Don’t trust an archaeologist about genetics, don’t trust a geneticist about archaeology

By Razib Khan | October 15, 2012 2:38 pm

Who to trust? That is the question when you don’t know very much (all of us). Trust is precious, and to some extent sacred. That’s why I can flip out when I realize after the fact that someone more informed than me in field X sampled biased their argument in a way they knew was shady to support a proposition they were forwarding. What’s the point of that? Who cares if you win at a particular bull-session? You’re burning through cultural capital. And not that most of my interlocutors care, but I’m likely to never trust them again on anything.

In any case, this came to mind when I ran across a James Fallows’ post at The Atlantic. Here’s a screenshot of the appropriate section, with my underlines:


The PNAS link is wrong. The correspondent is actually linking to an article in Quaternary International. And they do point out that there are possible problems with draft quality sequences due to contamination. But I didn’t find the paper too persuasive. There are two issues. First, the Denisova genome is very good quality. So you can be more confident about those results. And those results themselves should increase your probability for the validity of Neandertal admixture; Denisova admixture was much more unexpected and surprising. In contrast, Neandertal admixture is positively banal. Additionally, one of the citations that they list prominently as supporting problems with poor quality and D-statistics actually is from a group which strongly supports Neandertal admixture. This doesn’t mean that the group has absolute control over how their papers are cited/interpreted, but I think it’s rather misleading to cite a paper in this way, because it gives the sense that the authors of the cited paper are skeptical of admixture, when they are not.

Second, I’m rather sure that Fallows’ correspondent was confusing the above paper with the one from PNAS a few months ago which I mentioned in large part because friends and acquaintances were telling me that it wasn’t a very good paper. Since the correspondent doesn’t mention the substance of this paper I suspect they weren’t familiar with the details. Rather, they simply interpolated the name of a more widely known journal, PNAS, for the real journal, Quaternary International, while recalling the content of the latter’s paper.

The moral here is troubling, but it is worth pondering for all of us. James Fallows had no idea about this field, so he simply relayed a very confused correspondent. Second, the correspondent, an admitted archaeologist, probably has no way to evaluate the plausibility of papers in human genomics. So they forgot the content of the more prestigious article in PNAS from a more well known group, for a paper in Quaternary International, from Fudan University in Shanghai. I assume this is not a well known group. The archaeologist who contacted Fallows probably meant well, but they shouldn’t be using their academic status as a scholar in archaeology to pass along muddled opinions about a field which they’re not competent to evaluate. As for Fallows, I really do hope he knows that the 5% value he’s quoting is a genetic inference, and not an archaeological one, so that an archaeologist shouldn’t sway him too much either way (I think he should remain skeptical, though if he got the results from Geno 2.0, I know that that SNP-chip has a lot of Neandertal markers).

MORE ABOUT: Human Evolution
  • http://www.isteve.blogspot Steve Sailer

    The contamination issue is a nagging one that seems difficult to rule out totally. I hope that we someday see some testimony against interest — somebody who is on record as doubting Neanderthal or Denisovan admixture due to possible contamination now saying that we uncovered a bone and took superduper precautions against contamination and … it turns out we were wrong, there really was admixture.

  • Chad

    Read the protocols…..they did take “superduper precautions against contamination”

  • Aylwyn Scally

    The authors of the high-coverage Denisova paper presented convincing evidence by three different measures that the level of present-day human contamination is less than 0.5%. If there are reasons to doubt the inference of archaic admixture in modern humans, contamination is not a good one.

  • Amos Zeeberg (Discover Web Editor)

    Hit Fallows up on the Twitters. He seems reasonable; bet he’ll listen.

  • Bryan Howie

    Thanks for pointing this out; I had the same reaction to the “expert” that Fallows quoted in his post (although I hadn’t noticed that the link did not match the citation — good catch). I find it especially annoying when non-experts propagate headline results from “good journals” rather than evaluating the specific claims of a paper.

    I brought this up to JF on Twitter a couple of days ago, and I tried to point him toward recent commentary from better experts. I didn’t get a reply, but I understand that he’s a busy guy and this Neandertal business is just trivia for him. I see that you forwarded this blog posting to him — it would be great if this spurred him to do a follow-up post on the subject.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    #5, re: journal quality. it’s an OK quick & dirty filter on the front end (we’ve seen the problems with relying on ‘good journals’ like *science* in the recent past). but if you’re bringing it up in your explicit argument, then my skepticism goes up, because the quality of the paper should speak for itself. though to be fair i probably put more weight on the group that’s producing the paper…but people outside of a sub-discipline are totally blind as the implicit rank order research groups in terms of credibility.

  • gcochran

    James Fallows was also prominent among those who concluded, around 1988, that Japan had the secret of lasting economic growth and technological progress. Back then, I coined the word “dunderkid” just for him.

  • http://johnhawks.net/weblog John Hawks

    What I don’t get is the archaeologists who care enough to write “corrections” in to the Atlantic, but don’t care enough to get the facts…

  • http://opines.mythusmage.org Alan Kellogg

    Have you ever had the desire to bash a postal clerk about the head with a club?

  • Nick Patterson (Broad)

    (I was an author of both the Green et al (Neandertal) and Reich et al (Denisova) papers)

    When thinking about contamination it’s important to realise that contamination
    will look like modern human gene-flow -> archaics. But we find very strong evidence
    for flow in the reverse direction.

  • DK

    Yeah, given the precautions taken, it’s practically impossible to get contamination on a 5% level. It’s just not a real issue.

  • https://plus.google.com/109962494182694679780/posts Razib Khan

    does anyone know what #9 is trying to say?

  • Simon

    Very curious what his mDNA is!

  • Jake

    Re: #12
    I think it’s his idea of a Neanderthal admixture test.

  • http://shinbounomatsuri.wordpress.com Spike Gomes

    I’ve had *a lot* of experience with archeologists on a professional level, though I can’t be overly specific because it will get me canned. In general, genetics just doesn’t seem to be something they consider much. Not that they’re hostile to it (though a few are). Just doesn’t seem to be something they consider much, except in regards to concerns with burials (i.e. the natives don’t like it when you mention anything that even hints of it). Granted, though, I think that folks attracted to the field are the sort that love surveying and testing in the field, but hate the nitty-gritty stuff like weighing and sorting midden and soil samples and doing official write-ups of jobs with uninteresting results. Genetics is like a C-14 dating spreadsheet with even more incomprehensible math.

    Of course this is all anecdotal on my part, and I live someplace that’s very atypical in regards to archeological concerns and how it’s practiced.

  • Eurologist

    @#13
    I am, too, but I suspect it’s nothing too exciting, something like some H5a subclade that simply isn’t very common.

  • stargene

    Since I’m a happy amateur in all this, often rushing in where angels
    fear to tread, and am drawn to bright, shiny objects, my opinions
    are suspect. But, Razib… 5% Neanderthal DNA?… your clearly
    stated love for habaneros seems a dead giveaway. As is my
    unrequited passion, against my wife’s advice, for kim chee and
    really greasy steaks. Doubtless a remnant of chasing wooly
    mammoth blubber across Siberia. Here’s to happy admixtures.
    Good hunting.

  • sniper

    I was also scratching my head about the contamination issue….contamination from what? From the Neanderthal or Denisovan who took the sample?

  • BJM

    Re: does anyone know what #9 is trying to say?

    Something about not suffering fools gladly? Poor postal clerks, often used as stereotypical incompetents. I doubt there are more incompetents in their ranks than in any other profession.

  • Nathan

    As I read this blog entry headline and read Razib’s bolded comment , I immediately thought about what Steve Farmer said very recently about the inaccuracy of mutation rates (in past papers) and how some well known geneticists have not been vociferous in cautioning the jump to conclusions, rather it seems they partly welcomed it because it drew attention to their papers.

    ” Despite our arguments, the papers were cranked out regularly for over a decade
    by well-known population geneticists. When we pointed out the problem to them
    they privately admitted we were right but argued that tossing in discussions of
    “hot” political topics in their abstracts drew needed attention (and funding!)
    to their work.

    We’re talking about the best-known population geneticists, at Stanford and
    elsewhere. ”

    http://groups.yahoo.com/group/Indo-Eurasian_research/message/16092

    S.Farmer mentions the California Textbook controversy; fudging mutation rate data takes a sinister turn when well known Indian geneticists from well known institutions misrepresent and or fudge data to promote an ethno-nationalist / casteist pov.

  • http://opines.mythusmage.org Alan Kellogg

    Exactly!

    “Science Made Stupid” and “Am I a Neanderthal” (cf)

NEW ON DISCOVER
OPEN
CITIZEN SCIENCE
ADVERTISEMENT

Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com

ADVERTISEMENT

See More

ADVERTISEMENT

RSS Razib’s Pinboard

Edifying books

Collapse bottom bar
+

Login to your Account

X
E-mail address:
Password:
Remember me
Forgot your password?
No problem. Click here to have it e-mailed to you.

Not Registered Yet?

Register now for FREE. Registration only takes a few minutes to complete. Register now »