Saturday, June 06, 2009

Oh, so that's what it's called!

Had a conversation with a new postdoc in my lab who is trying to publish some leftover papers from her PhD work.

I guess this is a pretty common predicament nowadays, to be a postdoc who has actually never been through the experience of scientific publishing.

There are several things that are really baffling about the "process".

1. Formatting

This used to make sense in the days of yore printing, but it makes less and less sense as most of us get our journals online.

2. Anonymous reviews

They asked for WHAT??!! Often leads to the question of who is really your peer and what the hell they are doing writing reviews.

3. Editor-speak

As in, when the response is actually favorable but it sounds like it's not. Or, as is more often the case these days, the response reads as if they really didn't understand what was written in the reviews.

4. Reject means resubmit

Even when a paper is soundly rejected, the tradition is fast becoming to resubmit anyway, and browbeat the editor into sending the paper back out.

5. How long this all takes

So let me get this straight, she said. It's going to take a month or two to get the reviews back? What am I supposed to do in the meantime? Take out my crystal ball and try to guess what they'll ask for?

6. How little time you have to address the reviews

Most journals give you 2 months to do any and all experiments, but you're supposed to know that you can negotiate for more (even though it's not at all clear that this is negotiable if you read the journal websites).

7. How political it all is

Whether it's better to have presented the work in public first very close to when it will be submitted; or not at all. Whose names are on the paper; whether the reviewers you suggest will be the ones the editor uses; whether people with a conflict of interest will recuse themselves (no, they won't!).

8. Who's really going to get the credit when it comes out

Your PI. Whether s/he had anything to do with any of it or not.


In related news, this week I learned there is a term for what has been going on that is ruining my field. Apparently Richard Feynman called it Cargo cult and I think the description on wikipedia is totally accurate. Since I saw this on a blog but now can't remember where, apologies and thanks to the person who wrote about it.

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At 12:20 PM, Anonymous Anonymous said...

glad you found Feynman. You should read more of his stuff.

I have a few comments for your 8 points.

In general you have more power than you think but you should use it sparingly because it affects your reputation in ways that you might not understand.

2. You can always refute the validity of a reviewer's request. Tangential studies to satisfy someone's curiosity, work that goes beyond the scope of the conclusions of your study, impossible or uninterpretable experiments, absurdly redundant studies. You are well within your right to refuse to do these things. You can also temper your conclusions. Not everything is generalizable. You have to justify these decisions to the editor moreso than to the reviewer.

4. If you or your PI can browbeat an editor they must be very special. My lab routinely gets stuff in that tier of journals just below C/N/S with 1 C/N/S paper every ~3-4 years but has absolutely no leverage with editors when a manuscript is rejected. This barrier should be respected and for every example where someone gets crap published in a too high tier journal we all suffer - I can think of a couple studies a year over the last decade in my subfield and it pisses me off and makes me an exceptionally tough reviewer when I get sent one of their manuscripts.

6. If you don't realize that all things are negotiable, you will not succeed. Some journals keep a manuscript submission open for resubmission UP TO A YEAR after you get reviews back without you even asking (and they still formally give you 6-8 weeks to reply). To a one, including C/N/S, they will give you at least double the time they say to do the work if it is extensive. Most of the time, though, they say that addressing all reviewers comments does not mean that they will publish your paper. And if you take too long responding to comments your manuscript may no longer be timely enough to warrant high impact publication.


8. IF YOU ARE GOING TO BE FIRST AUTHOR IT IS ALWAYS WORTH PUBLISHING (at least until you get tenure) even if someone else is the corresponding author. If it is a huge burden to get the manuscript written and you made a substantial contribution to the origination of the study as well as the work and authorship of it, negotiate to be a co-corresponding author with the senior author especially if you have (multiple) other papers with them.

At 3:14 PM, Blogger Mikael Vejdemo-Johansson said...

For me, both 3 and 4 popped up during my PhD studies.

First off, I'm in mathematics. No big labs, no page-long author lists. I just now - during my first year of postdocing - got a coauthored paper out, and I still have never coauthored anything with either my advisor or my PI.

Nevertheless, even though some things are different in different areas, others seem very constant across the board.

So, my first attempt at a paper during my PhD was rejected. With good reason, in retrospect, and with a very nice and solid recommendation from the referee to work more on the project and resubmit once more results were present. We have our suspicions about the identity of the referee - and he is very favourable to my advisor and his work...

My second paper out for review was on a substantial portion of my thesis. The review came back, and had a typo in it as well as the "Sounds like condemnation but isn't really." It pointed out the entirety of section 3 of the paper as being already well-known and having WAY too many too long proofs of well-known ideas.
Reading this devastated me completely - as section 3 was devoted to the actual original research portion of the paper, and I read it as telling me that all my ideas were lousy and already well-known. On my advisor's explicit order, I ended up emailing the editor and asking for clarificiation - upon which it turned out that there was a typo: it was section 2, the background survey, that had too many proofs and stated well-known results (duh!); and contingent basically only on my cutting out the proofs from section 2, the paper was accepted.

Which is a marvelous thing to hear. If you're actually able to read that from the text you receive.

At 8:48 AM, Blogger Schlupp said...

"As in, when the response is actually favorable but it sounds like it's not."

Yes, this one puzzled me back when....

"I guess this is a pretty common predicament nowadays, to be a postdoc who has actually never been through the experience of scientific publishing."

... I was a graduate student. Now, I can understand there may be differences between fields and everything, but isn't that a MAJOR problem if you go through your PhD without having published? Or do you just mean that these students were sheltered, because someone else took care of the, ahem, 'technical details'?

At 11:48 AM, Blogger Ms.PhD said...


2. Yes and no. If the editor is an idiot, you are screwed.

4. If your PI has browbeaten editors in the past, and your current reviewers are trying to punish your PI when it is actually your paper- does this seem fair to you? Maybe you should consider that the first author might be somewhat helpless in these situations?

6. Agreed. But again the PI has to agree that it's worth doing. My thesis advisor, for example, did not understand this and did not believe me when I explained that this is how it works now.

7. This makes great sense- unless the number of people you are allowed to exclude is much smaller than the number who are against you. Also, in reality, editors are not required to respect your request, and frequently will send your paper immediately to whomever is on that list of "please don't".

8. Negotiate, ha. Great idea. Too bad it doesn't always work, and many of us are under the thumb of "advisers" who refuse to distribute credit fairly or accurately.


What a great story! Glad to hear that your advisor gave you good advice and that it all worked out in the end.


No, I do not mean technically or sheltered from the details. I mean, never having published any papers. This is much more common than most people realize, I guess. But just ask the people who review postdoctoral fellowships for NIH. They've been trying to make it essentially a requirement that you've published at least 1 first-author paper in order to win one. They must see a LOT of applications that lack even that minimal requirement.

At 6:04 PM, Anonymous Anonymous said...

MsPhd- re: your re: to point 7. I actually don't think this is as dire as you think. At a summer program, a C/N/S editor came to speak to us, and this is something he was asked about. He said that editors are completely used to this, and that it does not reflect badly on you to exclude people, because they know that all kinds of things can happen that would change how objective people can be. The editor also isn't likely to send it to them, because he'd want an unbiased non prolonged and dramatic review process.

I think it does work to exclude. We have a competing lab that doesn't like us much, and because of the heavy overlap in topic, many of the members are highly likely to be selected as reviewers for us- we routinely ask to exclude the PI, and some of the particular people from the group closest to the work in the paper, and as far as I can tell they never get sent to them.

At 9:24 PM, Anonymous Anonymous said...

You use the word idiot a lot. Perhaps you should consider reframing this projection. The people who review your work are likely often ignorant and sometimes biased, but they are rarely idiots. It is your job to educate them, through your cover letter and manuscript, to the importance, timeliness and novelty of your results.

Editors, reviewers, academic promotions and tenure committees, etc all need to be educated (briefly) at each interaction. Few have time to appreciate the subtleties, there is a broad array of applicants that come before them.

At 9:26 AM, Blogger Ms.PhD said...

Anon 6:04,

I'm just speaking from personal experience. Like I said, there are too many jerks in my field to exclude them all.

Anon 9:24,

Yeah, rarely, uh huh.

I think you'd be surprised at some of the idiotic comments I've received. How idiotic they are, and how frequent.

I understand ignorance, I understand bias. I don't expect everyone to have all the information about what I work on, far from it.

And personally I think we should try to be aware of our biases, but most scientists refuse to admit that we have any. I would love to see a review that said "Admittedly, I'm biased because of ___ but I think you should do ___ experiment to address ___, just to rule that out."

And yet, that's rarely what they write, isn't it.

I personally disagree with a process where any editor who is not an idiot can clearly see that the reviews are biased, but sends them along routinely in spite of that-! Which leads me to conclude that some of these editors must be idiots.

I do agree with educating the audience. I'm a huge fan of that. But how am I going to educate them, in a cover letter, as to how biased their whole search process is? How they shouldn't overlook me if my CV isn't as strong as the Blond Guy's?

To be really educational, I can always include a copy of several of these reports reviewing how bias works against women at all levels from publishing to funding to search committees... but somehow I don't think they would appreciate that.

And it's funny how irrefutable data can bring out the idiot/asshole faster than you can say "But I'm really very smart!"


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