Friday links: vaccine prioritization vs. conditional probability, Am Nat vs. PubPeer, and more

Also this week: 1930s Japan vs. the US right now, the #pruittdataversary, R vs. Groundhog Day, Haldane’s diary, and more.

From Jeremy:

I know that for many of you it’s a welcome escape to read an ecology blog for a few minutes rather than spend yet more time paying attention to the appalling events in Washington, D.C. earlier this week. But although I certainly don’t have anything to say about those events that’s worth reading, they don’t feel to me like events that should pass totally unmarked even on an ecology blog. So here are a few things I read this week that I thought were good. If you only want the ecology links, just scroll down a bit.

The lessons of the right-wing coup attempts in Japan in the 1930s. I learned a lot from this.

Once again, police were permissive towards right-wing rioters.

On cynical political theater and its uncontrollable consequences.

Normal politics isn’t enough.

Other links:

Ambika Kamath on why she studies animal behavior, and on serendipity. Very wide-ranging and personal posts that defy brief summary; I found them all the more interesting for that.

Worried that updates to R packages will break your (or other people’s) old scripts? Arguably, you should be. Now there’s a easy to use solution, in the form of an…R package (ht Stephen Heard) Related: Meghan’s old post on how R improved the reproducibility of her work. Whether you think R is good or bad for reproducibility depends on what you’re comparing it to.

Am Nat EiC Dan Bolnick on how Am Nat handles concerns and complaints about papers it publishes, including anonymous PubPeer comments and comments from others who wish to remain anonymous. Speaking as an Am Nat editor: Am Nat has had a lot of experience with this issue in the past year; other journals should learn from us.

Andrew Hendry with the first and second in a series of posts on how he taught online-only intro bio to 600 students at McGill this past fall. My immediate reaction is that Andrew took full advantage of McGill’s early decision (compared to many other institutions) to go to online-only instruction. They gave their profs months to prepare.

Epidemiologist Whitney Robinson on the controversy over prioritizing coronavirus vaccine recipients. Precise and insightful. Also a good example for intro biostats classes.

Epidemiologist Deepti Gurdasani on the contributions of children attending in-person schooling to Covid-19 transmission. Useful clarifying thread; curious to hear what others think of it.

This is charming:

It’s approximately one year since the #pruittdata saga began. Somehow it seems appropriate to mark the #pruittdataversary* like this: there’s now a correction for Pinter-Wollman et al. 2016 Am Nat, a paper on which Jonathan Pruitt is last author. Summarizing briefly: this is mostly a theoretical paper, and no concerns have been raised about the theoretical portions. But a small portion of the paper refers to data collected Pruitt, which contains anomalies that Pruitt was unable to explain satisfactorily. Kudos to Pruitt’s co-authors for doing the right thing and promptly agreeing to the correction once they were made aware of the anomalies. Depressingly but unsurprisingly, Pruitt did not agree to the correction. Oh, and after the correction was published, an alert PubPeer commenter noticed that the anomalous data seem to have been duplicated in large part from Keiser & Pruitt 2014 Behav Ecol (a paper that itself already has an Expression of Concern attached for data anomalies). Here’s the kicker: according to Keiser & Pruitt 2014, the anomalous data in question were collected on spider species from Tennessee. According to Pinter-Wollman et al. 2016, the anomalous data in question were collected on different spider species from, um, Africa. Which is not in Tennessee. I have many…thoughts on this, but I am not going to share them right now because I can’t even. Instead, maybe I’ll go see if there’s anything good on Netflix.

*What do you get someone for their one year #pruittdataversary? One year anniversary is “paper”, right? What’s an appropriate paper gift? 🙂 😦

I just discovered Desert Island Discworld–the first podcast I’ve ever listened to. If you, like me, prefer rereading Terry Pratchett to reading new books because you can’t find anything else that measures up, you’ll like it.

And finally, we now go live to my laptop as it tries to calculate 350+ cumulative random effects meta-analyses:

12 thoughts on “Friday links: vaccine prioritization vs. conditional probability, Am Nat vs. PubPeer, and more

  1. Who is Terry Pratchett?

    A question I have answered many times. I also lover rereading Pratchett books. But I have not read them all. Thanks for the alert to the podcast.

    • I haven’t quite read them all. I decided never to read Raising Steam and haven’t regretted the decision. I want to remember Pratchett from before the “embuggerance”. I’d found that his books had been going downhill towards the end, and I felt like reading Raising Steam would just mean I’d end up disappointed. And I haven’t read that hard sci-fi novel he wrote jointly with someone else near the end of his life.

      Haven’t read the Bromeliad either, but planning to read it to my son soon. (EDIT: my wife reminds me that in fact I did read them to my son, and somehow forgot when I first wrote this comment!)

      I’ve been rereading some of the Discworld books this fall and winter. It’s been so long since I read some of them, I can’t remember them at all. Which is fun because it’s almost like I get to reread them again for the first time. But only *almost*, because having read them all once, and read some of them several times, I find my tastes have changed over time. Like every fan, I have my own favorites now, and so I find I’m not that interested in revisiting the ones that are very different from my favorites.

      Although perhaps listening to this podcast will change my mind, because I’ll get to hear new perspectives on some of the books. Like, Kate Nyx’s favorite Discworld book is Monstrous Regiment? Really?! I remember being disappointed in Monstrous Regiment when I first read it because you could see the “twist” coming from 10 miles off. The whole thing just seemed like a very heavy-handed treatment of themes that other Discworld books handle much better. Saying that Monstrous Regiment is your favorite Discworld book seems to me like saying that your favorite Beatle was Ringo. So I’m really curious to hear why someone would say that. Maybe I’ve been missing something about Monstrous Regiment all these years!

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  3. “Am Nat has had a lot of experience with [the issue of handling concerns and complaints” in the past year; other journals should learn from us.”

    Am Nat under the leadership of EIC Dan Bolnick has been an exemplary citizen in their evenhanded and transparent handling of a particularly difficult situation. I don’t dispute that other journals should learn from American Naturalist; I just don’t think they will. I attempted to submit a formal comment to Ecosphere on an article that I argued was fundamentally flawed. The response was that they would consider it if I promised to pay the $1500 APC. Other OA journals have similar policies. One has to have a major grudge or a benefactor with a vested interest in discrediting a published paper to make it likely for commenters to pay up expensive APCs to write with concerns. Neither of those two seem like a good thing to me. I think this makes it highly unlikely that the formal letter to the editor will be the forum for commentaries on OA articles. Apparently, some EICs just can’t be bothered with critical comments (https://retractionwatch.com/2020/06/22/tortuous-and-torturous-why-publishing-a-critical-letter-to-the-editor-is-so-difficult/).

    • Interesting. I wonder if the signal of this shows up in the frequency with which author-pays OA journals publish comments. It might not, since comments are rare even at subscription journals.

  4. Thread:

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