Razib Khan One-stop-shopping for all of my content

June 30, 2018

Imperium did make the least of us richer

Filed under: Economic History — Razib Khan @ 1:38 pm

After reading the section on Rome in War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, I realized I had changed my mind over the past 10 years on the issue of differences in wealth in the past. Following the treatment in A Farewell to Alms: A Brief Economic History of the World or Contours of the World Economy 1-2030 AD: Essays in Macro-Economic History, I held to the position that before the pre-modern world, and back to the Paleolithic, the vast majority of people had been roughly at the same standard of living at the Malthusian limit.

Basically, a British peasant in 1500 was no more poor or rich than a Japanese peasant in 1500 who was no poorer than a Paleolithic hunter-gatherer who lived in 15,000 BC. The reason being that in the pre-modern world economic growth rates were so slow that population growth always caught up, and the populace was back to immiseration on the Malthusian margin. Yes, there were some differences of detail, but not worth mentioning.

In David Warsh’s Knowledge and the Wealth of Nations there is a great deal of emphasis on economic growth being driven by gains in productivity, which are driven by innovation. This is common sense. We all know that people are wealthier and healthier because of technological growth and development over the last few hundred years. But there’s another variable: the demographic transition. After all, modern middle-class Westerners could have huge families and spend all their discretionary income raising children. They don’t.

Malthus’ logic was actually right. He even understood that productivity gains and efficiency were going to occur. But the iron law of human reproductive fecundity seemed to be an inevitability…until it wasn’t. It is always important to move beyond logic. It seems clear that productivity gains in the pre-modern world were low…but there was variation in consumption and quality of life, even though it was nothing like what we see today.

Books like The Fate of Rome: Climate, Disease, and the End of an Empire and The Fall of Rome: And the End of Civilization have convinced me that the Roman Peace wasn’t simply a propaganda coup. That it wasn’t simply a great con by the elites to steal surplus wealth from the masses and channel it into public works which reflected their glorious and status and secured their immortality in the memory of future generations (though it was that!).

This doesn’t necessarily mean you’d rather be a Roman citizen or subject than a barbarian living beyond the frontiers. That depends on how much you value your life as opposed to your freedom. But whereas 10 years ago I would stay that the attraction of Romanitas was simply a function of elites attempting to capture the best extractive institutional mechanisms, I do think there was a “trickle down” in consumption goods through classical dynamics described in Adam Smith’s Wealth of Nations. Trade, specialization, and peace did bring dividends, both to the high and the low. On the margin being 25% wealthier on a low base may not seem like much to us, but it was probably a lot to them. How much do you value dishware?

The decline in South Asian poverty

Filed under: Economics — Razib Khan @ 12:47 pm

It has long been asserted that South Asia may make average strides economically, but it is still in absolute terms the locus of most of the world’s grinding poverty. This may not be true much longer. In particular, some estimates now suggest that India is no longer the world’s “leader” in extreme poverty in absolute terms. From Brookings, The start of a new poverty narrative:

According to our projections, Nigeria has already overtaken India as the country with the largest number of extreme poor in early 2018, and the Democratic Republic of the Congo could soon take over the number 2 spot (Figure 1 below). At the end of May 2018, our trajectories suggest that Nigeria had about 87 million people in extreme poverty, compared with India’s 73 million. What is more, extreme poverty in Nigeria is growing by six people every minute, while poverty in India continues to fall. In fact, by the end of 2018 in Africa as a whole, there will probably be about 3.2 million more people living in extreme poverty than there are today.

Bangladesh has been making progress as well, from the World Bank:

Bangladesh has made remarkable progress in reducing poverty, supported by sustained economic growth. Based on the international poverty line of $1.90 per person per day, it reduced poverty from 44.2 percent in 1991 to 13.8 percent in 2016/17. In parallel, life expectancy, literacy rates and per capita food production have increased significantly. Progress was underpinned by 6 percent plus growth over the decade and reaching to 7.3 percent in 2016/2017, according to official estimates. Rapid growth enabled Bangladesh to reach the lower middle-income country status in 2015. In 2018, Bangladesh fulfilled all three eligibility criteria for graduation from the UN’s Least Developed Countries (LDC) list for the first time and is on track for graduation in 2024.

Here’s GDP for South Asian countries in 2005 dollars:

I left Bangladesh in 1980. Not too long after I was born. I went back to visit in 1989 and 2004. In relation to 1980, per capita GDP was 1.15x. in 2004 it was 1.6x. In 2016 it was 2.9x. So over the past 14 years there’s been a 2x increase in GDP per capita in Bangladesh! The equivalent figure in the United States is 1.1x.

The decline in South Asian poverty

Filed under: Economics — Razib Khan @ 12:47 pm

It has long been asserted that South Asia may make average strides economically, but it is still in absolute terms the locus of most of the world’s grinding poverty. This may not be true much longer. In particular, some estimates now suggest that India is no longer the world’s “leader” in extreme poverty in absolute terms. From Brookings, The start of a new poverty narrative:

According to our projections, Nigeria has already overtaken India as the country with the largest number of extreme poor in early 2018, and the Democratic Republic of the Congo could soon take over the number 2 spot (Figure 1 below). At the end of May 2018, our trajectories suggest that Nigeria had about 87 million people in extreme poverty, compared with India’s 73 million. What is more, extreme poverty in Nigeria is growing by six people every minute, while poverty in India continues to fall. In fact, by the end of 2018 in Africa as a whole, there will probably be about 3.2 million more people living in extreme poverty than there are today.

Bangladesh has been making progress as well, from the World Bank:

Bangladesh has made remarkable progress in reducing poverty, supported by sustained economic growth. Based on the international poverty line of $1.90 per person per day, it reduced poverty from 44.2 percent in 1991 to 13.8 percent in 2016/17. In parallel, life expectancy, literacy rates and per capita food production have increased significantly. Progress was underpinned by 6 percent plus growth over the decade and reaching to 7.3 percent in 2016/2017, according to official estimates. Rapid growth enabled Bangladesh to reach the lower middle-income country status in 2015. In 2018, Bangladesh fulfilled all three eligibility criteria for graduation from the UN’s Least Developed Countries (LDC) list for the first time and is on track for graduation in 2024.

Here’s GDP for South Asian countries in 2005 dollars:

I left Bangladesh in 1980. Not too long after I was born. I went back to visit in 1989 and 2004. In relation to 1980, per capita GDP was 1.15x. in 2004 it was 1.6x. In 2016 it was 2.9x. So over the past 14 years there’s been a 2x increase in GDP per capita in Bangladesh! The equivalent figure in the United States is 1.1x.

June 29, 2018

Human genomics will uncover a lot of treasure in Southeast Asia

Filed under: Human Population Genetics,Negritos — Razib Khan @ 12:25 am

On this week’s podcast on “Isolated Populations” I mentioned offhand to Spencer that I believe it is a bit ridiculous to bracket a host of Southeast Asian populations as “Negritos,” as if they were an amorphous and homogeneous substratum over which the diversity of modern South and Southeast Asian agriculturalists were overlain.There was almost certainly a great deal of population structure which accrued over the Pleistocene. Another issue, which I didn’t mention, is that Southeast Asia is also very geographically expansive. Modern Indonesia alone spans the length of North America.

Of course, you could say the same for Europe, from the Urals to the Atlantic. And yet we know that European hunter-gatherers were relatively homogeneous (albeit, with some structure!) at the beginning of the Holocene. I think the difference though is that Europe was a landscape into which hunter-gatherers expanded during the Last Glacial Maximum, while Southeast Asia, like Africa, has long been a refuge for human populations even during the coldest and driest periods of the Pleistocene.

There are three major classes of “Negrito” peoples in South and Southeast Asia.  To the west, are the indigenous peoples of the Andaman Islands. These tribes probably arrived from what is today Myanmar during the Pleistocene, when sea levels were lower. In peninsular Malaysia you have groups such as the Semang. Though physically very different from their neighbors, these people speak the Aslian form of Austro-Asiatic languages. They are not linguistic isolates like the Andaman tribes.

This speaks to the reality that unlike the Andaman Islanders the Negritos of mainland Southeast Asia have long been interacting with local populations. The languages they speak reflect interactions with Austro-Asiatic rice farmers. Curiously though, the dominant people amongst whom they live no longer speak Austro-Asiatic languages. Rather, they speak Austronesian or Tai dialects. These two groups are later arrivals on the Southeast Asian scene, and both seem to have assimilated Austro-Asiatic groups culturally and genetically, except in Cambodia and Vietnam (and to a lesser extent in pockets of Thailand and Myanmar).

If you are curious about the relationship between the various modern Southeast Asian groups, then two ancient DNA papers, Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia and Ancient genomes document multiple waves of migration in Southeast Asian prehistory, should do the trick. Some of the migrations are historically or semi-historically attested. In particular, the intrusion of the Tai, the long occupation of what became Vietnam by the Chinese, and the settlement of Han officials amongst the local people, and the migrations of the ancestors of the Hmong into Laos.

Others processes are vaguer and poorly understood. It has long been clear that the Austronesian probably assimilated Austro-Asiatic rice farmers in much of maritime Southeast Asia. And yet unlike mainland Southeast Asia to my knowledge, there are no Austro-Asiatic populations in Indonesia. Additionally, it has been brought to my attention that the ~ 3,000-year-old sample from Myanmar has no clear Austro-Asiatic signature, despite the common sense suggestion that Austro-Asiatic languages must have entered India via that region (it has affinities to modern Tibeto-Burman individuals). And, importantly the Austro-Asiatic populations themselves seem to have been deeply mixed between a dominant element strongly related to the Han Chinese, and a minority component which was basal Southeast Asian, for lack of a better term. This means that the Munda populations within India have several distinct components of ancient South and Southeast Asian substratum.

Aeta family

But speaking of this substratum, probably the best paper recently focusing on these groups is from last year, Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. In many ways, it just reinforced the results of Reich et al. 2011. All the Negrito groups are only distantly related to each other. The Negritos of the Andaman Islanders and those of peninsular Malaysia seem to be somewhat closer to each other than either is to those of the Philippines. And, the groups in the Phillippines seem to be somewhat closer to the peoples of Melanesia. To some extent, this is just geographically expected, but there are also interesting details.

The Negritos of the Philippines, in particular, those from the northern island of Luzon, have some of the highest fractions of Denisovan ancestry of any human populations outside of Melanesia. No one is clear whether the admixture is from the same event as the one that leads to the high fractions in Melanesians, or whether there were separate mixing events (not implausible). The western Negrito groups have far lower fractions of Denisovan.

Another surprising result is that the Negritos of the southern Philippines seem very distinct from those of the northern Philippines. This may be an artifact of particular admixture history, but I wouldn’t be surprised if these islands preserved a lot of diversity which has been homogenized elsewhere.

Like many people, I believe that human evolutionary genomics will have a lot to say about Africa in the next 10 years. But, outside of Africa Southeast Asia may be one of the most fertile regions in terms of exposing deep history. This was an area that was always amenable to habitation by modern-like Africans. It seems very likely now that the predominant modern human ancestry found in the Negrito substratum, and shared with all other non-Africans, is actually not the signal of the oldest modern humans to be present in Southeast Asia. Second, there seem to be many archaic human species which made their homes in Southeast Asia.

Humans arrived in Southeast Asia a long time ago. Our speciosity and census sizes were high. With more ancient DNA and better deep whole genome sequence analysis, we’ll uncover some surprising things. I guarantee.

June 28, 2018

Have your exome sequenced for $29.99

Filed under: DNA,Genetics,sales,science — Razib Khan @ 9:11 pm

Just a reminder that for the rest June Helix DNA kits with the cost of an Insitome app. Buy Regional Ancestry, Metabolism, or Neanderthal, and start your lifelong DNA journey with Helix for just $29.99! A great gift idea.

That means for the cost of an app Helix will sequence more 30 million markers in your genome. In contrast, rival genotyping companies only look at 500,000 to 1,000,000 markers.

Cost of use: FREE

The 30 million markers Helix sequences include your whole exome. The part of your genome which is involved in coding for proteins, and so impact your appearance and function. The Helix system also includes markers outside of the exome to further map your genome more effectively.

Insitome’s apps, whether it be Regional Ancestry, Metabolism, or Neanderthal are windows into the whole landscape of modern day personal genomics. Once Helix sequences you the data is banked for later use.

When new apps are developed on the Helix platform, your future purchases will only include the cost of the app! Entering the ecosystem now means that you will never have to pay the initial cost of the sequencing kit.

What are you waiting for? Get the Helix DNA kit and jump into the ecosystem now!

Have your exome sequenced for $29.99 was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Harlan Ellison, R.I.P.

Filed under: science fiction — Razib Khan @ 3:03 pm

Harlan Ellison has died.

I Have No Mouth and I Must Scream is one of the most disturbing things I have ever read. Over 20 years after reading I still remember how appalled I felt as I finished the last sentence.

Ellison was a powerful writer. Some of his innovations have become cliche (e.g., Ellison pioneered time travel plots which have now become overused). One thing I remember from Isaac Asimov’s autobiography was how much he loved Ellison for his loyalty and devotion as a friend.

With his health failing over the past few years it is not surprising he finally died. But he surely lived a very full and eventful 84 years. Ellison made a difference, and he’ll be remembered.

June 27, 2018

Genetics of uniqueness

Filed under: Genetics,indigenous-people,science — Razib Khan @ 1:54 pm
Ati woman from the Philippines
Hui Chinese Muslim man

True genetic isolation is hard to pull off. Human populations tend to mix when they are in close proximity.

Consider the Hui people. These are Muslims who live across China and speak the local Chinese dialect of their locale. The Hui claim descent from Central Asians and Persians who arrived in China around 1,000 years ago. But the vast majority of their genomes are no different from the Han Chinese. Physically they are impossible to distinguish from Han Chinese unless you take note of their attire.

How can that be when they are so culturally different? For example, as Muslims the Hui do not eat pork and consider it unclean. In contrast, for the majority Han pork is dietary staple.

Imagine that the Central Asian ancestors of the Hui arrive 1,000 years ago to China. The historical record suggests that is roughly correct. Each generation is 25 years long, so that’s 40 generations. Since the population of Muslims is small in comparison to the native Chinese, we can ignore the latter, while focusing on the former. If on average 1 out of 20 marriages was between a Han Chinese and a Muslim within the Hui community per generation, after 1,000 years 88% of the ancestry within the Muslim community would be traceable to Han Chinese ancestors. Even though in each generation the overwhelming majority of marriages were within the Muslim community, over time the genetic distinctiveness of the Muslims would diminish.

The lesson is that even a small degree of intermarriage can even out the differences between groups. Similarly, in population genetics one individual moving between two groups per generation is enough to prevent them from becoming distinct. In small populations, which diverge fast, one individual is a substantial proportion of a population. In large populations the divergence is going to be much slower, so even one individual is enough.

An Andaman Islander

So how do populations remain genetically distinct if mixing and homogenization is so easy? The simplest way is simply geography. Consider the Andamanese. These slim and dark-skinned people are the natives of the Andaman Islands, in the middle of the Bay of Bengal. To the knowledge of archaeologists and historians these people have been hunter-gatherers since time immemorial. The only verified continuous such tradition in all of Asia.

The Andamanese likely arrived in the islands during the Pleistocene, when sea levels were lower, and the Andaman Islands were much more accessible from the Southeast Asian mainland. But over the past 10,000 years, as much of the world adopted agriculture, and population turnover occurred in South Asia and Southeast Asia, the Andaman Islands remained relatively untouched due to their isolation.

But it wasn’t just geography. Over the past 2,000 years the Indian ocean has become a major thoroughfare of trade and travel. The Andaman Islands were on a route between India and Southeast Asia. Because of this fact they were often a convenient stopping point to refresh water supplies. But these traders never settled the islands. The local people had a habit of attacking any vessel which tarried too long in their waters.

Pygmies from Central Africa

Unlike many animals humans have complex and evolving cultural practices. The Andaman Islanders discouraged contact with outsiders by maintaining a savage and hostile reputation.

But other groups have remained genetically distinct through symbiosis rather than separation.

The Pygmy peoples of Central Africa are distinguished from their neighbors by their small stature, and hunter-gatherer lifestyle. But they invariably speak the languages of their neighbors. Anthropologists have observed that Pygmies and the farmers who they live nearest to seem to exist in some form of interdependence. Hunter-gatherers can obtain resources from the deep rainforest inaccessible to famers, while the farmers offer the Pygmy people goods which they themselves could not produce.

African farmers and hunter-gatherers have lived in close proximity for over 2,000 years, and yet the Pygmies remain different physically and genetically from their neighbors. Some mixing has occurred, but the Pygmies are as much a separate caste as a different people. Their lifestyle is so different that farmers and Pygmies view each other as profoundly alien and peculiar, despite speaking the same language and occupying nearby geographical space.

Roma in Romania

Isolation then can be both a physical and psychological phenomenon. Some groups, such as the Andamanese, are physically separated from other humans. They add cultural adaptations which reinforce this separation. Others, such as the Pygmies, or the Roma of Europe, are culturally very distinct, and occupy a specific role in the social ecology of their region. In both cases the isolation is strong enough to result in genetic differences between populations of the majority and the isolate.

In many cases these populations are not so isolated in the modern age. In the Andaman Islands most of the tribes now interact with settlers from the Indian mainland. Only the people of North Sentinel island remained truly isolated and cut off from the rest of the world. Meanwhile, the Pygmy people of Central Africa have been caught up in the massive civil wars that have wracked that region of the world since the 1990s. In other cases, as with the indigenous Negrito people of the Philippines, their biological and cultural assimilation into the dominant Austronesian mainstream is proceeding to such an extent that they may no longer being a distinctive people by the end of the 21st century.

For many peoples the 21st century will be the twilight of their solitude, as they merge into the world.

Interested in learning where your ancestors came from? Check out Regional Ancestry by Insitome to discover various regional migration stories and more!

Genetics of uniqueness was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Open Thread

Filed under: Open Thread — Razib Khan @ 10:14 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

South Asian Genotype Project, Summer 2018 Update

Filed under: Genetics — Razib Khan @ 7:38 am

Just an update on the South Asian Genotype Project.

It seems Brahmins from Maharashtra are like Brahmins from South India. Brahmins from Gujarat are like Brahmins from North India.

South Asian Genotype Project, Summer 2018 Update

Filed under: India Genetics,India genomics,South Asian Genotype Project — Razib Khan @ 12:54 am

I’ve put another update on the South Asian Genotype Project. If you’ve contributed since March check it out.

Again, if you are interested: send me a 23andMe, Ancestry, MyHeritage, Family Tree DNA raw genotype file to contactgnxp -at- gmail.com.

In the subject please put:

  1. “South Asian Genotype Project”
  2. The state/province your family is from
  3. Ethnolinguistic group
  4. If applicable, caste

I decided to some poking around with some of the higher quality samples people have given me. 180,000 SNPs with almost no genotyping error. I also removed “relatives.” That means that a lot of Muslim groups from Pakistan had individuals dropping out. In the PCA above you can see 4 Burushos left! Not too many Pathans either.

Click to enlarge!

First, I decided to look at the Brahmin samples I had.

– Uttar Pradesh, Bihar, and the Gujarati Brahmin(s) I had are one cluster
– South Indian Brahmins (mostly Iyer) are another

To my surprise, the two Maharashtra Brahmins that I have are firmly in the South Indian cluster. The Bengali Brahmin is more like the North Indians. But there is a subtle skew toward the distant Bangladesh cluster. This individual seems less East Asian than even the typical Bengali Brahmin, but I think Bengali Brahmins can be modeled as North Indian Brahmin with non-Brahmin (and therefore East Asian) ancestry.

Click to enlarge!

Next, I wanted to look at Gujaratis. The 1000 Genomes has a large number of this population…but there’s not group identity. Years ago Zack Ajmal of Harappa DNA concluded that a large and relatively related cluster in these data were “Patels.” Someone who is a Bohra Muslim of presumably Patel background sent me their data. They did not fall in the Patel cluster. Rather, they were in the “Gujurati_ANI_1” group, which is more like Pakistanis than other Gujuratis. In fact, the Gujurati Brahmin is not in this cluster. An individual whos Solanki seems to be more ASI-shifted, like the Patels and Gujurati_ANI_4.

Overall, Gujarat has a lot of population structure in a rather small state (yes, I can’t spell Gujarat as you can see in my population labels).

Click to enlarge!

From Maharashtra, right to the south of Gujarat in western India, I have two Brahmins and one Kayastha. For non-South Asians, my understanding is that Kayasthas are literate non-Brahmin castes. In Bengal, they take the places of the Kshatriya in the caste hierarchy, and with Brahmins formed the traditional Hindu educated classes. I have seen Bengali Kayastha genotypes, and they look rather like other Bengalis (my mother’s father’s family is from a Kayastha family before their conversion to Islam judging from their customary surname).

There are Kayasthas in other parts of South Asia. I have a Kayastha sample from Maharashtra. Curiously on the PCA this individual is in the same position as the two Brahmins from the region, and South Indian Brahmins. I don’t know what this means.

Click to enlarge!

Next some odds and ends from the northwest of the subcontinent. I have a few Jatts who are not related. This group from Punjab is quite ANI-shifted. Someone who claims to be a Rajput from Rajasthan is where they should be on account of geography. The Punjabi 1000 Genome group is quite diverse. I have a Ramgarhia individual who seems to be somewhere between Punjabi_ANI_1 and Punjabi_ANI_2. The Jatt are on the edge (ANI-shifted) of Punjabi_ANI_1.

I have two individuals who claim to be Kashmiri. A Butt and a Syed. I have no idea what that means. But both are Punjabi_ANI_2…but they look somewhat East Asian shifted. This is not surprising. The curious thing about Kashmiris is that they are culturally and geographically quite distinct from Indians to their south. But genetically they are not so different. In fact, they are “more South Asian” (ASI) than Jatt, and considerably more than Iranian speaking groups like Pathans.

Finally, there is a Marwari individual. This community is from Rajasthan, though they occupy a mercantile role across the subcontinent. Strangely (or not?) they are very close to the Patels. Much more ASI-enriched than the Rajput.

Click to enlarge!

Shifting to South Indian samples, I plotted the Chamar samples, who I believe were collected from Uttar Pradesh in the north. These Dalits actually seem to cluster with a subset of the 1000 Genomes Tamil and Telugu samples I believe are Scheduled Caste (Dalit) as well. The Chamar are somewhat distinct. They are more ANI-shifted. But notice that the bulk of Tamils and Telugus are still more ANI-shifted than the Chamars are! This surprised me.

I have some Velama individuals, as well as a Reddy from Andhra Pradesh and a Padmashali. All these individuals are in the main distribution of South Indians. I do have a Mudaliar Tamil sample, and this individual is placed among the Chamars. Though not really in the Tamil Scheduled Caste group.

Click to enlarge!

Finally some odds & ends. The Nasrani samples from Kerala are between the South Indian Brahmins and middle caste South Indians. I suspect this is due to the origin of the Nasranis in the Nair community, who have mixed some with Brahmins. The Vania sample from Gujarat is clustered with South Indian Brahmins. The Dusadhs, an agricultural group from Uttar Pradesh and Bihar, that is depressed in some manner in relation to the dominant groups, are not quite Chamars, but they are quite ASI-shifted.

Some of you will be asking about admixture. I ran K = 4 unsupervised on the data set. You can find it here.

June 26, 2018

Height differences across Europe could be less effected by selection than we had thought

Filed under: GWAS,Height,Human Population Genetics — Razib Khan @ 8:43 am

Like an Old Testament prophet of yore Graham Coop has been prophesying that cryptic population stratification may be a major confounder in analyses for as long as I’ve known him with any degree of familiarity. So it’s no surprise he’s an author on one of two preprints which have rocked the genomics world:

Reduced signal for polygenic adaptation of height in UK Biobank:

There is considerable variation in average height across European populations, with individuals in the northwest being taller, on average, than those in the southeast. During the past six years, a series of papers reported that polygenic scores for height also show a north to south gradient, and that this cline results from natural selection. These polygenic analyses relied on external estimates of SNP effects on height, taken from the GIANT consortium and from smaller replication studies. Here, we describe a new analysis based on SNP effect estimates from a large independent data set, the UK Biobank (UKB). We find that the signals of selection using UKB effect-size estimates for height are strongly attenuated, though not entirely absent. Because multiple prior lines of evidence provided independent support for directional selection on height, there is no single simple explanation for all the discrepancies. Nonetheless, our current view is that previous analyses were likely confounded by population stratification and so the conclusion of strong polygenic adaptation in Europe now lacks clear support. Moreover, these discrepancies highlight (1) that current methods for correcting for population structure in GWAS may not always be sufficient for polygenic trait analyses, and (2) that claims of polygenic differences between populations should be treated with caution until these issues are better understood.

And…Signals of polygenic adaptation on height have been overestimated due to uncorrected population structure in genome-wide association studies:

Genetic predictions of height differ significantly among human populations and these differences are too large to be explained by random genetic drift. This observation has been interpreted as evidence of polygenic adaptation, natural selection acting on many positions in the genome simultaneously. Selected differences across populations were detected using single nucleotide polymorphisms (SNPs) that were genome-wide significantly associated with height, and many studies also found that the signals grew stronger when large numbers of sub-significant SNPs were analyzed. This has led to excitement about the prospect of analyzing large fractions of the genome to detect subtle signals of selection for diverse traits, the introduction of methods to do this, and claims of polygenic adaptation for multiple traits. All of the claims of polygenic adaptation for height to date have been based on SNP ascertainment or effect size measurement in the GIANT Consortium meta-analysis of studies in people of European ancestry. Here we repeat the height analyses in the UK Biobank, a much more homogeneously designed study. While we replicate most previous findings when restricting to genome-wide significant SNPs, when we extend the analyses to large fractions of SNPs in the genome, the differences across groups attenuate and some change ordering. Our results show that polygenic adaptation signals based on large numbers of SNPs below genome-wide significance are extremely sensitive to biases due to uncorrected population structure, a more severe problem in GIANT and possibly other meta-analyses than in the more homogeneous UK Biobank. Therefore, claims of polygenic adaptation for height and other traits, particularly those that rely on SNPs below genome-wide significance, should be viewed with caution.

I haven’t read both preprints through and through, but my first thought (along with others), is the same as Casey Brown:

Note that no one has responded to his question.

Finally, recall that population structure within Europe is relatively weak and the distances between the groups low. It reminds you of how difficult polygenic traits are to analyze due to the small and subtle effects, and how they might be overwhelemed even by subtle population structure. And recall, even the British population has some of that… (albeit, an order of magnitude or so less than what you can find across Europe).

A shock is a surprise because it’s a shock

Filed under: History — Razib Khan @ 7:08 am

Reading Thomas Childer’s The Third Reich: A History of Nazi Germany reminds me a lot of reading The Red Flag: A History of Communism. These strange and extreme ideological systems seem likely to be eternally marginalized…until they aren’t. The dream of revolution is a fantasy until it isn’t. The rot within these societies, their anomie and disharmony, could be papered over and suppressed for a time. But the revolution took root in rich soil fertilized by the decay and necrosis of the old order.

Human social and cultural systems go through the evolutionary process in a gradual fashion. But quite often they don’t. In fact, compared to biological systems I’d say cultural evolutionary processes are more nonlinear and protean. We may attribute this to exogenous shocks, but with hindsight, we often see that there were endogenous parameters setting the system up to collapse with the first “push” from the outside or an unexpected variable.

And one of the curiosities of humans is our tendency to maintain public fictions all the while knowing that private realities are different. With the chaos of the 1st century B.C., social unrest, the rise of successive strongmen, it was clear to observers of the time that the Roman Republic was sick. The final victory of Augustus and the end of the “republican” chaos is often depicted as a relief for most Romans and their subjects, with the exception of a few aristocrats who were pushed into a purely servile and ceremonial role.

Still, the public fiction continued. Augustus famously was the “first citizen,” princeps. The term imperator became more ubiquitous with the reign of Vespasian a century later, as the Roman Empire recovered from the fall of its first royal dynasty. Nevertheless, the forms of the Republic were maintained despite the reality that Rome become an autocracy. Only around 300 AD did princeps fall into disuse. Diocletian began to exclusively use the term dominus. Lord.

Other public fictions persisted even then. The office of consuls, which date to Roman prehistory, was maintained down to the 6th century A.D., the reign of the Justinian. The last of the Roman Emperors coincidentally who grew up as a native Latin speaker.

Obviously, the tendency toward public fictions is not an artifact of Rome. To a great extent, Constitutional Monarchies are public fictions. When around 200 A.D. the emperor Septimius Severus did away with the fiction that the laws enacted were derived from the will of the Senate of Rome, he did away with a practice that had maintained a republican facade for centuries. The shocks and violence of the 3rd century, when the Roman system almost collapsed, was the coup de grace. Though Diocletian and the military emperors which came after him were never self-styled kings, due to the taboo around the term in Roman society, their forms and manners were inherited by the monarchs of medieval Europe. The radiant crown that Westerners perceive to be prototypical of the form is a Roman inheritance was popularized by the sun-worshipping emperors of the late 3rd century. Julian the Apostate, a reactionary who abhorred the new, did away with many of the imperial accretions added by his recent predecessors, with all the pomp, ceremony and glamor (though his reign was an aberration in more ways than that). The Romans never had kings, but showed kings how to be kings in substance and style.

In the pre-modern world, these fictions were quite resilient. The Zhou dynasty persisted centuries after it no longer had any power to speak of. The Abbassid Caliphs were kept as puppets in Mamluk Egypt for 250 years before the Ottoman conquest. The Merovingian dynasty’s last 100 years was to be as symbolic puppets for the lords of the Franks.

The moral of the story is that public fictions can last quite a bit longer than the reality form which they are spun. With hindsight, the chaos and disrepute ushered in by the reign of Commodus clearly signals the end of the old Roman Empire with its republican fictions. But that was not clear then. The frog continued to boil, until from the outside barbarians threw in a dash of scalding water.

June 24, 2018

Open Thread, 6/24/2018

Filed under: Open Thread — Razib Khan @ 7:58 pm

I recently read John Keay’s Midnight’s Descendants: A History of South Asia since Partition. No particular reason. But I’ve read earlier books on the history of India and China and I sort of wanted to fill a hole in my knowledge. I would recommend if you don’t know much about this period and place. It’s probably somewhat important in the future.

Thanks to all the readers of this weblog who have given iTunes ratings to my podcast. We’re almost to 100 ratings, so you won’t be hearing me go on and on about it.

Though speaking of the podcast, we’re going to talk to Ian Morris, author of War! What Is It Good For?: Conflict and the Progress of Civilization from Primates to Robots, soon. So subscribe now.

Erdogan’s Election Win Gives Him Vastly Expanded Powers in Turkey.

The Trailer for The Man Who Unlocked the Universe Is a Gorgeous Mixture of Science and Action. This looks like a good complement to Lost Enlightenment: Central Asia’s Golden Age from the Arab Conquest to Tamerlane.

It’s curious how many Central Asian warlords were patrons of culture. Mahmud of Ghazni, for example, supported Ferdowsi.

Just found out that Reihan has a new book out this fall, Melting Pot or Civil War?: A Son of Immigrants Makes the Case Against Open Borders.

Demographic inference in a spatially-explicit ecological model from genomic data: a proof of concept for the Mojave Desert Tortoise.

Bangladesh’s Secular Bloggers: Risking Their Lives for Freedom. A lot of atheist podcasts aren’t really “edgy” anymore. The Secular Jihadists is an exception.

Evolution of correlated complexity in the radically different courtship signals of birds-of-paradise.

The citizen scientist who finds killers from her couch.

Human demographic history has amplified the effects of background selection across the genome.

Most people have always thought human sacrifice was bad

Filed under: Anthroplogy,Cultural Evolution,History,Human sacrifice — Razib Khan @ 4:00 pm

A few days ago a minor controversy about the cultural context of human sacrifice in Mesoamerica cropped. A writer at Science, wrote a piece, Feeding the gods: Hundreds of skulls reveal massive scale of human sacrifice in Aztec capital. The article was good. But it elicited some emotional responses from readers. As one sees in the earliest writings of the Spanish, the Aztec penchant for human sacrifice often results in a moralistic reaction.

The writer of the piece took to Twitter to disagree with the moralistic tone of many who read her article. It being Twitter, her original series of comments were easy to misinterpret or exaggerate, and she had to post a follow-up clarifying some issues. Below is a response to one of her original assertions.

Basically, I agree that our feelings about sacrifice today are irrelevant to understanding it. To understand human history and something scientific that relates to humans it is important set-aside feelings, at least for the moment. That being said, let me remind the reader that this is not the attitude of many science writers when a story has a “social justice” angle. We all know if a science article has a social hook which appeals to emotional or moralistic impulses in the readership, it will probably be injected into it for purposes of clicks and adding an extra layer of meaning and relevance. For various reasons, Aztec human sacrifice is better presented in a dispassionate manner, as Mesoamerican human sacrifice doesn’t lend itself easily to a standard social justice narrative (i.e., the “villians” are not white).

The Aztec Empire, or the Triple Alliance if you prefer, was built on brutality. From what we can tell it was an analog in the New World to what the Assyrian Empire had been in Eurasian antiquity: a polity bound together through brutal coercion.

Here is one tale from Aztec history that is well known:

In 1323, they asked the new ruler of Culhuacan, Achicometl, for his daughter, in order to make her the goddess Yaocihuatl. Unknown to the king, the Mexica actually planned to sacrifice her. The Mexica believed that by doing this the princess would join the gods as a deity. As the story goes, during a festival dinner, a priest came out wearing her flayed skin as part of the ritual. Upon seeing this, the king and the people of Culhuacan were horrified and expelled the Mexica.

Note that the legend is recounted whereby the other native peoples of Mexico were horrified by the Aztec behavior. This highlights the reality that human sacrifice seems to elicit negative reactions generally. It’s not arbitrary. In Carthage Must Be Destroyed the author spends a great deal of time exploring the reality of child sacrifice in that society. A practice in decline in the Phoenician homeland, for some reason it reemerged in the western Mediterranean much more vigorously. Classical observers found the practice grotesque, and their descriptions of Carthaginian child sacrifice were suspected by many scholars as being scurrilous. Fortunately, or unfortunately, the truth has been established by the discovery of bones of children in urns. The key point to note is that ancient observers were just as judgemental as modern people.

Though human sacrifice persisted in some form in many antique societies, it is clear that what was once a common occurrence in the Bronze Age world became rarer with time, until it was no longer socially or ethically acceptable. Researchers in the field of cultural evolution have explored the emergence and decline of human sacrifice. Though there are no current definitive conclusions, it seems likely that it crops up in societies which have transitioned toward being highly inegalitarian. But, it declines again in societies which scale large enough to the point where more abstract ideological and political systems must bind groups of people together. The Classical Western world, India, and China, all seem to be marked by a recollection of normative human sacrifice (e.g., Iphigenia), and a turn away from it.

The inequality aspect is important. Though some people willingly gave themselves as human sacrifices, there are recurrent themes of low-status individuals within the group (e.g., slaves) or outsiders (prisoners of war) being given to the gods. There is debate as to the nature of the Aztec “flower wars”, but one traditional explanation is that they were driven by the need for victims of human sacrifices.

In other words, Aztec human sacrifice can be contextualized in a generalized framework. But that is not where the writer of the original piece went on the Twitter thread. Rather, she seems to have bracketed the practice by modern social and political considerations, “centuries of colonial oppression and destruction.” To be frank, it is a strongly Eurocentric narrative where everything before European colonialism is viewed as a prologue to the true story. The only story that matters. The context of Aztec human sacrifice that matters to many people steeped in this way of thinking is what the Spaniards did to the native peoples of the New World after the conquest of the Aztec Empire. Like ethical tachyons the present blasts back into the past, and reshapes our whole perception of it in current terms. The Aztec tendencies toward brutality, oppression and grotesque customs such as human sacrifice, are inconvenient to this framework.

The cultural conditioning isn’t that of a Western individual who lives in a consumer society at the tail end of a two-century path of growth, domination, and maturation. Rather, the cultural conditioning is of a whole class of intellectuals steeped in understanding all social and historical relations as but mirrors of the one which defined the 19th and 20th century. This viewpoint also asserts that this period, these people, are sui generis. It is profoundly Eurocentric to the bones.

To me when considering the ethical and historical frame of human sacrifice two facts jump out to me. First, it’s an empirical fact that at certain levels of social complexity human sacrifice seems to emerge, and at later levels of social complexity tends to be dampened and abolished.  The reason that it tends to be dampened and abolished is probably the reason that the Spanish found it easy to obtain native allies against the Aztec Empire: human sacrifice is a costly and brutal way to foster social cohesion. Across societies, there has been a general tendency to abandon the practice and create psychologically satisfying substitutes which don’t have the bloody downsides.

The second aspect is more primal: humans don’t like to die. It is true that humans will sacrifice themselves, or in the case of Carthaginian nobles, their own children, in exigent circumstances. Human nature exists, and many aspects are universal. The abhorrence of human sacrifice doesn’t emerge out of particular and unique elements of Western colonial culture,  it has cropped up in many societies, and I would suggest that the shoe is on the other foot here: those who argue for human sacrifice have to make the argument for it is necessary. And that is why so often humans who are sacrificed are those who can least choose to give their own lives. Slaves, children, prisoners, and criminals.

Unfortunately, the Western colonial narrative looms so large for many moderns that other cultures and other histories are erased in all their complexity. They gain depth and richness only as handmaids to the deconstruction and critique of the Western colonial narrative.

June 22, 2018

Midnight’s Descendants: A History of South Asia since Partition

Filed under: History — Razib Khan @ 11:21 pm

I recently read John Keay’s Midnight’s Descendants: A History of South Asia since Partition. Like his earlier books on the history of India and China, this is a work written by a journalist, not an area specialist (though Keay seems to take a particular interest in South Asia judging by his oeuvre).

To be frank I’m not sure if I learned that much…and I don’t know much about South Asian history after 1945. But, it reaffirmed my intuitions that some of the ideologues who bandy extremely high casualty rates are doing a disservice to the real tragedies that have marred the subcontinent over the past century.

In any case, I do recommend this book to the 50% of the readers of this weblog who are not South Asian.

Note: I don’t have the time or interest to read Guha’s India After Gandhi. Also, my friend Reihan Salam has indicated to me it’s a more tendentious work than most are willing to admit.

Beware scientists laundering their credentials

Filed under: Journalism — Razib Khan @ 12:19 am

Recently Vox had a really bad piece up, How a pseudopenis-packing hyena smashes the patriarchy’s assumptions: Lessons from female spotted hyenas for the #MeToo era. The first thing you’ll notice is the crass inverse naturalistic fallacy that seems to be operating here. That is, you think of a state you’d find desirable (in this case, “matriarchy”), and then look at nature to find an illustrative instance to draw some lessons. I don’t always oppose this, but the people sharing the Vox piece are also the sort who’d find it “problematic” if others did the same (e.g., lobsters).

Reading the piece, I thought back to the fact that mammals as a whole tend to be rather polygynous, with males investing far less in their offspring than, for example, birds. This is why genomic imprinting and sexual genetic conflict is a thing for our broad class of tetrapods. I happen to believe humans are rather different in nature because of our evolutionary history from our mammalian cousins. Also, cultural forces are important to us. Our social complexity is hard to understand without acknowledging our plasticity, even though that plasticity is bounded in some serious was by our dispositions.

But Katie Herzog in The Stranger reports that researchers who study hyena behavior are angry about the Vox piece because it gets the science all wrong.

This is entirely expected. The author is “a Ph.D. student in microbiology and immunobiology at Harvard University.” Someone who has this particular training can’t be expected to be up-to-date on the latest literature in zoology and behavioral ecology, let alone organismic knowledge about a particular species (usually, one might make an exception if she was studying the microbiome of hyenas!).

Science is very specialized. I can’t speak for others, but just because someone is a “biologist” doesn’t mean that they really know much about biology in a broad sense. Most biologists outside of population genetics have somewhat woolly intuitions about population genetics. I know the difference between a dendrite and an axon, but I don’t know much about neuroscience.

When a scientist opines on a field in which they have some distant relationship to, such as a microbiologist offering their thoughts on the relevance of the evolutionary and behavioral insights from hyenas, be very careful, because whether they know it or not they are laundering their authority from one discipline into another where it does not apply.  A few years ago a scientist on Twitter with a background in ecology was explaining to an undergraduate that “epigenetics has rewritten the genetics textbooks.” This was just flat out wrong. Many ecologists have as much understanding of genetics as a layperson, and many geneticists have as much understanding of ecology as a layperson. Yes, most ecologists have probably taken a genetics class as an undergraduate, but they don’t know the literature, nor do they think much about genetics day to day. Similarly, most geneticists have probably taken an ecology class as an undergraduate, but they don’t know the literature, nor do they think much about ecology day to day. And really, classes aren’t worth much. I’ve taken introductory and advanced ecology courses on the undergraduate level, and graduate level ecology courses. I still don’t know much about ecology.

And these specializations are unfortunately quite narrow. I don’t study translational mechanisms in yeast. Talk to me about population genetic inference, especially in the context of diploid organisms which reproduce sexually.

It’s unfortunate that many science journalists are generalists who have a difficult time navigating specialized disciplines. But at least science journalists are not going to present themselves as experts. They are conscious of their limitations. I wish many people with a scientific background were too.

June 21, 2018

The fault in our parameters

Filed under: Population genetics — Razib Khan @ 10:49 pm

Of the books, I own Elements of Evolutionary Genetics is one I consult frequently because of its range and comprehensiveness. The authors, Brian Charlesworth and Deborah Charleswencyclopedican encyclopediac knowledge of the literature. To truly understand the evolutionary process in all its texture and nuance it is important to absorb a fair amount of theory, and Elements of Evolutionary Genetics does do that (though it’s not as abstruse as something like An Introduction to Population Genetics Theory).

When I see a paper by one of the Charlesworth’s, I try and read them. Not because I have a love of Drosophila or Daphnia, but because to develop strong population genetics intuitions it always helps to stand on the shoulders of giants. So with that, I pass on this preprint, Mutational load, inbreeding depression and heterosis in subdivided populations:

This paper examines the extent to which empirical estimates of inbreeding depression and inter-population heterosis in subdivided populations, as well as the effects of local population size on mean fitness, can be explained in terms of estimates of mutation rates, and the distribution of selection coefficients against deleterious mutations provided by population genomics data. Using results from population genetics models, numerical predictions of the genetic load, inbreeding depression and heterosis were obtained for a broad range of selection coefficients and mutation rates. The models allowed for the possibility of very high mutation rates per nucleotide site, as is sometimes observed for epiallelic mutations. There was fairly good quantitative agreement between the theoretical predictions and empirical estimates of heterosis and the effects of population size on genetic load, on the assumption that the deleterious mutation rate per individual per generation is approximately one, but there was less good agreement for inbreeding depression. Weak selection, of the order of magnitude suggested by population genomic analyses, is required to explain the observed patterns. Possible caveats concerning the applicability of the models are discussed.

June 20, 2018

Three drinks for the ages

Filed under: Alcohol,Coffee,Genetics,milk,science — Razib Khan @ 9:33 pm
Irish Coffee

The “Irish coffee” is a a delicious concoction. Coffee, alcohol, and dairy. What more can you ask for? Man does not live on bread and water alone. Cafes and bars are thick on the ground in large cities, but also grace country roads. Coffee and alcohol are congenial to conviviality among settled peoples, while milk is the staff of life for many pastoralists, consumed raw or turned into cheese.


Of the three, coffee is a new on the scene, discovered within the past 1,000 years. The consumption of milk, whether raw or as cheese, goes back to prehistory. But on the geological scale it a recent cultural development. In contrast, the imbibing of alcohol in some form is probably as old as humanity itself, albeit not as a pint in the pub.

Alcohol is produced naturally by the fermentation process, a metabolic pathway which is far more ancient than the oxygen metabolism that has been dominant for the past few billion years. Humans are omnivores, and our ancestors consumed overripe fruit which had fermented to the point of producing alcohol byproduct. Meanwhile, “good bacteria” in our guts also produced alcohol.

This is not a bad thing. Alcohol is nutritious in that it provides calories.

Though in modern societies we “count our calories”, and the richness of a deep and dark beer is not always a selling point, for the vast majority of our species’ history those calories were a feature, not a bug.

Early civilization ran on beer. The Sumerians even had a goddess of beer, Ninkasi. The workers who built the pyramids of Old Kingdom Egypt were given rations of beer. In other words, the wonders of the ancient world were fueled by alcohol!

And this is not just forgotten history. Until very recently much of the world was awash in alcohol, whether it be beer, wine, or various distilled spirits. Public and private drunkenness were one of the major reasons behind the emergence of the American “temperance” movement. Though Prohibition was deemed a failure, American alcohol consumption has never recovered to its earlier highs.

One of the reasons that Americans, and many other peoples, drank so much is that alcoholic beverages is that not only did they provide calories, but they were often more potable than conventional water. Ancient humans in hunter-gatherer bands did not have to contend to cholera, but the first village societies, and those who lived in early modern cities, lacked modern sanitation. Safe drinking water was one of the major achievements of 20th century engineering, and obviated the role that alcohol had traditionally played in quenching the thirst of the common man.

But alcohol is not a matter just of history, biochemistry and engineering. Humans differ in their ability and capacity to metabolize alcohol due to variation on their genes. In particular, ADH and ALDH2. The ADH genes produce enzymes which breakdown alcohol for processing by later biochemical steps, one of which is catalyzed by the product of the ALDH2 gene.

If you’ve ever seen someone with the flushed face characteristic of having had too much to drink, they may have a mutation on ALDH2 which means that they don’t process acetaldehyde very well. As the cells build up acetaldehyde, a host of physiological reactions kick in. Research has shown that those who exhibit these reactions are much less likely to be alcoholic.

In contrast, those with mutations on ADH tend to process alcohol very well indeed. But in the process they produce more acetaldehyde than the body can handle, resulting in physical discomfort. And similarly to the ALDH2 mutation these individuals are less likely to become alcoholic.

Genetic variation in the ability to process alcohol is a consequence of the long history of human omnivory. In contrast, the evolutionary history around our consumption of milk is much more straightforward and strange. For the vast majority of our species’ existence adults have not had the ability to digest milk sugar, lactose. This is a characteristic we share with all other mammals. The adaptive reason for this is likely that it encourages and forces weaning, so that mothers can bear other offspring.

And yet a minority of modern human adults today can digest milk. How? Why? The LCT gene produces an enzyme lactase, and mutations in this gene allow humans in Europe, parts of Southern Asia, East Africa and the Near East to continue to drink milk into adulthood. Over the past 5,000 years unique mutations in Europe and South Asia, in Arabia, and in Africa, have all been strongly selected.

In Denmark the mutant allele is now at frequencies as high as 90%.

Ancient DNA tells us that the ability to digest milk sugar into adulthood did not arise with agriculture and sedentary lifestyles. It is not implausible that Neolithic people who domesticated goats and sheep fermented milk to produce cheeses, where the sugar was broken down to make it more palatable. But the adaptation to a predominantly dairy dependent lifestyle only emerged with full-blown pastoralism, over the past 4,000 years. The earliest pastoralists on the Bronze Age Eurasian steppe carried the lactase persistent genetic variant, but only at low frequencies.

Dairy is an essential part of the modern food pyramid, at least for the USDA. But perhaps it tells us more about our evolutionary present than the evolutionary past. So often we talk about evolution as a dynamic of the deep past. But with lactose tolerance we see evolution as a process which is just initiating.

Finally, there is coffee. Though variation on the CYP1A2, Cytochrome P450, effects how fast caffeine is metabolized, coffee is such a recent cultural invention that it is unlikely that there are any adaptive dynamics related to it on a genetic level. Rather, CYP1A2 is locus which controls processes designed to cope with toxic chemicals by breaking them down. Caffeine in some ways is such a chemical, and those who metabolize it fast need to drink more coffee to feel its effects than those who have more efficient metabolization.

The effect of caffeine on humans is literally inefficiencies of bodily detoxification.

Milk nourishes. Alcohol both nourishes and alters the mental state of those who imbibe it. In contrast, caffeine does not nourish, but stimulates. For the past few million years our species likely never interacted with caffeine, but we were pre-adapted because of our consumption of a wide range of plants which manufacture chemical defenses.

The legend of coffee dates back 1,000 years, when an Ethiopian goatherd saw one of his animals behave strangely after eating a coffee plant. Within the next five hundred years coffee beans were cultivated across the hillocks of the lands around the Red Sea, from Ethiopia to Yemen, and became part and parcel of Islamic culture. To this day the coffeehouse is a major social and cultural nexus in the Middle East, though colonialism has taken it far afield, from Java to Colombia.

By the Renaissance coffee had reached Europe, and the proliferation of coffeehouses, and their stimulative effects, may have triggered the early modern Enlightenment intellectual revolution. While alcohol softens and dims the outlines of world around you, coffee is a stimulant which sharpens our perceptions and accelerates our cognitive pace.

Coffee, alcohol, and milk, are such central aspects modern culture that it is hard to imagine our existence without them. Though there is genetic variation in how we can process them, their relevance to our lives transcends biology, and extends to economics, history, anthropology, and in the case of wine, religion. Though they may not be the ambrosia of the gods, modern civilization arguably stands on the shoulders of these beverages.

Wondering if you are lactose tolerant based on your genetics? Check out Metabolism by Insitome.

Three drinks for the ages was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Open Thread, 6/20/2018

Filed under: Open Thread — Razib Khan @ 8:19 pm

I try to limit the shilling, but since readers of this weblog know what this means: Helix has a sale on kits until the end of the month. The three Insitome products can be purchased for app-only cost ($29.99) as an entrance into the ecosystem. In other words, for $29.99 you can get millions of markers in your exome sequenced, as well as some positions in the rest of your genome. Helix keeps the data, but there will be no kit cost if you see a future app that you want to purchase.

* Regional Ancestry
* Metabolism
* Neanderthal

If you are not subscribed to my total feed, you might not know that my review of She Has Her Mother’s Laugh went up at National Review Online. One thing that I’ve reiterated: it’s a very big book. A single review can’t really cover many aspects of what Carl touches on, and unfortunately even during the podcast I didn’t get to chimeras.

We’re almost at 100 reviews on iTunes on 10 on Sticher. I’ll stop bugging when we reach those milestones.

It’s been obvious to me that more and more people are protecting their Twitter accounts. Instead of a conversation the platform is about snooping on blow-ups and controversies.

In rapidly adapting asexuals, the orientation of G can reflect selection rather than functional constraints. Evolutionary, population, and quantitative genetics have been long-term interests of mine, so I love stuff like this. Adding a little genomics would be even better.

The most important study of the Mediterranean diet has been retracted and The collapse of a $40 million nutrition science crusade. Basically, it seems you should just eat what you want. Probably avoid processed food and trans-fats.

Diverse haplotypes span human centromeres and include archaic lineages within and out of Africa. Centromeres are crazy.

Harvard Office of Institutional Research on Discrimination Against Asian-American Applicants. I will blog about this at some point…and I’ve been making semi-serious/jokey tweets. But people are probably not clear on my “position.” My main irritation about Harvard is the extent of the doublethink that they get away with. Drew Gilpin Faust’s pablum about inclusion and diversity being central values at Harvard is a classic “Shaggy defense”. Faust helms a finishing school for the overclass, and as such accepts the necessity of discrimination when it comes to anointing future overlords. Some hypocrisy is necessary for the ruling caste, but the juxtaposition between “neoliberal” reality of what Harvard is, and the “progressive” rhetoric of it presents to the gullible and ignorant public, is starting to become indecent.

Speaking of overclass, Tim Draper is a third generation member of the capital class, and still defends Elizabeth Holmes.

With tantalizing early results, Sarepta’s gene therapy for Duchenne raises hopes for ‘real change’.

Close inbreeding and low genetic diversity in Inner Asian human populations despite geographical exogamy.

Genetic ancestry and population differences in levels of inflammatory cytokines in women: Role for evolutionary selection and environmental factors.

Population Genomics blog. The author is Chad Rohlfsen.

Re-identification of genomic data using long range familial searches.

Inference of species histories in the presence of gene flow.

How Much Does Education Improve Intelligence? A Meta-Analysis. It’s probably time to start reviewing stuff on psychometrics. The Ian Deary book is pretty good.

Open Thread

Filed under: Open Thread — Razib Khan @ 10:12 am

Please keep the other posts on topic. Use this for talking about whatever you want to talk about.

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