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

January 16, 2019

The state of Neanderthals in early 2019

Filed under: Neanderthal,Neanderthal admixture — Razib Khan @ 5:17 pm
PNAS has published a paper, Limits of long-term selection against Neandertal introgression. It’s from a preprint which I blogged this summer. What are the major takeaways here? It’s been about 10 years since the draft Neanderthal genome was published. At around that time everyone realized that there was archaic introgression into the modern human genome. […]

How your Neanderthal functions in the human genome

Filed under: Human Evolution,Neanderthals,science,Selection — Razib Khan @ 2:28 pm

What does it mean that you have Neanderthal ancestry? Everyone agrees now that that ancestry exists, but does it make you any different from what you’d be otherwise? From a scientific perspective, one might ask what the function of Neanderthal genetic variants are. What do they do in your body?

The truth is that they do many things. The human genome has many genes. About 20,000. Across those genes, there are ~3 billion base-pairs. A, C, G, and T. The best estimate if you are not African is that there is a 1–2% chance that a base is from a Neanderthal ancestry. Modern humans don’t have the same 1–2%, so around 30% of the Neanderthal genome can be reconstructed from living people alone!

For many years researchers have examined patterns of Neanderthal admixture within the genome, and over time (looking at ancient DNA). Because the ancestors of Neanderthals separated from modern humans 700–900 thousand years ago, there are some genetic incompatibilities, and Neanderthal variants are likely to be selected against. The most recent research, though not the final word, indicates that much of this selection happened very early on.

In other words, most of the very incompatible Neanderthal variants were removed from the human genome within ~10,000 years of the admixture.

But within the genome, there are differences as to where Neanderthal genes are found. Early work indicated that Neanderthal ancestry was overrepresented in the vast majority of the genome that does not code for proteins (“junk DNA”). This was suggestive of the likely that Neanderthal ancestry was usually bad when it coded for proteins.

Today a closer look, as implied in the figure the left, suggest that selection against Neanderthal variants was less about protein coding, and more about regulation. Though the human genome has only about 20,000 genes, how those genes are expressed in tissues, and how they are expressed, plays an essential role in differentiating us from other mammals. This is why the vast majority of our genome can be similar to a chimpanzee, or a Neanderthal, and yet modern humans are creatures very different.

It may turn out that our unique Neanderthal ancestry may play a greater role in rearranging how genes express themselves more than anything else.

Discover your Neanderthal story today!

How your Neanderthal functions in the human genome was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

To understand Neanderthals we need to understand ourselves

Filed under: Evolution,Genetics,Genomics,Neanderthals — Razib Khan @ 1:56 pm

In 2010 researchers sequenced the whole genome of a single Neanderthal. From comparing this genome to that of humans alive today they concluded, to their surprise, that many modern human populations had Neanderthal ancestry! More specifically, all populations outside of Africa seem to have some Neanderthal ancestry.

Over the last decade, researchers have come to agree that this finding is a true one. That is, modern humans do have Neanderthal ancestry. In fact, most scientists now believe that there is also ancestry from a third human population, Denisovans, across eastern Eurasia and Oceania.

But there is more to the story than we understood in 2010. Then, researchers argued there was a single admixture as humans left Africa. Today, some researchers contend there were multiple Neanderthal admixtures, with East Asians having more Neanderthal ancestry than Europeans. Others argue that European Neanderthal ancestry is diminished by later mixing with a human population without Neanderthal ancestry! Finally, some researchers have suggested these differences can be explained by natural selection, whereby Neanderthal genes are removed from the population due to their selective effects, which had different power across different populations (the larger the population, the stronger natural selection is)

Despite the widespread agreement about Neanderthal ancestry in modern humans, the discovery has triggered many more questions.

A new paper in PNAS, The Limits of long-term selection against Neandertal introgression, aims to resolve this muddle by two primary means:

  1. Use multiple Neanderthal samples of different relatedness to modern humans to obtain a better estimate of proportions.
  2. Add complexity to our understanding of the interactions between various ancestral human populations, and see how that affects estimates of Neanderthal ancestry.

The authors conclude that the decline in Neanderthal admixture discovered in Europeans may, in fact, be an artifact. First, it neglects gene-flow between African populations, as well as from Eurasian populations back into Africa (in particular, from European and Near Eastern groups). Second, using two Neanderthal samples, one much more closely related to the group which contributed to modern humans, allows for more precise direct estimates.

Though the authors found some evidence for natural selection, these results suggest that this force is not necessary to explain the differences between modern human populations.

This is unlikely to be the final world. The moral of the story is that moving beyond simple models and a few samples add complexity and nuance to our understanding of how our Neanderthal ancestry fits into the broader narrative of our ancestors’ tales.

Discover your Neanderthal story today!

To understand Neanderthals we need to understand ourselves was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Supporting the Brown Pundits “BrownCast”

Filed under: Podcast — Razib Khan @ 2:47 am

When Zach, Omar, and myself began the BrownCast I said that at some point we’d have to think about how we could make it self-supporting. Some people are already complaining about the production quality.

There’s a reason for that: I’ve been doing all the editing. I literally had never used Audacity before, and as most of you know I’m a geneticist, not a sound engineer.

For those of you who think no production is involved, listen to this clip I edited out from the most recent recording with myself, Slapstick, and Zach.

I would like to get a person who has skills and can devote time, to this project. I have someone in mind. But I’m already paying Zencastr bills out of pocket. So I’m asking listeners to chip in. Please consider giving to my Patreon. Since there is a wide range of abilities to pay I’m not stipulating a specific amount.

As a patron benefit, I have just posted links to the next two podcasts on Patreon. A podcast with Omar, Ali Minai, and Charles Cameron which focuses on Urdu literature and before shifting to artificial intelligence and the nature of Western culture is up. As well as another where Slapstick explains “generative grammar” in the context of Sanskrit.

We are unlikely to post podcasts more than once a week. But I often edit them together considerably earlier, so Patrons will get them in batches well before everyone else.

If you are not in a position to be a patron, please rate us positively on iTunes and Stitcher.

Liberty and justice for all

Filed under: Feminism — Razib Khan @ 12:20 am
Saudi Teenager Who Fled Family Embraces All Things Canadian. (O.K., Maybe Not Winter.): She wants to go to college to study architecture. She would like to take English classes. She is wondering about how to harness her newfound media stardom. … In Saudi Arabia, Ms. Alqunun was a first-year university student, studying basic science and […]

January 15, 2019

Open Thread – Brown Pundits

Filed under: Uncategorized — Razib Khan @ 11:57 am

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

An Iyer in the Whitehouse

Filed under: Kamala Harris,Politics — Razib Khan @ 11:10 am

As most of you probably know, <<<Kamala Harris>>>’ <<<mother>>> (who raised her after she was divorced from Harris’ father was an immigrant from India. A Tamil Brahmin physician, Dr. Shyamala Gopalan Harris instilled a sense of Indian culture in her daughter. At least according to Harris’ Indian.

The weird thing about Harris for me is she looks a lot like an Iyer friend of whenever she smiles.

Because of her mainstream/corporate Democrat credentials, I suspect Harris is far more likely to become President than Tulsi Gabbard.

Open Thread, 01/14/2019

Filed under: Open Thread — Razib Khan @ 12:40 am
Robert Alter has a new translation of The Hebrew Bible out. I really like Alter’s work. In particular, Genesis: Translation and Commentary. But read all his stuff! NPR has an interview with him up right now. He admits that he did the translation in longhand! Genome-wide association analyses of risk tolerance and risky behaviors in […]

January 12, 2019

A Hindu in the Whitehouse?

Filed under: Hinduism — Razib Khan @ 10:54 am

Tulsi Gabbard is running for President. She is a devotee of Gaudiya Vaishnava Hinduism. Her father is half-Samoan, and due to her dark looks and Hindu religion, she is often assumed to be South Asian. And, she does have connections to South Asian culture through her religious affinities.

That being said, I assume this is a way for her to increase her profile more than a plausible chance to win the Presidency (though I think the same was true of Trump!). Gabbard is a somewhat heterodox Democrat who strikes a Left pose, but her background in her youth was in social conservatism, and the truth is that aside from some oddballs there’s not much light between different factions in the Democratic party in 2018. For this, and other reasons, she is under fire from the usual pundit-class commissars who punish deviationism.

But what I’m curious about the attacks that are made on her religion:

The idea that Gabbard is a cultist probably comes from a piece in The New Yorker, The making of a charismatic, unorthodox Democrat.

Since I’m not on the Left, I don’t care/know about all the internecine conflicts/moves that define these sort of coordinated couterattacks. But it’s really interesting to me that unless you are a very liberal cultural Hindu, it’s open season from certain quarters of the Left. In a way, this is similar to Christianity, but not Islam, where conservatively devout individuals are acceptable so long as they keep their social views on the down-low.

(I have a friend who is Gaudiya Vaishnava who has to explain to her Hindu American friends that not all Hindu Americans are pantheist/Deists who are OK with beef-eating. She is, by the way, a very liberal Democrat)

Note: Kamala Harris is a Baptist, but her mother was an Iyer.

January 11, 2019

Forgetting the past

Filed under: History,Vedas — Razib Khan @ 12:24 am

How could the Indo-Aryans have been from somewhere else if it is not recorded in their traditions? This is a common question that comes form many Indians. It is an entirely Indo-centric perspective. This is a description, not a critique. After all, the Indo-European Greeks have no lore of migration in the Hesiod. Many, such as the Athenians, consider themselves autochthonous. The Egyptians have no lore of migration. In contrast, the Sumerians seem to have had legends of migration from the “south” (perhaps marshland to the south of Mesopotamia proper). And the oldest Sumerian city does happen to be the most southern one (Eridu). The Norse have no history of migration from elsewhere, but it is almost certainly a fact that the Nordic Bronze Age cultures came out of the post-Bell Beaker and Corded Ware societies after 2000 BC, whose roots lay ultimately to the south and east.

Finally, as I have written elsewhere, in the space of less than 200 years the Celtic Britons of what became England abandoned their native language and cultural memory and replaced it with that of pagan Germans. We know from both fine-scale modern genetic analysis of the British Isles, as well as ancient DNA, that the majority of the ancestry of the modern English dates to the period before the arrival of the Anglo-Saxons. And yet pre-Germanic language and cultural folkways had only a trivial impact on the English. Even royal houses, such as those of Wessex, who were likely of native British origin (the earlier rulers in the genealogy have Celtic forenames!) “retconned” their origin to be from the Germanic god Wotan.

If, as I believe, the Indo-Aryans are rooted primarily in the Sintashta culture which flourished around ~2000 BC, and the Vedic culture flourished in South Asia by ~1500 BC, that allows for only five centuries to “forget.” Your mileage may vary, but 20 generations seems a bit short to forget this when these people were punctilious in matters of antique ritual.

To answer this conundrum, I propose something entirely conjectural and hypothetical, but not impossible: the Brahmin caste emerged as a fusion of Indo-Aryan ritualists and pre-Aryan priests. In terms of total ancestral contribution, the latter is actually more preponderant than the former. Though the language of the former is dominant, most people accept that the Vedic culture was somehow synthetic. A hybrid. Perhaps the pre-Aryan priesthood was culturally more dominant than we may suppose, and as its roots were deeply indigenous, they promoted the ideology that their hybrid caste was in India in toto immemorial?

January 10, 2019

The genetic palimpsest of the Horn of Africa

Filed under: Uncategorized — Razib Khan @ 11:09 pm
Over the last few days I’ve been looking at genetic data related to the Middle East, and as part of that process, I added some Ethiopian samples (in particular, Beta Israel). Which has brought me to thinking about the issue of the origins of the Ethiopians. In 2012 Pagani et al. published a paper which concluded […]

January 9, 2019

The diversity of modern Arabians

Filed under: arabia,Saudi Arabia — Razib Khan @ 9:01 pm
Genetic variation of Arabians

At the confluence of Europe, Asia, and Africa, it is no surprise that the Middle East is genetically diverse and varied, just as its complex history would suggest. With numerous ancient peoples, from Egyptians to Sumerians, and Arabs, Persians, and Turks today, along with minorities such as the Armenians, Assyrians, and Kurds, the region is a palimpsest of cultures.

And so it is genetically due to its central position. The plot above shows results for people from different parts of the world. To the right are people from India. At the top of the plot are Africans from Kenya. In blue and green at the bottom, you see Greeks and Lebanese. Of note is that people from Saudi Arabia, Qatar, and the United Arab Emirates exhibit much more genetic variation in relatedness to Africans and Asians than either of these two groups.

A Dhow

Though the Arabian peninsula is one of the most arid inhabited regions of the earth, with no perennial rivers, it is surrounded by seas and oceans on three sides. Arab sailors pushed down the coast of East Africa, and on eastward toward the Spice Islands of modern Indonesia. The legends of Sinbad the Sailor are based on these voyages, with the Elephant Bird of Madagascar likely being remembered in the legends of the giant Roc.

Gene-flow from Africans to Saudis

The legacy of African slavery is felt the world over, and it has also left its imprint in Arabia, with large populations of African origin, identity and ancestry spread through the indigenous Arab population. If you model the genetic distances between the groups in the plot above, you see that an arrow representing gene-flow often points to one of the Arabian groups from Africans. The plot to the left illustrates that to a great extent the difference between Saudis and Lebanese is the ancestry Saudis have from Africa.

Further east, in the United Arab Emirates and Qatar, the influence of Persians and Indians makes itself felt. For thousands of years, there has been a connection between this part of Arabia and the lands which border the seas to the east. As early as 4,500 years ago, during the time of the Sumerians, Indians were traversing the islands and peninsulas of eastern Arabia, north to Mesopotamia. This is seen in the genetic analyses, as Qataris and Emiratis in particular, are shifted toward Indian populations.

Philip the Arab, Roman Emperor

History teaches us about the Arabs who left the peninsula to make their fortunes in the wider world, from the Roman Emperor Philip to the armies of Islam which swept from the Indus to the Atlantic. But the genetic evidence from the modern people of the Arabian peninsula shows that people also came and settled down from Africa and Asia. Today Mecca is one of the most diverse cities in the world due to its role in the Islamic religion, and believers from all over the world arrive every day. Historically a certain number would settle down, and intermarry with the local Hejazi people of western Arabia.

To the east, Persians, Indians, and Malays arrived and made their homes in the towns relying on trade. Over time they intermarried with the Arabs who shifted between the sea and the desert and laid the foundations of the cosmopolitan city-states which stud the modern Gulf.

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

The diversity of modern Arabians was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

On the edge of Africa and Eurasia

Filed under: Evolution — Razib Khan @ 5:43 pm
Rub’ al Khali

The sands of Arabia harbor romantic allure for many, despite their desolation. At the nexus between Eurasia and Africa, the Arabian peninsula serves as both a conduit and barrier for trade and migration. On its northern fringe arose the first civilizations, while far to the south the bleak deserts give way to the mountains and fields of what the Romans termed “lucky Arabia,” the verdant highlands of Yemen. From the sands of the north the armies marched, while the coasts of the south are where trade routes across the Indian ocean began.

From the Queen of Sheba to the rise of Islam and the centrality of oil in the modern economy, Arabia plays a pivotal role in the history of the world.

But the importance of this peninsula on the southwest edge of Eurasia is much deeper in an evolutionary sense. To the north in the mountains of modern Iraq were the southern edges of Neanderthal occupation in Eurasia, in the caves of Shanidar. To the northwest, just outside of Arabia proper, were the Skhul and Qafzeh hominins, a group of modern humans who flourished ~100,000 years ago, and whose roots seem to have been Africa.

Hominins have been present outside of Africa for nearly two million years. And yet their origins are ultimately in Africa. Both Neanderthals and modern humans derive from migrations from Africa within the last one million years. Logically Arabia must have been a stopping-off point for humans for millions of years.

Citation: Petraglia, M. D., Breeze, P. S., & Groucutt, H. S. (2019). Blue Arabia, green Arabia: examining human colonisation and dispersal models. In Geological Setting, Palaeoenvironment and Archaeology of the Red Sea (pp. 675–683). Springer, Cham.

Just as the complex geography of Arabia made it the nexus of history, so the scaffolding of water, mountains, and deserts have made it a central element of the human evolutionary odyssey. Humans have two plausible avenues of migration out of Africa. In the north, through the Sinai, or in the south across the Bab-el-Mandeb strait between Yemen and the African mainland.

The reality is that both routes may have been important, as the region seems to have been witness to many migrations of humans over the past two million years, as well as movements back toward Africa, whether it be the Neanderthal shift south during cold periods or the movements of agriculturalists from the Fertile Crescent over the past 10,000 years. Because of variations in climate over this time, multiple routes may have opened up, whether due to reduced sea levels, or the existence of perennial rivers on the Arabian peninsula during times of greater precipitation.

The mountains of Yemen in southwest Arabia

And Arabia may not simply have been a transit point. The latest ancient genetic work suggests that the humans who left Africa were separated into two primary ones. One population did not mix with the Neanderthals to the north and east. While another group did. This second group became the ancestors of all the humans today found in Europe, Asia, Oceania, and the New World. The first group seems to have remained close to Africa and mixed eventually with the first group, giving rise to the various peoples of West Asia and North Africa.

The historical romances set in Arabia are well known today, but in the future, this peninsula may hold the keys to the origin of humans outside of Africa!

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

On the edge of Africa and Eurasia was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Brown Pundits – Episode 7, Sarah Haider, Islam, identity, and the “public life”

Filed under: Podcast — Razib Khan @ 12:03 pm

The latest BP Podcast is up. You can listen on Libsyn, iTunes 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.

The guest this week is Sarah Haider. She is executive director of Ex-Muslims of North America.

Sarah and I are friends so I switched into a more informal register. The contrast between her very polished speaking style and my own is pretty striking and unsurprising. Also, please note that an outraged two year old child kept attempting to take over my home office, and you can hear him now and then.

If you want to hear more from her, please check out her speaking on YouTube.

January 8, 2019

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 11:57 am

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

January 7, 2019

Open Thread, 01/07/2019

Filed under: Open Thread — Razib Khan @ 7:55 pm
Because of BookBub I get notified of a lot of book deals. For example, The Roman Empire and the Silk Routes: The Ancient World Economy and the Empires of Parthia, Central Asia and Han China is now $1.30 on Kindle. This is like when The Shape of Ancient Thought was steeply discounted a few years […]

Toward a mature conservatism

Filed under: science — Razib Khan @ 1:51 pm

India scientists dismiss Einstein theories:

In 2014, Prime Minister Narendra Modi told medical staff at a Mumbai hospital that the story of the Hindu god Ganesha – whose elephant head is attached to a human body – showed cosmetic surgery existed in ancient India.

In 2014, Prime Minister Narendra Modi told medical staff at a Mumbai hospital that the story of the Hindu god Ganesha – whose elephant head is attached to a human body – showed cosmetic surgery existed in ancient India

I don’t comment much on Indian politics for two reasons. First, I think macroeconomic conditions and trajectories are more important than politics as such for a developing nation like India. Second, the details of the cultural and political dynamics within any given nation are really hard to grok from the outside.

That being said, the widespread percolation of this sort of pseudoscience and pseudohistory on the Indian Right is a problem and has analogs with instances in other nations (e.g., Mike Pence is almost certainly a Creationist). These beliefs are often (though not always) harmless in and of themselves, but they are indicative of deeper maladies in terms of epistemological hygiene.

I have Hindu nationalists who are broadly on the same empirical page as me. We differ on details of values and emphases. And I know they are somewhat embarrassed by these weird ideas about nuclear weapons in ancient India. The key is to keep a lid on it so it doesn’t capture the commanding heights (ergo, why I’m quoting Modi).

Addendum: One issue for me is that I have a hard time taking Indian pseudoscience seriously just as I have a hard time taking Creation Science seriously. Sincere, earnest, and sometimes bright, people taking absurd claims seriously and constructing models out of them strikes me as farcical and funny more than threatening.

January 6, 2019

The variation in religion and our evolutionary history

Filed under: Religion — Razib Khan @ 3:13 am
As my post on intelligence was quite successful, I thought perhaps I would offer up something similar on religion, since that’s a topic where I have been giving opinions based on fragments of my own views for some time. The point in this post is to unpack the general set of ideas and frameworks that […]

January 5, 2019

How is Austin getting less diverse? Not racially

Filed under: Austin,geography — Razib Khan @ 2:17 pm
Lawrence Wright has a new book out, God Save Texas: A Journey into the Soul of the Lone Star State. One thing I see him saying is that Austin is less diverse. Since he’s lived there for many decades, he has some personal data to bring to the table. And yet I wasn’t sure that […]

January 4, 2019

Why Indian forms dominated Chinese forms in mainland Southeast Asia

Filed under: History,Southeast Asia — Razib Khan @ 5:32 pm
On Twitter Peter Turchin had a question in response to me tweeting a new preprint on bioRxiv: I am particularly interested in what the data say about Indian genetic contributions — I thought that SE Asia just got Indian culture, without any substantial population movements involved — Peter Turchin (@Peter_Turchin) January 4, 2019 This was […]
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