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

April 30, 2019

Is the social justice exterior overwhelming the Indian nationalist interior?

Filed under: Politics — Razib Khan @ 11:33 pm

One of the most interesting things I have experienced over the past 15 years or so interacting with young Indian Americans, usually of Hindu background, is the disjunction between the scripts that they are inculcated with in their education in broader society, and the quite nationalistic/parochial perspectives that are imparted to them by their parents.

You can say many things about me, but there isn’t much of a disjunction in what I will say you to privately about controversial topics and what I will say in public about controversial topics (the main skeptics of this view are some Hindu nationalists and Zionists, who are convinced that I’m an Islamic supremacist sleeper agent).

So, I when I began to spend some time around Indian Americans one of the peculiar things I was a bit surprised by his how different their extremely social justice Left external presentation could be from what they might say privately over some drinks, or if they perceived you to be an intimate acquaintance. Since my views on Islam were well known many of them felt quite free to openly state their privately skeptical views on the religion of Islam and the practices of Muslims, which reflected what their parents had told them, while in public these people might still denounce Islamophobia. People who would criticize caste privilege in public forums might still be privately smugly proud of their family’s caste background. And, the same people who might perceive American patriotism as to be jingoistic and declasse would express Indian nationalism that they had absorbed with their mother’s milk in private in the crassest of terms.

But there does come a time when you leave your parents’ home, and their influence. And I don’t interact much with Indian Americans on a day to day basis, but I do wonder if many progressive Indian Americans are bringing their two aspects into alignment, and shedding their private chauvinistic reflexes?

An analogy here might be young American Jews, who until recently were quite liberal in the American context, but might align with more ethnonationalist views in relation to Israel (even if they supported the Left parties in Israel, those parties are still more nationalistic than similar parties in the United States). Today the two views are coming into coherence, as most younger American Jews who are not orthodox are starting to distance themselves from Israel.

Surfing into the genomic future

Filed under: Genetics,Genomics,Human Genome,human-genome-project — Razib Khan @ 7:16 am
The decline in cost per genome

Within genomics circles, the chart above illustrating the crash in sequencing costs since the year 2000 is famous. The reason it is famous is that it shows that genomic technology began to outrun the famous “Moore’s Law”, that computing power doubles every 18 months, around 2008.

The genomic revolution is arguably like no other information revolution of the 21st-century.

In 1983 there were 800 known genes with locations within human chromosomes. This is for all humans. The field of genetics had existed since the first decade of the 20th-century by this point. But the methods of the 20th-century were laborious, and not well suited to human genetics (we are a slow reproducing organism that one cannot experiment upon).

20th-century human genetics

Since the turn of the century, the sequencing of hundreds of thousands of human genomes has transformed our understanding of the landscape of inheritance. In 1983 scientists had no sense of how many genes humans had. They guessed 100,000, a suspiciously round number.

We now know that humans have 19,000 genes. We have also cataloged, more or less, all 3,000,000,000 positions in the genome. Genomics has finally allowed scientists to grasp the scale of variation among humans on the DNA level. To put a specific number to that variation (~100,000,000 polymorphisms), and assign specific places within the genome.

A “map: filled with “Here Be Dragons” has been transformed into something that one can perform a scientific GPS upon.

21st-century human genomics

Fundamentally the discipline of genetics has always been one of the transmission of information across the generations, but the emergence of “next-generation sequencing” (NGS) resulted in such a gusher of data that genomics and computer science have developed symbiotically in this century. For many researchers, the size of genomes is measured as often in computer memory as it is in base-length or classical recombination map-length.

But all of this fancy technology wasn’t developed so that computer scientists could work on interesting algorithms and data-mining techniques.

Though genomics has applications to basic science, as well as animal breeding and crop development, the original rationale for the Human Genome Project was to further the goal of human health and longevity. This promise has arguably been a disappointment. We have not won the war on cancer, nor has healthcare at the point-of-delivery been transformed.

But how likely were the promises in the first place? What could a single human genome tell us? Rather than be a pot-of-gold at the end of the rainbow, the first genome is more likely a map that points us to the future.

The growth of “personal” genomics

Many futurists contend that the transformative power of technology is often overestimated in the short-term, but underestimated in the long-term. Humans don’t anticipate what the broader market will respond to through reflection. Rather, there needs to be a trial and error process.

The internet exploded on the scene in the 1990s. It certainly transformed communication, but initial attempts to provide services and goods failed as the “dot-com bubble” collapsed. But the ashes of such failures gave rise to a whole new economy, which has transformed our lives in ways we can’t imagine account for. Remember anonymity before Google and social media?

The first decade after the first human genome saw little progress because it was fundamentally a blue-sky technology restricted to academic laboratories. The second decade of genomics has seen the explosion of the consumer market, from 100,000 users to 30,000,000 as of 2019.

Millions of consumers and dozens of companies means that the dynamic and adaptive power of the market will shape the future of genomics. The current “killer app” is genealogy, for fun and forensics. But as the whole American population gets whole-genome sequenced in the next generation the opportunities for personalization will open up. Instead of a single sequence, one can imagine consumers getting sequenced repeatedly over their lifetime, from different tissues, as healthcare professionals track the mutational arc of one’s life. And from the genome, consumer firms will explore the microbiome, the epigenome, and the transcriptome.

Information science will flood genetic science.

And once science becomes a technology, breaking out of the laboratory, the outcomes and changes can be unpredictable. Even protean.

In the years after 2000 what we would call “smartphones” existed, but they were luxury goods in the age of the “candy bar” and “flip” phone. The rivals to Apple were skeptical about the iPhone when it came out. But it turned out that the iPhone created an industry, and transformed many others (remember cheap digital cameras and paper maps?). Nevertheless, even Steve Jobs did not anticipate the proliferation of “apps”, and their centrality to the modern smartphone experience.

Apple’s ecosystem of applications developed organically, and its magnitude and importance were not anticipated. Jobs and his executive team clearly viewed the iPhone as a phone that had deluxe music functionality. As it turns out, Jobs had unveiled the next iteration of the computer! Today, a smartphone is really a computer with some phone functionality.

The genomic future likely will exhibit the same arc.

Genomics will transform our lives. That I can state with confidence. But how it will transform our lives, if I hazarded a guess I’d surely be wrong. History is more surprising than anything our imaginations can come up with.

Surfing into the genomic future was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 29, 2019

Reader Survey for The Insight

Filed under: Podcast,The Insight — Razib Khan @ 11:05 am

Reader Survey for The Insight podcast

After 50+ episodes and 200,000+ downloads, Spencer and I have decided that we want to know a little bit more about the listeners to our podcasts, as well as taking some feedback for the future direction of The Insight.

With 11 simple questions, it should take a few minutes at most to complete. If you are a listener to The Insight please take a little time to help us improve the podcast and give us a sense of who is listening!

Take The Insight listener survey.

Reader Survey for The Insight was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 28, 2019

Browncast Episode 33: an ethnography of doubting Darwin

Filed under: Uncategorized — Razib Khan @ 3:33 pm

Another BP Podcast is up. You can listen on LibsyniTunes, Spotify,  and Stitcher. Probably the easiest way to keep up the podcast since we don’t have a regular schedule is to subscribe at one of the links above.

You can also support the podcast as a patron (the primary benefit now is that you get the podcasts considerably earlier than everyone else…). Would appreciate more positive reviews.

Today I am posting a podcast that I decided to record on a lark. I talked to Benjamin Dierker, the author of Why One-Third Of Biologists Now Question Darwinism. To be frank, this is a case where you need to read beyond the title…

Dierker and I had a lot of common ground and his main project is not a defense of Intelligent Design, as much as an ethnography of it. We hashed out what Neo-Darwinism means, as well as how conservatives should bury the hatchet when it comes to their historical enmity to evolutionary theory. In fact, we discussed extensively how the left’s revolt against human nature in the past generation opens up an avenue for conservatives to be on the side of science.

Open Thread, 04/28/2019

Filed under: Open Thread — Razib Khan @ 3:27 pm

Reading The Race for Paradise: An Islamic History of the Crusades. A bit too many names and battles (narrative), rather than social and economic dynamics. But it’s a good inversion of the traditional narrative, and illustrates just how chaotic and fractions the Islamic world in the last decades of the 11th-century was. Western European society was coming back to Roman levels of density and complexity after 1000 A.D., and for various reasons, the last half of the 11th-century was a period of disunity in the lands of Islam, so the Crusades were timed very fortuitous for the Franks.

Speaking of the Crusades, Christopher Tyreman’s God’s War: A New History of the Crusades is one of my favorite books (I remember staying up to 3 AM on worknights reading this book). But for some reason, it has much worse Amazon reviews than Thomas Ashbridge’s The Crusades: The Authoritative History of the War for the Holy Land. Does anyone know why?

Interesting historical fantasy I stumbled across, The City of Brass. The author is a white ethnic woman from New Jersey who converted to Islam as a teen, and now has a last name which is associated with Bengali Brahmins (she also pronounces very peculiarly). The reviews are good, but I’m not a fan of historical fantasy. Mixing the real and fantastic doesn’t appeal to me.

Dante is still selling 30x WGS for $229 as of this writing. No, I have no idea how Dante works in regards to this price point. But apparently, it’s not a fraud.

Speaking of personal genomics, this week on The Insight I’ll be talking to Rodrigo Martinez, an officer at Veritas. Follow the link above to see the different ways you can subscribe.

Endgame is worth watching.

Speaking of podcasts and the like, I’m told that three people on a single Extremely Offline podcast that will go live next month will all have been podcasts on the Browncast. Can you guess who? It shouldn’t be too hard.

Evolutionary dynamics of culturally transmitted, fertility-reducing traits.

A genetic hazard score to personalize prostate cancer screening, applied to population data.

This thread is worth reading:

Gencove announces Phase I SBIR grant to validate polygenic risk score estimation from low-pass sequencing.

Angiosperm speciation speeds up near the poles. “Overall, our results show that speciation rates follow an opposite pattern to global variation in species richness.”

The continuing impact of an ancient polyploidy on the genomes of teleosts. “…lend support to recent suggestions that the TGD was the source of a morphological innovation in the structure of the teleost retina.”

Darwin Devolves: The New Science About DNA That Challenges Evolution. Michael Behe has a new book out. Richard Lenksi has responded in detail on his weblog.

I read Darwin’s Black Box and Michael Denton’s Evolution: A Theory in Crisis 20 year ago. Not convinced. That being said, people without a scientific background can be impressed easily. I still remember the stupid reader who incredibly blown-away by the pig-headed sophistry in R. J. Stove’s Darwinian Fairytales: Selfish Genes, Errors of Heredity and Other Fables of Evolution. I read the book because the reader was impressed, and the reader was someone who I didn’t have a strong opinion about. I came away concluding that the reader must be kind of a moron since the book itself was just plain ignorant in the literal sense.

I’m still trying to place a piece in The Federalist on evolution. They gave me a few suggestions. Friends who have read my draft were already impressed, so I’m 90% sure I can get this placed in the conservative media. I actually interviewed the author of this piece, Why One-Third Of Biologists Now Question Darwinism, for the Browncast. The podcast will go live tomorrow.

Genome-wide sexually antagonistic variants reveal long-standing constraints on sexual dimorphism in fruit flies. This is a really interesting paper. The citations are interesting too.

Efficient use of genomic information for sustainable genetic improvement in small cattle populations.

Direct-to-Consumer Genetic Testing and Potential Loopholes in Protecting Consumer Privacy and Nondiscrimination.

April 27, 2019

African genomics tells us about deep structure and history

Filed under: African Genetics,Human Evolution,Human Genetics — Razib Khan @ 11:36 pm

Two interesting papers in Genome Biology that are open access, Whole-genome sequence analysis of a Pan African set of samples reveals archaic gene flow from an extinct basal population of modern humans into sub-Saharan populations and African evolutionary history inferred from whole genome sequence data of 44 indigenous African populations. Since they are open access you should just read both of them.

I believe they are the first in a series of papers over the next few years using whole-genome analysis to understand the population structure within Africa, and how it relations to the people who branched off from Africans. Eventually, this will also lead to research focused on medical and population genomics, looking at characteristics and forces beyond phylogeny.

The results confirm at a finer-grain and with more precision what we’ve known before. The strangest result (to me), which has been confirmed over the past several decades or so (starting with uniparental lineages), is that the hunter-gatherers of Sub-Saharan Africa are broadly related more closely related to each other than they are to the agriculturalists of Sub-Saharan Africa. The relationship is deep (see the figure of the NJ-tree). The Baka and Mbuti Pygmies of the west and east of the Congo are deeply diverged themselves from each other, and even more so from the Khoisan people of southern Africa, or the Hadza of Tanzania.

But the missing piece of the puzzle has to be the “Bantu expansion.” As was pointed out to me by Nick Patterson about a decade ago, the Bantu-speaking people are genetically very closely related, as benefits a demographic expansion that began on the order of ~3,000 years ago from a small region of the Cameroon-Nigeria border. Curiously, a similar expansion did not occur to the west, as West Africa remains linguistically much more diverse, though genetically it is broadly similar to “Bantu Africa.”

Even on the furthest southern edge of the Bantu expansion, the majority of the ancestry remains similar to their linguistic relatives in Cameroon-Nigeria region, even if a substantial minority of the ancestry is Khoisan. Similarly, the Bantu speakers of East Africa often have some Eurasian ancestry, probably mediated by pastoralist Cushitic-speaking people who were already present.

The genetic variation of contemporary Africa is an artifact of the recent Holocene. This was clear after the publication of Skoglund et al. a few years ago. It also means that a lot of the fine-grained inferences from modern populations must be taken with a grain of salt, as there was probably more admixture and movement in the early Holocene which is not visible to us, let alone in the Pleistocene.

That being said, the figure at the top of the post captures the major features since 1) they’re in keeping with our understanding of the interaction of deeply diverged lineages 2) there has been other work with other methods detecting the same dynamics.

Most scholars did not accept the likelihood of Neanderthal admixture until the genome of this ancient hominin was published. Then we discovered the Denisovan contribution due to another genome. Both of these discoveries should update our prior expectations of any given model. The model above utilizes a complex ABC-framework. If you know what that means, you know I’m not going to get into the details. But I trust computers only to a point… I expect the ABC model does reflect realities of archaic admixture, but I’m not sure that the typology of the tree is totally settled.

That’s because of the reality that human genealogies are more like graphs with edges of different thicknesses. There’s always some gene flow, especially between close lineages. These models often infer that the Khoisan diverged ~200,000 years ago from other lineages. And, that the African ancestors of modern Eurasians diverged ~100,000 years ago. The model above even suggests that there is “anatomically modern human” (so African) admixture into Neanderthals. It is highly likely that this was detected in the Altai genome, so I think this is likely.

But is it likely that the Khoisan were a long and isolated branch over 198,500 years ago when some admixture with a Nilotic or Cushitic populace broad Eurasian ancestry? I doubt it. I suspect these divergence/coalescence times mask deeper and more recent branches, which fused together, and so give us an average mid-point coalescence. Archaics aside, I suspect that some of the Khoisan ancestry is probably deeply basal, and some of it is less basal.

Finally, the divergence time of the ancestors of Eurasians is  ~100,000 years ago. Archaeology tells us that the expansion of the ancestors of modern non-Africans occurred 50-60,000 years ago. What was going on in that interval? First, of course, all these estimates need to be taken with a grain of salt, even beyond the confidence intervals. But, I’ve read enough of these papers to see a number >>>60,000 years for the divergence to think it’s real. It strikes me that the ancestral proto-Eurasians were on the fringe of Africa or in Arabia for a long time before the expansion. A deep divergence between Eurasians and Sub-Saharan Africans is probably a function of the fact that most ancient African populations left no descendants (or very few). This seems common in large parts of Eurasia. If the proto-Eurasians were liminal, it is possible all the intervening populations between it and the ancestors of West Africans just went extinct.

The structure and history of African genetics is not just important for medical and population work. It is probably also essential to scaffold some of our inferences about cultural evolutionary processes. At a minimum, half of modern human man history has been within Africa (if modern humans were outside Africa in Arabia 100,000 years ago).

April 26, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 11:28 pm

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

Also, I’ve posted a new linguistic podcast on the patron page. It’s 1 hour and 20 minutes, and really dense with information and wide-ranging. There were five people, but I didn’t say much, and Zach was mostly asking questions. So there were three with a huge amount of knowledge engaging with each other. I have to say that this serves as a good model/example for future podcasts.

April 25, 2019

Having a common name in a post-Dunbar’s number world

Filed under: Culture — Razib Khan @ 3:04 pm

I’m not sure I believe the model outlined in Robin Dunbar’s Grooming, Gossip, and the Evolution of Language. I’m not even sure about the specific details of Dunbar’s number. But, the overall insight, that the vast majority of human history has been defined by small groups with people you see again and again had an impact on our psychology seems robust.

The connotations of the very word “stranger” are complex but generally lean to the negative. And I think that makes sense. One of the tasks of cultural norms and values is to figure out a way that strangers can be interacted with in non-zero sum relationships.

All of this is to preface a banal assertion about interaction in day-to-day life if you are a middle-class professional. I get a lot of emails from people with common names, and it’s a non-trivial cognitive load to figure out if I should pay attention or not. Names like “David”, “John”, and “Omar” are so common that I’ve actually ignored people I shouldn’t because I didn’t realize it was that David or Omar. I’ve almost even responded to the wrong person when two people with the same first name are emailing me at the same time.

In a premodern village or a Paleolithic hunter-gatherer tribe, having a common name on a population-wide scale wasn’t a big deal. The people you would address by name regularly was far less than 100 over a year. But in today’s world, some people have to interface with ten different strangers per day, along with all the “regulars.”

If I was a parent considering names, this would be something that I would take into account. It’s probably not optimal to have a very rare name, because people might misspell it or misremember it, though it will be salient. But having a very common name can also be annoying, to the point where many people with common names now go by their middle name or a nickname. Rather, a familiar but not-so-common name is probably optimal.

To give an example, the name “Dennis” is not too common for people my age (as opposed to “David”). If I get an email from a “Dennis” there is only one or two people it could be.

The many ways of being Brown Diasporic

Filed under: Culture — Razib Khan @ 12:43 pm

An admission: I have no idea what half of Zach’s posts are about. More clearly, they’re written in English, but there are so many references to Indian/South Asian pop-culture and drop-ins of Hindi-Urdu words that I have no idea what he’s talking about. It might as well be Greek. Often after 30 minutes of Google, I get it, but it’s pretty funny because technically we’re both English-speaking brown people living in Anglo countries.

There are different kinds of brown people. Some of them are well talked about. For example, ABCD vs. “FOB” culture. But it’s way more subtle and diverse than that.

For example, I have a friend who grew up in Canada, who is from a South Indian Brahmin background. But, it turns out that the only Indian language she knows is Hindi, because of the people she grew up with. I am not good with languages. I have primitive fluency with Bengali, though I can’t read it, and absolutely no firsthand knowledge of Hindi or Urdu. A lot of Diasporic South Asians through in Hindi-Urdu words into their speech and a lot of us have no idea what you are talking about (I share this reaction with a lot of people of South Indian background raised in the USA, who don’t know Hindi).

Zach is a “Third Culture” person in a traditional sense. I really am not…my parents left Bangladesh in 1980, and did not raise me among many Bengalis or even South Asian people. Better to describe me as American culture + an accent/perspective of something very different.

April 24, 2019

The Genetics Of The St. Thomas Christians, part 2

Filed under: Indian Genetics,Nasrani,St. Thomas Christians — Razib Khan @ 10:34 pm

Last year I posted The Genetics of the St. Thomas Christians. Recently I got some more samples. Of these, four were clearly self-identified as Southist/Knanaya Christians (as opposed to Northist Christians). The Knanaya are a bit different in their traditions than the broader much larger St. Thomas Christian community.

In the PCA above the bottom left are Middle Eastern groups. Druze and Yemeni Jews. Toward the top are Lithuanians. Green are Iranians. From the bottom right, up a diagonal axis, you see south-north Indian cline from low caste Telugu Christians, to Jatts from Punjab.

It does seem in relation to the other more generically labeled St. Thomas Christians the four Knanaya show some noticeable Middle Eastern shift.

Here’s an admixture plot:

The St. Thomas Christians have more yellow “Druze” cluster than other South Indians, with variation (the Knanaya have more).

I ran some Treemix. Didn’t detect major gene flow, but the Knanaya group was different from the other St. Thomas Christians, having a closer position to West Eurasians. When I ran a three-population test, it was the St. Thomas Christians (Nasrani above), and not the Knanaya, which registered admixture with Middle Eastern groups. It’s probably an artifact that the latter was not detected.

The Christians of Kerala are very similar to other peoples of Kerala. But, I now think it is more than 50% likely that they do have detectable Near Eastern ancestry above what you should expect.


The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans

Filed under: Denisovans,Podcast,science,Uncategorized — Razib Khan @ 2:55 pm

The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans

The Dali skull, 200,000 years old. A Denisovan?

This week on The Insight (Apple Podcasts, Spotify, Stitcher and Google Podcasts) Spencer is back, as we go back to our old two-man show format (at least for this episode). We discuss “deconstruct” the Denisovans, one of the newest human species discovered by science.

The Altai

But before we dug into the paleogenomics, Spencer discussed the human and physical geography of Inner Asia, and in particular the Altai region. In the 1990s Spencer had the opportunity to sample the native peoples of the region, which eventually turned in the Eurasian Heartland paper.

We put the critical role of Inner Asia in a broader historical perspective, from the early Indo-Europeans, down to the Mongols and Turks, and finally the “Great Game” of geopolitical rivalry between Britain and the Russian Empire in the 19th century.

The Altai in many ways has been at the center of Inner Asia. Spencer reflects on the fact that this is where there are Shambhala is often located, a mythical utopian kingdom. While the region is surrounded by cold deserts and forbidding mountains, with the Siberian vastness to the north, the Altai region harbors some relatively sheltered valleys through which nourishing rivers flow.

Inside the Denisova cave

Denisova cave also happens to be in the Altai. This means that not only has the Altai been of historical and mythic importance, but it has been at the center of the understanding of human evolution, and perhaps at the center of human evolution!

We discuss the multiple Denisovan individuals which have been sequenced from the cave. And, the first human ‘hybrid’, a woman whose father was Denisovan, and whose mother was Neanderthal, ‘Denny.’ Denisova cave was inhabited both by Neanderthals and Denisovans, with the Neanderthals having some evidence of modern human admixture, and the Denisovans Neanderthal admixture (and perhaps late Homo erectus).

But the Denisovans were not just a Siberian species. New work suggests there were three deeply distinct Denisovan populations, at least. The people of New Guinea may have had at least three mixing events with Denisovan people, while the admixture in China is almost certainly from a different Denisovan population than that in Oceania.

Finally, we talk about Homo luzonensis, and what the diversity of human across eastern Eurasia means in relation to what it “means to be human.”

The Insight Show Notes — Season 2, Episode 24: Deconstructing the Denisovans was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

April 23, 2019

Denisovans and the human story

Filed under: Denisovans,Human Evolution,Neanderthals,science — Razib Khan @ 1:38 pm
The Siberian cave where a new human species was discovered

We are all aware of the iconic fossil finds which mark the various milestones of our understanding of human evolution. The story of how our species became what it is today. Raymond Dart’s Taung Child helped establish that Africa might be the original home of our species. Lucy, which put the spotlight on some of the earliest upright ancestors of hominins. Even frauds like Piltdown Man go down in the history books, at least reflecting something of a particular Zeitgeist, wrong as it was.

And yet our past is haunted by a very small collection of remains indeed. Humans were never numerous (until recently). Our ancestors were fossilized thanks to luck, giving us a sense of the shape their form and bearing. The fossil trail of the upright line of apes which eventually lost their fur, and left Africa two million years ago, is quite tenuous.

Denisovan teeth from which DNA was extracted

But in the 21st-century new varieties of humans, species perhaps, are not discovered just by fossils alone. Rather, genetic science has now become adept at retrieving DNA from even the most ancient of human remains. Geneticists can then reconstruct the history of peoples long gone from their sequence, and compare them to modern people or other ancient genomes.

In the spring of 2010, the first whole Neanderthal genome was published, a landmark in the development of paleogenetics. Of course, Neanderthals have a long and storied history in paleoanthropology. They’ve been dehumanized and rehumanized and dehumanized many times. The surprise results out of the Neanderthal genome was that humans outside of Africa were all related to the Neanderthals. In other words, a few percent of the genome of non-Africans could be attributed to descent from them.

But wait! 2010 had more surprises in store for us. At the end of the year, a paper reported the genome of a new species of human. Previously unknown to science, these were the Denisovans, named after the cave in Siberia in which the remains were found. Because there was a genome of Neanderthals already sequenced, scientists could tell that the Denisovans were closer to Neanderthals than to modern humans. About ~750,000 years ago the ancestors of Neanderthals and Denisovans left Africa, separating from our own ancestors. Soon after, the Neanderthals and Denisovans began to diverge, becoming two distinct lineages, far more distinct than any two modern groups.

But why were they distinct?

To answer the question one must look at a map. While Neanderthals occupied Europe and ranged east into the heart of Eurasia, Denisovans likely inhabited the zone between eastern Siberia down into Southeast Asia. Differences develop between populations with common ancestors when they are geographically separated, and by and large (though not exclusively), Denisovans and Neanderthals were separated by the vast arid heart of Eurasia.

While the Neanderthals were a northern population, despite the discovery of Denisovans in a Siberian cave, they may have been used to warmer climes more often than not.

Papuan Woman and Child

One reason this seems likely is that Denisovans have descendants today. But they are not an obscure group in Siberia…they are the Papuans of New Guinea! This population has about ~5 percent of its genome from Denisovans. The descendants of these ancient people are also more widely scattered across Oceania, though to varying degrees.

While the Australian Aboriginals and Negritos of the Philippines have significant Denisovan ancestry, the native tribes of the Andaman Islands have little. This suggests that not all indigenous peoples of South and South Asia mixed equally with Denisovans.

More recent work has revealed that much lower levels of Denisovan ancestry are present across much of South and East Asia. And, importantly, the Denisovan ancestry in groups like the Chinese seems to be from a different group than that mixed into the Papuans. The genome from Denisova cave likely belongs to the people who mixed with East Asians and contributed adaptative functions such as high altitude adaptation in Tibetans.

So what we know now is that for hundreds of thousands of years a widespread group of humans, Denisovans, occupied eastern Eurasia. Unlike Neanderthals, they were not a single homogeneous group. Some research groups have detected three different Denisovan populations mixing into modern humans, while others have suggested that the Denisovans carry ancestry from even earlier hominins, who likely arrived in Asia before them.

But unlike Neanderthals or our African forebears, we have not been able to reconstruct a full skeleton of an individual who is Denisovan.

There are skullcaps, teeth, and stray bones, but not enough identified remains which could give us a sense of what these people looked like, how they were built (though the fragments from Denisova cave indicate to many the Siberian population was robust). Despite what we know was their expansive range, and the fact that they lived in eastern Eurasia for hundreds of thousands of years, to a great extent Denisovans remain genetic ghosts. They are digital shadows of their physical bodies, telling us about their relationships to other humans, details of their physiology, and immune system, but elusive in corporeal form.

The discovery of a new human on the island of Luzon, the existence of hobbits on Flores, and the diversity of Denisovans suggest that the eastern range of humanity during the Pleistocene was filled with many species of humans. The very existence of the Denisovans was window upon the vast ignorance of science in regards to the complexity of the Pleistocene world.

While Neanderthals have been the subjects of many books, they may have been a relatively homogeneous population with very precise adaptations to their northern Eurasian abode. A literal evolutionary sideshow. In contrast, Denisovans ranged from Siberia to the islands of Southeast Asia. From the edge of the tundra to the hot savanna of Sundaland.

They reflect in greater fullness the range of human experience.

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

College educated conservatives are divided on evolution

Filed under: Intelligent Design — Razib Khan @ 10:27 am

A few years ago an academic friend of mine mentioned offhand that it must be difficult for me to be an evolutionary biologist (of sorts) and a conservative (of sorts). As someone in touch with many “elite conservatives” (people who work at think-tanks and the like), that’s not true at all. Though Creationism has substantial support at the grassroots (the only time I have encountered evolution-skepticism in the last ten years has been from people who grew up fundamentalist), the reality is that at the elite levels in the conservative movement it is not a widespread position.

But, conservatives are still divided. Looking at the General Social Survey EVOLVED variable, and limiting to non-Hispanic whites, you see that while there is nearly total unanimity among self-identified liberals with college educations or higher that humans developed from animals, college-educated conservatives are split.

If you run some regressions you will see a lot of this is due not to politics, but to what politics is correlated with. Self-identified conservatives are much more likely to be religious conservatives. Those conservatives who are not religious conservatives are not very skeptical of evolution.

But one issue that I am wondering about: if most elite conservatives have no issue with evolution, and even college-educated conservatives are split down the middle, why is there so little “balance” at conservative publications? That is, periodically there is a report or opinion favorable to Intelligent Design published. But there is rarely a counter-response, even though attitudes amongst the readership are surely mixed?

I may personally attempt to change this a bit by submitting “pro-evolution” pieces here and there. We’ll see how that works out.

April 21, 2019

Indians are just as stupid as Americans

Filed under: India — Razib Khan @ 9:49 pm

You people. You people….

I specifically avoid using the term “secular” because I long ago learned what that means to Indians (just like we all know what “family values” meant in the 1990s in America).

(also, this idiot follows me on Twitter…at least as of when I posted this)

The expansion of modern humans ~50,000 as part of a regular Poisson process

Filed under: Human Evolution,Uncategorized — Razib Khan @ 4:58 pm

Last of the giants: What killed off Madagascar’s megafauna a thousand years ago?:

The first job is to understand exactly when the megafauna died out.

Radiocarbon dating of over 400 recent fossils demonstrates that animals under 22 pounds lived on Madagascar throughout the last 10,000 years. For animals over 22 pounds, there are abundant fossils up to 1,000 years ago, but relatively few since. The biggest decline in number of large animals occurred rapidly between A.D. 700 and 1000 – practically instantaneous given the long history of their existence on the island.

According to new dates on fossil bones with cut marks on them, humans arrived on Madagascar 10,500 years ago, much earlier than previously believed. But whoever these early people were, there’s no genetic evidence of them left on the island. New analysis of the human genetic diversity in modern Madagascar suggests the current population derives primarily from two waves of migration: first from Indonesia 3,000 to 2,000 years ago, and later from mainland Africa 1,500 years ago.

So it seems that people lived alongside the megafauna for thousands of years. How did the humans interact with the large animals?

Our new study found dozens of fossils with butchery marks. Cut and chop marks provide compelling evidence as to which species people were hunting and eating. Evidence of butchery of animals that are now extinct continues right up to the time of the megafaunal crash. Some people on Madagascar hunted and ate the megafauna for millennia without a population crash.

The abrupt land use change might hold some clues. The transition from a forest-dominated ecosystem to a grassland-dominated ecosystem appears to be widespread….

This research about Madagascar is important. If it turns out correct, I think it gives us deep insights about the expansion of modern humans outside of Africa ~50,000 years ago, and why their arrival resulted in the extinction of so many other human lineages. A generation ago we might have posited that some massive bio-behavioral change is what triggered this, but I am coming closer to the idea that cultural changes are punctuated enough that that may actually explain things. The culture changes first, then genes follow the culture.

Perhaps one might posit a model with massive turnovers in the hominin lineage due to this cultural dynamic occurs periodically, as if it’s a Poisson process.

Open Thread, 04/12/2019

Filed under: Open Thread — Razib Khan @ 3:52 pm

Just a reminder for people to check in on The Insight this week. Lots of talk about Denisovans between Spencer and myself. We’ve also got a follow-up podcast scheduled with a researcher working in Denisovan genomics in a few weeks (we’re on Spotify now by the way).

Our three new hires at George Mason economics. These look good.

Sri Lanka Suicide Bombings Targeting Christians Kill Hundreds. The most likely culprits seem to be a jihadist group active in southern South Asia.

A Transient Pulse of Genetic Admixture from the Crusaders in the Near East Identified from Ancient Genome Sequences. I think the “Crusader genes” are hard to find in the Near East because the collapse of the Latin kingdoms was gradual enough that “Franks” and their scions mostly managed to get out and go back to Western Europe.

Whole-genome reference panel of 1,781 Northeast Asians improves imputation accuracy of rare and low-frequency variants.

Anxious Times In Pakistan’s Pagan Valley.

Why One-Third Of Biologists Now Question Darwinism. I’m writing a response to this piece for The Federalist. Rather than a response to Intelligent Design, I want to represent what evolutionary biology really is.

Evidence for Early European Neolithic Dog Dispersal: New Data on South-Eastern European subfossil dogs from Prehistory and Antiquity Ages.

April 20, 2019

Easter Attacks in Sri Lanka

Filed under: Politics,Sri Lanka — Razib Khan @ 11:29 pm

Sri Lanka blasts: At least 137 dead and more than 150 injured in multiple church and hotel explosions:

More than 137 people have been killed and more than 150 injured after coordinated bomb blasts hit a number of high-end hotels and churches in Sri Lanka on Sunday.

The blasts, reported to have occurred in the cities of Negombo, Batticalo and the capital Colombo, targeted at least three hotels and three churches as worshippers attended Easter services.

Bodies of the dead have been received at Colombo National Hospital, according to hospital sources. Most of those injured were also taken there, hospital officials said.

Please post updates in the comments.

Gene Wolfe, death of a master

Filed under: Gene Wolfe,science fiction — Razib Khan @ 7:19 pm

Gene Wolfe, Acclaimed Science Fiction Writer, Dies at 87. Wolfe’s prose could be challenging to read. I actually read The Book of the New Sun trilogy twice because of some elements of impenetrability in the style, though there’s a reason Wolfe was acclaimed. In general, I’m not a fan of “science fantasy” or the “dying Earth” genre, but Wolfe really made it work.

One thing about Wolfe that is of interest is that like J. R. R. Tolkien he was a Catholic convert, whose religion influenced his work. Arguably more directly and consciously in the case of Wolfe. But it is subtle enough that it doesn’t distract or warrant notice. In fact, I’d argue that Severian is much less clearly a Jesus-figure than Paul in the Dune series to the naive reader.

I’m not someone who minds authors telegraphing their viewpoints and ideologies into narratives, no matter what it is. But I think there’s no point in putting it into “speculative fiction” if it’s too direct. For example, I think one reason C. S. Lewis’ Narnia cycle is less popular than Tolkien’s work is that it reads as Christian fantasy, rather than fantasy with inflections from the author’s Christian viewpoint.

Wolfe, like Tolkien, had strong personal views. But he did not let them saturate his stories. The Christian outlines and themes in The Book of the New Sun are clear after someone points them out. But they aren’t salient at all when you are reading it without foreknowledge.

April 19, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 11:27 pm

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

Let the genomic die fly!

Filed under: Human Genetics,Polygenic Risk Score — Razib Khan @ 11:19 pm

A new “polygenic risk score” (PRS) paper is making some waves, Polygenic Prediction of Weight and Obesity Trajectories from Birth to Adulthood. Since it is open access I suggest you read it.

But basically, they took ~2 million common variants (there are about ~100 million common variants in the world population) in ~300,000 individuals in 4 cohorts, and used it to predict weight. A genome-wide polygenic score statistic. The correlation with BMI of the score is 0.29. This is pretty modest. But it seems to me that the biggest and most important finding is that it seems to capture a lot of the people at the tails of the distribution.

I’m becoming more and more convinced that the best things these PRS scores can do in the near-term is to identify people who are possibly at these tails. In a complex trait context, the tails are where for diseases a lot of the people who are going to have issues later in life exist. People with BMI in the range 25-30 may have a modest increase in risks, but someone who is very obese, with BMI above 35, is at much greater risk. Over 40% of the people in the top decile here were obese. Only 10% of people in the bottom decile were.

This research comes out of the context of earlier work on the heritability of BMI. It’s around 0.75 or so. That means it runs in families. Combined with the fact that in the recent past, or in other nations, there is a great variation in median size and distribution, one can intuit that genetic dispositions and environmental context both help explain the variation we see around us. The modern American environment is clearly obesogenic. When most of the American population were involved in physical jobs on farms the environmental context was very different.

Over the next few years, there risk scores for BMI will get better, and expand to other populations. One thing that some people are pointing out is that we know it’s heritable, so why not just look at your family? As many of you know, Mendelian segregation means that siblings may have quite different risk profiles on the genomic level. Polygenic risk score prediction is I think going to be extremely interesting and informative in the case of traits which are known to be found within families across generations (e.g., autism), but don’t seem to impact everyone. Perhaps we’ll find for a given characteristic expression is random, due to some life event or cofactor such as infection. Or perhaps we’ll find that differences among siblings have some genetic basis in variants inherited from parents?

Addendum: One of the authors, Sek Kathiresan, has been answering questions on Twitter.

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