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January 30, 2019

How ancient DNA illuminated the dark cave

Filed under: Ancient DNA,Paleoanthropology,science — Razib Khan @ 9:23 pm

Unfortunately, we do not have a time machine, nor is there any likely possibility of any such thing in the near future. The laws of physics are what they are. That is why those of us who are interested in the human past must make recourse to disciplines such as history, archaeology, and paleontology.

But all of these have their limits. History’s reliance on the written text means that there is a bias toward the records of the powerful and privileged because for much of history writing was the purview of elites. Archaeology focuses on material remains and artifacts, but there is only so much insight one can squeeze from pottery shards. Finally, paleontology must rely on bones which are very rare and do not provide a fully-fleshed picture of human life (literally!).

Of course, these methods improve over time. The decipherment of cuneiform in the 19th century opened up the pasts of the Babylonians, Akkadians, and Sumerians. In the 1950s the decipherment of Linear B meant that historians could confirm that the Mycenaean peoples of the Bronze Age were Greek-speakers. Radiocarbon dating transformed the ability of archaeologists to produce chronologies of cultural change over time at any given location with incredibility certainty. Finally, paleontologists have been able to utilize modern technology to “scan” fossils and so obtain much more information from any given sample than was possible in the post.

Into this landscape stepped ancient DNA. Analysis of genetic remains and material dates back to the 1990s, pioneered by Swedish paleogeneticist Svante Pääbo. But Pääbo’s work really came to the attention of the mainstream when his team sequenced the whole genome of a Neanderthal in 2010. Consider how amazing this is in light of the fact that the draft of the first human genome was only completed ten years earlier!

And it turned out that the Neanderthal genome had surprises in store for paleoanthropologists which they had not anticipated. For decades the relationship between Neanderthals and modern humans had been debated. The primary question being whether the former were ancestors of the latter. Or not, as was the orthodoxy in 2010 in much of paleoanthropology!

Pääbo himself held to this orthodoxy, and earlier work sequencing the mitochondrial DNA passed from mother to daughter, confirmed that Neanderthals were distinct from modern humans. No modern humans seem to carry a Neanderthal mitochondrial lineage. Case closed.

But the data had other plans. When the researchers compared the genome of the Neanderthal to that of modern humans, they found that modern humans were very different. This was to be expected. But, they noticed a peculiarity in the relatedness: modern humans outside of Africa were all somewhat closer to Neanderthals than modern humans within Africa. Assuming that modern humans descend from a population that expanded out of Africa relatively recently, the most plausible explanation for this pattern is that some of these non-Africans mixed with Neanderthals in their migration outward.

Denisova Cave

The ancient genome changed everything because now there was a definite benchmark for comparison, rather than all the indirect attempts that had been performed in the past. The ancient DNA was a game changer, confirmed by the finding later that year that remains from Denisova cave in Siberia belonged to a previously unknown lineage of human, closer to Neanderthals than modern peoples. It turns out this mysterious population also contributed ancestry to the peoples of Papua New Guinea, far to the south and east. So a single ancient genome transformed our understanding of the past, and shed light on patterns in the present.

Now, it isn’t as if geneticists were not using their techniques to make inferences about the past for decades. The “Out of Africa” model rested on genetic inferences, looking at variation in living people, and concluding from that that the ancestry of modern humans likely derives from an ancient African population. At such a broad level a method which relied on modern variation was sufficient. The results have held up. But when it came to narrower questions the methods which looked at the “tips” of the phylogenetic trees, the extant populations today, have been far less successful.

We know this because ancient DNA from the past 40,000 years has shown that there were massive population turnovers and mixtures all across the world. Using modern DNA to make projections of the past rely on assumptions of geographic stability of human groups…which turn out to be wrong. If one thinks of the human past as a phylogenetic tree, ancient DNA allows one to fill in “nodes” upstream of the “tips” of the tree. This resolves ambiguities, confusions, and corrects for mistakes in assumptions.

Ancient DNA cannot tell researchers “who” a people were. What language they spoke. Or how they lived. What it can tell you without debate is how people were related to each other in the past, and how they are related to people today.

We know, for example, that very few of the ancestors of modern Europeans derive from the people who drew the enigmatic cave paintings of the Upper Paleolithic. We also know that no modern people descend from the Cro-Magnon bands who replaced Neanderthals in Europe. These artistic creations are in some meaningful way the true legacy of these lost peoples.

Humans are one of the most mobile mammals, occupying six of the seven continents by 10,000 years ago. The tools, the technologies, of ancient DNA are another quiver in the arsenal of prehistorians. The migration of peoples is not everything, but it is an essential thing because without migration we wouldn’t be the most successful large mammal of the past 60 million years.

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


How ancient DNA illuminated the dark cave was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

The Insight Show Notes — Season 2, Episode 12: The New York Times takes on Ancient DNA

Filed under: anthropology,DNA,Genetics,science — Razib Khan @ 3:42 pm

The Insight Show Notes — Season 2, Episode 12: The New York Times takes on Ancient DNA

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts)we discussed the controversy that has erupted over a 12,000-word piece in The New York Times Magazine, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps? Many researchers associated with this work, including the primary focus of the article, David Reich, have taken issue with the reporting. We talk to Bastien Llamas, a researcher in Australia who has worked with Reich and is involved in the field of ancient DNA himself and been vocal on Twitter about the piece.

Much of the discussion is hard to understand without reading the piece in The New York Times Magazine, but also David Reich’s new book, Who We Are And How We Got Here, also helps.

As Bastien makes clear, the field of ancient DNA has gone from basically nothing to thousands and thousands of samples in less than a generation. But, we talk about the fact that a single whole-genome sequence has enough information to infer the history of a whole population.

In the piece, there is a reference to the fact that some labs seem to have technological monopolies which exclude other research groups. Bastien outlines exactly and in detail the “other side” from the perspective of Svante Paabo.

We also discuss the debate around the peer-review of a paper on the genomics and history of Vanuatu, and how the “full story” is more complex, nuanced, and different, from what you might take away from simply reading the piece.

There was extensive discussion about the different technologies utilized in the field of ancient DNA, in particular, “shotgun whole-genome sequencing” vs. “SNP-capture array.” The technological debate is embedded in the reality that the field to a great extent is an oligopoly, with a few big labs and consortiums dictating the direction of the research questions and methodologies. We talk about this reality, as well as the nature of science now and the possibilities of the future.

The New York Times Magazine also takes for granted the idea that David Reich and colleagues are resurrecting old racist theories about the migrations and replacements of peoples, which archaeologists rejected after World War II due to their ideological valence. But an anthropologist points out that this is not actually what happened, and that the change from “cultural-history” to “processualism” had as much to do with the data available and scientific fashion as it did with broader cultural currents.

Finally, we discussed working in Australia and future directions in ancient DNA.

If you want to get a more academic understanding of the field, please see this opinion in PNAS, To curate the molecular past, museums need a carefully considered set of best practices.

David Reich’s lab website has two updates relating to the article.

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


The Insight Show Notes — Season 2, Episode 12: The New York Times takes on Ancient DNA was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

January 29, 2019

Millennials turn away from Creationism

Filed under: creationism — Razib Khan @ 8:05 pm
When I was younger dealing with Creationists was something I had to do as a matter of course. Like many members of “Generation X” I haunted Usenet groups in the 1990s where the “evolution-creation” debate raged, always defending the consensus science from detractors. Even in the early years of this weblog, we tackled Creationists now […]

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 11:59 am

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

January 28, 2019

Various Asiatic raps

Filed under: Culture,Rap — Razib Khan @ 8:27 pm

I was watching some Mongol rap:

Then I wondered…found some stuff. Thoughts?



Open Thread, 01/28/2019

Filed under: Open Thread — Razib Khan @ 2:27 pm
If I haven’t made it clear, I highly recommend The First Farmers of Europe: An Evolutionary Perspective. A very readable book. One thing I haven’t emphasized is that the early European farmers seem to have been big consumers of cheese. This is curious as it doesn’t look like they have the modern European lactase persistence […]

January 26, 2019

Brown Pundits BrownCast episode 10, with Josiah Neeley

Filed under: Podcast — Razib Khan @ 11:14 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. You can also support the podcast as a patron (the primary benefit now is that you get the podcasts considerably earlier than everyone else).

This week I spoke to Josiah Neeley of the R Street Institute. A policy analyst by day, Neeley is also a host of the excellent Urbane Cowboys podcast (I’ve been a guest twice).

We talked about what it’s like to be a “Trump-friendly” intellectual on the Right in the United States, and whether being a Trump-supporter means you are of course a racist.

China seems to be a topic that comes up on this podcast often, and this was no exception. Josiah and I spoke about how we as Americans need to handle new geopolitical realities and their impact on internal politics.

We discussed the future of Republican politics and the decline of a “white Christian America”, and the rise of something new…which we don’t know yet.

Finally, the conversation ended with musings about whether America was heading toward an Idiocracy-like political system. Josiah recommended Helen Andrews’ excellent essay in First Things, Bloodless Moralism.

January 25, 2019

Notes on Brown Pundits “BrownCast”

Filed under: BrownCast,Podcast — Razib Khan @ 10:07 pm

I’ll be interviewing my friend Josiah Neeley tomorrow about politics and policy in Trump’s America. Since this is Brown Pundits my outline has a lot of brown-themed questions, but we’ll range. If you are reading this before ~2 PM PDT feel free to drop-in questions. Josiah’s podcast, Urbane Cowboys, has had several brown people on. Of these, three are Bengali American. Myself, Reihan Salam, and Avik Roy.

On Sunday I’ll be talking to Carl Zha, who produces the popular CLASH! podcast. Feel free to suggest questions for Carl.

To paid-up patrons: I am posting the podcasts ahead of time on the patron page. These two podcasts won’t drop until February, so if you want to hear them earlier, you know how. I’ve already posted Zach’s podcast on Indian numismatics. That will probably drop tomorrow or Sunday, when Zach writes up some show-notes and pushes it live.

The diverse origins of the Bengali gentry

Filed under: Indian Genetics,Kayasthas — Razib Khan @ 7:24 pm
I’ve been rather busy with other things and the South Asian Genotype Project has fallen a bit by the wayside. But, I plan on allocating a day on a weekend soon to getting through the backlog. But, before that, I thought I would submit something that might clarify or illuminate an aspect of South Asian […]

The European Neolithic, in fits and starts

Filed under: Agriculture,Europe,LBK,Migration — Razib Khan @ 12:34 am
On this week’s episode of The Insight I discussed the field of cultural evolution with Richard McElreath. The author of Mathematical Models of Social Evolution, he was in a good place to explain why the field is relatively formal. This is in contrast for example to modern American cultural anthropology. Basically, formality keeps you honest […]

January 23, 2019

The Insight Show Notes — Season 2, Episode 11: Cultural Evolution

Filed under: anthropology,Cultural Evolution,Culture,Evolution — Razib Khan @ 4:45 pm

The Insight Show Notes — Season 2, Episode 11: Cultural Evolution

This week on The Insight (Apple Podcasts, Stitcher and Google Podcasts)we discussed the field of cultural evolution with Richard McElreath of Max Planck Institute for Evolutionary Anthropology. The past, present, and future possibilities within this discipline.

Genealogically the modern study of culture in an evolutionary context goes back to L. L. Cavalli-Sforza and M. W. Feldman’s Cultural Transmission and Evolution: A Quantitative Approach. This approach was extended by Peter Richerson and Robert, such as in their book Not By Genes Alone. McElreath himself has written Mathematical Models of Social Evolution, illustrating the formal bent of this field.

We discussed the difference between the methods within cultural evolution, which borrow heavily from population and quantitative genetics, and cultural anthropology. While cultural anthropology is descriptive and avoids generalities, cultural evolution leans heavily on mathematical modeling. McElreath points out that today there is a society for his field, the Cultural Evolution Society.

Differences between cultural evolution and evolutionary psychology were discussed. While the former is mathematical as well as depending on fieldwork, the latter is a branch of social psychology informed by evolution that is more verbal and experimental.

The relevance of group selection to cultural evolution and its irrelevance to evolutionary genetics was also explored.

Two papers that McElreath was involved with, Greater wealth inequality, less polygyny: rethinking the polygyny threshold model and Sustainability of minority culture when inter-ethnic interaction is profitable, were discussed.

Finally, we also alluded to a non-obvious finding from cultural evolution: that social cognition explains cultural complexity we see around us, rather than individual intelligence. This is a central theme of Joe Henrich’s book The Secret of Our Success.

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


The Insight Show Notes — Season 2, Episode 11: Cultural Evolution was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

January 22, 2019

Humanity is smarter than the sum of its individuals

Filed under: Culture,science — Razib Khan @ 10:46 pm

We live in a world of wonders. Airplanes take us across the world, computers connect us digitally, and antibiotics cure us of infections. But how does any of this work? Do you know? Does your neighbor know? Billions of humans beings use mobile telephones. But could any single human build a mobile telephone from scratch? Could they even repair their phone if there was a defect?

The answer is obvious. A single human being, no matter how smart, is likely to be able to create a smartphone. A single human being is not able to master all the disciplines, from software engineering to solid state physics, that would allow them to design such a device in the first place. And a single human being does not have access to the specialized and efficient economic system that allows for the production of modern technology. The mobile telephone is the product of a system.

In our current age, we are wont to chalk this up to the interdependent economics of an advanced society. Everyone specializes, and complex supply chains interact dynamically through the “invisible hand,” to provide for us incredible productivity gains. But the truth is that this is how it has always been for our species.

Imagine being asked to create a bow and arrow. A functional clay pot. Or raise a crop of wheat. Though none of these things are highly “advanced” technologies, individual humans without specific skill would be at as much a loss as if they were asked to build a car from “scratch.” Specialization, compartmentalization, and almost miraculous social coordination has been part of our species’ toolkit since the beginning. It was true during the Middle Ages. During the time of the Roman Empire. And during the Stone Age.

Humans may have very large brains for our body sizes, but the truth is that our brains have been about the same size for the past 200,000 years. And yet our innovativeness did not stop 200,000 years ago. Rather, the rate of cultural innovation has increased over time, despite the fact that individual humans have had the same hardware. If human cultural complexity is due to the size of our brains, it is curious that our brains have not changed while our culture has. Something else is going on.

Human cultural evolution operates not simply through shaping our biology in the form of our brains but embedding in social memory a distributed set of skills and abilities which develop cumulatively over tim

Human societies are “hive minds,” and even if individual constituents of that hive mind have not changed for many millennia, the mind itself has been evolving over time. Adapting and reshaping itself. The distributed network has allowed for the development of specialized individuals with particular skills.

A few hundred years ago the vast majority of humans were farmers. Today, one occupation is not dominant, and most people fill specialized niches. As individuals, we lack the general flexibility of our Paleolithic ancestors. Take us into the wilds and many of us perish. But as a social unit, we are far more advanced because the “memes” that have come to define us at the level of societies are far beyond anything our ancestors had access to.

No single human being was responsible for getting our species to the moon. Rather, the collective wisdom of our species was responsible, across the world, and going back in deep in time.

Though evolution in a genetic since has continued since the Paleolithic and continues today, perhaps the most riotous explosion of evolution in the past 10,000 years has been culture, not biological!

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


Humanity is smarter than the sum of its individuals was originally published in Insitome on Medium, where people are continuing the conversation by highlighting and responding to this story.

Open Thread – Brown Pundits

Filed under: Open Thread — Razib Khan @ 3:58 am

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

One thing, thanks to everyone who has donated to the Patreon. Weirdly it makes me feel a little more appreciated when I’m editing these podcasts late at night after my work and family are over 😉 Since the “patrons” have some “skin in the game” definitely going to be taking input from them in terms of what the directions are that our podcast, and to some extent the blog, will follow. I started this weblog with Zach seven years ago without any real goal or endpoint, so it’s evolving….

January 21, 2019

David Reich strikes back!

Filed under: David Reich,Historical Population Genetics — Razib Khan @ 8:03 pm
David Reich submits Five Corrections to The New York Times. As you know, in the fact-checking process I was sent more than 100 statements of which a very high proportion (more than half) were incorrect. For example, as I mentioned to you in my letter of January 7, 20 of 49 statements presented to me […]

January 20, 2019

Open Thread, 01/20/2019

Filed under: Open Thread — Razib Khan @ 10:58 pm
Peter Turchin recommended The First Farmers of Europe: An Evolutionary Perspective. It’s dry. But good. It is also one of those academic books where the cost of the Kindle version is $50 less than the hardcover version. Two for Tea is a good podcast. One the most recent one they interviewed two anthropologists, both known to […]

David Reich drops the mic

Filed under: David Reich,Historical Population Genetics — Razib Khan @ 12:04 pm
Didn’t mean to post so much about that crappy piece in The New York Tines Magazine. But there’s so much tendentious crap in it. That being said, I am probably not going to post much more on this, because David Reich’s response is up: Letter in response to Jan. 17 article in The New York Times […]

January 19, 2019

On “big science”, ancient DNA, and David Reich

Filed under: David Reich,Human Population Genetics — Razib Khan @ 5:52 pm
A lot has happened in the last few days in backchannel conversations and social media in relation to the piece in The New York Times Magazine which put the spotlight on ancient DNA, and David Reich, for the general audience. Unlike Carl Zimmer’s ancient DNA column in the science section of the paper, the people […]

January 18, 2019

The hammer of the All-Father

Filed under: Genetics — Razib Khan @ 3:48 am


Unless you have been sleeping under a rock, a mildly slanderous piece in The New York Times Magazine has taken aim at David Reich and his band of paleogeneticists, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps? I address this piece at my other weblog.

One of the major themes of the piece are the legends and myths of the people of Vanuatu:

I asked him about how the concept of Lapita migration to empty islands had been received by people whose oral traditions said they came from a stone or a coconut tree.

The reason this is relevant is that paleogeneticists have probed the history of Vanuatu. And yet this is the past. The future is that the Reich lab is collaborating with other paleogeneticists to crack the nut of the history of the Indian subcontinent with ancient DNA. They’ve been working on this for years, and they are working on it now. There are 275,000 people who live in Vanuatu. There are 1.7 billion people who live in the Indian subcontinent.

Within the next year I believe that the Reich lab will publish results which will falsify the beliefs of a substantial number of Indians about the nature of the origins of the native peoples of the region. This will shatter world-views, undermine mythologies, and rock peoples’ worlds. There will be sophists who live in denial, but the truth will be plain to those who see.

I understand that some of you reading this disagree with this assessment. Ultimately I don’t care because the data are coming, and if I’m wrong, that’s OK too. I don’t have emotional baggage invested in alternative models. But, I do wonder why the mythological traditions of “non-indigenous” people seem to warrant less attention than smaller nations or premodern tribes.

January 17, 2019

The ancient DNA oligopoly and the stories people tell about David Reich

Filed under: David Reich,Historical Population Genetics — Razib Khan @ 1:16 pm
There is a very long piece in The New York Times Magazine, Is Ancient DNA Research Revealing New Truths — or Falling Into Old Traps?. It’s the talk of DNA-Twitter for obvious reasons. The very fact that you have a long piece in The New York Times Magazine on this topic means that David Reich is […]

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. […]
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