Archive for July, 2011

Liberals more politically picky in mates?

By Razib Khan | July 31, 2011 9:08 pm

In the early 2000s I recall Joel Grus telling me how reality television would become a pretty powerful exploratory tool for social science. I’m not quite sure of that now (there here’s a game-theoretic analysis of Survivor!). For example, consider The Bachelor and The Bachelorette. If you watched this series you might think that we’re still living in the same country where a episode of Star Trek was not shown in the South because of an interracial kiss. In some ways “appointment television” has become a lagging indicator.

Rather, it looks like firms whose bread & butter is “the social web” are where the gold in social science is. Consider the OkTrends blog, which is affiliated with and has access to OkCupid. These companies have sample sizes not in the thousands, but in the millions! The Financial Times has a fascinating piece on the “secret sauce” of Match.com, Inside Match.com: It’s all about the algorithm:

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: Culture, Data, dating

Probability of pregnancy by age

By Razib Khan | July 31, 2011 2:25 pm

I just finished reading My Fertility Crisis, which is excerpted from a longer piece you can get on Kindle for $1.99. The author is a single woman in her early 40s who is going through IVF treatments, without success so far. She outlines the choices she made over her life which may have influenced her current situation.

After reading the piece I came back to an issue I’ve wrestled with before: it’s often really hard to find information on probability of pregnancy online in the form of charts. The reason is that there’s so much information, and much of it is skewed toward people who are undergoing treatment for infertility. But why look when you can generate your own visualization? I  found a pregnancy probability calculator online which I cross-validated with some of the literature. Here is the best case scenario for probability of pregnancy if you are trying in the natural fashion (the probabilities exclude women who are clinically infertile, which is a rather slippery category strongly dependent on age, so the older cohorts are probably much larger overestimates than the younger ones):

The main focus is really the decade of the 30s for women. Here is a figure from Ovarian Aging: Mechanisms and Clinical Consequences which shows a finer-grain decline in fertility:

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CATEGORIZED UNDER: Culture, Data Analysis, Health
MORE ABOUT: Fertility, GSS, infertility

A world full of children

By Razib Khan | July 31, 2011 12:07 am

The figure to the left is from a new paper in Science, When the World’s Population Took Off: The Springboard of the Neolithic Demographic Transition. It reports the findings from 133 cemeteries in the northern hemisphere in regards to the proportion of 5-19 year old individuals. When calibrated to period when agriculture was introduced into a specific region there seems to be a clear alignment in terms of a demographic transition toward a “youth bulge.” Why? A standard model of land surplus explains part of it surely. When farmers settle “virgin land” there is often a rapid “catch up” phase toward the Malthusian limit, the carrying capacity. Another possibility though is that sedentary populations did not need to space their offspring nearly as much as mobile hunter-gatherers. Whatever the details, the facts remain that the data do point to a shift in the age pyramid during this period. The author wonders as to the possible cultural implications of this. There is an a priori assumption that a young vs. old age profile in a society constrains its choices and channels its energies (e.g., think the “baby boom” generation in the USA). A final interesting point is that the authors note that today we are seeing the last gasp of this transition toward large numbers of children, as fertility drops toward replacement all across the world. That too may have some cultural consequences.

Here’s a podcast with the author. Link via Dienekes.

CATEGORIZED UNDER: Culture, Environment

Friday Fluff – July 29nd, 2011

By Razib Khan | July 29, 2011 1:08 pm

FF3

1) Post from the past: Why does race matter for women?

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CATEGORIZED UNDER: Blog
MORE ABOUT: Fluff, Friday Fluff, Katz

Who is chilled out about warming?

By Razib Khan | July 29, 2011 9:52 am

Chris Mooney pointed me to a report on a study which finds that white males are the most sanguine in relation to climate change. Unfortunately there wasn’t a link to the full report that I could see. But no worries, the GSS added a variable, TEMPGEN1, which asks: “In general, do you think that a rise in the world’s temperature caused by climate change is….”

1 – Extremely dangerous for the environment
2 – Very dangerous
3 – Somewhat dangerous
4 – Not very dangerous, or
5 – Not dangerous at all for the environment?

Below is a bar plot which illustrates the result by demographic:

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CATEGORIZED UNDER: Politics
MORE ABOUT: Climate Change

Quest for the Malagasy genotype

By Razib Khan | July 28, 2011 11:35 am

I would like to throw out the word that I am looking for a person with Malagasy ancestry for the African Ancestry Project. To my knowledge there are no thick marker autosomal analyses of the Malagasy people. After my recent exploration of Southeast Asian genetics I think even one individual would be highly informative.

As usual I would guarantee that these data are entirely private, and I do not share it with anyone. But in this case I would like to make an exception and stipulate that Joseph K. Pickrell, a graduate student at the University of Chicago, would also be very interested in access to a Malagasy genotype for the purposes of research. Since this is an undersampled population the marginal returns to a Malagasy genotype would be enormous for science, a public good rather than just a private gain.

Also, I am still looking for a Tutsi genotype so that I can ascertain the origin of this population.

Please contact me at africanancestryproject -at- gmail -dot- com.

Francais:
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Smart educated men less likely to think cheating always wrong

By Razib Khan | July 28, 2011 10:44 am

Lots of commentary below on my post about extramarital sex. I guess that’s fine, but I’m really not too interested your theories, I can do basic logic after introspection too. In fact, I can go down the street and ask a random person and I’m sure they could offer up after the fact rationales for the results I reported (people are always interested in sex and sharp about models to explain it). Instead, here’s the variable you need to use in the GSS: XMARSEX. I assume forms and graphical user interfaces worthy of 1997 are not too intimidating to readers of this weblog even if they perplex Matt Yglesias?

In any case, here’s some more results. First, I wanted to double check that there was in fact decreased tolerance of extramarital sex over the years. Let’s break it down by sex:

Some of you were curious about the demographic correlates of this behavior. Please note that all the following charts are limited to the year 2000 and later. The sample sizes for XMARSEX were rather large, so I saw no reason not to make it relevant to contemporary attitudes.

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: Extramarital sex, GSS

How Chinese genetics is like Chinese food

By Razib Khan | July 27, 2011 3:46 pm

Representatives of Szechuan and Shangdong cuisine


The Pith: The Han Chinese are genetically diverse, due to geographic scale of range, hybridization with other populations, and possibly local adaptation.

In the USA we often speak of “Chinese food.” This is rather peculiar because there isn’t any generic “Chinese cuisine.” Rather, there are regional cuisines, which share a broad family similarity. Similarly, American “Mexican food” and “Indian food” also have no true equivalent in Mexico or India (naturally the novel American culinary concoctions often exhibit biases in the regions from which they sample due to our preferences and connections; non-vegetarian Punjabi elements dominate over Udupi, while much authentic Mexican American food has a bias toward the northern states of that nation). But to a first approximation there is some sense in speaking of a general class of cuisine which exhibits a lot of internal structure and variation, so long as one understands that there is an important finer grain of categorization.

Some of the same applies to genetic categorizations. Consider two of the populations in the original HapMap, the Yoruba from Nigeria, and the Chinese from Beijing. There are ~30 million Yoruba, but over 1 billion Han Chinese! Even granting that the Yoruba seem excellent representatives of Sub-Saharan African genetic variation (not Bantu, but not far from the Bantu), there are still more Han Chinese than Sub-Saharan Africans (including the African Diaspora). So it’s nice that over the past few years there’s been a deep-dive into Han genetics. A new paper in the European Journal of Human Genetics focuses on the north-south difference among Han Chinese, using groups flanking them to their north and south as references, Natural positive selection and north–south genetic diversity in East Asia.

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Tolerance of extramarital sex by sex

By Razib Khan | July 27, 2011 3:22 pm

Are Empowered Women Driving Reduced Tolerance Of Extramarital Affairs?:

My girlfriend’s theory about this, which makes sense to me, is that as women’s labor market opportunities have improved their dependency on husbands for economic security has declined and, in turn, their willingness to put up with misbehavior has gone down. Looking at a gender breakdown of responses might shed some light on this, but I can’t figure out how to work the General Social Survey website.

He’s talking about a chart which shows decline in tolerance of extramarital sex by education:

I just replicated but broke it down by male and female:

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CATEGORIZED UNDER: Culture, Data Analysis
MORE ABOUT: Culture, GSS

DIY admixture analysis

By Razib Khan | July 27, 2011 11:24 am

Dienekes Pontikos has just released DIY Dodecad, a DIY admixture analysis program. You can download the files yourself. It runs on both Linux and Windows. Since I already have tools in Linux I decided to try out the Windows version, and it seems to work fine. It is somewhat limited in that you start out with the parameters which Dienekes has set for you, but if you don’t want to write your own scripts and get familiar with all the scientific programs out there, I think this is a very good option. Additionally, it seems to run rather fast, so you won’t spend days experimenting with different parameters.

Dienekes has already run me, but I put my parents’ genotype files through the system. Here are the results:

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The force was with him!

By Razib Khan | July 27, 2011 10:58 am

In my post below where I focused on patent law it was noted that even more obviously blatant abuses of the spirit of intellectual property occur in copyright. So I was interested to see that George Lucas has lost a law suit in the United Kingdom in relation to the idea of “storm troopers”:

Nevertheless, the High Court rejected the multi-billionaire director’s claim and the focus switched to design rights, specifically whether the helmets sold were works of art or merely industrial props.

If Lucasfilm could convince the courts the 3D works were sculptures, they would be protected by copyright for the life of the author plus 70 years.

If not, the copyright protection would be reduced to 15 years from the date they were marketed, meaning it would have expired and Mr Ainsworth would be free to sell them.

The High Court and Court of Appeal found in Mr Ainsworth’s favour, and despite Lucas being backed by directors Steven Spielberg, James Cameron and Peter Jackson, the Supreme Court has now followed suit.

Someone on twitter quipped that Lucas should be paying royalties to the Germans for the idea of stormtroopers. But I immediately recalled that many of the ideas which set the frame for the Star Wars series are actually lifted whole cloth from pre-World War II pulp science fiction. In particular the ideas of E. E. Smith and his Lensman series.

CATEGORIZED UNDER: Science Fiction
MORE ABOUT: Star Wars

When sociology meets statistical genetics

By Razib Khan | July 26, 2011 7:40 pm

In Dr. Daniel MacArthur’s post on Roots into the Future Blaine Bettinger left an interesting comment:

It will be interesting to see how 23andMe deals with the pool of people that respond to the 10,000 free kits. Doesn’t seem like they can pre-screen applicants, since African American heritage is sometimes more sociological than genetic (based on previous genetic studies, anyway). In other words, who’s to say who is an African American and who isn’t?

And how will they deal with the unscrupulous people who apply with the full knowledge that they have no recent African ancestry? Certainly they won’t be screen those people out, even with surveys or other methods.

My concerns probably won’t apply to the genetic association studies, since they can look for test-takers that have, for example, a certain % of African American ancestry, or can look for African American ancestry in the region of the genome where the association is believed to reside (after it’s predicted to exist).

However, my concerns will certainly apply to any conclusions they might make about African American genetic ancestry. For example, a conclusion such as “XX% of African Americans have less than XX% of African American DNA,” or “XX% of African Americans have European Y-DNA signatures.” These calculations will unfortunately be biased by the “unscrupulous”, even if they ask for surveys or other methods to deter bias. The best they might be able to do is “XX% of African Americans with 5% or more of African American DNA have European Y-DNA,” and conclusions that take the “unscrupulous” bias into account.

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Ingenuity's flight toward rents

By Razib Khan | July 26, 2011 11:53 am

Andrew Oh-Willeke, Esq., observes:

One example of cyclicality that continues to today is the practice of law. The basic principles of Roman private law and the complaints that people made about lawyers and litigation were remarkably similar in the 300s to what they are today.

In the 6th century Justinian the Great sponsored a compilation of the body of law which was being widely practiced in the Roman Empire at the time, what is now known as the Corpus Juris Civilis. This is not an abstract or obscure point in the history of modern law:

The present name of Justinian’s codification was only adopted in the 16th century, when it was printed in 1583 by Dionysius Gothofredus under the title “Corpus Juris Civilis”. The legal thinking behind the Corpus Juris Civilis served as the backbone of the single largest law reform of the modern age, the Napoleonic Code, which marked the abolition of feudalism.

Imagine that the astronomical models of Ptolemy served as a basis for modern astrophysics! There’s only a vague family resemblance in this case. The difference is that law is fundamentally a regulation of human interaction, and the broad outlines of human nature remain the same as they were during the time of Justinian and Theodora. In this way law resembles many humanities, which don’t seem to exhibit the same progressivity of science. Our cultures may evolve, but there are constraints imposed by our nature as human beings. Human universals in humanistic enterprises speak to us across the ages. The story of Joseph and his brothers in in Genesis speaks to us because it is not too unfamiliar from our own. The meditations of Arjuna are not incomprehensible to the modern, even if they come from the imagination of Indians living thousands of years in the past. The questions and concerns of the good life are fundamentally invariant because of the preconditions of our biology.

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CATEGORIZED UNDER: Culture, Economics, Science

Zack Ajmal's public domain genotype

By Razib Khan | July 26, 2011 10:34 am

See his announcement: Genome in the Wild. If you don’t know, Zack is the driving force behind the Harappa Ancestry Project. Seeing how the Indian scientific-bureaucratic complex still seems to be retarding rapid progress in human genomics (how many people have heard of the Indian Genome Variation Consortium? Their blog, which is hosted on blogspot, was last updated 1 year ago!), I think it can be argued that Zack has done more for the understanding of the population relationships of the Indian populations in the last 6 months than the Indian government has in 60 years! I’m hoping I’ll be proven wrong with a list of awesome and result rich publications in the comments.

CATEGORIZED UNDER: Personal Genomics
MORE ABOUT: Public Genotype

Roots into the Future

By Razib Khan | July 26, 2011 8:47 am

23andMe is announcing a new research initiative into African American genetics today. Dr. Daniel MacArthur has blogged it so well that I recommend you just read him: Personal genomics: not just for rich white folks. This looks like it will focus more on diseases associations than ancestry inference for individuals. Very necessary and useful.

CATEGORIZED UNDER: Personal Genomics

War in Pre-Columbian Sumeria

By Razib Khan | July 26, 2011 12:05 am

For most of my life I have had an implicit directional view of Holocene human culture. And that direction was toward more social complexity and cultural proteanism. Ancient Egypt traversed ~2,000 years between the Old Kingdom and the fall of the New Kingdom. But it s rather clear that the cultural distance which separated the Egypt of Ramesses and that of Khufu was smaller than the cultural distance which separates that of the Italy of Berlusconi and the Italy of Augustus. Not only is the pace of change more rapid, but the change seems to tend toward complexity and scale. For most of history most humans were primary producers (or consumers as hunter-gatherers). Today primary producers are only a proportion of the labor force (less than 2% in the USA), and there are whole specialized sectors of secondary producers, service workers, as well as professionals whose duty is to “intermediate” between other sectors and smooth the functioning of society. The machine is more complex than it was, and it has gotten more complex faster and faster.

This is a accurate model as far as it goes, but of late I have started to wonder if simply describing in the most summary terms the transition from point A to Z and omitting the jumps from B to C to … Y may hide a great of the “action” of human historical process. My post “The punctuated equilibrium of culture” was inspired by my deeper reflection about the somewhat staccato character of cultural evolution. Granting that the perception of discontinuity is a function the grain at which we examine a phenomenon, I think one can argue that to a great extent imagining the change of cultural forms as analogous to gradualistic evolution or the smooth descent of a ball toward the center of the earth is deceptive. The theories of history which many pre-modern peoples espoused can give us a window into perception of changes in the past: history was quite often conceived of as cyclical, rising and falling and rising. And yet even in the days of yore there were changes and increases in complexity. The Roman legions of Theodosius the Great in 390 A.D. were more complex institutions than those of Scipio Africanus in 200 B.C. The perception of stasis, and even decline, is due to the fact that the character and complexity of societies did not seem to exhibit direction over the short term toward progress. And that short term can be evaluated over centuries. Far longer than any plausible human lifetime. So while it is all well and fine to focus on the long term trend line, the details of how the trend emerged matter a great deal when attempting to construct a model of the past which can allow us to make robust and rich inferences. The people of the past made robust inferences over any scale of time which mattered to them. The world was nearly as likely to get less rich as more rich.

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CATEGORIZED UNDER: Anthroplogy, History
MORE ABOUT: Anthropology, History, War

Dominance, the social construct that confuses

By Razib Khan | July 25, 2011 1:31 pm

A story in The Los Angeles Times seems to point medical implications of being a sickle cell carrier, Sickle cell trait: The silent killer:

At least 17 high school and college athletes’ deaths have been tied to sickle cell trait during the past 11 years. The group includes Olivier Louis, a player at Wekiva High School near Orlando, who died on Sept. 7, 2010, following his first football practice.

You have surely heard about sickle cell anemia. It is a recessive disease which expresses in those who carry two sickle cell alleles. T-boz of TLC has the disease for example due to her homozygosity. But the allele also famously confers some resistance against malaria, which explains its concentration in regions which have historically been malarial. Sickle cell is arguable the classic case of heterozygote advantage driving the emergence of a recessive disease. The frequency of the allele is balanced at the equipoise between the proportion of people who are more susceptible to malaria if its proportion is too low and those who express sickle cell anemia if its proportion is too high. This advantage is obviously context sensitive. The standard assumption is that in a non-malarial environment selection pressure against anemia will drive the frequency of the allele down over time as heterozygotes don’t impose a floor in the proportion of the mutant allele. This seems to have occurred among African Americans, they’re ~80% West African, but their frequency of the sickle cell anemia allele is less than {0.80*(the West African proportion)} from what I know (remember that the median number of generations which an African American’s black ancestors have been in the USA is probably ~10).

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CATEGORIZED UNDER: Genetics, Health, Medicine

~1 month into the new social network order

By Razib Khan | July 25, 2011 2:08 am

I am only being added to Google+ “circles” at a clip of half a dozen per day. This is off the peak of nearly 20 or so per day a little over a week ago. I’m now at nearly 500 people in my Google circles, though only 5 were individuals whom I added proactively. I honestly have no idea who 2/3 of these people are, though it seems that most of them know me through my blogs. About ~75 people I know rather well, though fewer than 50 are people who I’ve met in real life (many of these only once or twice). In contrast on Facebook there are hundreds of people I’ve met and known and know in real life. Very few of my college or high school friends have “added me” to their circles. In contrast, the people who I am socially engaged with currently have added me. It’s like Google+ is a vast and shallow circle extending outward into my present social space, both explicit (people I know) and implicit (those who know me through my web presence). In contrast Facebook has more historical depth. Though it’s been around a lot longer too, so the comparison isn’t fair.

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CATEGORIZED UNDER: Technology
MORE ABOUT: Facebook, Google

Around the Web – July 25th, 2011

By Razib Khan | July 25, 2011 1:44 am

I assume you’re hot?

Killings in Norway Spotlight Anti-Muslim Thought in U.S.. I’ve read Gates of Vienna before. Despite my anti-multiculturalist attitudes I generally departed with them over their sloppy marshaling of history. Two wrongs doesn’t make a right. Ironically I was introduced to the blog mostly by someone who is now a moderately scary Muslim (they converted, at the time they were very not Muslim. Now they engage in quasi-apologia for reactionary Muslim behavior like death threats against blasphemers).

What should evolutionary psychology comprise? Also see John Hawks.

Epigenetic ‘Memory’ Key to Nature Versus Nurture. Epigenetics is trending.

Rival Debt Plans Being Assembled by Party Leaders. No comment.

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CATEGORIZED UNDER: Blog
MORE ABOUT: Links

Why the human X chromosome is less diverse

By Razib Khan | July 25, 2011 12:37 am

The Pith: The human X chromosome is subject to more pressure from natural selection, resulting in less genetic diversity. But, the differences in diversity of X chromosomes across human populations seem to be more a function of population history than differences in the power of natural selection across those populations.

In the past few years there has been a finding that the human X chromosome exhibits less genetic diversity than the non-sex regions of the genome, the autosome. Why? On the face of it this might seem inexplicable, but a few basic structural factors derived from the architecture of the human genome present themselves.

First, in males the X chromosome is hemizygous, rendering it more exposed to selection. This is rather straightforward once you move beyond the jargon. Human males have only one copy of genes which express on the X chromosome, because they have only one X chromosome. In contrast, females have two X chromosomes. This is the reason why sex linked traits in humans are disproportionately male. For genes on the X chromosome women can be carriers of many diseases because they have two copies of a gene, and one copy may be functional. In contrast, a male has only a functional or nonfunctional version of the gene, because he has one copy on the X chromosome. This is different from the case on the autosome, where both males and females have two copies of every gene.

This structural divergence matters for the selective dynamics operative upon the X chromosome vs. the autosome. On the autosome recessive traits pay far less of a cost in terms of fitness than they do on the X chromosome, because in the case of the latter they’re much more often exposed to natural selection via males. In the rest of the genome recessive traits only pay the cost of their shortcomings when they’re present as two copies in an individual, homozygotes. A simple quasi-formal example illustrates the process.

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