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The above is a figure from a new paper in PLoS ONE, Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats. Here’s the abstract:

The Black Rat (Rattus rattus) spread out of Asia to become one of the world’s worst agricultural and urban pests, and a reservoir or vector of numerous zoonotic diseases, including the devastating plague. Despite the global scale and inestimable cost of their impacts on both human livelihoods and natural ecosystems, little is known of the global genetic diversity of Black Rats, the timing and directions of their historical dispersals, and the risks associated with contemporary movements. We surveyed mitochondrial DNA of Black Rats collected across their global range as a first step towards obtaining an historical genetic perspective on this socioeconomically important group of rodents. We found a strong phylogeographic pattern with well-differentiated lineages of Black Rats native to South Asia, the Himalayan region, southern Indochina, and northern Indochina to East Asia, and a diversification that probably commenced in the early Middle Pleistocene. We also identified two other currently recognised species of Rattus as potential derivatives of a paraphyletic R. rattus. Three of the four phylogenetic lineage units within R. rattus show clear genetic signatures of major population expansion in prehistoric times, and the distribution of particular haplogroups mirrors archaeologically and historically documented patterns of human dispersal and trade. Commensalism clearly arose multiple times in R. rattus and in widely separated geographic regions, and this may account for apparent regionalism in their associated pathogens. Our findings represent an important step towards deeper understanding the complex and influential relationship that has developed between Black Rats and humans, and invite a thorough re-examination of host-pathogen associations among Black Rats.

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Last of the Spanish Habsburgs

The New York Times has a long piece out, Can the Bulldog Be Saved? To a great extent it is a parable of the problems with purebred dogs. Domestic dogs are much more homozygous than humans. That is, for their two gene copies they are much more likely to exhibit similarity than humans. This is usually due to inbreeding, where a few ancestral dogs with the required traits are bred, and then selection operates upon the progeny to reduce the effective population size even more. This means that many dog breeds are in danger of pedigree collapse, where they are so inbred that going back enough generations results in a convergence of the family tree.

But the story of the bulldog isn’t just about inbreeding: it’s about correlated response. If you select upon a trait of interest, you generally produce side effects due to pleiotropy. That is, you shift the allele frequencies at locus X, which produces the outcome you want on trait 1, but also incidental outcomes on trait 2 to trait n. As stated in the piece: “Bulldogs could be as outbred as mongrel dogs in the streets of Calcutta, but if they keep that phenotype, they are not going very far.” The bulldog is profoundly unnatural in shape and gait. In other words, the issues here are not just genetic, but they’re biophysical.

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Genomes Unzipped, Size matters, and other lessons from medical genetics:

…Smaller studies, which had no power to detect these small effects, were essentially random p-value generators. Sometimes the p-values were “significant” and sometimes not, without any correlation to whether a variant was truly associated. Additionally, since investigators were often looking at only a few variants (often just one!) in a single gene that they strongly believed to be involved in the disease, they were often able to subset the data (splitting males and females, for example) to find “significant” results in some subgroup. This, combined with a tendency to publish positive results and leave negative results in a desk drawer, resulted in a conflicted and confusing body of literature which actively retarded medical genetics progress.

An easy thing to pick on is the reliance on “p-values,” thresholds of statistical significance. Just because something is statistically significant doesn’t mean that it is substance. Statistical significance is just a number, and blindly adhering to a numerical standard in most human endeavors often results in a creeping bias and “gaming” of the measurement. There’s going to be a random distribution of p-values, and for publication you just need to fish in the pool below the 0.05 threshold. It just goes to show that you can’t beat taking a step back, and actually thinking about what your results mean and how you came to them.

(as indicated in the post, this is a problem in many domains, probably most worryingly in medical and pharmaceutical studies)

We’ll be talking about Iran a lot in the near future in the United States. I doubt we’ll invade the country (thank god). But one thing I think needs to be emphasized: on social issues Iran is more “progressive” than many of our close allies in the region, like Saudi Arabia, and one of the more progressive nations in the region. This is neither here nor there in the domain of geopolitics, but to convince a public about something it is often necessary to make a cartoon or caricature the enemy. I think it is important to remember though that aside from Israel our closest allies in the region are techno-feudal monarchies like Saudi Arabia, not those nations, like Iran, which have made a more thorough accommodation with modernity out of necessity (because oil can’t support the whole economy). It also reminds us that labels like “Islamic Republic” may not be totally useful.

As a gauge of modern outlook, as understood in the West, I poked around the World Values Survey. The results are for wave 4, around ~2000. The question asked was: A wife must always obey her husband. Possible answers:
– Agree strongly
– Agree
– Neither agree or disagree
– Disagree
– Strongly disagree

Below are two tables with nations which responded to this question. I stratified by sex and educational level of respondents. The sample sizes are in the “Total” column. The other numbers are percentages, summed along the rows to 100%. There are some surprises, but I’ll let the data speak for itself….

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There’s a piece in The New Republic, Mormonism’s Surprisingly Deep Affinity For Progressive Politics. It’s interesting, but I think that the niche for these sorts of pieces relies on the reality that there’s a deep lack of interest in American history on the part of the moderately educated public. Many of the “trends” or “surprises” we see today can actually be understood and made more explicable with a marginal amount of historical knowledge, something that came home to me when I began to read some American history in depth and detail ~2008.

The first thing to recall about Mormons and politics is that a greater proportion of Utah’s vote went to Franklin Roosevelt than in his home state of New York in 1932. Utah had a higher rate of voting for socialist Eugene Debs in 1912 than the national average. This can be explained by simple materialism. In the early 20th century Utah was a poor state which benefited from federal public works programs which developed and subsidized its economy.

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What We Don’t Know About Suicide:

CNNMoney reports that Ilya Zhitomirskiy, one of four co-founders of the social networking site Diaspora, died over the weekend, and that suicide was the likely cause of death. He was 22.

I gave some money to Diaspora. It seems like it didn’t pan out. So? But that’s easy for me to say, I just gave a little money. I suspect many of us have faced with panic the likelihood of failure. Personalities differ in how we can process that failure. I remember in college reading the story of a kid who killed himself because of shame over a credit card debt on the order of a few thousand dollars! We make a big deal today about how failure is critical to ultimate success, but we don’t put enough spotlight on the day to day toll that failure necessarily takes on many people….

There is a specter haunting the intersection of conservation biology and public policy, the specter of the biological species concept. Coyote-Wolf Hybrids Have Spread Across U.S. East:

Scientists already knew that some coyotes, which have been gradually expanding their range eastward, mated with wolves in the Great Lakes (map) region. The pairings created viable hybrid offspring—identified by their DNA and skulls—that have been found in mid-Atlantic states such as New York and Pennsylvania.

Now, new DNA analysis of coyote poop shows for the first time that some coyotes in the state of Virginia are also part wolf. Scientists think these animals are coyote-wolf hybrids that traveled south from New England along the Appalachian Mountains.

Most of the wolf ancestry in the lower 48 states might be in “coyotes!”

A few days ago Kevin Drum put up a post with the title “Being Poor in America Really Sucks”. He linked to a Pew survey which reported that the United states seems to have a stronger correlation between parent-child socioeconomic outcomes than most other nations. The implication here is that social mobility in the United States is lower than in other nations, in contradiction to our national mythology. This seems generally correct, in that I’ve seen this result reported repeatedly for the past decade (I’m sure you could slice and dice the finding to show it wasn’t quite right, but to a first order approximation you’d still have to start with that result before deconstructing it). But the finding itself is not what caught my attention. Drum goes on to say:

But in the United States they do a lot worse. The Pew chart is normalized so that children of middle-educated parents score in the 50th percentile and other children are compared to that standard. In Canada, the least-advantaged kids manage to score at the 37th percentile. In the United States they score at only the 27th percentile.

Now, it’s pretty unlikely that Canadian kids with low-educated parents are genetically unluckier than American kids with low-educated parents. Genes may account for some of the overall difference between rich and poor kids, but not for the difference between Canada and the U.S. That has a lot more to do with how we raise our kids and what kind of attention we give them at early ages. On that score, the United States does wretchedly. We simply don’t give our poorest kids a fair start in life.

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Anthony Shadid has a poignant piece up, … But There’s a Slim Hope in History, on the specter of extinction facing Arab Christianity in the wake of the Arab Spring. This is an issue which I think most of my Left-liberal friends simply seem unable to confront forthrightly: ethnic and religious cleansing are often the consequences of populist national self-determination. This isn’t a speculative proposition, the history of Europe is a testament to this, as well as what occurred in newly independent European colonies (e.g., the fate of Indians in Burma and Chinese in Vietnam). This reality is often emphasized by a sort which is very rare in the United States: cosmopolitan imperialists. To these partisans of the old regimes the Austro-Hungarian Empire is often held up as an ideal. This ‘prison house of nations’ was notoriously fractious and muddled, held together only by the history of the House of Habsburg. To illustrate this in a manner accessible to modern Westerners, Jews were often arch-imperialists because they saw themselves as likely receiving a better deal in a situation of imperial ethno-linguistic pluralism than in the possible nation-states where they would be a prominent minority overshadowed by the majority (I think the subsequent history of Jews in the inter-war states does confirm this fear as being grounded in reality). Additionally, in the mid-19th century it was reported that some military units resorted to English as their lingua franca! (the language being popularized by migrants who had returned from the United States).

This section of the Shadid piece emphasizes the broader concerns in the Arab world today:

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Grassroot funding for science: A good idea?

Summary: Crowdfunding science is a good idea to add additional support to underfunded missions or to enable small projects. It is not a good idea to draw upon the public opinion to fund research projects from scratch. It might appear as if public money is put to good use, but that use is likely to be very inefficient and misdirected and doesn’t actually solve any systemic problem. If you must, go occupy Wall Street, vote, and make sure your taxes are put to good use.

I have a few of the same questions as Sabine overall. This despite the fact that I solicited funds in a genotyping project. The key is that if you’re going to do crowdfunding/crowdsourcing you have to be clear and precise about the aims. In the abstract I think most people understand that most science fails, but I think it will be hard to get funds if you continue to fail because you’re aiming for “home-runs.” Rather, the best option if you want to go in this direction is to be modest, and aim toward a low reward/risk project. This will minimize the disappointment on the part of your numerous funders, who are going to be more engaged and curious as to the specific result than the NSF or NIH would be.

Though one issue that does need to be pointed out is that at the early stage the people donating to these projects are not the typical citizen. I know the identities of the people who donated to the Malagasy genotyping project, and well over half of them were faculty, postdocs, or grad students. In other words scientists were funding science.

But I think the bigger issue here in terms of the “crowd” isn’t going to be in the area of funds. Rather, I suspect it will be collaboration and labor input. Something analogous to the open source movement. And just like open source software doesn’t mean that firms like Google and Microsoft aren’t eminently profitable, open source science isn’t going to replace “traditional” science. Rather, it’s going to complement.