When people ask me what they should read to understand genetics, I don’t really know what to say. But An Introduction to Genetic Analysis is what I reviewed for my genetics qualifying exam. If you want to understand what PCA is, the Wikipedia page should suffice, especially if you have taken linear algebra. Perhaps ironically for someone interested in evolution and genetics I’ve read only a few textbooks devoted to these topics. Rather, I try and read papers. And with the preprint revolution there’s really far less of an excuse to not engage with the literature in such a direct fashion if you are interested.
re: question about inferring admixture from allele, as opposed to genotype data. One could convert to diploid genotype. Or, one could use a PCA based admixture method which takes allele data as inputs.
The Great Ordeal finished with a bang. I’d recommend it, though it is a difficult and frustrating read. Even being conditioned by the previous books that the protagonist is pretty creepy, it went even further in The Great Ordeal. But R Scott Bakker shines where you’d expect, in world-building and haunting evocations and expositions of what had heretofore been beyond the horizon. In particular the sections in Ishterebinth illustrate Bakker’s ability to take a tired trope, elves (he calls them nonmen), and transform it into something novel and multi-textured. Interestingly, as I was reading these sections I began to think that the nonmen looked just like the engineers in the world of the Alien films, and someone also added that observation to their entry in the wiki.
Congo: The Epic History of a People is kind of like reading Oedipus Rex. It’s hurtling toward tragedy. For the section on the “Great War in Africa” I’d just recommend Dancing in the Glory of Monsters. One might ask, why read books like this? Because to confront reality is hard, but to understand the world one must expose oneself to horrible truths.
One of the aspects of American culture that I have long disliked is the inability to acknowledge that democratic polities will naturally lead to an element of populism, and the people are often illiberal. The Founders were aware of the pitfalls of democratic populism, but the skepticism of the 18th century gave way to the embrace of democracy in the Age of Jackson. I’ve long been skeptical of this, but it’s interesting to watch people attempt to deny legitimacy to popular will where in other cases that is all that matters.
Joshua Schraiber is looking to get some post-docs.
In other news, why do people with Ph.D.s aim to get post-docs so that they can get a job in the private sector? Shouldn’t the 5+ years in a Ph.D. program in the biological sciences train you for jobs outside of academia? If not, then we’re doing it wrong.
I don’t talk about contemporary politics much. That’s because I don’t have much to say. On some topics, such as international affairs, not to be immodest, I’m actually more well informed on history and ethnographic detail than many people who write columns. But because I know a fair amount I’m also conscious of how little we can say concretely. Stuff happens. Big coarse heuristics are probably for the best, because this isn’t like sending a probe to Jupiter. We just don’t have a good grasp of mechanics. As for domestic politics, my current attitude is to ask my friends every now and then what’s happening. My time is better spent on intellectual interests, working, and spending time with my family.
So are there neighborhoods where kids hang around on the block? A suburban cul-de-sac? That’s the childhood I want for my kids, but the streets seem to be empty of children. Are they playing video games?
Someone asked me about Game of Thrones a few weeks back. Everything seems to moving in directions you’d predict. I suspect that much of the narrative in the book is not going to be so pat. The show-runners for the HBO series seem to want to squeeze an incredible amount into the last two seasons, while Martin has at least two books to go, and probably three (his books are barely physically feasible, there are so many pages).
One thing watching the television show has impressed upon me: the average IQ of people watching television is much lower than those who read books. The “theories” promoted by those who primarily watch the television show are often far stupider than anything I remember from the message boards of the late 1990s and early 2000s, when those who read the books came up with plausible models such as R+L=J.
Unlike most of my friends I don’t have a problem with gentrification. If a city is expensive, then only people who can afford there should be able to live there. That might impact the cost or availability of services provided by low wage earners, but that’s just how life goes. But being a gentrifier myself it’s interesting to see neighborhoods in transition. The demographic switch can happen very rapidly (e.g., if I see young white women on a block I assume it’s safe). But there is the phenomenon of established businesses often being geared toward the lower-income population that was previously dominant. Eateries and churches might still be frequented by old-timers, who hang around in some way almost as ghosts, strangers in the neighborhoods that grew around them.
The Kindle version of The High Frontier: Human Colonies In Space was free yesterday, so I bought it. There are some awesome things going on in space right now, and it’s fascinating to look back to a time when this was the science which captured the public imagination. It strikes me we are in the golden age of planetary probes, so who is the Richard Dawkins of this field?
The whole DNC email leak and Debbie Wasserman-Schultz resignation strikes me as strange. Obviously I don’t follow politics, because everyone knew they were engaging in these shenanigans. Is it different because we know for a fact?
Detecting Heterogeneity in Population Structure Across the Genome in Admixed Populations. I think the method is a bit under-powered…but I think that’s because local ancestry deconvolution hasn’t progressed that far in the past 3-4 years. I hear things will change soon. Also, high-quality whole genome sequences will change things.
I’ve started a Blue Apron subscription. Pretty impressed so far in that it has “nudged” me to start cooking.