33% Malagasy. More recently I have sent a genotyping kit to someone who is Malagasy. Those results should come in within a month or so. But a few days ago I received a contact from a person of the Merina ethnic group of highland Madagascar. So of course I ran their data.

Here are the technical logistics. I wanted to look at their genotype through an African and a Southeast Asian lens. So I created an African loaded data set with 400,000 markers. Unfortunately the Southeast Asian data set I have has only 56,000 markers, and only 18,000 in common with this genotype. I ran ADMIXTURE on the former data set, K 2 to K 11. But at only 18,000 markers I think there just isn’t enough to run ADMIXTURE and make inferences of the grain which I want to make. So I ran EIGENSOFT to generate PCA’s. I did this for the African data set too. From dimension 1 to dimension 10.

I uploaded all the files to Google Docs. You can look at the Southeast Asian weighted PCA’s there. I’m not going to post them. The Asian ancestry of the Merina individual does look to be similar to that of Malays. What you’d expect. Below are K = 10 and PC’s 1 and 4.

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CATEGORIZED UNDER: Human Genetics, Human Genomics
MORE ABOUT: Genetics, Genomics

Friday Fluff – September 9th, 2011

By Razib Khan | September 9, 2011 10:13 am

FF3

1) Post from the past: Introgression in wolves & dogs.

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The gift of the gopi

By Razib Khan | September 8, 2011 2:12 pm


Krishna with milk-maids


Unlike in some Asian societies dairy products are relatively well known in South Asia. Apparently at some point my paternal grandmother’s family operated a milk production business. This is notable because Bengal is not quite the land of pastoralists. In much of North India milk and milk-products loom larger, in particular ghee. People don’t tend to consume what makes them ill, and even accounting for some processing in the form of butter, most researchers have assumed a substantial number of South Asians must be lactase persistent. That is, they can extract nutritive value out of the lactose sugar present in milk (in addition to fat and protein). Additionally, many South Asians have the well known -13910 C>T common in Western Eurasia. How do I know this? Because I share my genetic information with lots of South Asians, and some of them, especially Punjabis, come up as “lactose tolerant” on that allele.

A new paper in Molecular Biology and Evolution confirms this with a larger data set, over 2000 samples from South Asia. The geographical pattern is exactly what you’d expect:

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Why I'd "go short" on "genetic privacy"

By Razib Khan | September 8, 2011 1:13 pm

Patient Data Posted Online in Major Breach of Privacy:

A medical privacy breach at Stanford University’s hospital in Palo Alto, Calif., led to the public posting of medical records for 20,000 emergency room patients, including names and diagnosis codes, on a commercial Web site for nearly a year, the hospital has confirmed.

Since discovering the breach last month, the hospital has been investigating how a detailed spreadsheet made its way from one of its vendors, a billing contractor identified as Multi-Specialty Collection Services, to a Web site called “Student of Fortune,” which allows students to solicit paid assistance with their school work. Gary Migdol, a spokesman for Stanford Hospital and Clinics, said the spreadsheet first appeared on the site on Sept. 9, 2010, as an attachment to a question about how to convert the data into a bar graph.

Even as government regulators strengthen oversight by requiring public reporting of breaches and imposing heavy fines, experts on medical security said the Stanford incident spotlights the persistent vulnerability posed by legions of outside contractors who gain access to private data.

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CATEGORIZED UNDER: Personal Genomics

Racism, what about speciesism?

By Razib Khan | September 8, 2011 12:49 pm

One thing that came to the fore in late 2008 was the worry that a financial regulatory regime which had been exceeding lax was now more conscious of the excesses of the previous era. The problem being that one will not necessarily be prepared for the next crisis. Similarly, terrorist actions such as those of the 9/11 hijackers are probably unlikely in their specific details, because the element of surprise is gone. That’s what makes much of the TSA “security” measures so frustrating for many people, there is a strong suspicion that the authorities are aiming to prevent the previous operation, when real terrorists will naturally alter tactics.

I thought of that when forwarded a link to a new book by a friend, Race and the Genetic Revolution: Science, Myth, and Culture. Here’s the summary:

Do advances in genomic biology create a scientific rationale for long-discredited racial categories? Leading scholars in law, medicine, biology, sociology, history, anthropology, and psychology examine the impact of modern genetics on the concept of race. Contributors trace the interplay between genetics and race in forensic DNA databanks, the biology of intelligence, DNA ancestry markers, and racialized medicine. Each essay explores commonly held and unexamined assumptions and misperceptions about race in science and popular culture.

This collection begins with the historical origins and current uses of the concept of “race” in science. It follows with an analysis of the role of race in DNA databanks and racial disparities in the criminal justice system. Essays then consider the rise of recreational genetics in the form of for-profit testing of genetic ancestry and the introduction of racialized medicine, specifically through an FDA-approved heart drug called BiDil, marketed to African American men. Concluding sections discuss the contradictions between our scientific and cultural understandings of race and the continuing significance of race in educational and criminal justice policy.

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Of beasts and men

By Razib Khan | September 5, 2011 9:23 pm

“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”

- Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?

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What our ancestors did best

By Razib Khan | September 5, 2011 5:49 pm

I know I’ve posted this before, but in light of another paper on archaic admixture, this video from 10 years ago keeps going through my mind….

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Africans aren't pure humans either

By Razib Khan | September 5, 2011 3:38 pm

Last year when discussing the possible admixture of Neandertals with the ancestors of modern non-Africans I joked that Sub-Saharan Africans were “pure humans.” This was tongue-in-cheek in part because the results from the Neandertal genome shifted my assessment of the probability of archaic admixture within Africa as well. In other words, there may never have been a pure “human” type which expanded and assimilated archaic ancestry on the margins of its range. Species Platonism may be very misleading for our particular lineage. Rather, what it means to be human has always been in flux, a compromise between extremely different ancestral components.

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Creationism evolves!

By Razib Khan | September 5, 2011 3:37 am

One of the most interesting things to me is the nature of Creationism as an idea which evolves in a rather protean fashion in reaction to the broader cultural selection pressures. For me the weirdest example of this was an interlocutor who kept bringing up Fisher’s fundamental theorem of natural selection. This sort of argument is well above the standard set of talking points which are easily rebutted with Talk Origins. But to some extent it isn’t what people say, but how they say them. One reason that Creationism seems to be a position of the dull is that it is a position of the dull, and the dull are not as eloquent as the smart.

So I invite you to watch a clip of Richard Land defending Creationism (Intelligent Design) below:

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CATEGORIZED UNDER: Creationism
MORE ABOUT: Creationism
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