Thursday, November 17, 2016

How to tell if your aphid is done reproducing.

If you want to know if a parthenogenetic pea aphid is all done reproducing, look at her abdomen. If there are eyespots, she still has embryos in her. If not, she's done. If she is post-reproductive, she's likely to move to the edge of the colony, where risk of predator attack is highest. Details are here, in a paper written with some very talented undergraduates at Bates College.

How not to respond to unhelpful peer reviewers

For as long as I've been a scientist, and longer, there has been extensive discussion on the many ways that peer review is broken. Peer review is how, in theory, science gets evaluated and hopefully improved, before publication, and therefore hard to dispense with, despite being widely seen as inefficient, biased, and corrupt. It goes like this: Author submits manuscript to journal, journal sends it out to independent experts for feedback, these experts (the scientific peers of the author) decide whether they are expert and independent enough to give appropriate feedback carefully read it, think about it, identify its flaws, make constructive detailed suggestions, and finally recommend to the journal whether it should be published as is, fixed and then reevaluated, or just rejected. That is, at least ideally, how is supposed to work.

There are a great many ways in which that ideal can fail. I draw a great deal of schadenfreude from reading Retraction Watch, which is effectively a blog about cases where peer review failed in one of many ways, something was published, and mistakes or misdeed were later found out. I, like most scientists, know a few people whose work may show up all over Retraction Watch some day.

Which brings me to the fact that I am currently figuring out how to respond to a review that has failed with regards to independence, expertise, detail, fact, specificity and constructiveness. I would have suggested to the journal that this person could not be an independent reviewer, except that it never occurred to me that anyone would consider him to know anything about the topic of the paper. Explaining the long history of this interaction to the journal, we have now been assured that our re-submission would be sent out to different reviewers. Even so, in resubmitting, I have to respond to all the reviewer's comments, even those that are wildly counterfactual, have nothing to do with the current manuscript, or are just complaints about the reviewer's own work not being cited more extensively. And it has to be done politely and factually. So one must never include responses like these:
  • This highlights a fundamental difference in approach to science. Reviewer's comment, and publications, suggest that scientific papers should be fishing expeditions in which everything that can be gotten out of a data set is analyzed and those results that test significant published breathlessly. We started with one, a priori original question, gathered all of the available data to address it, and got a clear result, which we state concisely. While some authors would stretch the results section out to numerous exploratory paragraphs, expounding upon questions that were tailored to fit the results of the numerous analyses, that would surely be a disservice to science.
  • It is not clear what this means. Perhaps the reviewer did not find our Methods section. It is in there between the Introduction and the Results.
  • It does not seem that the Reviewer has any idea what kind of data we are using, despite the six paragraphs on the topic.
  • Furthermore, a reading of the manuscript would have revealed that no matrix models are employed. Reviewer's comments would seem to be hastily copied and pasted from review of an unrelated paper.
  • The Reviewer's publications are not relevant or useful here. Perhaps they were relevant to the paper for which most of this review was written?
  • This is counterfactual and the Reviewer has excellent reason to know that.
  • These quotes of the journal's rules are from an entirely different journal that the Reviewer often reviews for.
  • Not only can we find no mention of this statistical rule anywhere, we note that Reviewer's own papers don't follow it. We asked an expert in these methods about this 'rule.' She called it, "hilariously made up." 
I need some empenadas.

Wednesday, November 16, 2016

Ghosts of papers that may some day be

The world is full of science that only half exists: Experiments done but not written up, manuscripts waiting for revision, results too unimpressive to prioritize for publication. Where fetuses are gestated for months but born in hours, data sets often take longer to put out into the world than they took to create. Until it is published, academic research is only a nascent fluffy squishy wispy gelatinous downy larval effervescent ephemeral eufloccinaucinihilipilificatable translucent apparition, neither seen nor heard nor here nor there. Once published, research gains visibility, permanence, and perhaps even value.

While most scientists have things they would like to get around to publishing,  I feel like I've accumulated a particularly long list of research projects I need to push out. This summer and fall I've actually had some time to dedicated to that. I've made a goodly dent, but the list is still long, and new tasks and projects emerge like mosquitoes from an abandoned hot tub.

I've published four good papers this year, another is ready to go as soon as my coauthor has time to look at it, and a sixth just needs a few final touches, and should be submitted in a week or two. Both of those 'full term' papers will, hopefully, come out next year. I think that's pretty good considering I spent most of the last year on intensive teaching, had a months-long battle with epidemic keratoconjunctivitis, have moved my family four times in the last year and a half, and have three children five and under. There are days I wonder why I am so tired, and then there are days I remember why I am so tired. And on those days, I don't feel the least bit bad about keeping all those manuscripts, and coauthors, waiting.