I’ve been vaguely following the “mystery” surrounding A Gay Girl in Damascus blog. Turns out that “she” is a “he”, a 40 year guy who lives in Georgia. But that’s not why I’m mentioning this. The article linked above is from The Washington Post, and the author notes:
Other links between Amina and MacMaster quickly surfaced. In 2006, both were active participants in a Yahoo message group for people interested in the esoteric subject of “alternate history,” debating what might have been if major historical events had different outcomes.
Now, as someone interested in alternate history dating to the late 1990s (yes, I’ve read Harry Turtledove, and I used to check the Uchronia site periodically) I accept that this topic is ‘esoteric.’ But perhaps if the writers and editors at The Washington Post had more ‘esoteric’ interests they wouldn’t make bizarre errors such as the one below (screenshot in case they fix the mistake):
So It didn’t work out for LeBron this year. I suspect it will work in the near future. Remember that it took Shaq and Kobe four years to win their first championship. Talent doesn’t guarantee a championship, but it sure does increase the odds. For now though I’m savoring. Though perhaps not as much as the people in Cleveland.
The Pith: You are expected to have 30 new mutations which differentiate you from your parents. But, there is wiggle room around this number, and you may have more or less. This number may vary across siblings, and explain differences across siblings. Additionally, previously used estimates of mutation rates which may have been too high by a factor of 2. This may push the “last common ancestor” of many human and human-related lineages back by a factor of 2 in terms of time.
There’s a new letter in Nature Genetics on de novo mutations in humans which is sending the headline writers in the press into a natural frenzy trying to “hook” the results into the X-Men franchise. I implicitly assume most people understand that they all have new genetic mutations specific and identifiable to them. The important issue in relation to “mutants” as commonly understood is that they have salient identifiable phenotypes, not that they have subtle genetic variants which are invisible to us. Another implicit aspect is that phenotypes are an accurate signal or representation of high underlying mutational load. In other words, if you can see that someone is weird in their traits, presumably they are rather strange in their underlying genetics. This is the logic behind models which assume that mutational load has correlates with intelligence or beauty, and these naturally tie back into evolutionary rationales for human aesthetic preferences (e.g., “good genes” models of sexual selection).
J.B.S. Haldane proposed in 1947 that the male germline may be more mutagenic than the female germline…Diverse studies have supported Haldane’s contention of a higher average mutation rate in the male germline in a variety of mammals, including humans…Here we present, to our knowledge, the first direct comparative analysis of male and female germline mutation rates from the complete genome sequences of two parent-offspring trios. Through extensive validation, we identified 49 and 35 germline de novo mutations (DNMs) in two trio offspring, as well as 1,586 non-germline DNMs arising either somatically or in the cell lines from which the DNA was derived. Most strikingly, in one family, we observed that 92% of germline DNMs were from the paternal germline, whereas, in contrast, in the other family, 64% of DNMs were from the maternal germline. These observations suggest considerable variation in mutation rates within and between families.
In the 1980s my family went and visited friends in Queens for a week in August. Down the street from the house there was a small shop with an arcade machine with Legendary Wings. Every day I’d start out with a fistful of quarters and pop them into the machine to get round after round. Eventually I purchased a version of the game for the original NES, and got so proficient at it that I could win basically on mental autopilot.
I thought of that when listening to a story on the radio about the decline of the home video gaming industry as a revenue generator. Here’s the relevant section of the transcript:
In the post yesterday I reported what was generally known about the Horn of Africa, that its populations seem to lie between those of Sub-Saharan African and Eurasia genetically. This is totally reasonable as a function of geography, but there are also suggestions that this is not simply a function of isolation by distance (i.e., populations at position 0.5 on the interval 0.0 to 1.0 would presumably exhibit equal affinities in both directions due to gene flow). For example, you observe the almost total lack of “Bantu” genetic influence on the Semitic and Cushitic populations of the Horn of Africa, and the lack of Eurasian influence in groups to the south and west of the Horn except to some extent the Masai.
Tacking horizontally in terms of discipline, over the past few generations there has been a veritable cottage industry making the case for the recent origin of many ethno-linguistic populations through a process of cultural self-creation. Clearly there are many cases of this, some of them studied in depth by anthropologists (e.g., the shift from Dinka to Nuer identity). But there has been an unfortunate tendency to over-generalize in this direction. In some ways this is peculiar insofar as these models presuppose the infinite plasticity of culture without observing the sharp and strong norms which those very same phenomenon can enforce. The genetic isolation of non-Muslims in the Middle East after the rise of Islam seems rather well validated by the evidence from genomics. The norms of both Muslims and non-Muslims strongly biased them toward endogamy, and nature of Islamic hegemony and domination was such that Muslims were the ones who were likely to have cosmopolitan affinities with the “Islamic international.” In contrast, non-Muslim minorities began a long process of involution after the Islamic Arab conquests, only disrupted in the past century by emigration and to a lesser extent emancipation.
So back to the Horn of Africa. The vast majority of the people of the Horn of Africa speak an Afro-Asiatic language. Arabic and Hebrew are the most famous members of this group, but it is a very broad classification, ranging from the dialects of the Berbers in the Maghreb all the way to ancient Akkaddian. There are two large subfamilies of particular note and interest here: Semitic and Cushitic. The map above shows the distribution within the Horn of Africa. One can “quick & dirty” summarize the pattern here by observing that Semitic languages in Ethiopia tend to be concentrated in the north-central Christian highlands, while Cushitic is found everywhere else. Additionally, there is the confluence between religion and ethnicity, as there are Cushitic Muslims (Somalis, Afar, etc.) and Cushitic Christians (many Oromo, etc.). From what I can gather many Cushitic social and political elites have had a tendency toward assimilating into an Amhara Semitic identity (Haile Selassie’s mother was a Muslim Oromo). We could therefore generate a possible model where Semitic langauges arrived late to Ethiopia and spread through elite emulation, so the difference between Semitic and Cushitic peoples should be marginal in the genomic dimension (such as the marginal differences between Hausa and Yoruba in Nigeria). Or, we could posit that the Semitic element is distinctive from a pre-existent Cushitic substratum.
To make a long story short by running more ADMIXTURE with a Horn of Africa centered data set I have discerned that one can actually differentiate Cushitic and Semitic elements in the Horn and tentatively identify them with different ancestral components. First, the technical details….
In light of my last post I had to take note when Dienekes today pointed to this new paper in the American Journal of Physical Anthropology, Population history of the Red Sea—genetic exchanges between the Arabian Peninsula and East Africa signaled in the mitochondrial DNA HV1 haplogroup. The authors looked at the relationship of mitochondrial genomes, with a particular emphasis upon Yemen and the Horn of Africa. This sort of genetic data is useful because these mtDNA lineages are passed from mother to daughter to daughter to daughter, and so forth, and are not subject to the confounding effects of recombination. They present the opportunity to generate nice clear trees based on distinct mutational “steps” which define ancestral to descendant relationships. Additionally, using neutral assumptions mtDNA allows one to utilize molecular clock methods to infer the time until the last common ancestor of any two given lineages relatively easily. This is useful when you want to know when a mtDNA haplgroup underwent an expansion at some point in the past (and therefore presumably can serve as a maker for the people who carried those lineages and their past demographic dynamics).
What did they find? Here’s the abstract:
Archaeological studies have revealed cultural connections between the two sides of the Red Sea dating to prehistory. The issue has still not been properly addressed, however, by archaeogenetics. We focus our attention here on the mitochondrial haplogroup HV1 that is present in both the Arabian Peninsula and East Africa. The internal variation of 38 complete mitochondrial DNA sequences (20 of them presented here for the first time) affiliated into this haplogroup testify to its emergence during the late glacial maximum, most probably in the Near East, with subsequent dispersion via population expansions when climatic conditions improved. Detailed phylogeography of HV1 sequences shows that more recent demographic upheavals likely contributed to their spread from West Arabia to East Africa, a finding concordant with archaeological records suggesting intensive maritime trade in the Red Sea from the sixth millennium BC onwards. Closer genetic exchanges are apparent between the Horn of Africa and Yemen, while Egyptian HV1 haplotypes seem to be more similar to the Near Eastern ones.
Much of this is totally concordant with the results we’ve generated from the autosomal genome. Though the autosomal genome is much more difficult when it comes to implementing many of the tricks & techniques of phylogeography outlined above, it does offer up a much more robust and thorough picture of genetic relationships between contemporary populations. Instead of a a distinct and unique line of paternal or maternal ancestry, thousands of autosomal SNPs can allow one t o get a better picture of the nature of the total genome, and the full distribution of ancestors.
The map to the left shows the spatial gradients of the broader haplogroup under consideration, HV1. But what about the branches? Below is an illustration of the phylogenetic network of branches of HV1, with pie-charts denoting the regional weights of a given lineage:
Since I started up the African Ancestry Project one of the primary sources of interest has been from individuals whose family hail for Northeast Africa. More specifically, the Horn of Africa, Ethiopia, Eritrea, and Somalia. The problem seems to be that 23andMe’s “ancestry painting” algorithm uses West African Yoruba as a reference population, and East Africans are often not well modeled as derivative of West Africans. So, for example, the Nubian individual who I’ve analyzed supposedly comes up to be well over 50% “European” in ancestry painting. Then again, I”m 55-60% “European” as well according that method! So we shouldn’t take these judgments to heart too much. Obviously something was off, and thanks to Genome Bloggers like Dienekes Pontikos we know what the problem was: the populations of the Horn of Africa have almost no distinctive “Bantu” element to connect them with West Africans like the Yoruba. Additionally, a closer inspection shows that the “Eurasian” component present in these populations is very specific as well, almost totally derived from Arabian-like sources. When breaking apart the West Eurasian populations it is no surprise that Northern Europeans and Arabians are among the most distant pairs, even excluding recent Sub-Saharan African admixture. The HapMap Utah European American sample and the Nigerian Yoruba are very suboptimal for people with eastern African background. In contrast, African Americans are a mixture of West Africans and Northern Europeans, so the ancestry painting algorithm has nearly perfect reference populations for them. The results for African Americans may not be very detailed and rich, but they’re probably pretty accurate at the level of grain which they’re offering results.
Though I’m happy to give people of Northeast African ancestry more detailed results than 23andMe, one of my motivations for the African Ancestry Project was to obtain a data set which would allow me to explore the genomic variation in the east of Africa myself. This region is a strong candidate for “source” populations for non-Africans within the last 100,000 years, and, it seems to have experienced rapid population turnover within the last 2,000-3,000 years. My data set is not particularly adequate to my ambitions, yet. But I do now have 5 unrelated Somalis. To my knowledge there hasn’t much exploration of Somali genomics using thick-marker SNP chips, so why not? N = 5 is better than N = 0 in these cases of extreme undersampling.
Before I proceed to methods and results, I want to note that I put up most of my files here. It’s a ~25 MB compressed folder with images, spreadhseets, as well as raw output from ADMIXTURE and EIGENSOFT. I hope readers will take this as an invitation to poke around themselves.
In the post below, Moderate marginal value to genomics, I left some things implicit. It turns out that this was an ill-considered decision. In reality my comments were simply more cryptic and opaque than implicit. This is pretty obvious because even those readers who are biologists didn’t seem to catch what I had assumed would be obvious in the thrust of my argument.
The point in the broadest sense is that DNA and genomics are not magical. Genetics existed before either of them. Understanding the physical basis of genetics has certainly been incredibly fruitful, and genomics has altered the playing field in many ways. But there was a broad understanding of genetics before DNA and genomics, both in a Mendelian sense and in the area of biometrics and quantitative genetics. In the earlier post I indicated that the tools for predictions of adult traits due to the effect of genes have been around for a long time: our family history. By this, I mean that a lot of traits of interest are substantially heritable. A great deal of the variation within the population can be explained by variation of genes in the population, as inferred by patterns of correlation between individuals in their traits as a function of genetic relatedness. This is genetics as a branch of applied statistics. It has great “quick & dirty” power, especially in agricultural science.
Let’s look at something simple, height. It’s a continuous trait which is rather concrete. No one argues that “height” is a social construct. In Western societies height is ~80-90% heritable. That means that most of the variation within the population of the trait can be explained by variation in one’s family background. Tall people have tall children, short people have short children, and so forth. Here’s a “toy” scatterplot which shows the relation between mid-parent heights and adult offspring heights (I made up the numbers):
Nature has a very interesting piece up right now, Don’t judge species on their origins, which addresses the periodic bouts of hysteria which are triggered by ‘invasive species.’ I’ve addressed before the issue of biological terminology of convenience being transformed into fundamental and principled Truths. The separation between ‘artificial’ and ‘natural’ selection, or more archaically the division between ‘humankind’ and the ‘natural world.’ There are important reasons why these terms emerged the way they did, but we shouldn’t confuse the terminology for the truth. This seems definitely a problem when we humans talk about ‘invasive’ and ‘non-native’ species, as well as whether population X is worth being protected because it is a ‘species’ according to a genetic definition, or whether it is too ‘genetically polluted.’ We are after all an invasive species ourself!
Since the piece is behind a paywall I’ll extract the most relevant paragraphs:
In recent years, many scholars have explored the degree of polarization between red and blue states (red states are those carried by Republicans at the presidential level; blue states are those carried by Democrats). Some claim that red- and blue-state citizens are deeply polarized, while others disagree, arguing that there are only limited differences between the two groups. All previous work on this topic, however, simply uses difference-of-means tests to determine when these two groups are polarized. We show that this test alone cannot determine whether states are actually polarized. We remedy this shortcoming by introducing a new measure based on the degree of issue-position overlap between red- and blue-state citizens. Our findings demonstrate that there is only limited polarization—and a good deal of common ground—between red states and blue states. We discuss the implications of our work both for the study of polarization itself and for the broader study of American politics.
Generating a statistical construct of the distribution of liberalism and conservatism on social and economic issues the authors produced a set of plots which illustrate the differences between “red” (conservative) states and “blue” (liberal) states. In the figures below the blue line represents “blue states/regions” while the red dashed lines represents “red states/regions.”
In the comments below when it comes to genomic privacy I expressed a rather carefree attitude toward the future possibilities of dark prediction. Over at FARK.com the comments were rather uniformly alarmed, and influenced by Gattaca. For example: “It’s really kind of shocking how accurate Gattaca is turning out to be.”
Unfortunately I haven’t watched Gattaca. I read a negative a review when the film came out, and since I don’t watch many movies in any case I passed. This I’ve come to regret because of the influence of the film, whether it was great as a work of art or not, is strong enough today to routinely be referenced. It seems to have pretty good reviews on Rotten Tomatoes, and it’s got some staying power on Google Trends. I keep meaning to watch it on Amazon Instant Video, but then there’s the opportunity cost of time. So I did the second best thing, I read the plot summary on Wikipedia.
I would say The Mismeasurement of Man is one of the most commonly cited books on this weblog over the years (in the comments). It comes close to being “proof-text” in many arguments online, because of the authority and eminence of the author in the public mind, Stephen Jay Gould. I am in general not particularly a fan of Gould’s work or thought, with many of my sentiments matching the attitudes of Paul Krugman in this 1996 essay:
….Like most American intellectuals, I first learned about this subject [evolutionary biology] from the writings of Stephen Jay Gould. But I eventually came to realize that working biologists regard Gould much the same way that economists regard Robert Reich: talented writer, too bad he never gets anything right. Serious evolutionary theorists such as John Maynard Smith or William Hamilton, like serious economists, think largely in terms of mathematical models. Indeed, the introduction to Maynard Smith’s classic tract Evolutionary Genetics flatly declares, “If you can’t stand algebra, stay away from evolutionary biology.” There is a core set of crucial ideas in his subject that, because they involve the interaction of several different factors, can only be clearly understood by someone willing to sit still for a bit of math. (Try to give a purely verbal description of the reactions among three mutually catalytic chemicals.)
But many intellectuals who can’t stand algebra are not willing to stay away from the subject. They are thus deeply attracted to a graceful writer like Gould, who frequently misrepresents the field (perhaps because he does not fully understand its essentially mathematical logic), but who wraps his misrepresentations in so many layers of impressive, if irrelevant, historical and literary erudition that they seem profound.
Yes, I am aware that some biologists would disagree with this assessment of Gould’s relevance. But I remain generally skeptical of his arguments, though over the years I have become more accepting of the necessity of openness to a sense of ‘pluralism’ when it comes to the forces which shape evolutionary processes. And certainly there is interesting exposition in a book like The Structure of Evolutionary Theory, but there was no need for ~1500 pages (Brian Switek did fine with a little over ~300 pages in covering similar territory as the first half of the book). Whatever valid positions Gould staked out in opposition to excessive adaptationist thinking on the part of the neo-Darwinian orthodoxy of the mid-20th century, his penchant for self-marketing and repackaging of plausible but not particularly novel concepts was often destructive in my experience to the enterprise of a greater public understanding of science.
When I was in 8th grade my earth science teacher explained to the class proudly that he was not a “Darwinian,” rather, he accepted punctuated equilibrium. One must understand that much of his audience was Creationist in sympathy because of the demographics of the region, but I was frankly appalled by his explicit verbal rejection of “Darwinism,” because I knew how the others would take it (my best friend in the class was a Creationist and he kept chuckling about “monkeys turning into men” throughout the whole period). I remained after to further explore this issue with my teacher. I expressed my bewilderment as best as I could, and it came to pass that my teacher explained that he had arrived to his skepticism of the rejected model of Darwinism via the works of Stephen Jay Gould. With his silver tongue Gould had convinced him that the future of evolutionary science lay with punctuated equilibrium, which had already overthrown the older order. A 13 year old can only go so far, and so I moved on.
So A Dance with Dragons, A Song of Ice and Fire #5, is coming out in about a month. Honestly I’ve been wondering if it really would drop (at ~1000 pages, it’s literally going to be a heavy drop). Seems as if it’s for real, Publisher’s Weekly has a short review up (and Lev Grossman will be penning a positive review in Time soon). Overall from what I can glean it looks as if A Dance with Dragons will receive a straight-B grade. My own current plan is it to wait for the first assessments to come in on Amazon, and get the Kindle version if the star ratings remain above A Feast for Crows. It is strongly hinted in the Publisher’s Weekly review that this is basically another “bridge” book, suggesting that George R. R. Martin still hasn’t gotten the story under control yet. Nevertheless, it may be that we finally reach the threshold of the portion of Martin’s epic which shifts from Dark Age historical thriller to magical high fantasy, a transition the author has promised, and which helped me convince Alan Jacobs to give the series a second look after being disappointed by the lack of fantastical elements early on. Martin’s penchant for dark plot twists, and shades of gray in character and actions, certainly gave his work a level of verisimilitude which put it above and beyond other works of fantasy, but I’m honestly not too excited about a magicked-up version of the Book of Job. Whereas some fantasists use magic as a deus ex machina which transforms their narrative into farce in short order, at his point a little numinous wonder would do the characters of the A Song of Ice and Fire a world of good.
Also, I still haven’t see the Game of Thrones HBO series, but the incessant web-chatter about it certainly does remind me of A Song of Ice and Fire. I guess it’s doing some good in terms of marketing Martin’s brand.
Randy McDonald points me to this very nice Q & A formatted piece in BMC Biology from March, Who is H. sapiens really, and how do we know?. The lucidity and clarity is impressive. If scientists keep putting stuff out there like that open access then there’ll be no need for science magazines and science blogs!
The Pith: What makes rice nice in one varietal may not make it nice in another. Genetically that is….
Rice is edible and has high yields thanks to evolution. Specifically, the artificial selection processes which lead to domestication. The “genetically modified organisms” of yore! The details of this process have long been of interest to agricultural scientists because of possible implications for the production of the major crop which feeds the world. And just as much of Charles Darwin’s original insights derived from his detailed knowledge of breeding of domesticates in Victorian England, so evolutionary biologists can learn something about the general process through the repeated instantiations which occurred during domestication during the Neolithic era.
A new paper in PLoS ONE puts the spotlight on the domestication of rice, and specifically the connection between particular traits which are the hallmark of domestication and regions of the genome on chromosome 3. These are obviously two different domains, the study and analysis of the variety of traits across rice strains, and the patterns in the genome of an organism. But they are nicely spanned by classical genetic techniques such as linkage mapping which can adduce regions of the genome of possible interesting in controlling variations in the phenotype.
In this paper the authors used the guidelines of the older techniques to fix upon regions which might warrant further investigation, and then applied the new genomic techniques. Today we can now gain a more detailed sequence level picture of the genetic substrate which was only perceived at a remove in the past through abstractions such as the ‘genetic map.’ Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection:
I was having a discussion with some friends who have all expressed interest in being genotyped or have been about putting their information into the public domain. They were a pretty savvy lot (half of the six had been genotyped), but one expressed the common sense objection that “someone could find something in the future.” In other words, a really creepy stalker could keep running your data through Promethease. Imagine you’re a really strange person, and you have a bunch of gentoypes of people who you want to know about, and you design a program which scours the academic literature and constantly notifies you when the individuals in your database pop up with a large effect mutation. I have no idea why someone would do this. Perhaps you could be blackmailed by someone threatening to disclose to your employer than you had a 50% greater chance of a heart attack before the age of 60 than the general population? Whatever the details of the concern, they’re general, ranging from inchoate to eloquent.
Josh Rosenau has a post up discussing the impact of “New Atheism” on public perceptions of atheists. He mentions offhand that “New Atheism” as a movement really only crystallized in the mid-2000s, which made me wonder: what does Google Trends tell us about interest in atheism?
Unfortunately there wasn’t any information on “New Atheism.” The search query didn’t have enough volume, alas. But “atheist” did. So I compared “atheist,” “Christian,” “Buddhist,” “Hindu,” and “Muslim.” I limited the data set to the United States.
You can’t really tell what’s going because the volume for “Christian” is very high. So let’s remove that.
Sean already mentioned it, and now that I’m feeling a bit better I want to as well: The annual 3QuarksDaily science writing contest nominees are out. You can vote here. Too many of my friends are up for nomination, so I’m going to avoid making any endorsements. But it’s a nice curation of awesome blogs and posts.
1) I haven’t been feeling very well the last few days, and don’t have the energy or interest to go trolling through my archives. So I recommend you read Steve Brenner’s Does Arsenic Really Exist in the DNA from GFAJ-1?