Archive for April, 2012

The end of IE; the rise of Chrome

By Razib Khan | April 19, 2012 6:24 am

A comment below prompted me to recheck the browser stats on the web. People are now starting to give Google crap for not having really hit the jackpot on anything since Gmail, especially after the flubs with Google Wave and Buzz, and the mixed reviews at best for Google+. But it looks like Chrome may actually reach a plural majority this year. Back in the day (i.e., 1990s) control of the majority browser share was actually a big deal. My earlier hunch that eventually Chrome will start eating into IE’s user base more than Firefox’s seems to be panning out.

He’s a similar chart from the w3schools website (because it’s a tech oriented site IE automatically suffers a penalty, but the overall trends are similar):

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CATEGORIZED UNDER: Technology
MORE ABOUT: Browsers

The billion SNPs of Alba?

By Razib Khan | April 18, 2012 7:33 am


A man of astonishing multitudes?

Daniel MacArthur points me to one of the funniest historical genetic popular write-ups I’ve seen in years. Study reveals ‘extraordinary’ DNA of people in Scotland:

Researchers believe that Scotland’s location could be a factor in the “astonishing and unique” origins of people from the country.

In a statement, Dr Wilson and Mr Moffat said: “Perhaps geography, Scotland’s place at the farthest north-western end of the European peninsula, is the reason for great diversity.

“For many thousands of years, migrants could move no further west. Scotland was the end of many journeys.”

I am aware that modern Scotland does emerge from a rather patchwork ethno-cultural background. That is, it is the fusion of Gaels (the Scots), Picts, the Norse, the Strathclyde Britons, and of course the German speaking Anglo-Saxon populations migrating up from Northumbria. But the “astonishing and unique” genetic heritage of the Scots seems as plausible as the culinary delights of haggis. From what I recall genetic diversity drops off as you go north and west in Europe because the effective population drops (less gene flow with surrounding populations because there are fewer surrounding populations). Rather than gene flow in, like the British Isles as a whole it seems that there is likely to be a whole lot of Scot in the rest of the world due to the migrations of its Diaspora.

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CATEGORIZED UNDER: Human Genetics
MORE ABOUT: Scotland

The genome is a structure, not just an abstraction

By Razib Khan | April 18, 2012 5:02 am

Here’s a quick follow-up on the study which purported to illustrate the shortcomings in genomic risks prediction, and received major media coverage:

Neil Risch, PhD, a leading expert in statistical genetics and the director of the UCSF Institute for Human Genetics, agrees with one major conclusion presented by the study authors, the Times reporter, and other experts quoted in media coverage: genomic studies are more valuable for their potential to lead to a better understanding of diseases globally than for their predictive power for any individual patient.

This position has been “in the air” for a few years. But I think we ought to reiterate something: genomics intersects with structural and molecular biology, as well as statistics. In other words, genomes are concrete things in the world, and their biophysical nature naturally has great relevance for understanding the etiology of diseases, even if they are of limited use in a purely statistical sense. The field even has something for those who are suspicious of hereditarian arguments in general: epiogenomics.

CATEGORIZED UNDER: Genomics
MORE ABOUT: Genomics

Ancestry painting: true but trivial, or interesting but inaccurate

By Razib Khan | April 17, 2012 9:22 pm

23andMe has done some great things, and I highly recommend its service to friends. But I’m really glad that CeCe Moore is being consulted by them in regards to improving their ancestry feature set. Below are the “ancestry paintings” for myself & my daughter.

According to 23andMe I’m 40% Asian, and she is 8% Asian. Obviously something is off here. The situation easily resolved itself when I tuned my parameters and increased my sampled populations in Interpretome. But it just goes to show you the limits of this sort of thing without fine-grained control of the details of the analysis.

 

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: 23andMe

Grandparents as reality, not theory

By Razib Khan | April 17, 2012 9:18 am

I am not particularly mystical or sentimental about genetics. I favor openness. But I just started getting my daughter’s results back from 23andMe, and some of her coefficients of relatedness to her grandparents deviated sharply from 0.25. As I have blogged about this possibility I was obviously aware of the abstract probability here; but it is a different thing altogether to be faced with reality. How exactly does one go about explaining that one of your parents is ~50% closer genetically to their grandchild than the other? I don’t think it matters really in a concrete sense for them, but divulging this information makes me somewhat uncomfortable. Many, many, others are going to be confronted with these issues. We don’t have social norms yet. This isn’t cut & dried like paternity. Thoughts?

CATEGORIZED UNDER: Uncategorized

If you are not too stupid you can be in Mensa

By Razib Khan | April 17, 2012 5:30 am

Is 4-Year-Old as Smart as Einstein? Not Quite, Scientists Say:

One of the latest members of the high-IQ club Mensa is a mere 4 years old, with an IQ of 159 — but psychologists warn against pulling out the Albert Einstein comparisons just yet.

“All you’re doing with IQ testing is testing within a certain age group,” Lawlis told LiveScience, explaining, “You’re saying the 4-year-old is smarter than 99.5 or 99.8 of [her] age group, but that doesn’t mean you can compare to another age group.”

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CATEGORIZED UNDER: Data Analysis
MORE ABOUT: SAT, standardized tests

Standardized test scores: math and verbal

By Razib Khan | April 16, 2012 11:48 pm

Prompted by miko’s skepticism about the utility of WORDSUM (a vocab test) across subcultures, I went and looked for SAT data. My assumption was that math sections are more “culture-fair” (though from what I gather ETS tries hard in various ways to be culture-fair in general). The data was not hard to find:

You can also check the ACT results.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: SAT

Reprising genes & geography

By Razib Khan | April 16, 2012 11:25 pm

Comparing Spatial Maps of Human Population-Genetic Variation Using Procrustes Analysis:

Recent applications of principal components analysis (PCA) and multidimensional scaling (MDS) in human population genetics have found that “statistical maps” based on the genotypes in population-genetic samples often resemble geographic maps of the underlying sampling locations. To provide formal tests of these qualitative observations, we describe a Procrustes analysis approach for quantitatively assessing the similarity of population-genetic and geographic maps. We confirm in two scenarios, one using single-nucleotide polymorphism (SNP) data from Europe and one using SNP data worldwide, that a measurably high level of concordance exists between statistical maps of population-genetic variation and geographic maps of sampling locations….

There is concordance. But look at the figure below. On the left are populations where they were sampled, and the right shows the populations displayed in a manner to reflect genetic distances.

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CATEGORIZED UNDER: Anthroplogy

None dare call it eugenics!

By Razib Khan | April 16, 2012 9:37 pm

Well, almost no one:

“The unspoken central reason for the societal taboo and the penal ban on incest is the possibility of hereditary defects — a factor that Strasbourg only hinted at. But the intention behind the eugenic argument is one that is indefensible, and not just in Germany with its terrible Nazi past: The increased risk of hereditary defects does not justify a legal ban. Otherwise you would have to legally ban other risk groups, like women over 40 or people with genetic diseases, from having children. Does anyone truly want to prevent predictable disabilities using penal measures and thus deny disabled children the right to life in 2012? That’s absurd. And yet such fears of genetic damage are precisely what shape the punishibility of sexual intercourse between siblings.”


There are a set of arguments against near relation incest which strike me as generally ad hoc. And there’s social science to back that up. Incest is reflexively disgusting to most people (depending on how it is categorized). But disgust alone is not a sufficient grounds for banning a practice in educated circles today, so people create rationales after the fact. David Hume would not be surprised.

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

Common variant for "IQ gene"?

By Razib Khan | April 15, 2012 11:11 pm

A few people have forwarded me this paper, Identification of common variants associated with human hippocampal and intracranial volumes:

…Whereas many brain imaging phenotypes are highly heritable…identifying and replicating genetic influences has been difficult, as small effects and the high costs of magnetic resonance imaging (MRI) have led to underpowered studies. Here we report genome-wide association meta-analyses and replication for mean bilateral hippocampal, total brain and intracranial volumes from a large multinational consortium. The intergenic variant rs7294919 was associated with hippocampal volume (12q24.22; N = 21,151; P = 6.70 × 10−16) and the expression levels of the positional candidate gene TESC in brain tissue. Additionally, rs10784502, located within HMGA2, was associated with intracranial volume (12q14.3; N = 15,782; P = 1.12 × 10−12). We also identified a suggestive association with total brain volume at rs10494373 within DDR2 (1q23.3; N = 6,500; P = 5.81 × 10−7).

Look at the sample sizes. Beware of behavior genomics with small sample sizes. Paul Thompson, one of the many authors of this paper, is giving media interviews. To me that’s a good sign, as he’s a very smart guy. He has some confidence in this study. Here’s the section which is resulting in the forwards:

… In addition, the C allele of rs10784502 is associated, on average, with 9,006.7 mm3 larger intracranial volume, or 0.58% of intracranial volume per risk allele and is weakly associated with increased general intelligence by approximately 1.29 IQ points per allele.

I’m a homozygote for the T allele for what it’s worth. But that’s not surprising. Look at the population distribution of the C allele from the HapMap:

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MORE ABOUT: Genetics, Genomics, IQ

Group selection survey

By Razib Khan | April 15, 2012 7:43 pm

I don’t have time to do a detailed analysis of my group selection survey right now. So I’ve uploaded the raw results for anyone to play with (there is no personally identifying information obviously). You should be able to convert it into an appropriate format for R or something else pretty easily.

CATEGORIZED UNDER: Data Analysis
MORE ABOUT: Group Selection

The case of the white Cubans

By Razib Khan | April 15, 2012 6:11 pm

In a follow up to a post below, a new paper in PLoS Genetics has some data on American Hispanics. Specifically, Puerto Ricans, Dominicans, Mexicans, and Cubans, as well as assorted Central and South Americans. I am not too interested in the cases except Cubans; no one doubts the mixed heritage of the other groups, though the African ancestry of Mexicans, and some Central and South Americans may surprise (again, I have to note that this not surprising in light of history, and has been robustly confirmed in the genomic literature).

But Cuban Americans are somewhat a special case. The vast majority, specifically, 85 percent, identify as white. This is a higher proportion than the number of self-identified whites in Cuba, and a function of the skewed nature of the migration out of Cuba socially and economically. By and large the white elite of the island fled Castro’s revolution to a far greater extent than the black lower classes. And contrary to American stereotypes of Latin American ease and openness about race, Cuba was a relatively stratified society, albeit not characterized by hypodescent. Slavery was not abolished on the island until 1884. Additionally, Cuba did experience a relatively large wave of Spanish immigration in the early 20th century. I have taken the claims of “pure Spanish ancestry” on face value in the past because of this history. But further genomic evidence makes me reconsider the biases in the reporting of ancestry. For example, I have heard singer Gloria Estefan mention that her heritage was of recent Spanish immigrants from Cuba, but Wikipedia indicates that this is the origin of her maternal lineage. It leaves her paternal lineage unaccounted for. I have no doubt that her father’s family were white Cubans, but if their roots on the island were somewhat deep, I am also sure that they had non-trivial African, and possibly Amerindian, ancestry.

The reason for some of these assertions from are the genomic results, like figure below from the paper mentioned above (reedited for some clarity and specificity).

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CATEGORIZED UNDER: Anthroplogy, Human Genomics
MORE ABOUT: Race, white Hispanics

Microryza: A Kickstarter for science?

By Razib Khan | April 13, 2012 9:08 pm

A few days ago I was contacted by Microzyra, a Seattle based start-up. Their aim is do for science what Kickstarter has done for creative projects. Obviously I can’t vouch for them, but I am intrigued enough to eventually consider seeing if I can raise funds through this avenue once I have some time for the Afrikaner genotyping project that I have in mind.

Update: Also see Petridish.org.

CATEGORIZED UNDER: Uncategorized

Verbal intelligence by demographic

By Razib Khan | April 13, 2012 8:43 pm

A few years ago I put up a post, WORDSUM & IQ & the correlation, as a “reference” post. Basically if anyone objected to using WORDSUM, a variable in the General Social Survey, then I would point to that post and observe that the correlation between WORDSUM and general intelligence is 0.71. That makes sense, since WORDSUM is a vocabulary test, and verbal fluency is well correlated with intelligence.

But I realized over the years I’ve posted many posts using the GSS and WORDSUM, but never explicitly laid out the distribution of WORDSUM scores, which range from 0 (0 out of 10) to 10 (10 out of 10). I’ve used categories like “stupid, interval 0-4,” but often only mentioned the percentiles in the comments after prompting from a reader. This post is to fix that problem forever, and will serve as a reference for the future.

First, please keep in mind that I limited the sample to the year 2000 and later. The N is ~7,000, but far lower for some of variables crossed. Therefore, I invite you to replicate my results. After the charts I will list all the variables, so if you care you should be able to replicate displaying all the sample sizes in ~10 minutes. I am also going to attach a csv file with the raw table data. As for the charts, they are simple.

- The x-axis is a WORDSUM category, ranging from 0 to 10

- The y-axis is the percent of a given demographic class who received that score. I’ve labelled some of them where the chart doesn’t get too busy

All of the charts have a line which represents the total population in the sample (“All”).

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CATEGORIZED UNDER: Data Analysis, Demographics, GSS

Against Microsoft Word

By Razib Khan | April 12, 2012 4:21 pm

Until a few years ago if I had to use MS Office, I used Office 97. I’ve been using Open Office and its precursors going back to 2000, but sometimes people really want MS format, and the export and “save as” features of Open Office don’t always work the best.* Now that I have upgraded to the new Word I really miss the old version. I thought that was due to my huge gap in usage, as what was a gradual shift seemed like a radical rupture to me. This indicates I’m wrong:

I know only one person who loves working in Word: my 4-year-old. It’s valuable to him to be able to put the names of subway lines in their correct colors, or to spell out “autumn” with each letter a different falling-leaf hue, or to jump from Times New Roman to Comic Sans to Chalkboard in midstory. He also loves to write things on my old manual Smith-Corona. A tool that’s lost its purpose makes a great toy.

* I’m in Linux a fair amount too, so it often isn’t an option.

CATEGORIZED UNDER: Uncategorized
MORE ABOUT: Microsoft

Genes: still a pretty big deal

By Razib Khan | April 11, 2012 1:24 am

Many people say that having children gives you a much better sense of the power of genes in shaping behavior. At least in the abstract sense that is not true in my case. I accept the “conventional wisdom” from behavior genetics that “shared environment” (colloquially, parental input) is relatively marginal in effecting much long term change within reason (i.e., if you don’t beat your kid over the head with a baseball bat and such you don’t have much influence).

To review, on many bio-behavioral traits the different choices parents make seem to account for on the order of ~10 percent of the differences you see in the world out there amongst their (biological) offspring. Of the remainder of the variation about half of it is attributable to variation in genes, and the other half to unaccounted for non-shared environment. In The Nurture Assumption Judith Rich Harris proposes that that last effect can be reduced down to social environment or peer groups. Her line of argument is such that parents are important because of the genes they contribute, and, the environmental milieus which they select for their offspring.

On one level I find this banal to review. If it is not the orthodoxy, this position seems relatively uncontroversial, and the results fall out of the data with minimal manipulation. But as a society such facts have simply not been internalized. In the great framing of “nature vs. nurture,” appealing in its stylistic dichotomy, but not even wrong in its substance, the past few centuries have seen multiple swings between each stylized extreme. That has been a matter of ideology, not science. The popularity of public intellectuals such as Steven Pinker by the turn of the 20th century indicates to me that the high tide of post-World War II nurture-über alles has receded. But the media and popular culture are to some extent lagging indicators. They continue to trumpet correlations between parental choices and offspring outcomes as if there is a causal connection without pausing to consider the possibility both might be being influenced by a confound, genes.

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CATEGORIZED UNDER: Behavior Genetics

The Anglosphere American exception (?)

By Razib Khan | April 10, 2012 10:49 pm

PLoS ONE has another article up about admixture in Argentina. The interesting aspect is that in its self-conception Argentina, like the United States of America or Australia, is a European settler nation, and therefore unlike Mexico, Boliva, or Brazil, each of whom de jure or de facto espouse a multicultural and multiracial identity. Buenos Ares is in its mentality more a Southern European city situated in the antipodes, with a touch of old Mitteleuropa (Argentines are avid consumers of psychoanalysis). As noted in the PLoS article, ~1 percent of the citizens of Argentina identify as indigenous, but ~20 percent of the ancestry of Argentina’s population seems to derive from Amerindian sources! The paper itself adds little new here. Rather, it increases the sample size, and confirms that the Amerindian ancestry does seem to be lower in Buenos Ares, the magnet for so much Italian immigration.

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

DNA Replication

By Razib Khan | April 10, 2012 4:37 am

Most of you have probably seen this stylized graphic somewhere along the away (I think it was on PBS at some point). But it’s still cool….

CATEGORIZED UNDER: Biology
MORE ABOUT: DNA

The way we were

By Razib Khan | April 10, 2012 1:43 am

I found out today that a private equity firm has purchased the majority of the Yellow Pages from AT&T. Which prompts me to ask: when was the last time you used the yellow pages? A pay phone? In a similar vein, Google And The Death Of Getting Lost. In 10 years (2001 to 2011) wireless penetration in the USA went from ~40 percent to ~100 percent.* This is the difference between arranging a rendezvous ahead of time in precise detail, and being confident that you can just end it with “I’ll call you.”

Image credit: Wikipedia

* This is actually calculated by comparing the number of phones to people. Since some people have multiple phones, and businesses purchase them for their employees, “real” penetration is somewhat less than this. I suspect that it is a larger underestimate for 2001, as a larger proportion of phones were probably business-related.

MORE ABOUT: Technology

Understanding across cultures

By Razib Khan | April 9, 2012 11:37 pm

One of the non-science aspects of this weblog which I’ve been addressing over the past 10 years is attempting to get a grip upon cultural variation. There are two major dimensions in terms of the problem. One is positive, in that people don’t really have a good sense of cultural variation. This is simply a function of stupidity, or ignorance. In the latter case the primary problem is that the media and public intellectuals aren’t very good at concisely transmitting information (I don’t expect normally curious people to pick up ethnographic or historical monographs). For example, “elite” publications like Slate routinely flub facts which could be confirmed via The World Book Encyclopedia, such as whether Iran is an Arab country. Sometimes the confusions are more obscure, but nonetheless misleading. In 2004 I slammed an Iranian American writing for Slate (this publication deserves to be picked on because of its quasi-New Yorker superiority; it’s a “smart” webzine which doesn’t live up to its own billing too often in substance if not style) for asserting that Iran’s Islamic history has been predominantly a Shia one. Going back to that 2004 post, I realized now that it was written by Reza Aslan:

…On the contrary, Iran has been a continuous entity for nearly 2,500 years. Half of that time has been as an empire founded upon the ancient Zoroastrian ideal of the “just ruler”—the divinely sanctioned shah, or king, whose omnipotent rule reflects the authority of the gods. The other half has been as an Islamic, and distinctly Shiite, community anchored in the principle of the “righteous martyr,” who willingly sacrifices himself in the fight against oppression and tyranny….

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CATEGORIZED UNDER: Anthroplogy, Religion
MORE ABOUT: Islam, Turkey
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Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!
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