15-min Improv Blogging 2

1. I just received a revision of a paper I had previously reviewed. I gave them a very positive and enthusiastic first review, but required that they do two things, which I know they can do, as some of the authors have done them before on similar systems, and which I know would require a few weeks of work; the cost of the additional work is not onerous, as it’s computational. They came back not having done anything to the manuscript. They wrote a response in which they argued that what I had asked them to do was a great idea and something they should ideally do, but that it would take too much time (I disagree) so they just don’t want to do it right now.

A word of advice to anyone who will ever submit a paper for peer review: you should not expend all your time and energy on the response letter, arguing with the reviewer. If you don’t want to or cannot do what was required, then do something else instead. You have to make some edits in response to what was required. A comment, a reference, a paragraph of discussion along the lines of what the referee requested and why it is a good idea in principle but not right now and might be done later.

How can I accept your paper when you have made absolutely no edits whatsoever to it? As if  my first report never happened.

Err on the side of more editing rather than rebutting.

2. I am not an entrepreneur. I don’t want to be an entrepreneur. I just looked at the funding call from one of DoD agencies for technology transfer/small business proposals. Under one topic, they want to fund the development of a simulation tool that might well have the pics of me and my collaborator on it. But I don’t want to develop a commercial tool. I don’t want to have a company and sell the code. I don’t want to supervise people developing user interfaces. I want to develop codes to address scientific problems that are too complicated to tackle without computers.

In my area, dissemination of codes is not as common as it perhaps should be. There are all the usual culprits — people don’t want to lose the competitive advantage, they don’t have the time or resources to develop the user interface, they don’t have the time or personnel to provide user support for potential users of the code, and they are afraid that if they freely share the source code (which is generally not pretty or clean) they will be found lacking. Additionally, the lack of sharing in my area happens because of a big bad dragon (let’s just say a very difficult colleague) being very territorial about the existing dissemination resources; as the resources exist, it is hard to get money to develop new ones for free dissemination, yet the existing ones are basically under siege. Maybe I will just start posting source code on my group website with a disclaimer: Use “as is” and don’t bug us if you can’t. It’s free; how much user support do you expect?

3. It is starting to fully dawn on me just how much travel I have next year. It’s a lot. There are 9 trips I already know of. Ugh.

At least I got to lie low, sort of, this semester. But the time has come to pay the piper.

I spent a lot of time last night booking flights, paying registration (I am nowhere near done). Now all those receipts have to be submitted to accounting with appropriate justifications.
And of course once I am done with all of trips, reimbursement has to be filed.

Isn’t it awesome that PhDs get to spend many hours of their time doing travel booking and reimbursement? No need to hire administrative assistants when professors can do this work at no extra cost. Next, PhDs empty trash cans and clean the toilets at the university, then take over facilities management and do all the repairs themselves. This is an excellent use of their professional qualifications and as a side benefit no one has to hire cleaners or skilled repairmen. Imagine the savings!

20 comments

  1. I know…travel reimbursement is just annoying. I need to do mine for a conference almost two months ago!

    And yes, if we like clean offices we need to clean them. Just like home.

    Urgh.

  2. My DH lives on SBIRs! You don’t actually have to be an entrepreneur– there are lots of small businesses that run primarily on SBIR funding.

    “Next, PhDs empty trash cans” You laugh, but our university tried this for about half a year. (The increased extermination expenses caused them to switch to an outsourced sanitation company that uses the same workers as the ones they laid off prior to the faculty does the trash experiment, but pays them much less and gives them no benefits.)

  3. …The increased extermination expenses… ”

    “[The university] switch[ed] to an outsourced sanitation company that uses the same workers as the ones they laid off prior to the faculty does the trash experiment, but pays them much less and gives them no benefits.

    Both are disturbing; the second one is way worse.

  4. Re #1: I hate this. The worst I saw was when I asked a question about the robustness of a result to variation of some parameters. The authors wrote a very nice response letter, including a figure showing that there was no variation. However, they did not include any of this data or even a comment describing that data in the paper. It was fairly insulting, actually, since it implied that only I could possibly care about this information (or was dumb enough to not guess it immediately), and it was not worth their time to include it for the general public. (Or they wanted to save it for the longer version of the paper…) If they had just put in a little more effort, they could have saved themselves another round of revisions.

  5. Definitely hate #1. Like you wrote, it’d probably take less time in many cases to make the changes than to respond to the reviewers. And why would one want to unnecessarily piss off a reviewer.

    Rheophile, I really don’t get the hesitance of people to include data/figures that strengthen their conclusions. Nearly all journals have electronic supplements these days, so even if the authors didn’t want to mess with the flow of their paper or whatever, it’s easy to dump that sort of data into the supplement.

  6. I hate filing travel reimbursement paperwork. At the wealthy, private research university where I post-doc’d, the university policy was trips over 2 weeks couldn’t claim per diem. When I spent several weeks on an international sampling trip, I had to save all my receipts and then convert them to US dollars. That’s really the best use of my time? Or an administrative assistant’s time?

    At my university, we do have to empty our trash cans or at least put them in the hall to be emptied. The problem with the hallway is that 1) several days will go by without them being emptied and 2) when they finally are emptied, the trash cans are often taken. Of all the things I should be spending my time on, I’m pretty sure it’s not tracking down replacement trash cans and recycling bins for my lab because somebody has swiped them for the 4th time in a couple of months.

  7. Why do they expect students to respond to commentary if they don’t respond to their own reviewers’ comments? Why bother with the process of peer review at all? Ugh.

    Free the code! (Isn’t that supposed to be the whole point of open source?)

  8. It’s disgraceful that journals in your field allow publication of computational simulation results without requiring provision of the code to other scientists who request it. In the molecular biology and genetics fields, journals absolutely require that any recombinant DNA and genetically modified organisms be made available to other investigators. This is fundamental to the scientific principle that other scientists are entitled to reasonable access to information, reagents, or other materials required to replicate published results.

  9. CPP, we had this discussion before, I am not about to have it again.
    Source codes in computational physical sciences are not analogous to recombinant DNA or genetically modified organisms in biomedical sciences.

  10. Regarding the source code, a motivated undegrad (or a more programing-oriented grad) student might be able to clean it up a bit to release it as open source under a respectable open source license (GPL comes to mind). A very successul example is the free FDTD code MEEP, from MIT. It is not the most feature-filled code out there, but it is free, quite powerful and flexible (and very widely used and cited). I guess the key is to have the software be someone’s “baby”, and that this person is more interested in working on the code itself rather than using it to explore the science in deep. If the software ends up being successful, that person could provide (in a voluntary basis) support in a forum or mailing list. But, in my opinion, this would require a special person, as I don’t think it is something any random student should be pushed into doing.

  11. EarthSciProf: as it happens, the figure did end up in the supplement of the paper. The only reason I can think of for why someone might not want to add it (beside laziness) is publishing conventions in the field. Often, people publish a letter with a summary of results, and then additional details in a lengthened paper. I think this makes some people wary of adding too many details to their letter supplements, because it might prevent them from writing the later paper. I disagree pretty strenuously with this: letters ought to include sufficient detail to actually convince people and at least hint at how you could reproduce the result!

  12. I’m waiting for my university to install little payment boxes by the bathroom, to charge us every time we use it.

    I’m not kidding.

  13. “Next, PhDs empty trash cans…”

    Actually, our U recently instituted a policy where the cleaning staff will empty your office recycling bin, but not your trash can. We have to dump our own trash into hall way bins.

    I suppose this is to encourage more recycling?? I don’t think it really does.

  14. “journals absolutely require that any recombinant DNA and genetically modified organisms be made available to other investigators.”

    I mean in theory this is true but people “forget” to reply to emails all the time.

    In Bioinformatics and modeling right now there seems to be a split developing between those who always provide great clean code in public repositories (mostly from the computer science / informatics side) and those who will only give it to you kicking and screaming (mostly from the math/modeling/biology side). A colleague once told me, regarding sharing code: “Why should I give them the code, I told them how to do it with the math in the paper, they can rewrite the script themselves.”

  15. Love point 1–so true. I just edited a paper the Reviewers loved–they only asked for some very modest changes. Instead of making them or adjusting text to acknowledge the issues raised, I got a long list of arguments. DON’T do that! Address each and every comment in some way and everybody is happier. In my case I made the person do so, and then accepted the paper–I hope they learned a lesson.

    Point 3 is also so true……. sadly

  16. As a bioinformatician I see both sides of the “provide code” debate. I’ve had referees complain when I provided open-source code that I hadn’t compiled it for their version of Windows (I don’t have a Windows machine).

    There is also the problem that the code does not always reflect exactly what the paper claims for it, but if the code is provided, most people will just use the provided code and never notice that it isn’t what the paper claims. Forcing re-implementation forces validation of the method—computational experiments are not validated by rerunning the same code on the same data, but by changing the data or re-implementing the method.

  17. At my place (well-known private hospital/med school) we’ve been emptying trash and vacuuming/dusting our own offices for years. What I hate most is the paper recycling– as theoretically we may have protected health info to dispose of (not that we ever do in my unit), printed media have to be ripped apart and fed about 10 sheets at a time through a narrow slot in a locked bin for recycling. Either that or, you know, send it to the landfill.

  18. As a specialist within civil engineering (not-in-academe), I have to say that I deeply appreciate reviewers. What I write is generally not aimed at people in my specialty; instead, I write for other fields to explain how what I (we) do intersects with their parts of a project and how to make the design for the intersection(s) more efficient. The best reviewer for me is someone who knows something about my field, but not a lot, is deeply involved in their own field, and who is not afraid to tell me (s)he doesn’t understand what I am describing. This helps me see where I need to explain further and — as long as the reviewer is part of the target audience — what the interests of the readers may be. If I get a reviewer who is in my specialty, often I get comments that demand more theory and design detail that I feel is not helpful to the other not-my-field designers unless they are looking to change jobs. This especially is a problem and is likely when I am writing about elements that are not explicitly covered in the Codes. These are (a) more likely to require explanation for others because they are more specialized and less common and (b) frequently use a lot of unfamiliar-to-many applications of analysis.

    I love having comments to respond to and am grateful the reviewer(s) took the time.

    *+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+*+

    ” (The increased extermination expenses caused them to switch to an outsourced sanitation company that uses the same workers as the ones they laid off prior to the faculty does the trash experiment, but pays them much less and gives them no benefits.)”

    THIS is disgusting, much more so than vermin.

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