Friday links: four (!) more #pruittdata papers, remembering Ben Nolting, and more

Also this week: Covid-19 vs. in-person classes, logical positivism vs. Mike Tyson, and more.

From Jeremy:

Very sad news, to which I am a bit late: theoretical ecologist Ben Nolting has passed away much too soon. That link goes to a remembrance from his friend and collaborator Christopher Moore. Here is a link to his obituary. I never had the honor of meeting Ben, and I’m sorry I will never get the chance. I love his Ecology paper with Karen Abbott on quasipotentials as a way to quantify stability in stochastic systems. Just a great, great paper, introducing new technical concepts and techniques while also teaching the reader the intuitions behind those concepts and techniques. The rare paper that makes you smarter, and makes you feel smarter. Rest in peace, Ben–ecology will be poorer without you. You can remember Ben by donating to the student support scholarship that has been set up in his name.

Well, that was fun while it lasted. By “fun” I mean “predictably disastrous”.

In other UNC-related news, here’s outstanding ecologist Caroline Tucker’s blog post on why she’s leaving academia. Her choice is a loss for ecology, but as you’ll see from reading the post it’s clearly the right decision for her. Wishing you all the best whatever you do next, Caroline.

Here’s yet another Expression of Concern for a paper for which embattled spider behavioral ecologist Jonathan Pruitt collected the data. It’s DiRienzo et al. 2013 Animal Behaviour. This one is for a spreadsheet formula used to generate some “observations” of one of the variables. There were other anomalies too. The formula-generated “observations” weren’t used in the paper, but their unexplained presence casts sufficient doubt on the entire dataset that an Expression of Concern was warranted. The linked tweet thread includes a link to a detailed PubPeer description of the anomalies by first author Nick DiRienzo. Kudos to Pruitt’s co-authors and the journal for acting as they did, and for being so specific about the problems with the data.

On the other hand, Proc Roy Soc B refused to retract Pruitt et al. 2016 at the request of Pruitt’s co-authors, thereby forcing them to remove their names from the paper. The journal is going to let Jonathan Pruitt reanalyze the data and submit a correction on his own, even though the anomalies weren’t explained to the co-authors’ satisfaction. It may be that the journal is allowing Pruitt to submit a correction at least in part because the journal is under legal pressure. Note that it seems possible (?) the paper could be retracted if the correction is judged insufficient. But even though the final decision on the paper hasn’t been made, questions are still being raised about whether Proc B is proceeding appropriately here. Kudos to Dan Bolnick, Andrew Sih, Noah Pinter-Wollman, and Nick DiRienzo for pulling their names from a paper they’re no longer confident in. Here’s some further background on the story from Dan Bolnick. If you want a tweet length summary of why Pruitt’s co-authors no longer trust these data (which comprise waiting times measured in seconds), and why they don’t think Pruitt’s proposed re-analysis would make the data trustworthy, here you go:

Same story for Pruitt & Pinter-Wollman 2015 Proc B:

Due to recently discovered anomalies in the data collected and curated by J. N. Pruitt for the paper by J. N. Pruitt and N. Pinter-Wollman, ‘The legacy effects of keystone individuals on collective behaviour scale to how long they remain within a group’ published in 2015 in the Proceedings of the Royal Society B282, 20151766, which include formulas in the raw data file, duplication of portions of the data and an excessively high number of repeated values beyond what would be expected in an unbiased sample, N. Pinter-Wollman removes her authorship from this paper.

And here’s an Expression of Concern from Functional Ecology for Pruitt and Husak 2010. That work reported in that paper dates from Pruitt’s time as a grad student at UTennessee; the university is investigating concerns about the data. (aside: I’ll be very curious to see what they do if they’re told that the data are no longer available; Pruitt apparently told another investigation that some of his data no longer exist). Here’s a bit of background from co-author Jerry Husak. I think Jerry Husak is rather too hard on himself for collaborating with Pruitt without ever asking to see the raw data. It’s good for scientists to default to trusting each other.

Continuing with Jonathan Pruitt-related news, his lawyers issued a Freedom of Information request for the emails of…um…fisheries ecologist Trevor Branch. Yes, really. Revealing a grand total of…one email Branch received that peripherally mentioned Pruitt as part of a discussion of an unrelated topic. I’m completely baffled why Pruitt and/or his lawyers would think that Trevor Branch of all people is in any way connected to the various investigations into Pruitt’s work.

And here’s the latest Retraction Watch story on Pruitt. No new information that we haven’t linked to before, but useful if you want a compact summary of recent goings-on.

Ethan Zuckerman’s note to the next occupant of his office at MIT.

I knew this story, but some of you may not, so here’s the time when famed 77-year old Oxford philosophy prof A. J. Ayer defended Naomi Campbell (yes, that Naomi Campbell) from Mike Tyson (yes, that Mike Tyson).

4 thoughts on “Friday links: four (!) more #pruittdata papers, remembering Ben Nolting, and more

  1. Quite sad to hear about Ben Nolting. At a conference this week I saw a fantastic talk by Jody Reimer (Utah), and over email she shared that paper with me yesterday. I was quite blown away by how impressive it was for all of the reasons you list, but otherwise had not heard of the authors before.

  2. Kate Laskowski’s comments on the authorship removals are worth reading (thread):

  3. There are towards the best of my knowledge several ways how standardized observations on the social behaviour of spiders, in the field and/or in a lab, can be recorded.

    (1): write them by yourself in a note book / field diary / standardized form etc. when you are alone;
    (2): use an audio-recorder (various possibilities, including video, wildlife camera, etc.) to record your own spoken observations;
    (3): work together with one or more others who write down in a note book / field diary / stadardized form etc. your spoken observations;
    (4): use a (modified / simplified) keybord (which it attached to a computer) to enter by yourself the (standardized) observations;
    (5): work together with one or more others who use such a (modified / simplified) keybord to enter your spoken observations.
    etc.

    This list is for sure incomplete. All methods produce raw research data, also called primary research data. I have huge piles of them (note books / field diaries / standardized forms). I only need a scanner / digital camera / mobile phone to make digital copies of these pieces of paper.

    I was wondering if any of the co-authors of the Pruitt papers which are at the moment under discussion has even seen (parts of) such kind of raw research data. Am I right that all these co-authors have until now only seen Excel-files etc.?

    My question is also related to a report by Harvard University about Marc Hauser in which a committee of Harvard university had access to a large amount of video/audio tapes which were taken during the research of Marc Hauser. See for details https://www.harvardmagazine.com/2012/09/hauser-research-misconduct-reported

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