What should you do when Reviewer #2 says “Cite my papers”?

It’s been a rough couple of weeks for rose coloured glasses in biology. There’s the unfolding saga of paper retractions in social behaviour; and then there’s cite-my-paper-gate.  I don’t have much to say about the former (beyond expressing my admiration for the many scientists who are handling their unintended involvement with grace and integrity).  But the latter made me think.

If you didn’t hear about cite-my-paper-gate: someone (yet to be publicly identified) has been busted over all kinds of reviewing and editing malpractice.

The climbing metaphor, or where should we encourage students to send their papers?

This is a guest post by Bastien Castagneyrol.  This is an issue I’ve thought about (as have others), and like Bastien, I don’t quite know what action to take.  I like Bastien’s climbing metaphor.  In a related one, the journey from subscriber-pays paywall to author-pays-open-access crosses a very rugged landscape, with crevasses both obvious and hidden.

Disclosure from Bastien: what follows is not exhaustive and could be much better documented. It reflects my feelings, not my knowledge (although my feelings are partly nurtured with some knowledge). I’m trying here to ask a really genuine question.

The climbing metaphor

My academic career is a rocky cliff.

Turning our scientific lens on our scientific enterprise: a randomized experiment on double-blinding at Functional Ecology

Image: Experiment, © Nick Youngson via picpedia.org, CC BY-SA 3.0

I’m often puzzled by the reluctance of scientists to think scientifically and do science.  “Wait”, you say, “that’s a bizarre claim – we do science all the time, that’s why we’re called scientists”.  Well, yes, and no.

We love doing science on nature – the observations and experiments and theoretical work we deploy in discovering how the universe works.  What we don’t seem to love nearly as much is doing science on ourselves.

What copyediting is, and what it isn’t

Image: a snippet of the (excellent) copyedit for my forthcoming book.

Over the last six months, I’ve had several pieces of writing go through the copyediting process: a few papers, and one book.  Over my career, I’ve seen closer to 100 pieces of writing through copyedits.  It’s a stage of publication that was, for a long time, rather mysterious to me, but contrasting two of my recent experiences provides a pretty good illustration of what good copyediting is, and what good copyediting very definitely isn’t.

It’s been a while since I’ve been this proud of a paper

I don’t usually blog about my own papers, except in some rather meta ways, but last week saw the publication of a paper I’m really, really proud of.  And it has some interesting backstory, including its conception right here on Scientist Sees Squirrel.

The paper is called “Site-selection bias and apparent population declines in long-term studies”, and it’s just come out in Conservation Biology.  It started, back in August of 2016, with a post called Why Most Studied Populations Should Decline.  That post made a very simple point about population monitoring, long-term studies, and inferences about population decline.  That point: if ecologists tend to begin long-term studies in places where their study organisms are common (and there are lots of very good reasons why they might), then we should expect long-term studies to frequently show population declines simply as a statistical artifact.  That shouldn’t be controversial – it’s just a manifestation of regression to the mean – but it’s been almost entirely unaddressed in the literature.

A bunch of folks read that blog post.  Some were mortally offended.

Reconciling the two functions of peer review

Image: Gandalf the Gatekeeper, CC 0 via goodfreephotos.com

Peer review is arguably central to what we do as scientists – to a considerable extent it’s what lets us recognize an authentic scientific enterprise.  Consider, for instance, the distinction between peer-reviewed publications and hack pieces in predatory journals; or think about how peer-reviewed grant proposals differ from pork-barrel politics.  Given this key role, it’s rather surprising to find a great deal of disagreement about what peer review is for, how it works best, or even whether it works at all.

Along these lines, I was very surprised a couple of weeks ago to see a flurry of tweets from some folks who wanted journals to give them a simple thumbs-up or thumbs-down on their manuscripts.  No comments, please, and no suggestions for improvement, thanks, just a writ of execution or an ennoblement.

My most important work is not what I’ve always thought

Image: This mobile, hanging in my office, was given to me by my friend Mary Harris when I got tenure.  It’s driftwood from the Skunk River in Iowa.  I’d just gotten tenure, and it’s made of dead wood – get it?

A rather poorly-executed and very poorly-communicated study made a big splash last week, with the claim that half of all ecologists “drop out” of the field within just 5 years.  The many, many flaws in this way of measuring and communicating people’s career trajectories have been thrashed out in other places, so I’ll just note for the record that by the paper’s critera, I myself have “dropped out” of the field.* 

How long should you wait before nudging the journal about your manuscript in review?

Image: “Waiting”, Edgar Degas, circa 1882 (pastel on paper). Collection of the Getty Center, Los Angeles.  Public domain.

I’m sure it’s happened to you.  It’s happened to me.  With excitement, you punch the “submit” button, and celebrate your manuscript being off your desk and into peer review.  And then you wait.  And wait.  And you wait some more.  Sometimes, it feels like you’re waiting forever.  When that happens, is it appropriate to e-mail the journal office to ask what’s holding things up?  And if so, how long should you wait?

The “publication power-of-attorney”, and why you should have one

(This is a lightly edited version of a post that originally ran in January 2015. But you probably didn’t see it then.) 

Here’s a problem you might not have thought of: did you know you can submit and publish a paper with a coauthor who’s deceased, but not with one who’s in a coma and might recover?

A lot of people have never thought of this, and a lot don’t think it’s a problem worth worrying about.  Please bear with me, though, because I think it’s a more important problem than most of us realize – but also one that’s easily avoided.

The unavailable-coauthor problem is actually more general than my coma example.

Do you really have to rewrite your Methods for every new paper?

Image: Recycling logo by gustavorezende, released to public domain

Warning: long post.  There’s a TL;DR in the Summary at the end.

Is recycling Methods text from an old paper, to use in a new paper that applies the same techniques, efficient writing – or self-plagiarism?

We’ve all had the dilemma.  You write two papers that use (at least some of) the same methods.  For the first paper, you craft a lovely, succinct, clear explanation of those methods.  For the second paper, you’d like to just cut-and-paste the Methods text from the first one.  Can you?  And should you?