Friday links: Daphnia theme song, RIP PubMed Commons, Joy of Cooking vs. p-hacking, and more

Also this week: 50 shades of grey green, the best (?) pedagogical technique you’ve never heard of (?), and more.

From Jeremy:

Somewhat contrary to the speculation in last week’s links, the Canadian federal budget includes substantial new money for fundamental, investigator-driven research. More detailed commentary here.

In the Least Surprising News Ever, PubMed Commons is shutting down because hardly anyone comments and the vast majority of papers draw no commentary.

Do journals really need cover letters to accompany ms submissions? Interesting question, but contrary to the author of the linked piece I think the answer is “yes”, because the EiC reads the cover letter (and probably not the ms) and uses it to decide whether to assign the ms to a handling editor or reject it, with “reject” being the choice ~50% of the time at leading ecology journals. I think handling editors vary on whether they read cover letters, but I don’t know. Follow that second link for advice on how to write a cover letter. (UPDATE: second link fixed)

Can someone with more pedagogical training than me give a second opinion on this? Because this is the first I’ve ever heard of the pedagogical technique of “direct instruction”. Does it actually work as well as the data in the linked post suggest?

In a new meta-analysis of undergraduate academic performance (which I haven’t read; just passing the link along), the single best predictor of undergraduate student grades is class attendance. It beats SAT scores, high school GPA, and measures of student study habits and study skills, and is not especially collinear with those other predictors either. Note however that, in a smaller sample size, mandatory attendance policies only have a modestly positive effect on grades. That’s consistent with my anecdotal impressions–students who attend class do better both because attending class helps, and because the students who attend class are the ones who would do well even if they didn’t attend. (ht @noahpinion)

BuzzFeed got hold of a bunch of emails from the lab of prominent Cornell University nutrition researcher Brian Wansink. The emails reveal him systematically ordering his trainees to p-hack, in order to come up with results that would generate media interest. This sort of thing is very much not what our own Brian McGill had in mind when he praised exploratory statistics. I think Wansink’s example is a useful one for intro biostats courses, as an extreme (and thus clear) example of what “p-hacking” means. But I think Wansink’s behavior is very unusual in the context of science as a whole (maybe he’s less unusual in the context of nutrition research or social psychology?). So I don’t think you can use Wansink’s example to make the case for a systemic problem with X, whether “X” is “p values” or “the quality of statistical training” or “incentives to publish” or “researcher integrity” or whatever (note that Andrew Gelman disagrees.) Put another way, I don’t think reform of statistical training, or widespread adoption of Bayesian approaches, or whatever, would reduce the (already low) frequency of Brian Wansinks. I agree with Andrew Gelman that Wansink’s work is completely theory-free and so his research program would be a fruitless wild goose chase even if his individual experiments were all preregistered rather than p-hacked. But because Wansink has been doing intentional p-hacking, his case isn’t the best illustration of how hypothesis testing is a bad idea in the complete absence of theory.

Speaking of Brian Wansink, here’s one of his early, influential papers getting shredded by…[wait for it!]…the Joy of Cooking Twitter account. Yes, really. (ht @dsquareddigest)

How economists log-transform data with zeroes. I have never seen that transformation used in ecology. Interesting how different fields develop different “standard” ways of dealing with the same problem.

Ok, maybe the movie version of Annihilation is better than the book. Anyone seen it?

50 shades of green“: John Holbo on the sexiness of Erasmus Darwin’s poetry. I found this interesting and fun, and I’ve never even read Erasmus Darwin. Best line:

It’s like Tinder, but for plants.

In the comments, place your bets on how many hours Stephen Heard will spend reading Erasmus Darwin’s poetry this morning after clicking that link. I set the over/under at two hours. 🙂 #resistanceisfutileStephen

The previous link alerts me to this book, which looks interesting.

And finally, Meghan just plays this on a loop in her lab. Presumably. 🙂

From Meghan:

Kate Clancy, lead author of a really important study on the prevalence of harassment and assault during field experiences, testified before Congress this week in a hearing on sexual harassment and misconduct in science. Her testimony was 5 minutes long and is really, really worth watching. Here’s an article on the full hearing, which includes this quote from Clancy’s testimony:

While the come ons are the type of behaviors we see in articles about Harvey Weinstein and in sexual harassment trainings, the majority of sexual harassment are in fact the put downs. These are the kinds of behaviors most women in the workplace have experienced at least once in their lifetime, and many experience everyday. The offensive remarks, subtle exclusions; requests to make coffee, yes, but also starting rumors, sabotaging promotions, or ruining a career.

This matched what I’d learned in a recent seminar I attended on sexual harassment, which referenced this article when noting that, because they are so much more common, the “put downs” are at least as damaging as the “come ons”. Given this, it’s a problem that we focus almost entirely on the come ons when discussing sexual harassment.

Related to the above, the American Geophysical Union recently updated their definition of what constitutes scientific misconduct to include sexual harassment. (Here’s a Science piece on the AGU policy.) And the National Science Foundation has now set up a mechanism for reporting harassment directly to them; I think this is the portal, though it’s not totally clear to me how to report (would you just send an email to the address on that page?) and I’d love more information from others who know more. NSF also now requires institutions to report sexual harassment findings, with potential consequences for funding.

33 thoughts on “Friday links: Daphnia theme song, RIP PubMed Commons, Joy of Cooking vs. p-hacking, and more

  1. I’ve seen the argument against cover letters and I also had mixed feelings about it. I think we would need getting rid of them *only* if we would end up in the world that many open access advocates are dreaming of. In this world selective journals and their “gate-keeping” editors cease to exist and evaluating and curating of manuscripts is all done after peer-reviewing and publishing in Plos One-style journals.
    However, we do not (yet) live in such a world and therefore, in line with Jeremy’s argument, I think good cover letters are essential for publishing in highly selective journals and as long as publishing in these journals is important for one’s career prospects (and progress) I’ll keep honing my cover letter writing skills.

    • I wish I could’ve asked the author of the Rapid Ecology post about this point, but they don’t allow comments and Twitter doesn’t really work for me as a vehicle for serious discussion. Which is fine, it’s their blog, different strokes for different folks. But as someone who likes blog comment threads, I’ll get a bit of a chuckle if the most active discussions about Rapid Ecology posts happen in our comment threads rather than on Twitter.

      Note that I haven’t looked to see how much discussion of their posts is happening on Twitter. And it’s early days for them, the volume of discussion will ramp up as they build an audience. Which they surely will if they maintain their impressive start. They’re doing multiple posts a day! It’s a pleasantly old-school blog in that way so far.

      • Interestingly, I note that Rapid Ecology doesn’t ordinarily allow comments on posts–but they do allow trackbacks. We linked to one of their posts, and now there’s now a link at the bottom of it pointing back to our post.

      • Every author at Rapid Ecology, if they want a discussion on their post, can have the comments open. The default is ‘comments off’ but if any person posting wants comments, that’s an option. So for all folks reading here, if you’d like to have your own post at Rapid Ecology, with comments, go on ahead and submit.

      • You’ll notice that the Rapid Ecology crew has just started a weekly post as a comment thread. Where all posts there, and whatever else under the sun. can be remarked upon.

      • Interesting experiment. Kind of a hybrid of pure open thread and comment threads associated with each individual post.

        I’ve sometimes thought about trying open threads here at DE, but never have. Thought that we’d be unlikely to get comments, because as it is most of our comments come from people who comment only rarely. They break their usual silence to comment on particular posts when they feel they really have something they want to say. In contrast, in the blogs I’ve seen that have successful open thread posts, it’s because the blog is read by a community of people who just like to chat with each other in the blog’s comments. But obviously, you’re not doing pure open threads, your posts so far don’t allow comments, and your readership is still developing and isn’t set in its collective ways yet. So I think it’s a great idea to experiment and figure out what works. And who knows, maybe I’m totally wrong and if we tried some open threads here at DE people would comment a lot on them.

  2. OK, not going to lie, I did indeed click on the Erasmus Darwin link, and your over/under sounds about right.

    Two relevant observations.

    First, Linnaeus himself wrote somewhat erotically (for the time) about plants, and doing so raised the ire of at least one other botanist. The result: history’s first use of a Latin name to insult someone. Story here: https://scientistseessquirrel.wordpress.com/2018/02/26/less-than-a-tribute-when-latin-names-are-insults/

    Second, years ago I taught the plant part of 1st-year botany. I gave a lecture about plant sex in which I talked about tristyly and other forms of what I called “plant kinkiness”. About a year later, I was walking downtown late at night and a rather rough-looking young man was coming toward me on the sidewalk. I was actually feeling a little nervous, especially when I noticed him notice me and sort of drift towards me on the sidewalk. Then he grinned, pumped his fist, and yelled “Whoo, Dr. Heard, kinky plants!!!”. It turns out that when you teach, sometimes students listen and actually remember stuff… and kinkiness (of the subject matter!) may help.

  3. As a handling editor, I can tell you that I usually read the cover letter (as well as the ms). It helps me see quickly what the authors thought were the main hooks, which can help frame my thinking about interest level in this paper for that journal. And if I like the paper, having a nicely packaged way of summarizing those hooks can help me sell the ms to the editor in chief.

    • @ Robin,

      Your example nicely illustrates part of the issue here: different strokes for different folks. Handling editors vary, and at least some of them want to see a cover letter. So if it’s possible that the handling editor might want to see a cover letter, I think it behooves you as an author to write one. Even if you personally wouldn’t want to read one if you were a handling editor yourself.

      This does raise the question of what fraction of handling editors read cover letters. I bet it’s a substantial majority, at least at selective journals, but that’s purely a guess and I could be wrong.

      And again, even if the majority of handling editors don’t read cover letters, I bet most EiCs do, at least at selective journals. I doubt Brian McGill’s an outlier in reading cover letters and putting a lot of weight on them in his role as EiC at GEB.

  4. Gotta say that I’m disappointed in our readers that the Erasmus Darwin “Tinder, but for plants” link is among our least-clicked so far. Our readers are much more keen to read the Joy of Cooking Twitter account schooling Brian Wansink…

  5. I read about Direct Instruction years ago in Ian Ayres’ book “super crunchers”. I would have to read about it again to recall the details, but as I recall it, its a repetition-heavy, fully scripted method that gives the teacher almost no leeway, and thus teachers hate it, bur its quite effective

      • Ayres’ book gives a decent discussion of it. Apparently it is/was used in some schools in Baltimore.

        It’s interesting, you know here in Seattle there is a big discussion of pre-k and the amount of bullshit I’ve read about the purported benefits of pre-k is amazing. Statements are creatively phrased to give the completely wrong impression without actually lying. But will you ever hear about direct instruction? Nope. Not even charters are doing it!

  6. I wanted to share my opinion on Annihilation as someone who loved the book and recently saw the movie. Overall, I really enjoyed the movie and thought it very effectively created the atmosphere of the beauty and horror of area X. I am thrilled that this is the first movie I have EVER seen where a group of women go on an adventure together. They are each allowed to have different strengths and weaknesses and lives beyond their relationships with men. My husband also really enjoyed the movie (he hasn’t read the book) as someone who also likes this specific type of science fiction. So, especially if you like movies like Gattaca, Blade Runner, Ex-machina, The one I love, etc…, you might enjoy this movie.

    My only disappointment with the movie compared to the book (not a spoiler) is how they changed the main character (the biologist/Natalie Portman). In the book she is a kind of down and out field ecologist who struggles with her desire to be out in the wilderness vs. participating in society. In the movie, she is ex-military (7ish years), cell biology professor at John’s Hopkins University apparently in her early-to-mid thirties. There didn’t seem to be any necessary reason for the change, and, of course, I found her academic journey quite unrealistic for her age and experience. I also understand the critiques about the racial identities of the cast not matching the descriptions in later books (it was my first concern when I saw the casting), so I thought the inclusion of POC in other main roles as well as in the world in general was at least a step in the right direction where Hollywood has a long way to go.

    Anyway, it was driving me bonkers that Jeremy kept bagging on this book, so I wanted to share my recommendation and explain a little about why it was so meaningful to me as a female ecologist. I also universally recommend Black Panther (also deeply rich female characters, amazing world building, and much more of a sci-fi vs. traditional superhero movie) and can’t wait for Wrinkle in Time!

  7. Direct instruction was tried in an Australian indigenous school where there was a high turnover of teachers. I think the thought was that in such a situation perhaps a “teacher-proof” curriculum that could be handed to new teachers would be ideal. This one implementation, I believe, is seen by many as a pretty big failure in terms of student outcomes per dollar invested

    https://theconversation.com/what-went-wrong-at-aurukun-school-62175

    It’s unclear how much of that is due to scripts not tailored to the unique culture, strengths and weaknesses of the students seeing the material [as it is a US based product – and hence likely tailored to US students]. So it could have failed because of something wrong with DI or it could just be evidence that it needs to be tailored to each audience. There are likely other confounding factors as well.

    I’m not that familiar with DI, but I am not aware of any studies where it has been used in college classrooms, and my guess is that the higher you go up the educational ladder, the worse this kind of heavily scripted instruction might be.

    • Interesting, thanks.

      Yes, insofar as the scripts need to be heavily tailored to many different groups of students, that would seem to undermine what I understand to be one of the main arguments for direct instruction: that it’s “teacher proof”.

    • In the link you reference, the DI program was for kids with a learning disability, not for English Second Language kids. DI in general isn’t specifically for learning disabled children as far as I know, so it sounds like someone bought or was sold the wrong program.

      “the higher you go up the educational ladder, the worse this kind of heavily scripted instruction might be.”

      I don’t know if I agree with that, either! 🙂 As I recall, the pre-test study sessions for most of my undergrad courses consisted of me coming in with a list of questions and everyone else scribbling madly when the prof answered them.

      AT the study sessions that the students organized themselves, I often tried to convince them that their notes or their interpretation of them was incorrect, usually in vane (student: “no but Dr. X said this or that”; Me: “Well, no, he couldn’t have said that because it doesn’t make sense”). They always default to what they think they’ve been told rather than reasoning through the problem, so it’s not clear that the teaching is giving them any reasoning ability at all. At least with direct instruction, the steps would be broken down enough that they couldn’t come to the wrong conclusion, even if all the reasoning is done for them.

      • “As I recall, the pre-test study sessions for most of my undergrad courses consisted of me coming in with a list of questions and everyone else scribbling madly when the prof answered them. ”

        At the risk of derailing the thread, that’s why as an instructor I don’t like relying primarily or exclusively on review sessions for which I just answer questions from students. Typically, most students show up hoping somebody *else* came prepared with questions. Which only the best-prepared students (i.e. those least in need of a review session) typically do. Writing down the answers to somebody else’s questions is mostly not helpful for learning.

        “At the study sessions the students organized themselves…At least with direct instruction, the steps would be broken down enough that they couldn’t come to the wrong conclusion, even if all the reasoning is done for them.”

        Students do learn a lot from talking to one another as they think through problems. Even the best-prepared students learn from doing that. That’s one of the main rationales for why we teach intro biostats using a team-based format:

        https://dynamicecology.wordpress.com/2016/02/22/we-flipped-our-huge-intro-biostats-course-heres-how-part-1/
        https://dynamicecology.wordpress.com/2016/03/09/we-flipped-our-huge-intro-biostats-course-heres-how-we-did-it/

      • It just seems to me like over the years I’ve noticed many things that increasingly suggest to me that repetition, which Direct Instruction uses heavily, really is the key to learning. Isn’t it true that, even in college, students are still forming synapses? They *don’t have* all the physical tools yet – you’re helping to form the pathways that they’ll use to reason in the future, so it’s important that they be correct. Repetition of quality materials creates the appropriate connections.

        Could the “baby formula” moment be coming for education? Where we realize the new technology is inferior to thousands of years of natural experimentation?

        I don’t know that much about direct instruction, but the repetitive aspect of it seems almost certain to be effective. OTOH, most of the supposed “new” methods require a lot of careful data gathering – and I mean careful to avoid gathering some data – to get not very much benefit.

        From my professional experience, I assure you that 1 out of 25 students being prepared for anything is about par for the course. If every student learned nothing from university except to prepare ahead for everything, the world would be a much better place. Alas….

  8. I gave a presentation on Erasmus Darwin for a Darwin Day celebration here at UMN a couple weeks ago. One of the coolest things about him is the fact that he seemed to know nearly all of the luminaries of his time — James Watt and Matthew Boulton, who produced some of the first practical steam engines; Joseph Priestley, who helped discover oxygen (a word which, to my knowledge, first appears in English in one of Darwin’s poems); Josiah Wedgwood, the famous potter; Joseph Wright of Derby, who made some of the finest ever paintings on scientific subjects; and poets like Anna Seward and Samuel Taylor Coleridge. (Coleridge: “I absolutely nauseate Darwin’s poem.”) There are so many fascinating little anecdotes about his life. For example, after Darwin published “The Loves of the Plants,” George Canning — who would later become Prime Minister — became incensed by Darwin’s supposedly Jacobin tendencies and published a satire called “The Loves of the Triangles.” Reading about Darwin’s life, you really get a sense of how science, politics, religion, and the arts were intertwined during his time.

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