Hope the weather is good enough where you are that you’ll enjoy the weekend.
Tories Still Short of a Majority: Hix-Vivyan Prediction up to 26 April. Trendlines + 95% confidence intervals as shading. What’s not to like?
Tolerance and Tension: Islam and Christianity in Sub-Saharan Africa. In 1900 there were 50% fewer Christians than Muslims in Africa. In 1950 there were as many Christians as Muslims in Sub-Saharan Africa. Today there are twice as many Christians as Muslims. Christ was a black man, while Muhammad had white thighs.
Listening to (and Saving) the World’s Languages. I don’t get why there are always “languages of the world are dying” articles popping up regularly in the mainstream and scientific media. I mean there’s a great benefit to having one language unify diverse groups. It’s just like how Europeans gained efficiencies by ditching their local currencies and going with the Euro. Eh, well, perhaps not the best example right now….
What can you learn from a whole genome sequence? Dr. Daniel MacArthur seems to suggest that there isn’t a whole lot more you can learn that you couldn’t learn from a chip with hundreds of thousands of SNPs instead of all 3 billion base pairs. Seems about right. And remember the baseline, many people are highly skeptical of the marginal value of the SNP chips beyond what you’d know from your family history.
Absence of Evidence for MHC–Dependent Mate Selection within HapMap Populations. I’m starting to lean away from thinking that the MHC studies in humans are finding any real robust correlations. The studies are literally all over the place, with reverse signs of statistically significant correlations in some cases.
Below I stated:
…until the late 20th century the majority of the ancestry of the white population of the republic descended from those who were counted in the 1790 census.
A commenter questioned the assertion. The commenter was right to question it. My source was a 1992 paper that estimated that only in 1990 did the proportion of American ancestry which derived from those who arrived after the 1790 census exceeding 50%. In other words, if you ran the ancestors of all Americans back to 1790, a majority of that set would have been counted in the 1790 census (so people of mixed ancestry would contribute to the two components are weighted by their ancestry).
I am currently reading Peter Heather’s Empires and Barbarians: The Fall of Rome and the Birth of Europe. This is a substantially more hefty volume in terms of density than The Fall of the Roman Empire: A New History of Rome and the Barbarians . It is also somewhat of a page turner. One aspect of Heather’s argument so far is his attempt to navigate a path between the historically tinged fantasy of what its critics label the “Grand Narrative” of mass migration of barbarian tribes such as the Goths, Vandals and Saxons during the 4th to 6th centuries, dominant before World War II, and its post-World World II counterpoint. As a reaction against this idea archaeologists have taken to a model of pots-not-people, whereby cultural forms flow between populations, and identities are fluid and often created de novo. This model would suggest that only a tiny core cadre of “German” “barbarians” (and yes, often in this area of scholarship the most banal terms are problematized and placed in quotations!) entered the Roman Empire, and the development of a Frankish ruling class in the former Gaul, for example, was a process whereby Romans assimilated to the Germanic identity (with the shift from togas to trousers being the most widespread obvious illustration of Germanization of norms). I believe that liberally applied this model is fantasy as well. Being a weblog where genetics is important, my skepticism of both extreme scenarios is rooted in new scientific data.
A few months ago I blogged a paper in PLoS Biology which suggested that a common Y chromosomal haplogroup, in fact the most common in Europe and at modal frequency along the Atlantic fringe, is not pre-Neolithic. Rather their analysis of the data implied that the European variants were derived from an Anatolian variant. The implication was that a haplogroup which had previously been diagnostic of “Paleolithicness,” so to speak, of a particular population may in fact be an indication of the proportion of Neolithic Middle Eastern ancestry. The most interesting case were the Basques, who have a high frequency of this haplogroup, and are often conceived of as “ur-Europeans,” Paleolithic descendants of the Cro-Magnons in the most romantic tellings. I was somewhat primed to accept this finding because of confusing results from ancient DNA extraction which implies a lot of turnover in maternal lineages, the mtDNA. My logic being that if the mtDNA exhibited rupture, then the Y lineages should too, as demographic revolutions are more likely to occur among men.
But perhaps not. A new paper in PLoS ONE takes full aim at the paper I blogged above. It is in short a purported refutation of the main finding of the previous paper, and a reinstatement of what had been the orthodoxy (note the citations to previous papers). A Comparison of Y-Chromosome Variation in Sardinia and Anatolia Is More Consistent with Cultural Rather than Demic Diffusion of Agriculture:
Experiments in cultural transmission and human cultural evolution. I’ve read plenty of models of cultural evolution (Cavalli-Sforza & Feldman, Boyd & Richerson, come to mind), but a post which reviews some more empirical literature. One criticism of modelers of cultural evolution is that they’re all talk, no action, and so basically just mathed up versions of armchair humanists.
Wired for Sex. The existence of two sexes is of obvious evolutionary genetic interest; males are an “expensive” cost for a lineage. But obviously there are other angles to explore, including neurological. Because sexual dimorphism takes a while to evolve I think one possible way to get a good grip on sex differences in the brain might be to look at male vs. female anatomy, function and neuochemistry across the great apes + humans. Presumably many of the differences are basal characteristics.
Psychopaths and Rational Morality. Would Mr. Spock have been a psychopath?
The Arc of Evolution Is Long and Rarely Bends Towards Advantageous Alleles: Why Does Popular Science Ignore Neutral Theory? Love the title. I think writing a book like “Climbing Mount Improbable” is going to be easier than writing “Probably Random Walking All Over.”
Can’t Pivot to the Economy With Magic. I disagree. It’s a world filled with magic & mystery, we need to just open our eyes and appreciate it. We can can use magic & mystery as fuel to generate productivity gains. A wizard in every home I say!
Dr. Daniel MacArthur pointed me to this story, Conn. woman alleges genetic discrimination at work:
A Connecticut woman who had a voluntary double mastectomy after genetic testing is alleging her employer eliminated her job after learning she carried a gene implicated in breast cancer.
Pamela Fink, 39, of Fairfield said in discrimination complaints that her bosses at natural gas and electric supplier MXenergy gave her glowing evaluations for years, but targeted, demoted and eventually dismissed her when she told them of the genetic test results.
Her complaints, filed Tuesday with the U.S. Equal Opportunity Commission and Connecticut Commission on Human Rights and Opportunities, are among the first known to be filed nationwide based on the federal Genetic Information Nondiscrimination Act.
What probability do readers put in regards to this being a legitimate complaint? This seems a large firm, so I doubt that group insurance rates would change because of one person (I have heard of this occurring in small businesses where an expensive employee or employee’s family member can effect the rate for everyone else). So if it is legitimate the main issue would have been their fear of future illness, but the woman in question went through a double mastectomy, which I assume would obviate that concern. What am I missing? Are there expectations that she’d be taking medical leave in the future due to follow up operations or treatment?
Update: Brendan Maher has some follow up from Fink’s lawyer.
Change is quite in the air today, whether it be climate change or human induced habitat shifts. What’s a species in the wild to do? Biologists naturally worry about loss of biodiversity a great deal, and many non-biologist humans rather high up on Maslow’s hierarchy of needs also care. And yet species loss, or the threat of extinction, seems too often to impinge upon public consciousness in a coarse categorical sense. For example the EPA classifications such as “threatened” or “endangered.” There are also vague general warnings or forebodings; warmer temperatures leading to mass extinctions as species can not track their optimal ecology and the like. And these warnings seem to err on the side of caution, as if populations of organisms are incapable of adapting, and all species are as particular as the panda.
That’s why I pointed to a recent paper in PLoS Biology, Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory below. I am somewhat familiar with one of the authors, Russell Lande, and his work in quantitative and ecological genetics, as well as population biology. I was also happy to note that the formal model here is rather spare, perhaps a nod to the lack of current abstraction in this particular area. Why start complex when you can start simple? Here’s their abstract:
Many species are experiencing sustained environmental change mainly due to human activities. The unusual rate and extent of anthropogenic alterations of the environment may exceed the capacity of developmental, genetic, and demographic mechanisms that populations have evolved to deal with environmental change. To begin to understand the limits to population persistence, we present a simple evolutionary model for the critical rate of environmental change beyond which a population must decline and go extinct. We use this model to highlight the major determinants of extinction risk in a changing environment, and identify research needs for improved predictions based on projected changes in environmental variables. Two key parameters relating the environment to population biology have not yet received sufficient attention. Phenotypic plasticity, the direct influence of environment on the development of individual phenotypes, is increasingly considered an important component of phenotypic change in the wild and should be incorporated in models of population persistence. Environmental sensitivity of selection, the change in the optimum phenotype with the environment, still crucially needs empirical assessment. We use environmental tolerance curves and other examples of ecological and evolutionary responses to climate change to illustrate how these mechanistic approaches can be developed for predictive purposes.
On paper, that’s what Sudan’s 21-year civil war was all about. More than 2 million people died in that terrible religious-themed conflict between the Muslim, Arab-led north and the pagan and Christian black south. In reality, almost no one in the south bought the unity line except their charismatic (and autocratic) leader, John Garang. Garang, a favorite of the West, negotiated Sudan’s 2005 peace treaty, the Comprehensive Peace Agreement, that finally ended the war. The document was essentially written to ensure he would be elected Sudan’s first black president.
How is it that the current president of Sudan (picture to the left) isn’t black, but Barack Hussein Obama is black? I’m in the category of people who think the world “race” has some utility and maps onto real patterns of human variation, but sometimes it’s just funny. The distinction between the Arabs of Sudan and blacks of Sudan is kind of weird, because Arab is not a race, and Arabs can be of any race theoretically (there are even Arabs in Yemen’s Hadhramaut who have a lot of Malaysian ancestry because of international trade), though generally they are of the olive persuasion. Perhaps the Sudanese Arab elite wouldn’t want to be identified as black because that isn’t particularly prestigious, but they’d certainly be identified as such in other Arab countries. Anwar Sadat was the subject of some racist attitudes within Egyptian society because of his Sudanese ancestry (his mother was Nubian) and his dark skin.
Anyway, my amusement was mostly the fact that they went with this text, and, added a picture of a man who most Americans would identify as black but noted implicitly that he wasn’t black. American journalists are generally punctilious about following the rule of hyodescent when it comes to Americans, even when those individuals object to this framing, such as Tiger Woods (who is twice as Asian ancestrally as he is black). But I guess in an international context they will bend more. It reminded me of stories that Afro-Arabs were often allowed to stay at “whites only” facilities in the USA when segregation was the norm because they were foreign.
Note: Hypodescent isn’t just an American issue. There are controversies about a new biopic of Alexandre Dumas where he is played by Gérard Depardieu. Some people wanted a non-white actor cast because Dumas’ mother was mixed-race. But of course Dumas was mostly white, and he seems to basically have looked like a white guy. France of the 19th century was not the American South of the 19th century, and a drop of black blood did not make you persona non grate within white society. If you want real accuracy, perhaps cast Wentworth Miller as a young Dumas, he’s a white-looking mixed-race actor.
Image Credit: Slate & Whitehouse.gov
Adaptation, Plasticity, and Extinction in a Changing Environment: Towards a Predictive Theory. It’s beneficial to have a little give.
Enculturation and Wall Street. Rich, irrational herds? I think you can’t ignore the Magnetar strategy either. What may be rational for a firm or individual may result in the shrinking of the aggregate pie.
Peppers May Increase Energy Expenditure in People Trying to Lose Weight. No wonder so many people who like bland food are fat.
Crossing the Wallace Line. Patterns across species.
I listened today to an interview with Stephen Prothero, which outlined the argument in his book God Is Not One: The Eight Rival Religions That Run the World-and Why Their Differences Matter. Prothero is a professor in the Department of Religion at Boston University, and he certainly brings some heft to this argument. Not having read the book, but listening to his talking points in interview and discussion, he seems to have a problem as an empirical matter with the contention regularly made in interfaith circles that all religions fundamentally point to the same truth. The metaphor that Houston Smith used whereby religions are separate paths to the same mountain top is referred to repeatedly. Prothero suggests that this universalistic model denies the deep reality of sectarian difference in belief, practice and outlook, and tends to be favored by those of liberal bent at ease with multiculturalism. He also notes that the foundation of common unity can be traced back to the perennial philosophy. This philosophy lay at the heart of the Traditionalist School, of which Smith was arguably a member, as was Julius Evola. So the tendency that Prothero is putting into focus is not necessarily associated with liberalism, though in the American context it is because of the Right’s capture by low church anti-elitist elements.
Angst on the Aegean. Like many Third World countries Greece is characterized by familialism and rampant corruption typical of a low trust society (more on the familialism). Except thanks to geography Hellenes are like a boat being lifted by the rising tide of the dynamic economies of other European nations (the reason Mexico has a GDP PPP per capita of $15,000 and Colombia $9,000 probably has something to do the former’s more favorable location). Greek culture and government seems trapped in a particularly unfortunate equilibrium, and the buck stops soon. I have mooted that perhaps many nations in this position might benefit from the importation of a Suomalaiset bureaucratic class to “shock” the society to another state where virtuous circles of trust may arise. Such a mandarin caste would be congenitally incapable of eye contact, minimizing the ability to weasel out bribes.
Exploring the Complexities of Nerdiness, for Laughs. I’d probably watch this show if I owned a TV.
The Search for Genes Leads to Unexpected Places. Since this is a Carl Zimmer piece of course it’s worth reading. Turns out that there are many interesting insights one can glean from the tree of life which are of general import.
Lady Bugs to the Rescue in the Galapagos: Biocontrol of Insect Pest Is a Major Success, Entomologists Say. “Non-native species” become useful agents of “biocontrol” in the right context!
Ethnic Differences in Precursors of Type 2 Diabetes Apparent at an Early Age. It’s hard to be brown. Brown like me, not Gordon Brown, or faux brown.
“Save A Mother”: An Appeal. My friend Ruchira Paul is trying to raise money for a charity focused on Indian rural maternal health after she got to know the doctor who heads it. You can find out more here.
A few weeks ago I reviewed a paper on the the genetics of the Cape Coloured population. Within it there was a refrence to another paper, Deconstructing Jaco: genetic heritage of an Afrikaner. The title refers to the author himself. It was an analysis of his own pedigree going back to the 17th century, along with his mtDNA, his father’s mtDNA, and his Y lineage. The genetics is a bit thin, but the pedigree information is of Scandinavian quality from what I can tell. Praised the records of the Reformed Church!
The author’s utilizes an inversion of the typical method whereby a survey of a population may give some insight into individuals within that population. Rather, he leverages the thorough church records of his Afrikaner community, and his local roots, to paint a picture of his own ancestry. Then he compares the results to those of the community as a whole. Though an N of 1 certainly has limits it seems that the author concludes that he is relatively representative because some of the statistics that emerge out of pedigree analysis seem to fall in line with what genealogists working with the whole community have found. Additionally, it is clearly that he has deep roots within the historic Afrikaner nation, so assuming random mating and little population substructure, inferences from his pedigree may have some general utility.
Afrikaners apparently have some peculiarities genetically which has made them of some interest to scientists. It turns out that they seem to exhibit high frequencies of classical Mendelian diseases, a hallmark of inbreeding or population bottlenecks. This aligns well with the thesis that Afrikaners are the descendants of a small group of founders who arrived in the 17th century and entered into a long phase of demographic expansion, which culminated with their long Trek into the veld to escape English domination as well as perpetuate their practice of slavery (James Michner’s The Covenant is a fictionalization of this). As I have observed before the primacy of the “first settler” seems to loom large in the minds of demographers.
J. M. Greef, the author of the above paper, seems to refute this simple story in his own genealogy, though not the core aspect of the importance of the first founders. First the abstract:
Last week I was emphasizing the fact that someone from Max Planck seemed to really be positive about the University of New Mexico research which indicates that there has been “archaic” admixture into the modern human lineage derived from Out-of-Africa. This was curious because Svante Pääbo is at the Max Planck Institute, and he’s reconstructing the Neandertal genome. I wasn’t going to do more than hint at rumors, so I’ll point to Thomas Mailund (after linking to posts on the topic of admixture or not) :
I really look forward to reading the Neandertal paper and see what it has to say about gene flow between us and Neandertals. A few month ago, while I visited his group in Leipzig, Svante Pääbo actually promised to show me the draft, but it never happened. In Ohio in February I talked to one of the authors on the paper and he wouldn’t reveal anything… I guess I just have to wait and can only hope that it won’t be too long.
Remember that I didn’t say anything, Thomas Mailund did. Though he wasn’t explicit either, so whatever conclusions you draw are your own. But perhaps a reminder that when people are talking about things in public that might seem curious or a bit farther than the evidence warrants, it may be an issue of you not knowing what they know.
How do non-genic polymorphisms influence disease risk? It might be gene expression and regulation.
Law tackles U.K. caste discrimination. Britain’s doing a great job assimilating at brown people with their ‘authentic’ barbaric traditions, isn’t it? (of all religions) Viva la multibarbarism!
Why Belief in God Is Not Innate. I think the author is trying too hard, playing shell games with various types of non-Christianity. Unfortunately this area is dominated by pro and anti religious polemicists who wish to promote a strong and exclusive form of their prediction.
Complexity and Diversity. Frequency dependence is critical in maintaining variation on the intra and inter species level. Economists aren’t the only ones who need to move beyond equilibrium thinking.
Liars’ Brains Wired Differently. I think many of you will click this, so I’ll let the title speak for itself.
I heard an interview on the radio by the author of No Longer Separate, Not Yet Equal: Race and Class in Elite College Admission and Campus Life. The study focused on elite universities. I decided to poke around and see what I could find. The chart on probability of acceptance by SAT score broken down by race has no surprises.
Equalizing standardized test scores I assume everyone knows that at elite universities there’s an Asian penalty, and blacks and Hispanics tend to get a bonus, with whites as a reference population in the middle. The author warned though that looking at standardized test scores may not indicate any discrimination against Asians, as it didn’t include in other “soft” aspects of the application such as leadership, which Asians naturally must lack because of their conformist and collectivist nature (OK, I added the last part!). But the class chart was more interesting to me….
Several people have pointed me to Stephen Hawking’s warning about ‘First Contact’ with aliens. Specifically that we’d be on the short end of the stick. His worry reminded me of something I read as a child which shocked me somewhat when I encountered it, as I was conditioned by a post-Cosmos optimism. Here’s the author:
…I find it mind-boggling that the astronomers now eager to spend a hundred million dollars on the search for extraterrestrial life never thought seriously about the most obvious question: what would happen if we found it, or if it found us. The astronomers tacitly assume that we and the little green monsters would welcome each other and settle down to fascinating conversations. Here again, our own experience on Earth offers useful guidance. We’ve already discovered two species that are very itnelligent but less technically advanced than we are-the common chimpanzee and pygmy chimpanzee. Has our response been to sit down and try to communicate with them? Of course not. Instead we shoot them, dissect them, cut off their hands for trophies, put them on exhibit in cages, inject them with AIDS virus as a medical experiment, and estroy or take over their habitats. That response was predictable, because human explorers who discvered technically less advanced humans also regularly responded by shooting them, decimating their popualtiosn with new diseases, and destroything or taking over their habitats.
Any advanced extraterrestrials who discovered us would surely treat us in the same way….
That was Jared Diamond in The Third Chimpanzee. In terms of this particular concern I have to admit that my attitude is encapsulated by Arthur C. Clarke’s third law of prediction. An advanced alien race is basically going to have magical powers in relation to humanity, and I doubt anything we do will matter either way (i.e., I don’t think we could hide, or, get their attention). But my main question is why haven’t the von Neumann machines already co-opted all the matter and energy in the universe? The Fermi paradox is a real issue. There are still big questions that we have no idea or clue about.
Michael Arrington of TechCrunch has a post up, The Age Of Facebook. Facebook having superseded Google having superseded Microsoft. Unstated that Microsoft superseded IBM as a firm which defines an age through reach, power and influence. Two thoughts that come to mind:
1) It seems that each “age” has been shorter than the previous. IBM was computing for decades. Microsoft probably ten years or so depending on how you define it (I put the second derivate maximum at 1995). Google’s real ascent seems to date to around 2000, but its monopolistic plateau of the mindshare didn’t seem to last for very long as Facebook was already generating a lot of buzz by 2007 (the same principle operates across human history, the civilization of Pharaonic Egypt spanned 2,000 years, the same length as from Augustus to our own time!)
2) It also seems that the extent of a definite age of ascendancy for a particular firm is more muddled now, as creative destruction and innovation allow for many domains of excellence and supremacy, as well as the resurrection of bygone brands. Consider the revival of Apple’s fortunes. And if we are on the verge of the Age of Facebook does anyone believe that Google’s brand will collapse? Arrington notes that Microsoft is perceived to be passed its peak, but it has many years left of its cash cow products, perhaps at least another decade. IBM has reemerged as a software services company. And so on. On a relative scale Arrington’s argument seems to have some merit, but secure domination doesn’t seem to be what it used to be (also, one might need to distinguish between buzz and influence, and concrete metrics).
Alan Templeton, whose text Population Genetics and Microevolutionary Theory is right below Hartl & Clark in my book, recently published a strongly worded paper, Coherent and incoherent inference in phylogeography and human evolution. The possibility of statistical errors in published work is not shocking, I have heard that when statisticians are asked to sort through papers in medical genetics journals there are elementary errors in ~3/4 of those which have made it beyond peer review. That being said Templeton seems to be making a stronger case than simple refutation of basic errors, in particular he is suggesting that the “ABC” method which lay at the heart of the paper I reviewed last week is incoherent at the root. Here’s Templeton’s abstract:
A hypothesis is nested within a more general hypothesis when it is a special case of the more general hypothesis. Composite hypotheses consist of more than one component, and in many cases different composite hypotheses can share some but not all of these components and hence are overlapping. In statistics, coherent measures of fit of nested and overlapping composite hypotheses are technically those measures that are consistent with the constraints of formal logic. For example, the probability of the nested special case must be less than or equal to the probability of the general model within which the special case is nested. Any statistic that assigns greater probability to the special case is said to be incoherent. An example of incoherence is shown in human evolution, for which the approximate Bayesian computation (ABC) method assigned a probability to a model of human evolution that was a thousand-fold larger than a more general model within which the first model was fully nested. Possible causes of this incoherence are identified, and corrections and restrictions are suggested to make ABC and similar methods coherent. Another coalescent-based method, nested clade phylogeographic analysis, is coherent and also allows the testing of individual components of composite hypotheses, another attribute lacking in ABC and other coalescent-simulation approaches. Incoherence is a highly undesirable property because it means that the inference is mathematically incorrect and formally illogical, and the published incoherent inferences on human evolution that favor the out-of-Africa replacement hypothesis have no statistical or logical validity.
The method which Templeton favors is naturally one which he has pushed in the past. In any case, I don’t know the statistical details well enough to comment with much knowledge, but I see that a statistician has responded to Templeton already, so I would recommend checking that out. I immediately went looking for responses because the paper uses really strong and dismissive language, and I am somewhat wary of that sort of thing when attempting to tear down the fundamentals of a whole field of research (I want to emphasize that overall I enjoy Templeton’s work, but the paper reminded me a bit too much of Jerry Fodor). His citation of Popper in particular seems an appeal to authority that aims to convince the non-statisticians in the audience, and I don’t see the point of that besides rhetorical utility. I do tend to accept somewhat Templeton’s critique of models which assume very little gene flow between hominin populations before the Out-of-Africa migration, though from what I can tell it does seem that Africa has had relatively little back-migration south of the Sahara over the past 50,000 years, so perhaps this is an older dynamic as well. I am cautiously optimistic that DNA extraction from fossils themselves may put to bed some of these arguments over the dance of parameters, though naturally interpretation is always an issue outside of pure mathematics.
For what it’s worth, here’s the model which Templeton’s method favors: