Wednesday, August 19, 2009

Manuscript Update

I really should be working on my tenure case right now, but ... it's numbed my mind past the point of functioning at this point. So, since I said I would, here is my manuscript update and some thoughts on the process. So, I'm batting .500 (1 for 2) in my current spate of first author manuscript submissions.

1. Manuscript One: Sent it off to Applied and Environmental Microbiology only to get reviews telling me it was "too applied". Was told that it "... read like an engineer wrote it". Too applied? Written like an engineer? WTF? Well listen folks, when I write about an applied microbiological process, what do you expect? The system is actually used in an engineered management setting. It was a novel/interesting study because under similar situations experienced by other systems under these conditions (and we checked several), ours performed between 200% and 800% more efficiently. There was not a single previously published study which outperformed our system. That didn't seem to make much of a difference. Oh well. But, hey ... aside from a 100+ day wait through the peer process when we directed it towards another journal it wound up being accepted by said journal which has a higher impact factor than AEM. Win for me.

Take home message: Just because a particular set of reviewers doesn't like your paper doesn't mean your paper isn't worthy of publication. When you get back a review, sit down, check over those reviews and if they're a load of bullturd, make the revisions you do need, reformat it, and send it back out. Try to get that process done within a couple of weeks. There is no use, if you do not plan on making major revisions, to let it sit on your desk for much longer. All it will do is delay the time it takes to get it accepted elsewhere. If you get a similar review the next time, then you should reconsider your science, but if your science is sound, don't give up on the paper.

2. Manuscript Two: Sent it to my new favorite journal (Soil Science Society of America Journal). It received a quick turn-around, and I was able to watch the entire process online. Not only that, but the journal strives to make the peer review process double-blind. Within reason, all identifying information is stripped from the manuscript. Obviously, if you cite yourself a lot, figuring out who sent in the manuscript is not a problem, but overt naming of the manuscript submitter is taken out of the paper. I like this style of review. Unfortunately, the paper was not accepted (was told when I resubmit, I should submit it as a new manuscript since it would really amount to a new work). However, the three reviewers sent back to me the most detailed and helpful review I've ever received. In total, they spent about eight pages combined detailing my experimental methods and the interpretations of my data and told me what they agreed with, and what they disagreed with. When they disagreed, they spent considerable time telling me why. In essence, they left me with a blueprint of what they would accept for publication. The things they disagreed with really didn't come as too much of a surprise for me, and the bonus is that the things they did suggest, we've already done (and figured we'd use in another publication). So, now all I need to do is switch around the data in the two manuscripts and send it back off.

I'm not sure if they figured I was new to this field and wanted to walk me through their world, or if this is standard for the journal. I figure I'll find that out with my next submission. However I was stunned by the level of detail put into a review for what amounted to a rejected manuscript.

Take home message: Appreciate criticisms of your manuscript. While this may seem to contradict the first take home message, I think we can all tell the difference between a simply negative review and valid criticism. If the reviewer spends no time detailing why they disagree with your premise, but simply tells you to take it elsewhere, the peer review system has failed. That's not a review. It's passing the buck. So when you do get thorough reviews, appreciate them, take them to heart, let them allow you to grow as a scientific investigator.

Before these two manuscripts, I had never had a manuscript rejected before. Perhaps I was just lucky, but it was bound to happen eventually. Fortunately I learned valuable lessons with these two manuscripts. I do not delude myself into thinking that my pooh doesn't stink. In case #2 I definitely can see the areas where I stretched, and the reviewers didn't buy it. They figured the data I was presenting would be good for different analyses, just not the one I was trying to answer with that particular manuscript. I can buy that, and I'll do (have done) the work and get them back out as quickly as I can. The point for me is that I use this as a moment of growth. I could have gotten pissy and sent out #2 to a lower-tier journal and probably have gotten it in, but I saw this situation as different than situation #1. It also reinforces that I need to be thorough, helpful, and honest when doing my own peer-reviews. That is how the system succeeds and works as intended.


Genomic Repairman said...

Congrats, sounds like the SSSAJ will lead to better science and hopefully a better published paper. Batting .500 is not too shabby if I do say so myself. I mean if you could keep it up, the Mets might pencil you in for the 3,4 and 5 spots in the lineup (and I know they whipped up on Lowe today).

Philip H. said...

Congrats. Yep, .500 is a great batting average, though you imply higher based on cumulative totals. I'm also having a WTF moment on your Applied paper -if that's in the name of the journal, what exactly do they expect?

soil mama said...

thanks for the post, it's always good to hear other stories of the process. I'm glad SSSAJ was so good to you. I can't help but to be curious about the content of the paper... was it an ARISA one?

AEM confuses me at times. Sometimes they have such great papers, and other times I wonder how such obscure crap can get published there. care to share which journal it ended up at?

Thomas Joseph said...

GR: Bah, it's gotten so bad that I've stopped even following up on them. To top it all off, both of my fantasy teams have tanked as well. It's a lost year. Hopefully the Sooners can do something better than a Big XII Championship this year.

Philip: I certainly have my fair share of publications, and fortunately they're quickly expanding (5 papers [2 first author, 3 collaborations] in various stages of reviews, revisions, writing). The whole AEM process was clearly a WTF moment for me too, though it didn't phase my collaborators. They told me to send it right back out without any modifications.

soil mama: Yeah, I liked the way SSSAJ handled it, even though it didn't go in my favor. It did involve RISA, and overall they didn't have problems with the techniques, they just thought I was a bit too broad in my approach. I disagree somewhat, especially when I've seen similar approaches using Biolog plates for single carbon source measurements to determine overall diversity, and then link that to specific biochemical processes. They wanted me to get "more specific" and save the RISA for other analyses, which we'll do.

soil mama said...

oh, don't even get me started on Biolog! I understand the intent behind it, and I want to believe in it, but I just can't get over the "culture" aspect of it. I've heard there is a "new" biolog coming out that should overcome at least some of the issues with the current method... I think I'd rather just do a bunch of soil enzyme assays.