Mailund on the Internet

The paper I described in a previous post: Investigating selection on viruses: a statistical alignment approach, just got published online today.  Yeah us!

Following up on the last post, and an older one, I’m going to rant a little bit about the reviews I’ve gotten on two papers recently.

I’m not complaining about the reviews I’ve gotten for the Bioinformatics paper I mentioned in the previous post.  Those are detailed, thoughtful, relevant and all reasonable.  There my only problem is that I have a page limit that keeps me from adressing all the comments.

What I am a bit miffed about is two papers submitted to BMC Bioinformatics.  Do not take it as a critisism of that journal, though, I have also gotten nice reviews there.  I have another paper submitted there, that is getting nice reviews (in the sense that there are lots of suggestions to consider, not that they are just positive). Not so for the last two papers.

First of all, the review reports are very short.  Maybe 15-20 sentences.  Secondly, there aren’t really any constructive criticism. Not surprising with less than 20 sentences, of course. Thirdly, and this is the most annoying, they haven’t made any decision!

The “positive” reviews are just summaries of the paper (essentially paraphrasing the abstract).  The “negative” reviews are saying things like: “I do not really like this / I do not find it interesting” or “other people are doing something similar”.

Of course reviewers are permitted to not like a paper and to not find it interesting.  They shouldn’t make their decision on this, but on whether the results are novel and sound.  If they think that the results are too small an increment on existing work — and there will always be similar work out there, if I submit it to BMC; it it was truly novel I would go for higher impact — in that case they should say so, justify it, and reject the paper!

Telling me that they do not find the results interesting, and then telling me to resubmit is just crazy! How can I make any improvements if that is all the criticism I get?

If I resubmit, the paper will end up with the same reviewers, and they still won’t like it.

The form letter from the editor just asks us to resubmit and include a cover letter “addressing the reviewer concerns”.  That is of no help at all!  “To make the paper more interesting, we have included a Dilbert strip and a picture of a clown.”  Is that going to work?  I doubt it.

This is really pissing me off.

If, as a reviewer, you do not have any constructive criticism — good or bad — just make your decision and let us get on with our lives.  If the paper is rejected, it would probably also be rejected after a resubmission, but now I know that so I can decide on whether to abandon the paper or try somewhere else.

It is not just the reviewers that are the problem here, though.  In a situation like this, I think the editor has a lot of the responsibility.  The final decision is his, so he should get involved at some point.  By now, he should a good idea about whether the papers will get accepted or rejected.  After all, there are no additional experiments or improvements suggested, so the content of the papers are not going to change.

As a side note, BMC isn’t that bad in this regard.  We once had a paper at European J of Hum Gen in review for more than a year, where each iteration consisted of very minor changes but the form letter kept telling us that no decision was made yet.

We all want our papers as good as we can get them, so if you have made your decision then let us know!  If it gets rejected, we wont waste any more time on it, and if it gets accepted we will still address reasonable comments to improve the final version.

You are no more “unable to make a decision” at this point than you will be after a resubmission, if the reviews do not ask for any actual additional work!

Grrr!

This is a typical situation for me: I submit a paper to a journal or conference that is just to  under the page limit.  I get review reports back, and each reviewer has a few reasonable suggestions to additional experiments or possible extensions or papers worth referencing.  I want to do the extra work — it is reasonable and I will learn something from it — but there just isn’t room in the paper to write about it!

Right now, I’m editing a paper for Bioinformatics, where the page limit is seven pages.  I’ve done all the work suggested by the reviewers but I’m practically putting it all in the cover letter instead of the paper.  The cover letter is now as long as the paper itself.

What do you do in a situation like this?

The reviewers’ decision is based on the submitted paper, so there is a limit to how much I can remove.  I cannot completely rewrite the paper, since the journal want me to mark up all changes (and I doubt that they will be happy with markups showing that I’ve changed everything).  So with the submitted manuscript being seven pages, I can only make very minor changes to the paper, and I still need to find a way to address all reviewer comments.

It is an impossible task!

I guess I should always leave a page or so for the second submission, but usually I find it hard to get down to the page limit in the first place…

Sciencewomen describes a problem I know very well:

On a day when I am feeling increasingly dismal about the publication prospects of my current project, my mood was not lightened with the arrival of the table of contents for the current issue of a very high impact journal (say, cell/nature/science). One of the papers was right up my research alley and the lead author is someone junior to me. Why is it that the other guy is getting a very high profile paper and I’m struggling to get results that will merit publication at all?

I did my PhD in theoretical computer science, where high impact papers (high impact outside your own field, that is) are few and far between, and I didn’t really expect to write high impact papers then.

Now I’m doing bioinformatics, and that is a hot field, so now I do want to, but I am not particularly successful.  There’s a few that have received some interest, in particularly this one about the speciation of humans,  but I wasn’t the first author on that.

Lately, I do not seem to manage to be first author on any paper…

I’m in the weird situation where I am not senior enough to be last author on any paper, but I am spending too much time on too many different projects that I can focus enough on a single project to expect to be first author on a paper.

I feel like I’ve substituted quantity of publications for quality.  Of course, I have no one to blame but myself, so I just need to change my working habits, I guess.  Spending too much time blogging probably doesn’t help either.

Great, now I’m depressed.  What a way to start the day…  Oh well, I’ll head to the office to get some work done, that should cheer me up!

Bayblab asks: Publish and/or Perish — When to Submit that Manuscript?

There is a trade-off between the quality of a paper and the  time it takes to get it done.  Not so much the actual writing — it doesn’t take much longer to write a well-written paper than a poorly written one — but the research that goes into the paper.   In the long run, writing high quality papers is what matters (the metrics on productivity such as the h-index include how many other papers reference your papers, not only how many papers you have) but the quantity of your publications matters as well, especially early in your career.

This is an important question to consider whenever you are working on a paper.  In my own case, I think I consistently err on submitting a tad too early.  My problem is that I get bored with what I am doing.

A lot of my research is methods development, and there it is exciting to get the first 80% of the method up and running — and that usually takes less than 10% of the time needed to truly validate it.  After I have convinced myself that the method works, I need to explore the parameter space where the method is applicable, I need to compare it to other methods to judge strength and weaknesses, etc.  This takes ages and is pretty boring work, so at some point I just give up.  At that point, I either abandon the project all together, or I submit a paper to a lesser journal.

With experience, I am hoping to get better at picking the right experiments up front so I don’t have to go through the long experiments phase that just bores the hell out of me, but right now I am really struggling with it.