Archive for March, 2009

How big does the N need to be?

By Razib Khan | March 31, 2009 7:57 pm

Estimating the number of unseen variants in the human genome:

…Consistent with previous descriptions, our results show that the African population is the most diverse in terms of the number of variants expected to exist, the Asian populations the least diverse, with the European population in-between. In addition, our results show a clear distinction between the Chinese and the Japanese populations, with the Japanese population being the less diverse. To find all common variants (frequency at least 1%) the number of individuals that need to be sequenced is small (∼350) and does not differ much among the different populations; our data show that, subject to sequence accuracy, the 1000 Genomes Project is likely to find most of these common variants and a high proportion of the rarer ones (frequency between 0.1 and 1%). The data reveal a rule of diminishing returns: a small number of individuals (∼150) is sufficient to identify 80% of variants with a frequency of at least 0.1%, while a much larger number (> 3,000 individuals) is necessary to find all of those variants. Finally, our results also show a much higher diversity in environmental response genes compared with the average genome, especially in African populations.

The details of this matters for genetic architecture, especially for complex traits such as height & IQ.


Women are the genetic future

By Razib Khan | March 31, 2009 4:48 pm

Dan MacArthur has a post up where he discusses 23andMe’s outreach to “mommy bloggers.” This makes economic sense for any firm in this field. There’s only so much money to be made out of telling blue eyed nerds that they carry the gene for blue eyes. To use a computer analogy the way you can get the Apple II of personal genomics would be to convince millions of pregnant women of the utility of your tools.


Facebook is not a revolution

By Razib Khan | March 30, 2009 5:56 pm

A follow up to my earlier post on information technology, In The Age Of Facebook, Researcher Plumbs Shifting Online Relationships:

“You can ask somebody, ‘Of your 300 Facebook friends how many are actually friends?’ and people will say, ‘Oh, 30 or 40 or 50,’ “ said Baym. “But what having a lot of weak-tie relationships is giving you access to are a lot of resources that you wouldn’t otherwise have. Because we do tend to cluster in relationships with strong ties to people that are pretty similar to ourselves. So they don’t necessarily know a whole lot that we don’t know. They haven’t necessarily been a lot of places that we haven’t been. They can’t volunteer to show us around Sydney, Australia, or give advice on a good reading on a topic. So there are all of these little bits of information and wisdom and social support that people can provide each other when they have a weak-tie relationship — and they can really open up access to resources that we wouldn’t have otherwise.”

The 30-50 number should be familiar, as it is in the same range as what ethologists such as Robin Dunbar have been reporting for years in terms of how many friendships a human can plausibly manage. Social technology has limits in terms of how much it can leverage our innate capabilities. On other hand it seems plausible that the “long tail” of weak acquaintances can yield some utility in terms leaking more information into one’s social network from the outside. Quantitative shifts in network structure and scope on the margins may very well lead to qualitative changes in human societies, but I don’t think we’ve really thought through in much detail the substantive ramifications.


More skepticism of natural selection

By Razib Khan | March 30, 2009 5:47 pm

In the wake of last week’s paper, looks like another one is coming down the pipe, Hundreds of Natural-Selection Studies Could be Wrong, Study Demonstrates:

“These statistical methods have led many scientists to believe that natural selection acted on many more genes in humans than it did in chimpanzees, and they conclude that this is the reason why humans have developed large brains and other morphological differences,” said Nei. “But I believe that these scientists are wrong. The number of genes that have undergone selection should be nearly the same in humans and chimps. The differences that make us human are more likely due to mutations that were favorable to us in the particular environment into which we moved, and these mutations then accumulated through time.”
Nei said that to obtain a more realistic picture of natural selection, biologists should pair experimental data with their statistical data whenever possible. Scientists usually do not use experimental data because such experiments can be difficult to conduct and because they are very time-consuming.

Good luck on getting experimental data on humans! In any case the paper will be out in PNAS later this week. Doesn’t look like it’s on the website yet.

CATEGORIZED UNDER: Evolution, Genetics

Paternity rates by population

By Razib Khan | March 30, 2009 5:37 pm

A few years ago a paper came out, How Well Does Paternity Confidence Match Actual Paternity?:

Evolutionary theory predicts that males will provide less parental investment for putative offspring who are unlikely to be their actual offspring. Cross‐culturally, paternity confidence (a man’s assessment of the likelihood that he is the father of a putative child) is positively associated with men’s involvement with children and with investment or inheritance from paternal kin. A survey of 67 studies reporting nonpaternity suggests that for men with high paternity confidence rates of nonpaternity are(excluding studies of unknown methodology) typically 1.9%, substantially less than the typical rates of 10% or higher cited by many researchers. Further cross‐cultural investigation of the relationship between paternity and paternity confidence is warranted.

I’ve referred to this paper before, but I thought it might be useful to post the rates for various populations. See the original paper for sources & discussion.
Note that the second set of results from paternity testing laboratories obviously are subject to selection bias.

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One gene controlling ant behavior?

By Razib Khan | March 30, 2009 5:32 pm

Single Gene Shapes the Toil of Ants’ Fighter and Forager Castes:

Researchers studying the social behavior of ants have found that a single gene underlies both the aggressive behavior of the ant colony’s soldiers and the food gathering behavior of its foraging caste.
The gene is active in soldier ants, particularly in five neurons in the front of their brain, where it generates large amounts of its product, a protein known as PKG. The exact amount of the protein in the ants’ brains is critical to their behavior.

The article goes on talk to about correlates of PKG variation in humans….


Copy Number Variation in African Americans

By Razib Khan | March 30, 2009 10:08 am

The paper is pretty straightforward, Copy number variation in African Americans:

Employing a SNP platform with greater than 500,000 SNPs, a first-generation CNV map of the African American genome was generated using DNA from 385 healthy African American individuals, and compared to a sample of 435 healthy White individuals. A total of 1362 CNVs were identified within African Americans, which included two CNV regions that were significantly different in frequency between African Americans and Whites (17q21 and 15q11). In addition, a duplication was identified in 74% of DNAs derived from cell lines that was not present in any of the whole blood derived DNAs.

Also see ScienceDaily. The authors are interested for purposes of disease, one of the loci which exhibit a CNV difference seem to be related to a variant of mental retardation. They suggest that differences between whites and blacks on this locus might be due to difference in the frequency of duplication between the two groups (45% vs. 8% respectively). Though remember that we have a non-pathological example of CNV polymorphism in human populations. As the field gets saturated by analyses of SNPs one assumes that there will be more investigation of other types of genetic variation, such as CNVs.


Every Man A Media Mogul!

By Razib Khan | March 29, 2009 11:56 am

Portfolio & Wired have a one-two punch on the future of broadband up. I’ve read that it takes 3-4 months for a salary increase to be “discounted” so that individuals move up the consumption ladder and no longer feel flush. With internet speed the latency seems far more attenuated; there’s always a new application around the corner. The Portfolio piece notes:

Spurred by a new wave of Skype-linked families, Hulu-watching flash mobs, and HD-video downloaders, global internet traffic is likely to quadruple by 2012. That’s an internet 75 times larger than it was just five years ago. It will be generating 27 exabytes–nearly 7 billion DVDs worth–of data each month. Start stacking those DVDs on January 1, and you’d be at the moon by tax time.

Technology moves fast. Can you believe that it was as recently as 2003 that sales of DVDs surpassed VCRs? Remember VCRs? Yeah, vintage technology for antiquarians.
The Wired piece is more of a speculative think piece:

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Science & liberalism

By Razib Khan | March 28, 2009 2:38 pm

Faith in science and social conservatism:

Except for crime and gun control, faith in science is associated with socially liberal positions. For guns and crime, the direction of the relationship is liberal, but the relationships are not statistically significant.

I’ve dug through the GSS on this and this seems about right. Even on topics where many would assume that conservatives trump liberals, there isn’t a strong difference. For example, Genetically Modified Foods:

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Creationism in America & Europe

By Razib Khan | March 28, 2009 11:56 am

So I’m reading/hearing about something flaring up in Texas again in regards to Creationism. I always get these strange “articles” in my RSS for the “evolution” query on Google Alerts where an uninformed columnist rambles on how the theory has been disproved or brought into doubt. These arguments are not my brief, I’ll leave that to Josh Rosenau et al. Nevertheless one of the interesting things about the discussion in regards to Creationists has been the reality that the United States is swarming with them, though there are Creationists elsewhere, especially in the Islamic world. It is a difference of degree, not kind.
Attitudes toward Creationism vary across European countries, and even within European countries. But what about the United States? It’s not a coincidence that the same states crop up when it comes to Creationism vs. Evolution flair ups.
The General Social Survey has several variables which ask about evolution. SCITESTY, SCITEST4, EVOLVED and CREATION. Additionally it has regional divisions which break down along Census parameters:

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Expertise & entertainment

By Razib Khan | March 27, 2009 3:42 pm

Jonah Lehrer, author of How We Decide, has a post up where he notes how bad political “experts” are. Nevertheless, I’m a little confused, isn’t the whole point of political pundits & stock pickers to be entertaining, as opposed to expert? It seems that the premise that the public is rationally consuming expertise is just false.


Environment as the gene's handmaid

By Razib Khan | March 27, 2009 10:15 am

A few days ago The New York Times had a blog post up which addressed the relationship between genes & environment in shaping our behavior & choices (see Genetic Future). One of the authors even posted a follow up comment where they evinced some surprise at the bile of the responses. I have to say that some people are naive; statistical sciences are a good reflection of the tenor of society. If you say a trait is 50% heritable, that is a statement of fact, but individuals will “spin it” however they want to based on their own outlook and the preferences of their target audience. Years ago Steven Pinker recounted to Robert Wright that when he states that a trait is 50% heritable he is often accused of being a genetic determinist, even though it is a logical implication of his assertion that 1/2 of the variation in the population is due to non-heritable factors. In fact a regular reader of this weblog labeled me as a “genetic determinist” years ago (on his deleted weblog, so I can’t link to the exchange) when I suggested that only 50% of variation in religiosity was due to environment (since he held that 100% was due to environment, he was of course an environmentalist).

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Madoff & Merkin mensch?

By Razib Khan | March 26, 2009 10:26 pm

New York has a very long piece, Monster Mensch, which profiles Bernie & J. Ezra Merkin. Psychoanalysis can get kind of old, the profile is more interesting in terms of the light it sheds on other figures in Bernie’s world.


Whither the cloud?

By Razib Khan | March 26, 2009 3:16 pm

New Nail in Google Cloud Coffin:

Here’s what Google fears: If its cloud-computing system crashes, or inadvertently lets companies view their rivals’ confidential documents all over the world, the entire system of cloud-based business-information processing collapses. Companies’ most precious secrets are leaked, as are government files; suddenly, your tax history is available for anyone to read. The world’s governments and businesses panic and come fleeing back to software that is embedded in individual computers, but not before incalculable damage is done to the modern economy and the privacy rights of ordinary citizens.
Lately, the latter scenario’s been getting a little more likely. Last year, Gmail crashed three times, and Google Docs, the service that migrates word-processing and spreadsheet documents onto the cloud, crashed in July. In February, the company’s gmail froze for several hours, right in the middle of the business day in Europe. Earlier this month, a small percentage of word-processing documents were made available to people who shouldn’t have access to them. If people can’t guarantee that their private documents will stay private, they may never join the cloud utopia.

“Too Big To Fail” anyone? When it comes to something like gaming I can envisage consoles disappearing. You might get angry if your cable service goes down, but it isn’t “mission critical.” If Google Docs becomes ubiquitous in the office it seems like it is very amenable to the Black Swan criticism.


South Park, it's back!

By Razib Khan | March 26, 2009 4:21 am

Excellent episode. Should it be titled “In praise of fiat currency?”


Signals of recent positive selection, words vs. figures

By Razib Khan | March 25, 2009 9:50 pm

Dan MacArthur already posted some of the supplementary figures from Signals of recent positive selection in a worldwide sample of human populations, but he didn’t put up one that I thought was really striking. The text:

First, there is extensive sharing of extreme iHS and XP-EHH signals between Europe, the Middle East, and Central Asia, while overlap between other regions is much more limited. In fact, 44% of the genomic segments in the 1% tail of iHS in Europe fall in the 5% tail for both the Middle East and Central Asia (89% are shared between Europe and at least one of these two), while only 12% of European signals are present in East Asia by the same criterion. Second, XP-EHH signals seemto be shared on a larger geographic scale than iHS signals.

Below the fold the figures. Rather stark.

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Sexual selection & animal signals

By Razib Khan | March 25, 2009 8:35 pm

Nick Wade in The New York Times has a piece on a review on the relationships between male competition, signaling and sexual selection. If the topic interests you I strongly recommend Animal Signals, John Maynard Smith’s last book.

CATEGORIZED UNDER: Evolution, Genetics

Iceland, Elves & Inbreeding

By Razib Khan | March 25, 2009 5:11 am

There’s a critique up of Michael Lewis’ entertaining if somewhat less than illuminating (compared to the piece in The New Yorker) profile of the Icelandic financial meltdown. No surprise that Lewis spun here and there to extract more entertainment out of the straight story, but I have to take objection to a few points:

5. “Icelanders are among the most inbred human beings on earth — geneticists often use them for research.”
Now this is insulting. Icelanders’ DNA shows their roots to be a healthy mix between Nordic Y chromosomes and X chromosomes from the British Isles. The reason genetic-research company deCODE uses Icelandic genes for its research is not because the codes are so homogeneous, but because the population has kept excellent genealogical records dating back thousands of years.

What the author means is that the ancestors were males from Scandinavia and females from the British Isles. One can vary the proportions, but the skew is in the direction suggested above. But even if all the female ancestors of Icelanders were British and all the male ancestors Nordic, only 2/3 of the X chromosomes would derive from the British population. Males carry an X as well. That’s the pedantic point. The more substantive one is the idea that because an ancestral population originally had diverse origins (in this case, at settlement), the descendant population could therefore never be inbred by definition. Actually there is some evidence that Icelanders are a touch inbred, though that just means that they have a low longer term effective population and little gene flow with other groups.
By analogy, consider a set of biracial siblings. If the brothers and sisters started mating and produced inbred offspring, who themselves bred with each other, the resultant population would become progressively more inbred despite their diverse racial origins. That’s what inbreeding does; it cranks down effective population and starts to increase the power of drift so much that it removes a lot of the genetic variation. If human races aren’t that different, well, you aren’t starting from very different places in the race to get inbred, right?

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Black girls more likely to be bulimic?

By Razib Khan | March 25, 2009 4:29 am

Black Girls Are 50 Percent More Likely To Be Bulimic Than White Girls:

Rather, girls who are African American are 50 percent more likely than girls who are white to be bulimic, the researchers found, and girls from families in the lowest income bracket studied are 153 percent more likely to be bulimic than girls from the highest income bracket.
“As it turns out, we learned something surprising from our data about who bulimia actually affects, not just who is diagnosed,” says USC economist Michelle Goeree.

Surprised me. Then again, whenever when I watched Law & Order on the airplane I’m shocked at how many white people who live in the Upper East Side are suffering from crime in New York City….


Recent positive selection, or not, etc.

By Razib Khan | March 24, 2009 6:35 pm

Genetic Future’s summary of Signals of recent positive selection in a worldwide sample of human populations is an excellent complement to mine. Highly recommended.


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