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.
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.
…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
- Neither agree or 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….
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.
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….
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.
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:
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.
Ed Yong has a post up on a behavior genetic publication where the sample size is 23. The researchers report a correlation between a SNP on the OXTR locus and “prosociality.” To make a long story short the sample size suggested to Dr. Daniel MacArthur and Dr. Jospeh Pickrell that this was a spurious correlation. The bigger issue here is that there are functional reasons to assume that some genes are correlated with normal human variation in psychology and behavior, and a robust body of literature that these traits are heritable (trait value is highly predictive across relatives), but, the results associating a particular genetic marker with a given trait are much less robust.
But I immediately realized something interesting: a sample size of 23 may be small, but there is a sample size potentially of thousands! I know my genotype at this SNP from 23andMe. How about some 23andMe customers get together and produce some results, and then get published in PNAS? A sample size of 230 would be easy I think, and you could probably push it much closer to 1,000.
In a rambling column at Slate on (ir)religious intermarriage Jesse Berring observes:
Still, I concede that the irreducible alchemy of romance makes my cold logic rather difficult to apply to individual marriages. There are more things to a person—and to a relationship, one hopes—than religious beliefs. But since atheistic bachelors and bachelorettes are very rare specimens (there are no exact statistics available, but just 1.6 percent of the U.S. population self-identifies as “atheist”), deciding just how important it is to find a godless mate is indeed a real issue.
There are two small issues, and a big one. First, the 1.6 percent figure is a low one because the term “atheist” is somewhat taboo. Atheist as defined by those who don’t believe in God (as opposed to those who admit to being atheists) is closer to 5%. Second, the main issue with “atheist dating” is the sex ratio problem, though that’s more modest in younger age cohorts today than older ones.
But the broader point is that it’s totally ridiculous to assume that mating is random within the population. Jews are ~3% of the American population, but Jewish-Jewish pairings are not 0.03 × 0.03. I’m sure Bering saw that “religious nones” (of which 1/3 are de facto atheists) have a 50% probability of being with someone of the same lack of beliefs, despite being 15% of the population.
Overall I think it’s right that people should align reasonably well on big metaphysical questions for increased probability of amity. If possible. I don’t think metaphysics (or lack thereof) really matters much day to day, but it does start to matter when there’s a discordance. I just don’t get why Bering ends up writing stuff that’s plainly meant to provoke when there are serious and interesting questions which he is really addressing.
23andMe has a feature which allows you to check MHC compatibility. This is important for matching potential organ donors with those who need those organs. If a close family member is not a match (it’s a very polymorphic set of genes), then a co-ethnic is the next best bet. This is a major problem for those from ethnic minorities and of mixed-race. One day we’ll be able to “grow” organs from our own tissues, but until that day comes matching is still essential. Right now matching is done via drives and what not. But as more and more people get genotyped or sequenced, the information will be right there in the databases. Even racially mixed individuals with very rare combinations of alleles might find matches once the majority of the world’s population gets typed (though I haven’t done the math on this, has anyone?)!
On the other hand, imagine the ethical implications of an accidentally discovered unwilling match being pressured to donate.
From what I recall about half the people who end up being matched decline to be organ donors.* I think that expanding the pool of potential matches so that this situation is minimized far outweighs the cost of the risk Alex alludes to above.
* Donating is not trivial. Going to a drive to check for a tissue match is. So it shouldn’t be that surprising.
But change is afoot. Numerous teams of clinicians and genomicists (including two at my own institution) have come together to sequence patients’ genomes and/or exomes to identify disease-causing mutations.
Of course, doctors and researchers and genetic counselors are still bickering about when to sequence, whom to sequence, return of results, institutional liability, whether we are confusing research with patient care, and on and on. But for the moment, what everyone can agree on is that parents of kids with serious undiagnosed conditions likely to be genetic absolutely do not give a shit about any of those things.
They want help. They want answers. For two decades we have painted grandiose pictures of personalized medicine. Are we going to keep moving the goalposts? Are we going to tell them that we didn’t mean it?
There’s a chicken & egg problem with personal genomics. Until it gets ubiquitous and relatively transparent there is always going to be some letdown in terms of what it can, or can’t, tell us. But as long as there’s a letdown, it won’t become ubiquitous and transparent. That’s the main reason I put my genotype into the public domain. It doesn’t do me too much good or bad, but I wanted to show people that there’s nothing terrifying about it. Once the fear is gone, we can move forward and get some work done.
I haven’t had time to read a book front to back in 2 months. Probably the longest period I’ve gone like this since I was 13. I plan to “binge” as much as I can over the Holidays. Is there anything interesting you’re reading? And yes, I already have The Better Angels of Our Nature: Why Violence Has Declined on my Kindle.
Nice. We’re funded!:
Thanks to an amazing piece at the CNN blog Light Years by Ed Yong, the outpouring of support for the Roman DNA Project today has been astounding! In financial news, we have actually exceeded our $6,000 goal, after just 10 days. That goal was to fund analysis of at least 20 individuals (the immigrants to Rome that I found through Sr/O isotope analysis). Of course, we are accepting donations through mid-December, so additional funding will be put to good use – studying more ancient Romans!
And I’ve received a dozen or more emails today from people as excited as I am about this project, offering their encouragement, lab services, expertise, and knowledge about the ancient world. I will respond to all of them, I promise, but it might take a few days!
Again, thank you – all of you reading this – for making this project a reality!
Dienekes has a little extra commentary. In any case, congratulations are in order! This sort of genetic science seems to be “low hanging fruit.” It isn’t as if you need to fund a massive particle accelerator and what not. I hope that all the museums with assorted samples in their back rooms may now consider the possibility that they don’t have to wait for Max Planck to approach them….
There’s a variable in the GSS, GENEEXPS, which asks if genes play a role in personality. The options are:
- It’s genes which play a major role
- It’s experience which determines personality
First, let’s admit that the premise is stupid. Personality is heritable, but environmental variation also seems to matter. In other words it is noncontroversial to assert that both genes and environment can explain variation in personality (or perhaps more precisely genetic variation can only explain around half the variation for any given trait).
I was curious how this broke down by education and intelligence. To remove demographic confounds I limited the sample to non-Hispanic whites. For intelligence I used WORDSUM, with scores 0-4 being dumb, 5-7 being average, and 8-10 being smart.
A few months ago I pointed out that there’s strong circumstantial evidence that Rick Perry is not very smart. Or, he’s very lazy. While George W. Bush had a reputation as dull, his standardized test scores indicated that he wasn’t without any raw material. This makes sense in light of the fact that his father is reputedly bright, having graduated from Yale with an economics degree in three years. Perry in contrast may be the real deal in terms of a dumb authentic Texas politician.
All that being said, one reader pointed out that Perry did have the intellect to become an officer in the Air Force. Since the military uses standardized tests a fair amount you can put a floor on his intelligence. So I let the matter rest, especially since Perry dropped a great deal in the polls.
But all this came back to mind over the past few days, after Rick Perry’s famous brain freeze during the recent debate. I don’t judge Perry too harshly on this matter in regards to intellect, as I suspect a lot of the problem here is that he hasn’t campaigned very long with the same talking points. Nevertheless, he did forget about the Department of Energy, which should be high on his mental checklist recalling his priorities in this area.
Kevin Drum is in no mood for apologies: