RSS
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.
First CRISPR trial in humans is reported to start next month. In China.
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?
Uncle Sam Wants You — Or at Least Your Genetic and Lifestyle Information.
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.
Evolution Is Happening Faster Than We Thought.
I’ve started a Blue Apron subscription. Pretty impressed so far in that it has “nudged” me to start cooking.
English
Arabic
Chinese (Simplified)
Dutch
French
German
Hebrew
Hindi
Italian
Japanese
Korean
Persian
Polish
Portuguese
Russian
Spanish
Swedish
Turkish
Vietnamese
“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.”
On the left, political theorists such as Amy Gutman have been transforming the understanding of democracy to be more than procedural and Rawlsian, but also include SJW notions of race and gender, so that true democracy just IS progressivism. A huge swath of the American population is unaware of these trends among the intelligentsia, which is why we’re seeing a deeper misunderstanding of the “other side” in politics. We share fewer and fewer priors.
Re: post-docs for those heading to industrial careers — they aren’t needed for training purposes, but they provide a competitive advantage to the job-seeker in an environment where there are more PhD graduates than relevant job openings. We have the same phenomenon in chemistry.
Re: gentrification: Razib writes “only people who can afford there should be able to live there”. In the case of home-owners, the “affordability” that matters may be decades in the past, and gentrification becomes an age thing. Here in Toronto the average house price is about ten times the median household income, and prices have been going up around 5-15% per year consistently for the last 12-13 years (with a brief blip in 2008-9), so age ends up being a better predictor of home-ownership than income is.
Question for Razib or anyone who cares to answer: are the major races we recognize today genetically analogous to the more recent modern humans listed on the top of this chart or do we not know? I’m guessing the differences between Denisovan, Neandertal, Naledi, etc. are considered to be more profound than differences between African, Eurasian, Asian, etc. Would the extinct hobbit people be like today’s Pygmy people in terms of genetic distance to the others? I remember Steve Hsu cleverly hinting at this a while back but wasn’t sure how perfect of an analogy it is.
http://www.nhm.ac.uk/discover/the-origin-of-our-species.html
I know this is basic stuff but I don’t follow pop gen too closely.
Genetic distances between anatomically modern humans and archaic humans (Neandertals, Denisovans) are much greater than between races of AMHs. Recently, some 700,000 year old remains attributed to H. floresiensis were found, associated with stone tools; but my thought is that it might be too much of a stretch to say that they might have been to H. erectus what modern Pygmies are to other AMHs; it seems more likely that they derived from H. erectus and underwent island dwarfing. The parallel might have some value though - pygmy sized people have existed in many parts of the world associated with living in rain forest environments, even in Australia, so some of them might also be the result of 'rain forest dwarfing'. The Australian pygmy people basically disappeared when they were brought out of the rain forest and into the modern world; within a generation or so they no longer existed as pygmies. The same happens to African Pygmies when they interbreed with Bantu - they cease to be Pygmies. Jungle Maya are physically small.
Modern Pygmies have enough cognitive ability to interact normally with other modern humans, and interbreed with them, evidently without difficulty. Greg Laden is definitely worth reading on the subject of Pygmies - he did his anthropological fieldwork living among the Efe. Cognitively/culturally, and in facial shape, the people he describes belong clustered with AMHs, although the splits between Pygmies and all other AMHs, and between the San and all other AMHs, may have been a lot further back than previously thought.Replies: @Robert Ford
http://www.nhm.ac.uk/discover/the-origin-of-our-species.html
I know this is basic stuff but I don't follow pop gen too closely.Replies: @John Massey
I’m opinionating here, Robert.
Genetic distances between anatomically modern humans and archaic humans (Neandertals, Denisovans) are much greater than between races of AMHs. Recently, some 700,000 year old remains attributed to H. floresiensis were found, associated with stone tools; but my thought is that it might be too much of a stretch to say that they might have been to H. erectus what modern Pygmies are to other AMHs; it seems more likely that they derived from H. erectus and underwent island dwarfing. The parallel might have some value though – pygmy sized people have existed in many parts of the world associated with living in rain forest environments, even in Australia, so some of them might also be the result of ‘rain forest dwarfing’. The Australian pygmy people basically disappeared when they were brought out of the rain forest and into the modern world; within a generation or so they no longer existed as pygmies. The same happens to African Pygmies when they interbreed with Bantu – they cease to be Pygmies. Jungle Maya are physically small.
Modern Pygmies have enough cognitive ability to interact normally with other modern humans, and interbreed with them, evidently without difficulty. Greg Laden is definitely worth reading on the subject of Pygmies – he did his anthropological fieldwork living among the Efe. Cognitively/culturally, and in facial shape, the people he describes belong clustered with AMHs, although the splits between Pygmies and all other AMHs, and between the San and all other AMHs, may have been a lot further back than previously thought.
Genetic distances between anatomically modern humans and archaic humans (Neandertals, Denisovans) are much greater than between races of AMHs. Recently, some 700,000 year old remains attributed to H. floresiensis were found, associated with stone tools; but my thought is that it might be too much of a stretch to say that they might have been to H. erectus what modern Pygmies are to other AMHs; it seems more likely that they derived from H. erectus and underwent island dwarfing. The parallel might have some value though - pygmy sized people have existed in many parts of the world associated with living in rain forest environments, even in Australia, so some of them might also be the result of 'rain forest dwarfing'. The Australian pygmy people basically disappeared when they were brought out of the rain forest and into the modern world; within a generation or so they no longer existed as pygmies. The same happens to African Pygmies when they interbreed with Bantu - they cease to be Pygmies. Jungle Maya are physically small.
Modern Pygmies have enough cognitive ability to interact normally with other modern humans, and interbreed with them, evidently without difficulty. Greg Laden is definitely worth reading on the subject of Pygmies - he did his anthropological fieldwork living among the Efe. Cognitively/culturally, and in facial shape, the people he describes belong clustered with AMHs, although the splits between Pygmies and all other AMHs, and between the San and all other AMHs, may have been a lot further back than previously thought.Replies: @Robert Ford
thank you! very interesting
From my observations and experience, yes and yes.
Even in the same suburb or town, the situation with the children is different from block to block. The only way to find out is to conduct in-person and in-depth reconnaissance prior to purchasing a house. My wife and I were very fortunate to have several neighbors who have children of similar ages to ours. We were doubly lucky that they shared similar parenting philosophies as we did and encouraged their children to play outside.
But, my observation is that, due to 1) parents emphasizing a lot of extracurricular activities, especially among the upscale families and heavily scheduling such activities for their children and 2) the overall sedentary tendencies of most children today (TV, video games, iPads, etc.), there are definitely fewer – probably substantially fewer – children playing outside on average than, say, 30-40 years ago. Everyday I see children, even very small children, who are glued to their electronic screens.
My wife grew up in a very affluent suburb, but her family also had a considerable amount of country property, so she enjoyed the benefits of both lifestyles growing up. She played with her friends in the suburb, riding bicycles with the lot of them and roaming the suburban blocks, but she, her siblings, and cousins also hiked about their country property, hunting, fishing, swimming in a lake, catching frogs, building tree houses, and so forth. So she and I have replicated that experience for our children – we live in a Charles Murray “super zip” suburb, but also have a country farm property in a rugged area (little to no mobile phone reception) where the children have learned to grow up as hillbillies. The older of the children are quite appreciative of what they have had growing up.
This appears to be difficult for some (many?) people in the West who seemingly hope to build a paradise – a utopia – on earth. They don’t seem to realize that much of the world is disorderly and vicious where life is often “nasty, brutish, and short.”
I’ve seen firsthand how difficult it is to build what we in the West consider to be functioning and broadly representative institutions in such areas of chaos and anarchy and just how easy it is to destroy any semblance civilization.
Surely the average material condition of human beings has risen greatly and incredibly – to utilize that over-used word – over the past millennia. And certainly there are now wide zones of peace, security, and abundance. But the things I have seen and experienced in different parts of the world as well as some hints or impulses of people in crisis I have seen even in this country lead me to believe that human nature has not changed all much from the coarser days of our existence. So I am always keenly aware of how thin of a veneer civilization is.
“So are there neighborhoods where kids hang around on the block?”
When we moved back to Australia to live for a period, we moved into a low crime neighbourhood. But, coming from the vibrant street life in Hong Kong, the thing that really hit us was that, not only were there no kids playing in the streets, the whole suburb was like a ghost town. I drove through it daily, driving my daughter to and from university, which was an impossible commute by public transport, and I very rarely saw any sign of human life on the street. I also often bicycled around the suburb, and never saw anyone. People didn’t even appear in their front gardens, except briefly to mow the lawn or dig out some weeds. On the rare occasion that I saw women out walking for exercise, they were invariably in pairs, often accompanied by a sizeable dog, and they still looked nervous.
We deliberately used to go to a more distant very down-market shopping centre in what was essentially a ‘refugee’ suburb with high crime rates, just to get a bit of diversity and human interaction, while my wife shopped for ‘Asian’ foodstuffs. I could stand and chat amicably for half an hour with the Vietnamese guy and his wife who ran the news agency there, in a way that did not feel like I was wasting their time, and in a way that was simply not possible with white Australians, who have made themselves invisible and unapproachable by retreating en masse into their houses and back yards. In a year and four months, I had literally a small handful of short, polite, very non-committal conversations with our immediate neighbours on both sides and opposite (variously white South Africans, New Zealanders and Australians), but there was no sense of community at all. The relatively wealthy Muslim kids living across the road turned up at our door step at Halloween and were friendly enough when bribed with candies, but I never did get to have any kind of conversation with their parents, or even met them.
I have lived/worked in some fairly remote areas of Australia; areas where if my vehicle seriously broke down I would be in trouble, because there were no visible humans within 100 miles in any direction, and that kind of isolation and self-reliance never bothered me, but never did I feel so alone as I did living in that suburb, with people living all around me who evidently wanted no human interaction outside of their own nuclear families.
This is not what life was like when I was a kid growing up in the same city. At that time, street life was a normal part of life, and after school every day, all of the neighbourhood kids would be out playing together in the street.
Re robotic probes and who is Richard Dawkins. This is not the golden age of robotic probes. Far from it. Rather it’s the early dawn of the (yes, will take a long long long while) post human, autonomous robotic space exploration era. By this I mean, biologic humans are so ill suited for hard radiation and weightless space it’s only the Cold War mythos of 1960s Apollo heroics thats confusing people that it ever made sense to send humans into space instead of autonomous probes. Time is correcting this myth. Hence any “Richard Dawkins” of probes suffers from tension of truthfulness versus writing about robotic AI post human future. You sometimes see this slip out in Elin Musk occasionally getting off message. But mostly he sticks to pro human to keep getting investors. So there are people writing about this. But mostly they are ignored. Maybe another decade before Overton window shifts enough to make this an acceptable topic in polite company. Meanwhile government space funding talks and talks and talks of sending people to places like Mars, while incredible science gets ever cheaper with (ever more autonomous) robotic probes.
Robert, the way I think about it is in terms of mutation rates in humans which drive evolution, and the lengths of time of geographic isolation. Even if the Pygmies and San split from other AMHs and were geographically isolated from them and one another for as much as 200,000 years, that is a lot less than the period over which AMHs and Neandertals split from their common ancestor (H. heidelbergensis?) and were geographically isolated from one another (for 600,000 years?). All modern human races including those most distant from one another have no difficulty at all interbreeding and having fertile offspring (e.g. Africans interbreeding with Native Americans). Hybridising with Neandertals seems to have been somewhat more difficult, with some suggestion that male hybrids might have been infertile, and subsequently most Neandertal genes have been purged from the genomes of modern humans. Denisovans appear to be more genetically distant again, although the evidence from Melanesians is that they interbred successfully with AMHs, and some evidence that they also interbred with Neandertals.
Razib – On twitter, I noticed you discussing selection of embryos for high-IQ alleles. I am curious how effective you think that can be — it seems that the following would have to happen:
1) larger GWAS will yield more accurate polygene scores for IQ
2) single-cell genotyping or sequencing from 6-day old blastocysts would have to be highly accurate in order to generate accurate polygene scores from available embryos
3) the embryo(s) with the highest polygene scores would be chosen for implantation (standard success rates would apply, with potential risks of PGD reducing viability)
Assuming these technical/engineering issues are optimized in the coming years, it seems that there is still a limit to potential utility imposed by:
1) the amount of variance explained by polygene scores (much, much lower than the heritability estimates derived from family studies)
2) the very limited number of viable, testable blastocysts available in a given IVF cycle
Even ignoring potential risks from negative pleiotropic effects, how much of a difference would there be between the highest and lowest scoring embryo? Or, more relevant, between a randomly selected embryo and the highest scoring embryo?
Just screening embryos, the greatest difference would be the maximum hypothetically possible between siblings.
It is obvious that intelligence is inherited, but it is also usually easy to say which child is the smartest in a family, unless they are an only child. With proper screening, all of the 'only children' would also be like the smartest one out of ten (or one out of thousands if the parents screened embryos for years).
In fact, the most intelligent would be the most likely to start collecting and screening frozen embryos from an early age, but delaying their choice until much later.
Of course they would also screen for all other known non-intelligence related alleles, which would also have a great health benefit.
Even without genome modification, a few generations of high selection in embryos could have amazing consequences for those willing and able to afford it.
This information could be put to use immediately in the sperm donation/selling business, even without screening the embryos.
1) larger GWAS will yield more accurate polygene scores for IQ
2) single-cell genotyping or sequencing from 6-day old blastocysts would have to be highly accurate in order to generate accurate polygene scores from available embryos
3) the embryo(s) with the highest polygene scores would be chosen for implantation (standard success rates would apply, with potential risks of PGD reducing viability)
Assuming these technical/engineering issues are optimized in the coming years, it seems that there is still a limit to potential utility imposed by:
1) the amount of variance explained by polygene scores (much, much lower than the heritability estimates derived from family studies)
2) the very limited number of viable, testable blastocysts available in a given IVF cycle
Even ignoring potential risks from negative pleiotropic effects, how much of a difference would there be between the highest and lowest scoring embryo? Or, more relevant, between a randomly selected embryo and the highest scoring embryo?Replies: @Razib Khan, @Rick
one idea that a friend brought up: iterated embryo selection. the polygene scores would have to get better of course.
Those would be the first children whose parents were never born.
I would like to see that done to improve dog breeds, or exchange single alleles between strains of mice before it was tried on humans.
I know that this has been done with plants, but it is hard to avoid tumor-like situations arising from repeated in vitro growth stages.
This new article by Robert Plomin (Open Access) presents a pretty optimistic view of how much separation can be achieved even with relatively imperfect polygene scores (R2=.09)
Note especially Fig 2 and Fig S2.
However, number of testable blastocysts would still be a rate-limiting factor.
Your thoughts, Razib?
1) larger GWAS will yield more accurate polygene scores for IQ
2) single-cell genotyping or sequencing from 6-day old blastocysts would have to be highly accurate in order to generate accurate polygene scores from available embryos
3) the embryo(s) with the highest polygene scores would be chosen for implantation (standard success rates would apply, with potential risks of PGD reducing viability)
Assuming these technical/engineering issues are optimized in the coming years, it seems that there is still a limit to potential utility imposed by:
1) the amount of variance explained by polygene scores (much, much lower than the heritability estimates derived from family studies)
2) the very limited number of viable, testable blastocysts available in a given IVF cycle
Even ignoring potential risks from negative pleiotropic effects, how much of a difference would there be between the highest and lowest scoring embryo? Or, more relevant, between a randomly selected embryo and the highest scoring embryo?Replies: @Razib Khan, @Rick
“how much of a difference would there be between the highest and lowest scoring embryo?”
Just screening embryos, the greatest difference would be the maximum hypothetically possible between siblings.
It is obvious that intelligence is inherited, but it is also usually easy to say which child is the smartest in a family, unless they are an only child. With proper screening, all of the ‘only children’ would also be like the smartest one out of ten (or one out of thousands if the parents screened embryos for years).
In fact, the most intelligent would be the most likely to start collecting and screening frozen embryos from an early age, but delaying their choice until much later.
Of course they would also screen for all other known non-intelligence related alleles, which would also have a great health benefit.
Even without genome modification, a few generations of high selection in embryos could have amazing consequences for those willing and able to afford it.
This information could be put to use immediately in the sperm donation/selling business, even without screening the embryos.
What do you mean by iterated? Screening the embryos generated from in vitro production of sperm and eggs from the parents’ embryos?
Those would be the first children whose parents were never born.
I would like to see that done to improve dog breeds, or exchange single alleles between strains of mice before it was tried on humans.
I know that this has been done with plants, but it is hard to avoid tumor-like situations arising from repeated in vitro growth stages.
Ok, that makes sense, that’s kinda what I was thinking but without any detail. Thanks again!
Yes, in addition to Twinkie’s points, I’d emphasize that the density of children in neighborhoods is obviously not what it once was. From that, the increase in competition from organized activities and technology, reduce the number of kids available even further. The more kids, the more likely to find friends of your own age/interest/gender, the more likely to find alternative friends when necessary, the more likely to have group activities, etc.
The other factor is parents working. When I grew up most moms stayed home, and the kids were out and about. In my current neighborhood, there appears to be more kids hanging around than others because one parent is either working at a job from home or working part-time. My sense around here is that this is less likely in more expensive neighborhoods.
Have you read the andamanese paper in nature? I do not have access. The abstract is saying two things at the same time, single wave from Africa and descent from a homin in Asia.
https://www.unz.com/gnxp/ancient-archaic-admixture-into-the-andamanese/
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?
Perhaps. Sanders ran saying, “The system is corrupt and stacked against you, and Hillary is part of that system.” But he’s a pragmatist, and very much wants to change his message to, “Donald Trump is absolutely awful, so vote for and work for and give money to Hillary.”
This makes it harder to get his supporters on to the new message. Part of the story of the next three and a half months will how successful he and Hillary (and parts of the media) are in burying the old message and spreading the new one. In fact, the Hillary people will be trying to spread an even newer message, “With the changes in the platform and the welcome to Sanders, Hillary is now the anti-establishment, pro-reform candidate–but with experience and knowledge of “how to play the game.” Kind of a tight-rope walk. But a lot of people certainly want to believe that.
http://www.nature.com/mp/journal/vaop/ncurrent/full/mp2016107a.html
This new article by Robert Plomin (Open Access) presents a pretty optimistic view of how much separation can be achieved even with relatively imperfect polygene scores (R2=.09)
Note especially Fig 2 and Fig S2.
However, number of testable blastocysts would still be a rate-limiting factor.
Your thoughts, Razib?