Gene Expression

Most awesome post about Facebook ever  permlink

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At least in my book. How to split up the US. The author took social networking data and split up the United States into clusters. Here's the map:

Clicking through you can find the top fan pages of various nations. I noticed Megan Fox came up high on a list of many. She's #8 in Pakistan, and #2 in India. #7 in England. #6 in Saudi Arabia! Isn't that haram? #1 in Canada, #2 in Australia, #6 in USA and #4 in Mexico.

Anyway, read the whole post.

Posted by Razib Khan at 12:49 AM • 2 Comments

Gene Expression Survey  permlink

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That time of the year. Please take the Gene Expression Survey. I'll put up the analysis and the csv file next week. I have the usual questions, but also added a few more that might seem a bit weird. There are 30 questions total, and you don't need to answer all of them, but as I said the more you answer the more data there'll be. I did a trial run and it took less than 5 minutes; most people can answer a question about their sex or religious identity pretty quickly.

Update: You can view the results of the survey here.

Posted by Razib Khan at 4:07 AM • 18 Comments

Ooga begat Booga...lots of begats...Robert begat Charles  permlink

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In my discussion with Eliezer I referred to "recreational genetics." Basically, "for entertainment purposes only" genetics. For example, someone with blue eyes confirming that they have the alleles on OCA2 & HERC2 associated with blue eyes. Or a man with the surname O'Neill discovers that he has the Uí Néill Y chromosomal marker. Yes, people will pay money to find out these facts which are already highly probable.

I think the news that Charles Darwin was likely of the R1b Y chromosomal haplogroup falls into the recreational category, though due to Darwin's fame the media has really been running with it. Let me point to the Telegraph, Charles Darwin's genetic history unlocked by DNA project:

Published almost 200 years after the birth, the results reveal that the father of evolutionary theory, who struck upon the theory that all humans are descended from one common ancestor, comes from a long line of adventurers, his forbears being some of the first modern humans to leave Africa for the Middle East.

...

Tests on Mr Darwin's DNA, collected from a swab of his saliva, showed that his ancestors, and those of Darwin himself, were among the first wave of modern humans to leave Africa for the Middle East about 45,000 years ago.

From there, they travelled into Europe, surviving the Ice Age by migrating south to Spain, before moving north to England about 12,000 years ago.

The tests revealed that Charles Darwin belonged to the Haplogroup R1b, direct descendants of the Cro-Magnon people who dominated the human expansion into Europe and heralded the demise of the Neanderthals.

Read on »

Posted by Razib Khan at 6:35 AM • 5 Comments

Charles Darwin was a genius (I think)  permlink

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After watching Creation last week I decided to take the plunge and read Origin of Species. As I've mentioned before I did read Origin early in my teen years, but in hindsight with minimal comprehension. Since then I've occasionally started to read Origin, or perused an extract, but I've never made it from front to back as a sentient adult. At this point I'm 3/4 of the way through, and I need to get something off my chest: I now believe that Charles Darwin was a very smart man, a genius. I had heard other people to refer to Darwin in such a fashion, but reading his original works has brought home to me much more viscerally his incredible power of insight.

One of the reasons I hadn't reread Origin of Species was that I assumed that because it was the modern root of evolutionary biology what was correct would have been integrated into conventional wisdom and what was false would have been falsified. This impression seems to have been right. But I was shocked by the magnitude of Darwin's intellectual creativity, so many basic aspects of evolutionary biological orthodoxy are in evidence in Origin of Species, down to a very low level of specificity. Page after page I have encountered hypotheses and empirical observations which are seamlessly integrated into the body of conventional background wisdom within a modern biological education. Granted, he does not use contemporary terminology. For example, when Darwin discusses pleiotropic traits in depth he refers to "laws of correlation." But it is clear what is being elucidated in the section nonetheless, the substance has the same force even if the style is a bit peculiar.

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Posted by Razib Khan at 5:15 AM • 10 Comments

X chromosome marks the spot, again  permlink

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A few days ago I discussed a new paper which explores the patterns of natural selection in the genome of the X chromosome. As you know the X is "carried" disproportionately by females, as males have only one copy, so it offers up an interesting window into evolutionary dynamics (see The Red Queen for a popular treatment). Today Dienekes points me to a new paper in Genome Biology which puts the focus on the X chromosome again, Characterization of X-Linked SNP genotypic variation in globally-distributed human populations:

Background
The transmission pattern of the human X chromosome reduces its population size relative to the autosomes, subjects it to disproportionate influence by female demography, and leaves X-linked mutations exposed to selection in males. As a result, the analysis of X-linked genomic variation can provide insights into the influence of demography and selection on the human genome. Here we characterize the genomic variation represented by 16,297 X-linked SNPs genotyped in the CEPH human genome diversity project samples.

Results
We found that X chromosomes tend to be more differentiated between human populations than autosomes with several notable exceptions. Comparisons between genetically distant populations also showed an excess of X-linked SNPs with large allele frequency differences. Combining information about these SNPs with results from tests designed to detect selective sweeps, we identified two regions that were clear outliers from the rest of the X chromosome for haplotype structure and allele frequency distribution. We were also able to more precisely define the geographical extent of some previously described X-linked selective sweeps.

Conclusions
The relationship between male and female demographic histories is likely to be complex as evidence supporting different conclusions can be found in the same dataset. Although demography may have contributed to the excess of SNPs with large allele frequency differences observed on the X chromosome, we believe that selection is at least partially responsible. Finally, our results reveal the geographical complexities of selective sweeps on the X chromosome and argue for the use of diverse populations in studies of selection.

The low effective population of the X chromosome and the power of drift to produce greater between population difference comes up in this paper again, as it did in the one I discussed a few days ago. What's going on here is that noisy variation has no specific direction, so random genetic variation which accumulates within the genomes of different populations will tend to be different. A given locus in a large mixed population may have many alleles, a₁, a₂...a_n, at a given locus. If you divide the population into smaller clusters which no longer have any contact, and maintain the proportions of the alleles identical to the parental populations, the frequencies will begin to drift in different directions. The probability of any allele, a, fixing to 100% is the same in all populations, but the populations will likely fix different alleles. Ergo, they will start to exhibit greater between population differences. This is easily illustrated visually. The colors below represent different alleles. In the parental population three alleles are extant at 1/3, and in the initial daughter populations they are also at 1/3. Over time one notes that in these smaller populations different alleles fix, and the variance between the populations increases. If the X chromosome always is assumed to have a smaller effective population size, then it would be more strongly shaped by these dynamics than the autosome.

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Posted by Razib Khan at 5:00 AM • 3 Comments

Eliezer Yudkowsky & Razib Khan on bloggingheads.tv  permlink

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Posted by Razib Khan at 3:52 AM • 8 Comments

Katz  permlink

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Posted by Razib Khan at 4:44 PM • 2 Comments

Creation  permlink

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I went and saw Creation today. I enjoyed the film, though personally I am a bit tired of the religion vs. science angle. To some extent I felt that there was a conflation between the views & emphases of Thomas Huxley and Charles Darwin. Paul Bettany's character seemed to be expositing a view of evolution which was less subtle than what the real Darwin outlined so as to juxtapose his own stance cleanly against the simple narrative offered by traditional religion.

But a movie is a story about characters, not a perfect reenactment of history. One thing that struck me about Creation was the power of Jennifer Connelly's portrayal of Emma Darwin. I remember seeing Connelly in Labyrinth as a child, and remarking even then on her striking looks. No longer 16 years old, Connelly's form and comportment have both matured with grace. The Emma Darwin of Creation exhibited a regal quiet elegance. In contrast, despite being a bit of a hypochondriac I grew tired of Charles Darwin's sickliness and general ennui.

Finally, a picayune but interesting observation. The young actress who played Darwin's eldest daughter, Annie, had very dark eyes. Both Paul Bettany and Jennifer Connelly have light eyes. There is then a high probability in the real world that the genetics would be such that the probability of a dark eyed child emerging from light eyed parents is low enough that one might point to misattributed paternity as the cause behind the anomaly. I note this because one of the central issues which hovers over Creation is Charles Darwin's fear of the possibility that the illnesses which his children suffered, in particular Annie, were the outcome of the fact that he and Emma were first cousins. This concern occupies a central position within the narrative arc, so I couldn't help but always note the physical evidence which strongly implied that there was in fact no consanguinity at all in that specific instance.

Posted by Razib Khan at 4:54 AM • 3 Comments

The tales that the X chromosome tells  permlink

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Highly Punctuated Patterns of Population Structure on the X Chromosome and Implications for African Evolutionary History:

It is well known that average levels of population structure are higher on the X chromosome compared to autosomes in humans. However, there have been surprisingly few analyses on the spatial distribution of population structure along the X chromosome. With publicly available data from the HapMap Project and Perlegen Sciences, we show a strikingly punctuated pattern of X chromosome population structure. Specifically, 87% of X-linked HapMap SNPs within the top 1% of FST values cluster into five distinct loci. The largest of these regions spans 5.4 Mb and contains 66% of the most highly differentiated HapMap SNPs on the X chromosome. We demonstrate that the extreme clustering of highly differentiated SNPs on the X chromosome is not an artifact of ascertainment bias, nor is it specific to the populations genotyped in the HapMap Project. Rather, additional analyses and resequencing data suggest that these five regions have been substrates of recent and strong adaptive evolution. Finally, we discuss the implications that patterns of X-linked population structure have on the evolutionary history of African populations.

Remember that Fst is measuring the genetic variance between and within populations. As Fst approaches 1, that means all the variance can be partitioned between groups. For example:

Population A:
Allele frequency 1 = 1.0
Allele frequency 2 = 0.0
--------------------------------------------------------------------------
Population B:
Allele frequency 1 = 0.0
Allele frequency 2 = 1.0

All the variance is between the populations, not within them. There's no difference within the population, so it works by definition. By contrast, Fst approaches 0 when all the variance is within the population, and not between. For example:

Population A:
Allele frequency 1 = 0.5
Allele frequency 2 = 0.5
--------------------------------------------------------------------------
Population B:
Allele frequency 1 = 0.5
Allele frequency 2 = 0.5

There's a lot of variance within both populations, but none between. In other words, Fst is telling you whether there's any point in looking at population substructure. In the latter case obviously you can throw everything into a big bin and not lose any information (assuming HWE in both). In the first case, pooling the populations together would mask the fact that there's lot of between population variance, which might be important.

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Posted by Razib Khan at 4:10 PM • 3 Comments

Stuff scientists think  permlink

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Check out what has learned from being on ScienceBlogs. Some of the comments are funny.

Posted by Razib Khan at 2:42 PM • 0 Comments

How to be more ethical than the Swedes  permlink

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Population Will Come Down -- We Choose How:

So, as I once wrote, for a person to produce more than two children is unethical. If you want lots of kids, then adopt -- preferably from an affluent country, as you only make things worse if you move people from cultures with a small environmental footprint to a land of big cars and hamburgers.

We need to give little girls worldwide a good education, because that makes them have fewer kids when they grow up. And we need to combat various religious organisations that sow doubt about the efficacy and moral acceptability of contraceptives.

The whole thing about adopting from affluent countries only seems kind of mean really. I get Martin's point, but there are other terms for "small environmental footprint," and they wouldn't leave Jeremy Bentham smiling. In any case, here are the total fertility rates for nations below Martin's homeland of Sweden from Wikipedia:

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Posted by Razib Khan at 3:39 AM • 14 Comments

Inbred dogs & GWA  permlink

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Could be the title of the paper. Anyway, Genome-wide association mapping identifies multiple loci for a canine SLE-related disease complex:

...Incidences of specific diseases are elevated in different breeds, indicating that a few genetic risk factors might have accumulated through drift or selective breeding. In this study, a GWA study with 81 affected dogs (cases) and 57 controls from the Nova Scotia duck tolling retriever breed identified five loci associated with a canine systemic lupus erythematosus (SLE)-related disease complex that includes both antinuclear antibody (ANA)-positive immune-mediated rheumatic disease (IMRD) and steroid-responsive meningitis-arteritis (SRMA). Fine mapping with twice as many dogs validated these loci. Our results indicate that the homogeneity of strong genetic risk factors within dog breeds allows multigenic disorders to be mapped with fewer than 100 cases and 100 controls, making dogs an excellent model in which to identify pathways involved in human complex diseases.

In which case, skip the dogs. There are plenty of human populations where family reunions, not college, is where you find your "life partner":

They're running out of oil and water in Yemen, perhaps their unique local inbred clans could be of service to medical genetics, though I don't know the bioethics of paying for these studies. I do recall genetic homogeneity of Icelanders was one of the selling points of why deCODE was going to be a big success....

Citation: Nature Genetics , 31 January 2010 | doi:10.1038/ng.525

Posted by Razib Khan at 3:27 AM • 1 Comments

Goodbye Peace Dividend  permlink

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I got the following chart from Wikipedia, and it suggests that on a per capita inflation-adjusted basis we're spending more on defense today than we were during the Reagan build-up, or Vietnam! Is this for real?

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Posted by Razib Khan at 2:36 AM • 11 Comments

Why We Cooperate  permlink

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PLoS Biology reviews Why We Cooperate:

What makes us human, what sets us apart from other animal species, and which traits do we share with our closest living relatives? Ever since Darwin introduced the notion of continuity in his theory of evolution, humans have been obsessed with the question of how to distinguish themselves from all other species. In the postwar period, our species became known as "Man the Toolmaker," until in the 1960s Jane Goodall watched chimpanzees using sticks to fish for termites, and that was that. We then distinguished ourselves using the term "Man the Hunter," but the discovery that chimpanzees and other social carnivores engage in coordinated hunts refuted this type of collective action as the one decisive feature. More recently, the issue of culture has entered center stage. Trying to distinguish the cultural "haves" from the "have-nots" tends to generate more heat than light, and it seems much more productive to think about the cognitive prerequisites for social learning, attribution of mental states, and symbolic communication.

Posted by Razib Khan at 2:12 AM • 1 Comments

Why Pakistanis are more Muslim than thou  permlink

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A comment at Secular Right:

Ever since the Revolution the Mullahs have wanted to erase all traces of the pre-Islamic Persian society. They realized they couldn't go and raze Persepolis and other relics without losing the support of the people. I've heard that it is common for people in Iran to complain openly that worst thing to ever happen to them was the Arab invasion.

A similar strain in Egyptian Islamist clerics and leaders exists but again, they cannot destroy the pyramids without losing legitimacy. Too many Egyptians are attached to their history, whether for economic or cultural reasons.

The contradictions of Persians in relation to Islam and Arabs have always perplexed me, and my Persian American friends have never been able to unpack the sentiments coherently. On the one hand Persians are resolutely Muslim, have been by and large for over 1,000 years. Their script is derived from Arabic, Farsi has been strongly influenced by Arabic, and many Persians have names of Arabic provenance. Muhammad, Ali and Husayn were Arabs. On the other hand, Persians are often racist against Arabs, something which takes concrete form against Iranian Arabs. As far back as Ferdowsi's Shahnameh you see Muslim Persians looking back to a glorious past, and bemoaning their cultural enslavement by barbaric bedouins.

When it comes to the Islamic regime's ambivalence, and on occasion outright hostility, toward the glories of pre-Islamic Iran, the authorities need to tread a fine line. The Persians may be Muslims, and have synthesized their culture with Islam so that the religion is part & parcel of a modern Persian identity, but they also retain their ethnic-national identity as distinct from the Arabs, and later Turks, who ruled them. The customs, traditions and physical monuments from pre-Islamic Iran are witness to the concrete aspects of Persian identity which are prior, or independent of, Islam.

The issue with Egyptians is somewhat different, because the Egyptians became Arabs, abandoning the Coptic language, which descends from ancient Egyptian. After the decline of Baghdad Cairo became the cultural capital of the Arab world, and more recently was the locus of pan-Arabism. In contrast to the Persians the Egyptians subsumed their own identity with that of the Muslim Arab conquerors. But, they retain pride in their ancient civilization, which is still concrete in the form of the pyramids. I don't think this is particularly surprising; from what I can tell the Greeks take pride in the achievements of the ancient Greeks, the Chinese believe that the ancient Chinese invented everything, while black African and northern European racial nationalists have concocted an alternative history whereby all of antiquity was the handiwork of their own ethnic groups. If one's history includes Egypt of the Pharaohs, I am skeptical that any Muslim group would disavow it on account of it being pre-Islamic.

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Posted by Razib Khan at 9:19 PM • 16 Comments