Friday links: RIP Joe Connell, and more

Also this week: another retraction for Jonathan Pruitt, PubPeer vs. journals, and more

From Jeremy:

Very sad news: Joe Connell has passed away. He was 96. He was a giant of ecology. His Mercer Award winning 1961 paper on the population biology of barnacles pioneered field experiments as a research approach. His classic results on interspecific competition now feature in many ecology textbooks. He was also perhaps the most productive and influential developer of conceptual models in the history of ecology. Particularly models to explain the maintenance of diversity in the coral reefs and tropical rain forests in which he worked for much of his career: the intermediate disturbance hypothesis, the Janzen-Connell hypothesis for the maintenance of tropical tree diversity, and the Connell-Slayter classification of modes of succession. Not all of those conceptual models and hypotheses proved equally fruitful in the long run–I think the Janzen-Connell hypothesis has held up the best–but that takes nothing away from their importance to the history of ecology. Among his many awards and honors, Joe Connell received the ESA’s Eminent Ecologist award, and was one of just 12 Lifetime Honorary Members of the ASN. This 1985 appreciation accompanying his Eminent Ecologist award provides a good overview of his life and career to that point.

You know how national governments try to bury bad news by publishing it on Friday afternoon? Well, scientific journals apparently have learned to do that when it comes to retracting or expressing concern about Jonathan Pruitt’s papers. (I’m kidding. I hope.) Last Friday afternoon, Biology Letters retracted Costa-Pereira & Pruitt 2016. The retraction is for anomalous duplicated values in the raw data. Last Friday afternoon also saw an Expression of Concern for Keiser & Pruitt 2014 Behavioral Ecology. (ht Nick Keiser, who provides some backstory.) It’s for anomalous duplicated sequences of observations. It’s only an Expression of Concern rather than a retraction because the journal allowed the authors to reanalyze the data with the anomalous observations removed and the conclusions didn’t change. The Expression of Concern notes that the integrity of the remaining data is still in question, and says that “We will publish a more complete correction once the remaining data have been verified.” I think this is…[counts on fingers]…six weeks in a row with at least one retraction, EoC, or correction for Pruitt. Plus several retractions from back in the winter, of course.

In other #pruittdata news, the Google spreadsheet tracking the current status of investigations into all of Pruitt’s papers has been put back up by…someone. I understand (what I presume is) the intent, but confess to mixed feelings about this. Dan Bolnick, who started the original spreadsheet, had reasons for taking it down.

How should journals respond to critical PubPeer comments? Am Nat EiC Dan Bolnick weighs in. And here are a few further comments from Dan.

8 thoughts on “Friday links: RIP Joe Connell, and more

  1. In our 21st Century rush to publish ever more papers and generate ever more citations it’s worth reflecting on Joe Connell’s published output. As far as I can see from Web of Science (and this is a little fuzzy because there’s more than one JH Connell) he published fewer than 100 papers and his h-index was perhaps 40 at most. Yet, as you rightly say Jeremy, he was a real giant and enormously influential in the field. The legacy he leaves behind will be remembered long after we’ve forgotten the names of some “superstar” researchers with hundreds of papers and a stellar h-index. Or perhaps we’ll remember them for the wrong reasons.

    RIP Joseph H. Connell.

  2. I’m pretty uncomfortable with Dan Bolnick’s position on PubPeer.

    In particular, “the right to face your accuser” makes sense when it’s a matter of the accuser’s word against yours. But I don’t see how it is relevant when the statement in question is “Lanes 3 and 5 of this blot are identical.” It really doesn’t matter who is saying this: the question is whether or not it’s true. The anonymous poster might be a disinterested sleuth, or your worst enemy: either way those lanes should not be identical.

    What the right to face your accuser has meant in practice, all too often, is professional or legal threats against the accuser. The net result is that powerful people are insulated from criticism.

    Every time we put a barrier in the way of people trying to correct the scientific record, we discourage some of them from doing it. Looking at the state of the literature, I think that’s going in the wrong direction.

    • With respect, I think you might have misunderstood Dan’s position. Quoting from his post:
      “If valid well-justified and substantial concerns exist and are published on PubPeer, then the affected journal should respond.”

      “That said, whistleblowers sometimes hide their identity for good reason (e.g., not trusting that whistleblower laws offer sufficient protection). With this in mind, it might be worth considering whether journals might publish anonymizied Comments. That runs counter to the growing trend towards open peer review, but can protect vulnerable individuals when their complaint is valid and they have compelling grounds to be concerned about how their career is impacted.”

      “First, the PubPeer comments need to be brought to the Editor’s attention. Don’t assume that Editors take time to search PubPeer regularly; at least I don’t. Then, the journal begins an evaluation process that may include (1) forming a committee to evaluate the papers and the citicisms, and/or (2) contacting the author(s) for a response.”

      In his post, Dan is thinking out loud about all sides of an ongoing debate. He’s saying (in so many words) “on the one hand, on the other hand” because he thinks (rightly) that this is an issue on which all sides have a point and there are no easy, blanket right answers. With respect, I think it’s a little uncharitable to just pick out the bits of his post that you disagree with, and ignore the bits where he says “on the other hand” and agrees with you. Dan thinks you have a point! He just thinks that you’re not the *only* one with a point.

      I suspect that the reason you think Dan disagrees with you more than he actually does is that you’re *only* thinking about cases in which the PubPeer commenter has correctly identified strong evidence of scientific misconduct. Whereas Dan is *also* thinking about the cases where PubPeer commenters nitpick about debatable statistical choices, or mistakenly think that data are anomalous because they didn’t read the paper carefully, or etc. (Yes, such cases do happen. I don’t know how frequent they are relative to the sorts of cases you’re thinking about, but anecdotally they don’t seem vanishingly rare.)

      The other thing Dan is thinking about is the need for procedures to handle PubPeer comments that not only work, but that are *seen* to work by all. Procedures that everyone (or as many people as possible) buy into. Like it or not, it’s a fact of life that lots of scientists don’t like it when they first they hear about someone’s concern about their work is an anonymous public criticism on PubPeer. And it’s not just the rare scientists are dishonest or incompetent who don’t like it; lots of honest competent scientists who’ve made one-off honest mistakes don’t like it either. Now, in response you could say “who cares about their feelings, it’s correcting the scientific record that matters”. But here’s the thing: the record will get corrected more often, and faster, if it’s corrected via known procedures that everyone buys into. Correcting the scientific record goes more slowly when authors feel threatened and dig in to defend themselves. Dan knows that times are changing, and he is trying to develop new procedures for dealing with PubPeer comments, that everyone (or as many people as possible) will buy into! You should see that as a good thing, or at least better than the previous status quo. Right?

      In his post, Dan explicitly describes the procedure that he follows at Am Nat to deal with PubPeer comments that are brought to his attention. I quoted part of it above. So if you think his procedure is bad, what procedure do you think Am Nat should follow instead? Honest question. Dan would be the first to admit he’s not infallible. So if you have some better procedure in mind for how journals should handle PubPeer comments, spell it out!

      Related old post: https://dynamicecology.wordpress.com/2014/02/24/post-publication-review-signs-of-the-times/

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