We are not all Neanderthal: this is how science proceeds

by Matthew Cobb

You may recall that back in October we reported the amazing discovery that, as I put it in the headline, “Neanderthal genes are everywhere“. Up until then, it had been thought that only those human populations outside of Africa carried Neanderthal genes, as a consequence of our ancestors having mated with our Neanderthal cousins—mainly in Europe and the Middle East. People from sub-Saharan Africa, it was thought, did not carry those genes, because their ancestors did not leave Africa, and so didn’t meet the Neanderthals (whose ancestors had left Africa several hundred thousand years earlier).

What happened in October was that a group of researchers from around the world, led by Gallego Llorente of Cambridge University, studied the DNA of Mota, an Ethopian man who lived around 4,500 years ago. They found that he carried an unexpectedly high proportion of DNA from European populations, including DNA that had originally come from Neanderthals over 30,000 years earlier (Neanderthals went extinct around 35,000 years ago). The really exciting bit came next. As I wrote:

When they compared Mota’s DNA with those of modern African populations, they found that the European sequences he carried were also present deep in the continent, even amongst the Pygmies of the Congo. Even ‘reference’ African genomes, such as those from the Yoruba and Mtubi peoples, which were thought not to have been affected by interbreeding with Europeans, turned out to have around 6% of their DNA from European DNA, like Mota. (…)

The final novelty came when the researchers looked at Neanderthal DNA. Mota carried that DNA, just like me, because his ancestors had mated with Neanderthals tens of thousands of years earlier.

And it turned out that some of those Neanderthal sequences could also now be detected in African populations, too. They were very dilute – around 0.5% – but they were clearly there. They do not indicate that there were Neanderthals in Africa, but rather that when the offspring of Mota and others carrying migratory European sequences spread their DNA into Africa, they also spread small amounts of Neanderthal DNA, too.

This was amazing, and I excitedly changed the lecture I gave to my first-year students the next day. I’ve since explained in various public lectures that we all carry Neanderthal DNA, including those of Afro-Caribbean origin.

Now it turns out not to be true.

The authors have published an erratum notice to explain the error, along with updated versions of the figures and tables. If you want the technical explanation, here it is:

A script necessary to convert the input produced by samtools v0.1.19 to be compatible with PLINK was not run when merging the ancient genome, Mota, with the contemporary populations SNP panel, leading to homozygote positions to the human reference genome being dropped as ‘missing data’

What this means is that they forgot to run a particular computer programme (‘script’) that would harmonise  the outputs of two different programmes used to do the analyses of Mota and of modern sub-Saharan populations. When they did so, much of their effect disappeared.

As Ewan Callaway explains, the error came to light when two researchers, Pontus Skoglund and David Reich, tried to replicate the finding, doing their own analysis of the Mota genome. They failed, and alerted the original authors, who soon worked out their mistake. In an exemplary act of clarification, they let everyone know their error and have corrected their data.

The conclusion is that although there was migration back into Africa (what is delightfully called ‘back-flow’), this was less extensive in geographical terms than the authors claimed. The European genes carried by Mota did not flood all the way back down to Africa, and Modern sub-Saharan populations do not have unexpectedly high levels of European, and therefore Neanderthal, DNA. We are not all Neanderthals.

These two figures show the difference in the analyses. The first is from the October 2015 article, the second, corrected, version is from the Erratum:

Map showing the proportion of West Eurasian component, λMota,LBK, across the African continent. (Gallego Lllorente et al. 2015). THESE DATA ARE ERRONEOUS – COMPARE WITH THE FIGURE BELOW

Mota2

The lessons of this are multiple. Above all, hats off to Llorente et al, the original researchers, for making their data openly available, so that quizzical scientists like Skoglund and Reich could explore what they thought to be an unlikely result. And then even more kudos for publishing their correction so quickly. This is how science works – if something seems weird, and it is incorrect, it should get corrected by science’s inherent questioning, based on experimentation.

There is another lesson, too. A lot of modern research is based on complex analyses that can be difficult for those outside of the research group involved to understand. A lot is therefore taken on trust; had the result not been unusual, the mistake might never have been discovered. I have experienced a similar problem when some exciting results we had found eventually turned out to be an artifact, produced by an error in a computer script. Although the work has not been published, so we did not need to retract, we probably wasted about 18 months getting excited about something that turned out not to be there. . .

Finally – what about my students? I told them about the Mota paper, and how they all had Neanderthal genes, even those of Afro-Caribbean origin. I’m going to change the lecture for next year, obviously, but my students – many of whom will not take another course in human evolution – may never discover that what I told them was wrong. And what about next year’s students? Do I tell them the whole story as an example of how science proceeds? If so, I know from bitter experience that for a sizeable number of them, the thing that will stick in their memory will be the wrong result, not the scientific lesson. I think I’ll keep quiet in the lecture, but post links to this and the original post. I’ll also edit the original post, with a pointer to this correction.

82 Comments

  1. GBJames
    Posted January 30, 2016 at 10:25 am | Permalink

    If I were a university student again and I found myself in your class, Matthew, I’d welcome this example of how science works.

    • rickflick
      Posted January 30, 2016 at 10:41 am | Permalink

      Me two, but you’ve got to respect the probability that many will remember it wrnog. It seems to me, though, that it might be worth mentioning to students that there was some misleading evidence without making it big issue.

  2. Diana MacPherson
    Posted January 30, 2016 at 10:42 am | Permalink

    When I was a student some volcanologists discovered ancient dates of things were all wrong. I probably now have wrong dates of things still in my head but at least my professors told us about the results. However I’m sure generations of students were taught the wrong dates.

    I’m 2.7% Neanderthal according to 23andme.

    • GBJames
      Posted January 30, 2016 at 10:45 am | Permalink

      I’m 3%. My daughter is more Neanderthal than I am, at 3.1%. My wife hasn’t been tested but she’s obviously more Neanderthal than I am.

      • Daniel bertini
        Posted January 30, 2016 at 11:26 am | Permalink

        Wow!!

    • gravelinspector-Aidan
      Posted January 30, 2016 at 11:21 am | Permalink

      I wouldn’t stress over much about it, because the details of dating, once you get beyond the reach of documentary evidence, are always a series of successive approximations. With documentary evidence you can get to the day ; with dendrochronology you can get to the season or year (when the wood was cut ; how much allowance for seasoning/ working and then the working life of the artefact between manufacture and it’s passing out of use?) ; with C-14 you can get to fractions of a percent (increasingly better with multiple samples, site-wide Bayesian analyses ; but then you’re back to asking which samples are from the same stratigraphic context, and what are the relations of the contexts – which is what Flinders-Petrie was doing 50 years before radiocarbon dating was invented, and how that dating was calibrated).
      Some years ago – mid-2000s IIRC – the shifting collection of averages that combined to estimate the “age of the Earth” temporarily passed through the easily-memorable number “4567” million years. Which is very nice because it’s easily memorable. But since the process of building the Earth took an estimated 20-odd million years, any date in the 4557-4577 range is probably going to be “right”, for meanings of “right” that will vary between different geochemists. I mean, we don’t even know if that construction phase included differentiation of the planet or not, let alone how long that took?
      To a rough rule of thumb, a new dating technique will be introduced if it halves the uncertainty in dates. (It’s not really worth the re-dating work if it doesn’t do better, and equipment is expensive.) So for forensic work where you need to know who did what between 9 and 10 pm on the 24th, you need different precision than for a historian who needs to know where Mr X was on the 24th, or the archaeologist, who needs to know if the technology associated with the bones is appropriate for the second, third or 4th decade of the skeleton’s life …
      What was Ussher’s reasoning for the 24th Oct 4004 date? IIRC, he got the year by counting begats, then used some ritual arguments to get the season, day of week and week number. I think there’s an implication that a lunar calendar would have been in use there too.

    • John Conoboy
      Posted January 30, 2016 at 3:45 pm | Permalink

      I am 2.8% Neanderthal, so I now consider myself to be a Neanderthal-American and will use that when asked about race/nationality on government forms.

      • Diana MacPherson
        Posted January 30, 2016 at 5:26 pm | Permalink

        OMG thanks for the great idea of filling in the “other” for ethnicity. I’ve always wanted to be a smart as here, mostly because many such questionnaires confuse ethnicity and nationality.

  3. Posted January 30, 2016 at 10:48 am | Permalink

    How frustrating for the authors, but how great that this result was tested and corrected! I like to see science progressing in this way.

  4. Posted January 30, 2016 at 10:49 am | Permalink

    I think part of the reason the “we all have Neanderthal genes” story that might have been so attractive is that one of the arguments that’s been made against racism over the last couple of decades is the idea that human populations are overall more alike that different; that is, our species has far more within-group than between-group genetic diversity, and has far less within-group genetic diversity than chimps and other primates. Which is true to a point, but it doesn’t tell the whole story. The fact is, there are real differences in the presence of Neanderthal or Denisovan genes between populations. Also, there are groups like Australian aboriginals that did not develop agriculture and did not experience the resulting strong selective pressures and genetic outcomes that came with that, and due to relative (though not total) isolation, did not experience much gene flow from such populations. The worry is that this might be yet another thing the “Bell Curve” crowd will seize on.

    • gravelinspector-Aidan
      Posted January 30, 2016 at 11:26 am | Permalink

      Also, there are groups like Australian aboriginals that did not develop agriculture and did not experience the resulting strong selective pressures and genetic outcomes that came with that

      Hang on – aren’t the PNG Aboriginals part of the same migration as the Australian Aboriginals? And they HAVE developed agriculture. Strongly suggesting that the Australian non-farming habits are local adaptations, rather than any intrinsic lack.
      There’s also the point that the Australians did inflict huge changes on their environment, largely by use of fire.

    • Sastra
      Posted January 30, 2016 at 11:30 am | Permalink

      Among the woo crowd you can find a belief that Neanderthals were more intuitive and psychic than homo sapiens. Blame books like Clan of the Cave Bear for spreading this meme. So it’s possible that this might have been another, less significant reason that “We are all Neanderthal” was popular.

      Needless to say, aboriginal of all types — including native Africans — are also supposed to be more intuitive and psychic than modern humans. The original finding then would have dovetailed neatly into this. I can’t say that I’ve ever seen Llorente et al’s study cited in Spiritual circles, but then I haven’t really been looking.

    • Victoria
      Posted January 30, 2016 at 2:53 pm | Permalink

      I’ll admit my first thought when I read this headline was the suspicion that someone had been over-eager in promoting human unity.

      Egalitarianism would be deeply challenged by any meaningful differences between human populations. It’s much easier to be a right-thinking liberal, which most of us wish to be perceived as, if we believe that humans are blank slates with identical distribution of talents in different populates.

      Given how fantastically incapable people, even well-educated people, are at rationally distinguishing between group means, normal distributions, and individuals within a group, I’m almost inclined to say that even if true, scientifically-validated racial differences in ability would be the rare sort of science like nuclear weapons that were better off without.

      Steven Pinker has commented on this mindset. As a feminist I’ve seen just fervent, religious-like opposition to Evolutionary Psychology, by strict constructionists who want gender differences to be entirely socialised. for some reason it’s much easier to accept some innate gender differences than innate group-level racial differences beyond superficial phenotype.

      • Posted January 30, 2016 at 3:15 pm | Permalink

        I agree with everything you e written except this:

        “Egalitarianism would be deeply challenged by any meaningful differences between human populations.”

        Some people might be inclined to use genetic differences to rationalize their prejudice, but it would be an entirely rhetorical and disingenuous ploy. Egalitarianism need not be challenged at all by genetic difference, and Pinker acknowledges such in The Blank Slate.

        You judge individuals on their individual merits or demerits, you don’t prejudge them based on their genetic endowment. This can be done even while recognizing that humans are not blank slates.

        • Victoria
          Posted January 30, 2016 at 5:02 pm | Permalink

          I agree with what you state. I should have phrased it better. No group difference or even genetic aprofile could ever validate denying a person equal opportunity or a right to be judge on personal merit. I meant genetics might challenge people who conceive of “egalitarianism” as equal outcomes.

        • Posted February 1, 2016 at 11:44 am | Permalink

          Note that any conclusion of the above character has *two* possible (at least) outcomes. Suppose it turns out that group X is disadvantaged in respect Y due to some biological factor (“genetics”). Then either we can (a) discriminate negatively against X and prohibit them as a class from doing thus and so. Or (b) we can help them out – give Xs extra support in matters related to Y. (This is just a specific instance of Bunge’s “rule based on law” principle, showing the ethical neutrality of science.)

          *Because* in our current societies policies would be likely pushed in the (a) direction it is true that there is something of a risk, and in a way P. Kitcher and co. are right to point out it might be good to raise the burden of proof here. But note that this is because our societies are dysfunctional and (to this degree) bigoted – *not* because of the scientific finding itself.

          The more complicated case is with (b) and making the relevant *tradeoffs*. But these have to be handled case by case.

  5. Historian
    Posted January 30, 2016 at 10:54 am | Permalink

    This is a great example of the self-correcting nature of science. But, unfortunately, every time science self corrects itself, public confidence in the discipline is eroded. The public asks, “how many other errors are awaiting self-correction?’ This is particularly evident in the area of health where health protocols later turn out not only to be ineffective, but harmful. The classic example is that for many years menopausal women were advised to undergo hormone replacement therapy as a means of reducing heart attack risk and other ailment. It was later discovered that this therapy could be harmful to women. So, many people, myself included, always wonder when taking a drug whether it may be later discovered that it is doing more harm than good.

    This correction about the Neanderthals is primarily of academic interest. The public at large will not get excited about this. But, when supposedly good scientific research in the health area is later discovered to be not so good, public anxiety about the consequences of using a new discredited regimen rises dramatically. Unfortunately, there is little the scientific community can do about this and has no choice but to take the “hit” for offering erroneous research. Somehow, the scientific establishment has to establish new rules to reduce the number of errors, particularly in the health field

    • conservationtrust
      Posted January 30, 2016 at 11:26 am | Permalink

      And again, the supposed “harm” from hormone replacement probably had to do with certain factors in the study that were misinterpreted. If one reads the entire study (which I have done), it turns out that the population which was harmed had several confounding factors. First, there were two arms to the study. In the study which showed increases in cardiovascular effects, a) the hormone replacement was started in women who had already gone through menopause; b) the hormone used was Premarin, which is a combination of horse estrogen (from pregnant mares, hence the name), and Provera (a synthetic progesterone), which was given together continuously. Since they were already menopausal, many probably already had changes in their cardiovascular system which these hormones acted upon adversely. The second arm of the study was done in menopausal women who had undergone hysterectomy, and the hormone used was estradiol, which is a more bio-identical hormone, and NO Provera. This arm of the study did not have the same negative effects. So, what was never established was whether it was the type of estrogen, or the type of progesterone, or the continuous use of both (which in the female body doesn’t follow the continuous pattern levels — there is some indication that premenstrual symptoms correspond to the fluctuations). But the media picked up the results as “estrogen replacement is wrong!” and so it’s had a bad rap ever since. The fact that once post-menopausal, women have the same cardiovascular risk as men have right along has been essentially ignored.

    • GBJames
      Posted January 30, 2016 at 11:47 am | Permalink

      “But, unfortunately, every time science self corrects itself, public confidence in the discipline is eroded.”

      So?

      This is a problem with the level of education available to “the public”. The solution is to improve education. And that includes improving how “the public” understands what science is. You can’t do that if you hide errors.

      • Historian
        Posted January 30, 2016 at 12:02 pm | Permalink

        So? Here’s the so. Much of scientific research in this country is dependent on the receipt of public funds, i.e., tax money. If public confidence in scientific research is eroded, public funding is likely to be reduced. Do we really need to give more ammunition to the science deniers?

        Also, where in the world did you get the idea that I believe scientific errors should be hidden? Of course, they need to be made public. The effort needs to be to reduce the errors. Errors of carelessness, such as in the Neanderthal case, as well as outright scientific fraud, need to be more forcefully addressed, if not already being done so.

        • Posted January 30, 2016 at 12:48 pm | Permalink

          We have representative democracies, not direct democracies. The hope is that the representatives of the public elected as lawmakers will have a reasonably good understanding of things. They usually do.

          • Historian
            Posted January 30, 2016 at 12:52 pm | Permalink

            “The hope is that the representatives of the public elected as lawmakers will have a reasonably good understanding of things. They usually do.”

            I trust that you’re not referring to the party that controls both houses of the United States Congress.

            • Posted January 30, 2016 at 1:17 pm | Permalink

              I am wondering whether Republican politicians really believe in the stuff they tell their constituency, such as the “pro-life” stuff. The Republican president I’ve admired most was a professional actor. Presenting as someone other than who you are is in the job description.
              In contrast, the openness of Obama’s campaigns was terrifying to me. But I do not rush to the conclusion that Democrats are all open and honest to their voters. Being open about letting the world in free fall would not harm Obama. It would terrify only non-Americans like me, who cannot vote in these elections anyway.

              • pali
                Posted January 30, 2016 at 3:38 pm | Permalink

                “I am wondering whether Republican politicians really believe in the stuff they tell their constituency, such as the “pro-life” stuff.”

                Some don’t, but a lot do – and what matters isn’t whether they actually believe the nonsense themselves, but whether they vote the nonsense, and they do indeed vote the nonsense.

                And am I reading you correctly in that you think a politician actually meaning what he says is terrifying? I’m having trouble understanding your last four sentences.

              • Diane G.
                Posted January 30, 2016 at 9:17 pm | Permalink

                I am wondering whether Republican politicians really believe in the stuff they tell their constituency, such as the “pro-life” stuff…

                It’s been noted before that they often don’t. There have been quite a few Republican candidates who once were pro-choice but have had to insist they’re no longer so. Or who campaign for the pro-life vote, then see that the issue simply isn’t raised once elected (Dubya was said to be of this stripe). Or who proclaim their staunch anti-abortion bona fides while their wives publically disagree with them on the issue, serving as a dog-whistle for similarly closeted moderate Republicans.

        • GBJames
          Posted January 30, 2016 at 1:01 pm | Permalink

          You don’t advance the interest of science education by concealing the nature of science.

          Nobody that I know is in favor of making errors. If I’m wrong about that, please set my right with an example.

          What is at issue here is whether we pretend that errors don’t happen out of fear that a poorly public will misunderstand the nature of science. Errors are inevitable. Thinking that science without errors could possibly exist is profoundly mistaken.

          • Historian
            Posted January 30, 2016 at 1:16 pm | Permalink

            I will try for the third and for the last time to state my position, which apparently did not get through to your previously.

            1. I have never advocated concealing the nature of science.

            2. You said: “Nobody that I know is in favor of making errors.” Yes, this is true, but has as much relevance to the discussion as saying nobody is in favor of cancer.

            3. You said: “Thinking that science without errors could possibly exist is profoundly mistaken.” Did you miss the part where I said errors need to be reduced? Surely, you know the difference between reducing errors and eliminating them.

            • GBJames
              Posted January 30, 2016 at 2:18 pm | Permalink

              “Errors need to be reduced.” I think there’s a deepity there.

              I think my confusion results from my assuming that your comment somehow was relevant to the discussion of whether/how someone like Matthew should present situations such as “we’re all Neanderthal” as examples of how science works and how the process tends to be self-correcting.

              Yes. Errors should be reduced. This is true in all fields. And clean air is good, too.

              • Historian
                Posted January 30, 2016 at 2:26 pm | Permalink

                “Nobody that I know is in favor of making errors.” I think there is a deepity there.

    • Gregory Kusnick
      Posted January 30, 2016 at 2:31 pm | Permalink

      It seems to me the real problem (if there is one) is not that scientists sometimes make mistakes. It’s that people think making mistakes is a bad thing. Correcting mistakes should not erode public confidence in science; it should increase it. That’s how science converges on truth.

      So in my view it’s wrongheaded to focus on making fewer mistakes; that’s a recipe for timid, ineffective science. People should be taught to value science because of its willingness to be proven wrong, in contrast to the failed systems of infallibilist dogma it replaces.

      • Historian
        Posted January 30, 2016 at 3:00 pm | Permalink

        Educating the public about the scientific method and the ability of science to self-correct is certainly meritorious. But, when a scientific error, particularly in the area of health, results in a disaster to real people, the public will want the head of the person making the mistake. If you’re not familiar with the drug thalidomide, look it up. Do you think the creator of thalidomide could have quelled public outrage by saying, “Hey! That’s science. I wasn’t being timid.”?

        Obviously, all scientific mistakes can’t be eliminated. But, the scientific community must always be seeking new ways to reduce them, both for the integrity of the discipline and the need to retain public confidence.

        • GBJames
          Posted January 30, 2016 at 7:01 pm | Permalink

          I’m not really understanding your point, Historian. Do you think the scientific community is less interested in correcting errors than anyone else? Do you think there is some shortage of interest in accuracy among scientists compared to the population at large? Do you think that someone is advocating the spread of misinformation for some reason? You seem to think that errors (in this case regarding the spread of Neanderthal genes in populations) is intentional or the result of some kind of professional negligence.

          • Historian
            Posted January 30, 2016 at 7:47 pm | Permalink

            My comments regarding errors in scientific research were meant to be general in nature. This is why I concentrated on errors in health research. I was trying to make a simple point, which is errors in scientific research that impact the public can have very negative repercussions on the respect of science in the public eye, whether deserved or not. It seems to me that some scientists simply do not make as much as effort as they could to check their work. I base this on the replication problem, which has gotten much attention lately. If thousands of people are killed or made sick by faulty research (overwhelming non-intentional), to say that the error will eventually be corrected does nothing to help those already impacted. In other words, scientific errors of a certain type (such as health errors), even if relatively rare and eventually self-correcting, provides fodder to the anti-science right wing. My hope is that the scientific community can come up with new protocols to reduce scientific errors.

            The Neanderthal error and eventual correction will have virtually no impact on public opinion regarding scientific research because they have no effect on the daily lives of people. Thus, it makes no practical difference whether the error was corrected in a week or a year. Nor do I believe that the authors of the study intentionally published incorrect data. But, they did forget to run a critical computer program. This is gross carelessness. Before taking off, pilots go through a checklist to make sure that every system is running properly. These scientists, and perhaps many others, could use a similar one to avoid forgetting some critical step in the research.

            • GBJames
              Posted January 30, 2016 at 7:55 pm | Permalink

              Yes, errors are to be avoided when possible. I’m sure the scientific community will welcome this insight.

              • Historian
                Posted January 30, 2016 at 8:13 pm | Permalink

                Yes, errors are to be avoided to the same degree as snide remarks, which is about all you have left to say.

            • Gregory Kusnick
              Posted January 30, 2016 at 11:01 pm | Permalink

              If thousands of people are killed or made sick by faulty research

              You seem to be conflating two different sorts of error here. Earlier you mentioned thalidomide, but it’s not clear to me where you think the scientific error lies in that case. Marketing the drug to pregnant women without sufficient testing was clearly a bad decision in retrospect, but why pin the blame on the research team who developed it? How should they have done their jobs differently? In fact thalidomide remains a useful treatment for conditions unrelated to pregnancy.

              I agree that we should strive for fewer errors of over-interpretation or premature application, fewer fad diets based on uncorroborated findings. But the solution, it seems to me, is greater transparency about the provisional nature of such findings, not a revamping of research programs to discourage speculation on grounds that it may turn out to be wrong.

      • rickflick
        Posted January 30, 2016 at 5:39 pm | Permalink

        I think you’ve described an essential insight. It challenges society going forward. I imagine, in time, this will resolve in favor of a more widespread appreciation of the scientific enterprise.

    • peepuk
      Posted January 31, 2016 at 2:32 pm | Permalink

      “But, when supposedly good scientific research in the health area is later discovered to be not so good …”

      This happened already many times see f.i. http://www.sciencemag.org/news/2015/06/feature-cancer-reproducibility-effort-faces-backlash

      We still do cancer research.

      Science is a trial and error process; mistakes are part of the game. A far bigger problem is that a lot of falsified stuff isn’t reported.

      As long as corporations and countries are in competition with each other science will get funding.

      • peepuk
        Posted January 31, 2016 at 2:36 pm | Permalink

        Bummer, I didn’t notice Gregory Kusnick post.

  6. Frank Bath
    Posted January 30, 2016 at 10:57 am | Permalink

    Don’t be hard on yourself. I learned many wrong things in the science of the time but my interest helped me to keep up and make the necessary corrections as I aged, dilettante though I am. Four cheers for science!

  7. Posted January 30, 2016 at 11:00 am | Permalink

    Did the authors call these genetic elements “European” or it just you? It is strange, because the source of the (multiple) “back-migrations” was most likely the Middle East, generally South-West Asia. Those genetic elements are Eurasian, not partcilularly European.
    Nevertheless, a migration from the Middle East to Africa still pulls Africans closer to Europeans, because the Middle Eastern population is (and was) genetically much closer to Europeans that to (Sub-Saharan) Africans. Still, this won’t make Europe the source.
    (Neanderthal genetic elemenets are not European specific either and the bulk of the Neanderthal genes inside us came from a population mix in SW Asia with all likelity.

    • gravelinspector-Aidan
      Posted January 30, 2016 at 11:35 am | Permalink

      Palaeoanthropologists tend to taking the geological point of view of what constitutes “Europe”, with the Europe-Asia suture running along the Ural mountains, then down to the Caucasus. It then gets ill-defined, but would generally put most of the Middle East, including what we call “Turkey” and “the Levant” in Europe.
      You could make an argument to draw the line down the Dead Sea Transform Which makes good sense to a geologist, and none at all to an archaeologist. Or to a Babylonian warlord.

      • rickflick
        Posted January 30, 2016 at 4:58 pm | Permalink

        “You could make an argument to draw the line down the Dead Sea Transform…”

        Every web site should have a resident geologist for just this sort of thing.

      • Posted January 30, 2016 at 11:01 pm | Permalink

        I never heard anything like this. In the geological point of view the borders of Asia with Europe are at the Aegean – Sea of Marmara – Black Sea – Caucasus – roughly Ural river – Ural mountains. There is no classification where Asia Minor (the bulk of Turkey) would be in Europe, even articles about archaic genetics and human prehistory call it Asia, same for every Geology or Geography text I ever have read.
        (And the Dead Sea does not make any sense from Geological viewpoint.)

        • Posted January 30, 2016 at 11:17 pm | Permalink

          By the way, I have found a blog where they quote from the original article and the therm “Eurasian ancestry” is used there. So it is called “European” in this site, not in the original article.

        • gravelinspector-Aidan
          Posted January 31, 2016 at 4:00 am | Permalink

          The thinking goes back a pretty long way. Neanderthal hominids were first discovered in (surprisingly) the Neander Valley of Germany in 1840-something. Slowly, more specimens were found, but only in mainland Europe, so they were considered a “European” form (or species – arguments continue). Come the (hmmm, trying to remember, late 1940s ?) when fossils which were ascribed to the Neanderthal group were found in the Levant … people got a vaguely-defined idea that maybe climate conditions in the central part of Asia were too severe for these “proto-humans”, giving some vague reason to expect there to be a breeding-barrier between the NW-European population (“Neanderthals”) and the rest of the humanoid population of the planet.
          It was never a very well thought-out sort of idea, which has been thoroughly blown out of the water with the discovery of Neanderthals and Denisovans in the Denisova cave in the Altai (though not at the same time. Probably.) and of mammoth butchery in the high glaciation in the Yamal peninsula. Plus the genetics is also showing that the populations were certainly in contact with each other, and to a degree interbreeding.
          The evidence – and the subsequent models – of human evolution has increased considerably in the last few years. The terminology hasn’t caught up, because the new models still haven’t reached that magical stage called “consensus”.

          The northern margin of the Tethys Ocean goes by the name of “Europe” when you’re west of the Urals, “Asia” if you’re east of the Urals. The southern margin of Tethys was composed of what we now call the Arabian shield (recently separated from the Nubian shield, in Nubia) with chunks from island arcs which form parts of Iran, Afghanistan, Pakistan, and the Levant.
          That whole area between the southern margin of Europe and the NE margin of Africa-Arabia is a bit of a mess of consolidated microcontinent terrains. With three major faults running through it – full-thickness faults, from surface to Moho – along the north and south sides of the Anatolian peninsula (North and South Anatolian Faults, the NAF having given rise to many highly lethal earthquakes over the millennia, with a swarm marching towards Istanbul as we speak). And the third full-thickness fault is the Dead-Sea Transform. Exactly how those three intersect and interact with the remaining post-Tethys compression running off into central Asia (Altai, Tienshan, Kun Lun – all fault-bounded, active mountain chains) simply is not clear. It is a bit of a mess. Most mountain belts are.

          • Posted January 31, 2016 at 4:58 am | Permalink

            Thank you the detailed explanation. I knew the tectonic plates are not that simple, I should have used the term “geographical Europe” instead of geological.
            However even using tectonic does not justify calling the SW Asia Europe, because most of the Middle east is on the Arabian plate.

            More importantly, I do not think that the terminology of the post above comes from this. It is simply a mistaken simplification. (One that is apparently not used by the original article.)

            • gravelinspector-Aidan
              Posted January 31, 2016 at 4:03 pm | Permalink

              Certainly the description of the “Middle East” as being “SW Asia” is becoming more common these days. For a start, to increasing numbers of Chinese, Japanese, Oceanian and Indian people, it is a nonsensical term. The “SW Asia” description only requires people to know the N-E-S-W pattern, and the fact that north poles are where the rotation axis turns ant-clockwise. (For which you need the polarity of kaon decays or something equally esoteric to describe.)

  8. colnago80
    Posted January 30, 2016 at 11:33 am | Permalink

    Recalls the faster then light neutrino brouhaha a few years ago.

  9. Posted January 30, 2016 at 11:49 am | Permalink

    Reblogged this on The Logical Place.

  10. Mark Sturtevant
    Posted January 30, 2016 at 11:49 am | Permalink

    I was a bit puzzled about their earlier finding, but decided to wait to see how it panned out over time. I had decided some time ago that hot new results that revise established models need to ‘bake’ for a while before I change my lectures.
    An example right now is the recent announcement from researchers who found that the Great Impact Model for the moon formation needs to be revised. Rather than having the moon form from collision between the earth and another planet with a glancing blow, they say that it was a center-on collision. Right now I am going to stick to the original model.

    • Mark Sturtevant
      Posted January 30, 2016 at 11:52 am | Permalink

      Giant Impact Model (or Giant Impact Theory).

    • Torbjörn Larsson
      Posted January 30, 2016 at 1:12 pm | Permalink

      It is probably wise to stick closer to the original model.

      Though my take from just reading the abstract is that they think the results ” favor vigorous mixing during the giant impact and therefore a high-energy, high-angular-momentum impact.” That doesn’t exclude glancing impacts if they mix the outer part of the Moon well. The new result open up the impact phase space rather than closing it.

      One reason to stick with a glancing blow is that it is a likelier event than a bulls eye. (Cf Moon, Mars, Vesta largest impactors.) Here is a recent paper that elucidate how such an impact may have resulted in well mixed outer layer of the Moon:

      “Previously, scientists had considered that volatiles vaporised by the impact might have escaped before the Moon formed.

      “However, few volatiles may have actually been lost because the velocity needed to escape the Earth’s gravity is quite high,” said Canup. “The new research suggests instead that as the Moon completed its growth, volatile-rich melt was preferentially deposited onto the Earth, rather than onto the growing Moon.””

      “The models show that the Moon acquires about the final half of its mass from melt condensed in the inner portions of the disc, close to the Earth and just inside the Moon’s initial orbit. Over time, the Moon’s orbit expands due to dynamical interactions with inner disc material. When the Moon is distant enough, it can no longer efficiently accumulate inner disc melt, which is instead scattered inward and assimilated by the Earth.”

      [ http://astronomynow.com/2015/11/10/scientists-explain-why-moon-rocks-contain-fewer-volatiles-than-earths/ ]

      Such a model can have Earth’s volatiles sourced in several ways. Besides keeping much of the impactor volatiles, the ongoing impact flow from the system could have delivered volatiles preferentially to Earth over Moon. Bill Bottke et al has shown that stochastic impacts would make a ~1000:1 difference.

      Young has his ideas, but I find it interesting how the Mars sized impactor model has weathered all new results.

    • rickflick
      Posted January 30, 2016 at 5:04 pm | Permalink

      My suggestion is to describe the more standard explanation in detail, but don’t avoid the latest information. Present it as an afterthought or “on the other hand” note at the end of the lecture. Otherwise you risk disappointing the more attentive students who will wonder why you are not keeping up with developments.

  11. Posted January 30, 2016 at 12:08 pm | Permalink

    Scientists, being human, also sometimes make mistakes. New technology is a two-edged sword providing us with more sophisticated tools with which to increase knowledge, but with more potential for unintended error also. I admire the essential element of science that disseminates corrections when they are found. It is one reason scientific evidence can be trusted.

    In using the health field example referenced earlier, look how long we were “fed” the
    erroneous notion that low fat, high carb diets were healthy. The last 10 years or so of my father’s life were made miserable by this restriction on his diet intended to “improve” health by prevention of a heart attack or stroke, which he died of anyway.

    Having been taught about straight lines as a child, imagine my amazement when I was informed as an adult in a college History of Mathematics class that there is no such thing in reality.

    Virtually everything we are taught as factual
    changes over time as cultures intermix and change. This happens in almost all areas of knowledge, not exclusively science. When studying history, I was taught that historians reevaluate and modify history on the average of every 25 years. And, when studying myths in literature, I learned that change took place to meet the needs and understandings of divergent cultures. For example, the Prometheus myth changed many times from Aeschylus’ version to that of Camus. Many cultures have had differing versions of the creation myth (the Greeks vs, the Jews for example,or various Nordic cultures vs. various Native American cultures, etc.) When cultures combine, and later split, new nuances in interpretation have occurred in the “parent” mythology that remains as well as in that which migrates outward. Viva la difference! The universal body of knowledge changes in much the same way as individual human knowledge does (or vice versa.)

  12. Posted January 30, 2016 at 12:23 pm | Permalink

    Unfortunately this will give the so called “race realists” one piece of ammunition back. You know the idiots who believe white people are inherently more intelligent than blacks. One of their arguments is that it’s the neanderthal DNA which accounts for it.

    • W. Benson
      Posted January 30, 2016 at 12:33 pm | Permalink

      Geographic populations differ in hundreds of ways. Unfortunately, racists will always be tootin` their horns.

    • Posted January 30, 2016 at 1:01 pm | Permalink

      On the other hand, some sub-Saharan Africans could boast about being “the only true, pure Homo sapiens”. If one wishes to be racist, he will twist any facts to suit his agenda.

      Traditionally, Neanderthals do not enjoy a reputation of having been intelligent. In a sci-fi novel by S. Lem, humanity is accused in blood-thirstiness and one of the arguments is the genocide against the Neanderthals. Someone defends modern humans by claiming that they honor the Neanderthals as their ancestors who became extinct naturally. The accuser then directly addresses a human: “When you on Earth call someone a Neanderthal, is this a compliment or an insult?”

      Personally, I think that Neanderthals may have had rudimentary language but otherwise were quite intelligent. They resisted H. sapiens for many millenia. Modern humans needed almost as much time to spread into Europe as to reach and populate Australia.

    • Victoria
      Posted January 30, 2016 at 3:12 pm | Permalink

      It’s not a sign of strength when you have to misstate the position of your opponents. If you’ll forgive me, I notice a lot of older people are caught up in a black-white binary on race issues that does not reflect Western diversity.

      This is also insupportable because IQ research shows East Asians, not whites to be the highest performing group. Of what I have seen of the “race realists” while commenting at the Guardian and other general news sites, they seem to accept this reality when Asian commenters rubbed it in their face (which raises other questions).

      I’m not denying these self-described “race realists” have ulterior motives of racist policies. Even if race-intelligence differences were entirely true, it would not validate denying equal opportunity to a given individual. I think respect for the individual and meritocracy are much stronger argument against their views than simply denouncing them, lest they end up with more scientific evidence than we feel comfortable with.

    • Diana MacPherson
      Posted January 30, 2016 at 5:18 pm | Permalink

      I love telling racists that Africans are more pure Homo sapiens than all the while people from Europe. I get a little twinkle in my eye.

      • Victoria
        Posted January 30, 2016 at 7:01 pm | Permalink

        But would you go up to a non-African, non-European person (e.g. Japanese, Papuan, Dravidian) and make that same purity argument? I understand your point, but also see a lot of white people who erroneously imagine or oversimplify literal racism to some exclusively white prejudice. It is decidedly not, although some Regressive Leftists would very much like us to think otherwise.

        • Diana MacPherson
          Posted January 30, 2016 at 7:31 pm | Permalink

          No I would only say that to white racists. The point wouldn’t sting a racist who wasn’t white. Moreover, I realize it is over simplified but these racists are simple and this pisses them off.

      • Posted January 30, 2016 at 7:43 pm | Permalink

        “I love telling racists that Africans are more pure Homo sapiens than all the while people from Europe. I get a little twinkle in my eye.”

        🙂

  13. Torbjörn Larsson
    Posted January 30, 2016 at 12:52 pm | Permalink

    Ha, I used the earlier result as an example on Friday to illustrate how linguistic roots are separated from population mixtures, then read the correction later on the day. Now I have to go back and explain what happened.

    But I also read yesterday a result on how Austronesian languages could be separate from the Pacific population. That would make the Taiwanese (most likely) language root having a 20 % influential social strata promoting it, while the population migration may have started after the latest glacial.

    [By the way, in the context I read about the human populations and plants that were thought to be connected to the Pacific migration. But also one technique that for whatever reason was thought to have been invented once, the blow gun. So putatively introduced in the Americas, I see it spread up to North America, by Pacific visitors.]

  14. Billy Bl
    Posted January 30, 2016 at 1:02 pm | Permalink

    This story also illustrates the emotional ups and downs that doing science can provide. One of my worst days was when a negative control turned out to be positive. Oh no! I ran many other negative controls that all turned out negative, so then I had fun trying to figure out why the one was positive. Never did find out why, but many years later, others got similar results, so the positive negative control was likely to actually be positive. I went from dejected to puzzled to happy. We still don’t know what’s going on, though.

  15. JJH
    Posted January 30, 2016 at 3:19 pm | Permalink

    Matthew,

    Another superb post on the processes and progress of the knowledge arts.

    I don’t know the specifics of the courses you teach, so you may not have time to cover the subject in depth, but I think an overview of it an introductory lecture would be a powerful statement about how science in general works.

  16. Posted January 30, 2016 at 3:25 pm | Permalink

    Well, there’re not too many months between last October and today, so if it were up to me, I’d be inclined to get an assistant to send emails with the information/links to all the students who were in my class. It’s too easy to spread wrong info in that short sentence, “We all have Neanderthal genes”.

    • Posted January 31, 2016 at 6:21 am | Permalink

      Ha! Good idea! They’ve done the exam, but it’s worth letting them know.

  17. Posted January 30, 2016 at 3:44 pm | Permalink

    🔬

  18. douglasgscofield
    Posted January 30, 2016 at 6:01 pm | Permalink

    This is a nice example of science being self-correcting, but I am not so understanding of the fact that an error of this profundity and (in bioinformatic terms) simplicity failed to be discovered by that team prior to publication. Extraordinary results should immediately lead one to double-check pipelines and use alternative methods. The symptom of excess missing data should have been clear enough not have been missed.

    • Victoria
      Posted January 30, 2016 at 7:16 pm | Permalink

      Most science goes awry when the conclusion is tempting for non-scientific reasons. Cold fusion is the classic example with the Fleischmann–Pons and Taleyarkhan experiments coming to mind.

      You can see from other comments how much people would love for this study to be relevant in the population-intelligence debate by effectively making genetic clusters that sort of resemble traditional “race” categories less distinct from one another.

      This is why I argue for focusing on liberal principles of individual rights and meritocracy rather than scientific proof of antiracism. The former is an eternal principal and I’m not going to stake legal equality on science that is far from settled.

      Of course the Regressive Leftist who describe race as a complete “fiction” and social construct, as opposed to a difference without distinction – my preferred explanation – are the same one’s who assault the Enlightenment and the notion of objective truth.

  19. jeffery
    Posted January 30, 2016 at 8:16 pm | Permalink

    It seems to me that the main issue here is that of the “repeatability” of the results of an experiment being one of the criteria for judging the worthiness of a hypothesis. Was the original publishing of their conclusion based on only ONE running of the data through their program? Was the error discovered only upon a second, “outside” attempt to produce the same results? If this was the case, the researchers ignored the scientific standards for validating a hypothesis. Of course, I can imagine it’s possible they could have run the program many times, with the same “error of omission”, which would cause them to see the same results, but there’s no indication of it in any articles I’ve read on this matter. It would certainly help to clarify things to know as this would make it a more obvious example of science as “self-correcting”.
    Sadly enough, many hard-core racists will no doubt leap on this as “proof” as to genuine “differences” in racial groups, which I have seen extrapolated to the point of the insistence that there are definite cognitive/emotional characteristics that are more “lacking” in some groups than others. It is important to remember, however, that there may, indeed, be such differences, but they have not been formally proven by science.

  20. Posted January 31, 2016 at 6:02 am | Permalink

    Reblogged this on My Selfish Gene and commented:
    In a recent Kreationist Korner I outlined Neil Shubin’s work in finding Tiktaalik as an exemplary example of how to do good science. Here is another side of that same coin.

  21. Posted January 31, 2016 at 6:28 am | Permalink

    Thanks for another great post Matthew. And the comments, as always, are a mini-course in and of themselves. One thing that strikes me – the other side of this coin – is how much confidence we can have in foundational research that has been sliced, diced, and built upon for decades. This is how I wish this were approached publicly.

  22. Mike
    Posted January 31, 2016 at 8:04 am | Permalink

    The beauty of Science, w’eve discovered A! thats interesting I’ll replicate it. Sorry our results don’t match yours, ok I’ll check again, you were right , we haven’t discovered A ! sorry about that , bin A, move on.

  23. Eli Lingard
    Posted January 31, 2016 at 10:25 am | Permalink

    Thanks so much for notifying us first years of the error, and providing clear, concise details about its discovery and how it was dealt with. I think it’s really important that we students should understand that mistakes do happen in science, as they do in every other field of study, and that it’s not a bad thing if it’s acknowledged properly and learnt from.

    You’ve helped me (and I’m sure many other students) to understand that, and I’m really grateful.

    As usual, a really great and informative post 😀

  24. Posted January 31, 2016 at 10:33 am | Permalink

    Chances are, if those Afro-Carribean students’ ancestors were slaves in the Americas, then they do have Neanderthal DNA.

    According to the DNA sequencing company 23andMe, most American blacks have and average of 25% European DNA; I have about 20%, and due to that I also have 1% Neanderthal DNA.

  25. Posted January 31, 2016 at 10:58 am | Permalink

    Reblogged this on Anthropology Now.

  26. Posted February 1, 2016 at 10:21 am | Permalink

    “A lot of modern research is based on complex analyses that can be difficult for those outside of the research group involved to understand. A lot is therefore taken on trust; had the result not been unusual, the mistake might never have been discovered.”

    Yes, this seems to be the man bites dog signal. If a result doesn’t seem like news, we just move along and don’t question it. Which sort of makes sense, generally, from a null hypothesis standpoint.

    Still, we are probably missing a lot.

    But at least science (unlike “other ways of guessing”) has a mechanism for self-correction.

  27. Nik
    Posted February 17, 2016 at 12:52 pm | Permalink

    When I teach I usually take special efforts to tell my students that I’m almost certainly telling them terrible lies here and there, and that if they repeat what I’ve said at a cocktail party decades later and are profoundly embarrassed to discover that their bit of remembered trivia was overturned years ago, they’re welcome to curse my name for misleading them. They still need to know everything for the test, though, but also should keep a kernel of epistemic skepticism in the back of their heads.


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