Gossip in the Pop Gen World

Angela said:

In terms of indigenous people, I understand some of these results may be very unwelcome. They've been a bit unwelcome for me too. However, science is a search for the TRUTH, whether it hurts or not, and scientific inquiry shouldn't stop because it hurts a group's feelings. In the particular case the article highlights, the samples are available. Intellectual debate about them is healthy, concern about whether it conflicts with past beliefs is not.

Honestly, this is what I see all around me, in academia, politics, the media etc.: endless moaning, whining and complaining. That hurts our feelings; we're not getting a big enough share, and on and on. Just man up, people. Competition is tough. The truth is what it is. Deal with it. If you're not getting the recognition you think you deserve, here's a novel idea: try to improve your work product.

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To the Editor:


Gideon Lewis-Kraus (Jan. 17) profiles the nascent field of ancient DNA, which in the last few years has contributed to a transformation in our understanding of the deep human past. His article touches on important issues that we, as a field, have yet to deal with fully: including how to handle ancient remains ethically and in a way that preserves them for future generations; how geneticists and archaeologists can work in equal partnerships that reflect true respect for the insights of different disciplines; and how ancient DNA technology, which at present is applied efficiently only in large labs, can be made accessible to a wider group of scholars.


But Lewis-Kraus misunderstands several basic issues. First, he suggests that competition to publish is so extreme that standards become relaxed. As evidence, he cites a paper by my lab that was accepted on appeal after initial rejection, and another that was reviewed rapidly. In fact, mechanisms for appeal and expedited review when journals feel they are warranted are signs of healthy science, and both processes were carried out rigorously.


Second, he contends that ancient DNA specialists favor simplistic and sweeping claims. As evidence, he suggests that in 2015 I argued that the population of Europe was “almost entirely” replaced by people from the Eastern European Steppe. On the contrary, the paper he references and indeed my whole body of work argues for complex mixture, not simple replacement. Lewis-Kraus also suggests that I claimed that our first study of the people of the Pacific island chain of Vanuatu “conclusively demonstrated” no Papuan ancestry. But the paper in question was crystal-clear that these people could have had some Papuan ancestry – and indeed, to support his claim, Lewis-Kraus could only cite his own notes from an interview I gave him long after I had published a second paper proving that there was indeed a small proportion of Papuan ancestry.


Lewis-Kraus also suggests that I use small sample sizes to make unjustifiable sweeping claims. In fact, small sample sizes can be definitive when they yield results that are incompatible with prevailing theories, as when my colleagues and I described two samples that proved the existence of the Denisovans, a previously undocumented archaic human population. In my papers, I am careful to only make claims that can be supported by the data I have. In small-sample size studies, I emphasize that more samples are needed to flesh out the details of the initial findings. A major focus of my lab is generating the large data sets needed to do this.


Lewis-Kraus’s critiques are based on incomplete facts and largely anonymous sources whose motivations are impossible to assess. Curiously, he did not ask me about the great majority of his concerns. Had he done so, the evidence underlying his thesis that my work is “indistinguishable from the racialized notions of the swashbuckling imperial era” would have fallen apart. The truth, and the main theme of my 2018 book Who We Are and How We Got Here: Ancient DNA and the New Science of the Human Past, is exactly the opposite – namely, that ancient DNA findings have rendered racist and colonialist narratives untenable by showing that no human population is “pure” or unmixed. It is incumbent on scientists to avoid advocating for simplistic theories, and instead to pay attention to all available facts and come to nuanced conclusions. The same holds true for journalists reporting on science.


David Reich
Harvard Medical School and the Howard Hughes Medical Institute, Boston, Massachusetts

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Ygorcs said:

What could be more ludicrous than some apparently stubbornly outdated archaeologists complaining through that NYT piece about the fact that ACTUAL SCIENTIFIC DATA (that they might welcome as yet another great source of information for their own interpretation of the past) have been proving all the post-war strong emphasis on cultural diffusion and "pots, not people" wrong in many instances, using hundreds of samples in different circumstances and places? It's like they just lost their scientific curiosity and even the basic humility to feel astounded by the possibilities of this great new source of data about ancient peoples and by the fact that they can finally assess many hypothesis of past historians in firmer grounds, including - why not, what do they fear? - resurrecting very old theories that had been thought incorrect in the last decades. They seem to have taken it personally that geneticists are just doing their job and by doing so they're slowly forcing archaeologists to refine and revise some of their dominant current positions. That's so narrow-minded, so shallow for people who are supposed to be scientists.

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Angela said:

Sad that a great scientist felt he had to respond to this garbage.

Journalism used to be a half way honorable profession. No more. It's clear he never read the papers in question or he would never have made such easily falsifiable errors of fact. That's over and above the fact that he freaking can't write and there must not be any editors left at The Times.

Lazaridis has also tweeted on it in his usual calm and logical manner.

In my opinion this comes perilously close to libel, and if I were him I'd be talking to the best of the best attorneys in the field right now. Reckless disregard for the truth is actionable. I'd also never work with some of these idiots again, but he doesn't strike me as the type,lucky for them.

Disappointed in Khan' s piece. I saw two good ones for which I'll provide info as soon as I find them again. One was by Turchin.

I'm sure he has a good idea of the sources: archaeologists who can't bear that their dithering and endless speculating are beyond their expiration date, and lesser intellects in pop gen who can't stand being shown up over and over again.

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Ygorcs said:

What could be more ludicrous than some apparently stubbornly outdated archaeologists complaining through that NYT piece about the fact that ACTUAL SCIENTIFIC DATA (that they might welcome as yet another great source of information for their own interpretation of the past) have been proving all the post-war strong emphasis on cultural diffusion and "pots, not people" wrong in many instances, using hundreds of samples in different circumstances and places? It's like they just lost their scientific curiosity and even the basic humility to feel astounded by the possibilities of this great new source of data about ancient peoples and by the fact that they can finally assess many hypothesis of past historians in firmer grounds, including - why not, what do they fear? - resurrecting very old theories that had been thought incorrect in the last decades. They seem to have taken it personally that geneticists are just doing their job and by doing so they're slowly forcing archaeologists to refine and revise some of their dominant current positions. That's so narrow-minded, so shallow for people who are supposed to be scientists.

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ToBeOrNotToBe said:

Geneticists are going to wipeout everything archaeologists have worked towards since the 60s, just as the Indo-Europeans did to those "anarcho-communist feminist pacifist farmers" (guess which professionals came up with that descriptor) they replaced. Of course most archaeologists aren't so extreme, but a surprising amount are, and this surprising amount has its own fringe. Just today I saw this:

"In April 2011, it was reported that a deviant Corded Ware burial had been discovered in a suburb of Prague.^[47] The remains, believed to be male, were orientated in the same way as women's burials and were not accompanied by any gender-specific grave goods. The excavators suggested the grave may have been that of a "member of a so-called third gender, which were people either with different sexual orientation or transsexuals or just people who identified themselves differently from the rest of the society",^[47] while media reports heralded the discovery of the world's first "gay caveman".^[48][49] Archaeologists and biological anthropologists criticised media coverage as sensationalist. "If this burial represents a transgendered individual (as well it could), that doesn't necessarily mean the person had a 'different sexual orientation' and certainly doesn't mean that he would have considered himself (or that his culture would have considered him) 'homosexual,'" anthropologist Kristina Killgrove commented. Other items of criticism were that someone buried in the Copper Age was not a "caveman" and that identifying the sex of skeletal remains is difficult and inexact.^[50] A detailed account of the burial has not yet appeared in scientific literature."

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Eochaidh said:

Here is a link to Thor Heyerdahl's book on the Kon Tiki Expedition on Archive.com. It is not the little paperback, but a 900 page serious work. It must have weighed 5 pounds.

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January 21, 2019


To the editors:


I am writing to request 5 corrections to the article on ancient DNA that appeared in this week’s The New York Times Magazine.


Please note that this request is in addition to the letter to the editor that I submitted on Jan. 19, which was aimed at your primary readership, and which I believe should appear in print in the magazine.


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 for review on January 2 were incorrect, and 27 of the 36 statements presented to me for review on January 5 were incorrect. The high rate of errors was concerning as it suggested that the narrative based on them might not be supported by a solid set of facts. While a substantial number of these incorrect statements were removed through your fact-checking process, some errors got through, and I am therefore now requesting formal corrections of the following 5 errors that meaningfully affect the article, so it is important to set the record straight on them. (I have also identified additional errors, but those are for the most part smaller, so I am not requesting corrections in those cases.)


(Correction 1) The article wrongly states that Skoglund et al. Nature 2016 was accepted after appeal “over the steadfast objections of two of the three peer reviewers on its anonymous panel.”


This is false.


There were four reviewers on the panel when the paper was accepted. This is important, because the fourth anonymous reviewer was added as the arbitrator during the appeals process, and that reviewer’s involvement (not discussed in the article at all) and positive assessment was a key part of the rigorous appeal process that led the journal to the decision to accept.


Note that I pointed this out in my fact-checking reply on January 2, where I wrote: “On July 6 2016, we received second round reviews of the manuscript which included comments not just from the original three reviewers but also from a newly added 4th reviewer who was very positive.”


Please publish a correction of this statement.


(Correction 2) The article wrongly states that the revision of Skoglund et al. Nature 2016 “addressed very few of the other reviewer concerns.”


This is false.


The revision addressed every one of the reviewers’ scientific concerns (that is, concerns about the convincingness of the claims about population history based on the evidence provided). As evidence for this: (a) after receiving the revision Reviewer #2 wrote that “The first 5 revised points are acceptable” [this referred to all of the scientific points], and (b) Reviewer #3 did not identify any unaddressed scientific concerns from the initial set of reviews. Finally, (c) in Nature’s final decision letter sent to us on August 25th 2016, the newly added arbitrating Reviewer #4 wrote: “The latest revised version of the ms addressed all the issues that were previuosly raised by the reviewers.”


It is possible that the anonymous reviewer(s) told Gideon Lewis-Kraus that very few of their concerns were addressed by the revisions, but Lewis-Kraus never confirmed that with me, and I have evidence that contradicts it. With an anonymous source it is especially important to fact-check against available confirmatory information, and this was not done.


Please publish a correction of this statement.


(Correction 3): The article wrongly states that I claimed that the Skoglund et al. Nature 2016 paper “conclusively demonstrated” no Papuan ancestry in the Teouma Lapita individuals.


If Lewis-Kraus has a note that I said this I am sure that this note is in error or that the quote was out of context, as I never believed this and have never argued for this. The Skoglund et al. paper was crystal-clear in the main text that the Teouma individuals were consistent with some Papuan ancestry (up to 11%), and my conversations with Lewis-Kraus happened well after my colleagues and I published a second paper proving some Papuan ancestry in the Teouma individuals. Even if Lewis-Kraus was able to point to a quote from me that seemed to suggest this, it is not appropriate to cite this given that: (a) it is out of context, (b) it contradicted my view stated clearly in Skoglund et al. 2016, (c) it contradicted my view stated in Lipson et al. 2018, which was published well before my interview with Lewis-Kraus, and (d) it was a misunderstanding on Lewis-Kraus’s part of my views that I corrected in the fact-checking correspondence (see below).


To go into detail on that fact-checking correspondence, on Jan. 7 I sharply contradicted the statement that was sent me to check that “Lipson et al. applied higher-resolution analysis to the three Teouma skulls than had been done in Skoglund et al., and the resulting data showed higher traces of Papuan ancestry,” writing:


“Lipson et al. 2018 actually get lower estimates of Papuan ancestry than Skoglund et al. 2016, not higher as your fact-checking statement suggests:


3.4% ± 2.9% (99% confidence interval of 0-11%) Skoglund et al. 2016


2.4% ± 0.9% (99% confidence interval of 0.1-4.7%) Lipson et al. 2018


You nevertheless persisted in making this false assertion. In Cynthia Cotts’ fact-checking email of Jan. 10, I was told that: “The assertion that Lipson et al. reported higher levels of Papuan ancestry, and was thus a walking back of Skoglund et al., remains in the story. I am aware that you disagree. I will advocate that this be attributed to critics of your work.” I replied: “It’s a matter of scientific fact not academic disagreement — it would be an error in the article that would need to be corrected after publication if it stayed this way.”


In the final version of the story, the statement is essentially still there. However, now the only justification cited (all the other evidence had fallen apart) is Lewis-Kraus’ notes, which attribute a view to me that is incompatible with all other lines of evidence — what I had published, what I believed, and what I clarified through the fact-checking process.


Please publish a correction of this statement.


(Correction 4): The article wrongly states that in 2015 my colleagues I argued that the population of Europe was “almost entirely” replaced by people from the Eastern Europe Steppe. More generally, the article states wrongly that “Earlier paleogenomic results established thousands of years of heady mixture among long-forgotten ancient populations. With the relatively recent rise of everything we associate with “culture” — technologies like agriculture, metallurgy and eventually writing — much of this continuous “admixture” began to give way, it seemed, to discontinuous episodes better characterized as “replacement” or “turnover.” That is, about 5,000 to 9,000 years ago, human history was, at least in a few crucial places, less about various groups coming together and more about some groups blotting out their neighbors.”


This is flatly contradicted by the evidence and by my whole body of work, as well as the work of all my colleagues in ancient DNA, over the last few years.


Below left is Figure 3 of Haak et al. Nature 2015 (a key paper referenced in your article), showing that in no ancient and in no present-day European population is there evidence of anything close to a complete replacement by Eastern European Steppe ancestry around 5,000 years ago (Eastern European Steppe ancestry is labeled with a green color in the bar plot). In that paper, we were clear that mixture was central to what had occurred, and that southern Europe (a legitimate part of Europe) had very little Steppe ancestry.


Below right is Figure 4 of Lazaridis et al. Nature 2016, which shows how all West Eurasians are profoundly mixed due to events in the last 9,000 years — a model as different from replacement as possible.


Figures


Note that I corrected this in my fact-checking response of Jan. 2, writing in response to the statement “Some time in the last 10,000 years, admixture began to give way to replacement or turnover.” I wrote: “Not true. Admixture has continued intensively in the last 10,000 years, and many of my papers have been focused on demonstrating just this.”


Please publish a correction to this statement.


(Correction 5): The article wrongly states that Skoglund et al. 2016 “presumed to offer the final word on the history and ancestry of an entire region.”


The truth is provably just the opposite. The last sentence of the published paper reads:


“Systematic study of ancient DNA from throughout Remote Oceania should make it possible to provide a detailed chronicle of the population movements and sex-biased population mixtures that shaped the ancestry of present-day Oceanians.”


In other words, our paper is extremely careful to state that the small sample size analyzed in the study—while sufficient to disprove some prevailing theories which was the main result in our paper—is not able to reveal the detailed history. Indeed, we have always believed that our findings in that study (and, for that matter, in Lipson et al. 2018) are just the start and not the final word (any fair reading of "should make it possible" contradicts the claim that we thought we had the "final word").


Please publish a correction of this statement along with the four others above.


Yours sincerely,
David Reich


Harvard Medical School and the Howard Hughes Medical Institute, Boston, Massachusetts

https://reich.hms.harvard.edu/five-corrections-new-york-times

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Jovialis said:

Here's another response by David Reich, requesting for five corrections to be made to the piece.

For all the pretentious flowery language in the NYT piece meant to dazzle it's pseudo-intellectual audience; the author is clearly a mental-midget compared to Dr. Reich. If the NYT doesn't correct the article, I hope legal action is taken against them.

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Ygorcs said:

People today need to understand something very basic to see unpleasant results of scientific research, analyze them, accept them (or present a plausible counter-hypothesis) and then move on: it is people who have rights and deserve respect, and that's all. Beliefs, ethnic or national myths (no matter how solidly historical they may appear to be), mere ideas and abstractions, or, even more vaguely, mere "feelings" do not have the right to not be bothered, questioned and perhaps even cast aside by honest investigations on the objective (or as objective as possible) truth of things, even if they end up being ultimately proven incorrect, as it inevitably happens when people are truly trying to make something important and find solutions for big mysteries. I think we must respect the traditions and identities of people, but their strictly subjective beliefs, especially if they're based on received knowledge from many generations ago, and not in factual things (like monuments, tombs, actual pieces of the history of a people), are not sacred and set in stone. They should be aware that of course their own people's beliefs and self-conceptualizations changed along the time, and it will change again.

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Maciamo said:

... I also disagree with Lazaridis and al. when they say that "Modern Greeks resemble the Mycenaeans, but with some additional dilution of the Early Neolithic ancestry"...
... In other words modern Greeks are nothing like Mycenaean Greeks, and even less Minoan Greeks...

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Maciamo said:

That would make them mostly Mycenaeans if you reckon that Mycenaeans are themselves a blend of many populations. They had ancestry from Mesolithic SE Europeans, Neolithic Greeks, Neolithic Anatolians, Chalcolithic Iranians/Caucasians, Bronze Age Kura-Araxes, then of course Mesolithic Steppe (EHG), Neolithic Balkans, Bronze Age Steppe, etc. It's pretty meaningless to say that modern Greeks share 60-75% of DNA with such a heavily admixed population as the Mycenaeans, who shares lots of ancestry with all modern Europeans. With that logic, Albanians and Bulgarians could be just as close to the Mycenaeans.
Anyway, my point was that 25 to 40% of post-Mycenaean ancestry isn't trivial. That's much more than the whole Indo-European ancestry in India, even among the Brahmins (who have 15-20% of Steppe ancestry). According to the Haak et al. (2015) paper (which Angela loves to quote), modern Spaniards have only 20% of Steppe ancestry, while Albanians have a mere 13%. And yet both are considered Indo-European populations (because of the language they speak). This puts into perspective the 25% to 40% of post-Mycenaean European ancestry in modern Greeks. And I did not even include the post-Mycenaean Middle Eastern ancestry! There is no way to calculate this from the admixture data, but why wouldn't other Middle Eastern people have contributed to the modern Greek gene pool in the last 3500 years? After all Greece was part of the Macedonian, Roman, Byzantine then Ottoman empires, which had open borders between Greece and the whole eastern Mediterranean from 332 BCE to 1918 CE (2250 years). It's unthinkable that Europeans contributed 40% of modern Greek DNA and that during that time no population exchange at all happened within the empire to which Greece belonged! The genetic exchange with Anatolia would surely have been considerable over time, considering all the Greek-speaking cities in Ionia or the Pontus, and the displacement of all these Anatolian Greeks to European Greece after 1918. Iosif Lazaridis is himself a Greek whose family hails from the Pontus region. It's baffling that he shouldn't have considered the impact of over 2000 years of intermingling with neighbouring Anatolian populations on those Greek communities that later resettled in the modern state of Greece.
It's very hard to estimate how much DNA in modern Greeks came from Anatolia, or elsewhere in the Near East, in the last 2000 or 3000 years, but I am confident it is more than 10% and probably more than 20%. So overall it could be than less than half of the modern Greek DNA is directly inherited from the Mycenaean-age population.

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