One two many cooks ...

... so I've begun writing a new manuscript. We have a number of additional collaborators that we generally would not have, so I decided to, before I started my outline of the manuscript, email everyone and ask how they envisioned this manuscript taking shape. I detailed where I was thinking I'd take the manuscript (in philosophical terms ... not vacation destinations). I went so far as to let them know of the journal it was going to, and that I had already talked to the editor-in-chief of the journal about this manuscript (which is somewhat off the beaten path of what they routinely deal with) and that he was extremely receptive to this article.

I figured this was a nice courtesy email, and didn't expect much fallout from it. Yah, I was stupid. Turns out that everyone else has their own idea on the path this manuscript should take, and while some parallel my own ideas, the heaviest hitter on this manuscript (other than the one who is writing it, moi) is the most esteemed member of the group. So ... what to do? I can certainly see their point of view, but the approach they want me to take (and which other people have fallen in line with now), while it is the safe approach, does not bring the problems I wish to address front and center. It's not that I'm intending on making a huge splash with this paper, though if it happens to partly revolutionize the field I'll gladly take as much credit as people are willing to give me, but I really hate beating around the bush. My collaborators are much more conservative, thinking that you don't upset the status quo, you go for the sure bet, you play it safe, you don't fight the reviewers, you get results, and you accept it and be happy about it. With most publications, I'm happy to take that course of action. I did not want to take that action with this manuscript. Bollocks.

Fin!

Manuscript out the door. Now onto the next one. Fun fun!

In the meantime, I'm jamming to the following iTunes mix ...

Don't Talk to Strangers - Dio
Mexico - Incubus
Dream Brother - Jeff Buckley
Life in Technicolor - Coldplay
Dyers Eve - Metallica
Dam That River - Alice in Chains
Next To You - The Police
We Build Then We Break - The Fray
Get Off My Cloud - The Rolling Stones
Been Around the World - Cracker

A lot of writing ...

... but very little blogging. The push is on to get my latest manuscript ready for submission. All the figures and tables have been polished to a nice sheen, and now the text needs to be brought into line. Add to this that mid-year evaluations need to be submitted by the end of the month and I'm a busy fellow. Which means a drop in my blogging rate.

I'm sure I'll blurt something out now and again, but it won't pick up in earnest until this paper is out the door.

Can it be done?

Can I really, truly, make a resolution work? I have had limited success with New Year resolutions. The only one I can ever remember following through on was cutting out soda for an entire year ... but that only worked for the one year I did it, and now I can down a 2L bottle in an afternoon.

At any rate, my goal for this year is to write (and get accepted) three first author manuscripts this year. I have the data for two of them already collected so this should be an accomplish-able task. Also, since I have a paper already under review, that should count towards one of the accepted papers should things go favorably.

However, in order to achieve this level of success, I need to organize. It's not one of my strong suits, and my desk is a cluttered mess. I know where everything is, but I'm still not organized, and I need to get there. I know it behooves me, for my long term productivity and upward mobility in the ranks of research, to achieve this goal. So, I took my first step in this direction today ...Is increased productivity in my future?
I went out and purchased a daily planner. I tried this last year, with very mixed results ... but I have the fire in my belly this year. I swear! At any rate, I've already started filling out January, which is a good thing because I have a manuscript review and a grant review due in the next few days. I better get cracking!

You know what ...

... I really like reading review articles. I don't like writing them though.

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.

Ode To My Peer Reviews

AKA: The Manuscript Tracker Lament

O my dear Peer Reviews,
There you are! I can see you!
I logged on, and glanced inside,
And despite your efforts to hide,
I can see the dates within,
Next to each as they turned you in.
Since then, three long days have passed,
And yet, still nothing, so I ask.

What's taking so darn long?!?

Alas, I cannot help but continuously look.
Hour after hour, I return, but still forsook.
For me, now an obsession, an unsatiable drive,
My need to know your status, eating me alive!
Please lovely peer reviews, arrive at last.
Fly through the intertubes, pronto! Fast!
Give me respite, knowledge that my work is approved.
That what gave you birth is true, behooved.

What the?

So my collaborator on a recent co-first-authored paper informed me that they received their reviews back today. Sweet Jimminy! It took exactly 30 days for the submission and return of the reviews. Here in agriculture-review-land, I had to wait over 100 days for the reviews of my submission to be returned to me (which I now need to address). My current submission has been in for 8 days. Wonder if I'll hear anything back in the next 22?

One leaves, another one arrives ...

... so sent my manuscript out for review today.

Shortly afterwards, a request for the review of a manuscript arrives. Unfortunately, they were not asking me to review my own paper. Heh.

All told, this manuscript took me about 10 weeks from start to finish. If not for the bureaucratic red-tape, it would have taken closer to 7. Not sure if that's a good turn-around time from sitting down to write to getting it to the editors desk. All I know is that my next one needs to go out much quicker than that. But first, time to answer the reviewer comments from my last manuscript, which returned to me almost 4 months after it was sent out. There is no reason a review should take almost twice as long as it takes me to write the whole thing!

Sweet Release

All I need to do is finish the figure legends and then I can get this manuscript out to my collaborator! Within the next couple of weeks this manuscript should be on its way to the journal! w00t!

ETA: Done, and out!

ETA2: A couple of more hours and my ASM poster will be finished, and then it's time to move onto the next manuscript.

Manuscript Homestretch

Got the office door closed, playing some Mighty Mighty Bosstones (currently Someday I Suppose off of their Don't Know How To Party album), and configuring the dozen or so phylogenetic trees I'm including as Supplementary Material for my manuscript (over 500 OTUs will do that to you). Once that is done, its off for a final reading of the manuscript to find typos, clean up the other figures, and catch any minor errors that I may have passed over previously. Then, it's off to the collaborators for their review prior to submission.

And then, I get to turn right around and work on the next manuscript. Whee!

So, no more blogging for today (and probably tomorrow).

Continuing manuscript madness ...

... so not a lot of blogging today. However, I will take this time to complain about individuals who do not proof-read their manuscripts. My lab is currently working on a project looking at the denitrification pathway in various agricultural settings. So we're doing a combination of Real Time PCR (to look at gene copy density) and DNA analysis (RFLP and sequencing) to try to tease out some relationships. Well, there are several steps in the process, and all of them (save the final step) involve at least two enzymes. So we have a lot of analysis to perform.

Well, for the RFLP (restriction fragment length polymorphism) work we need PCR products which are long enough to be worthwhile to restriction digest. As you can guess, the "universal" primers we use aren't really universal, so it's a mixed bag. Add to this the fact that one of the primers we ordered IS WRONG and kept giving us erroneous results (about 300bp shorter than what it should have been). Turns out, the primer I ordered was based on a manuscript where the authors tacked on two 3' T's to the end of the primer (without an explanation) while citing the original paper. Figuring I had the correct primer sequence (should be identical in both papers, natch), I ordered it and didn't check it against the original. Doh!

At any rate, that drama consumed part of my day yesterday and I hope to close my office door, open up my manuscript word document, and spend a majority of today writing ... because tomorrow is filled with meetings.

Manuscript Madness

Going to spend the rest of the day writing, so no more blogging. Toodles for today!

Incommunicado

Manuscript craziness: Just had one published, waiting on the peer review results of another, and I'm in the process of analyzing data and putting together my first manuscript of the new year. Have another (plus a review) nipping at my heels as well. So I sort of have to play catchup. I'll be back, but first I need to put this introduction together.

I hate writing introductions.

Does this hold ...

... for manuscript rejections as well?

But in a modern world, our hypersensitivity to rejection can have surprisingly destructive consequences. When we're socially or romantically excluded, even in seemingly insignificant ways, it can lead to a host of negative psychological and physical side effects. That includes everything from lower scores on intelligence tests to a weakened immune system and increased aggression ...

I know I want to strangle someone when I get a less than stellar review on one of my manuscripts.

Acceptance!

Thank you, you love me, you really love me! - Jim Carrey in The Mask.

One paper accepted (the one from my graduate school days). Working on getting the other revised and sent back out for further review. Then, onto this years major project!

In the meantime, a white paper, and two presentations for customer workshops in early January. Which is only a couple of days away. How time flies!

Still revising ...

... though it's going much slower on a laptop, because my desktop whimpered and died on me. Graphic construction software (I use Gimp) is much more tedious on the laptop. As a matter of fact, I hates it. But, it's coming along. I hope to get it out by the first week of December ... and focus on the data analysis for my next manuscript.

Yup ...

... the desktop is still down for the count. Something about my 24" monitor being too much for the graphics card that currently resides in the bowels of that damned machine. It will need to be upgraded, but that won't happen until after Thanksgiving.

At least I managed to recover the data/text I need for the revision of my grad school manuscript. Now hopefully my co-author will come through today with the request I made of them, and we'll get this thing out!

Another manuscript ...

... in the oven with a deadline giving me only a few more days to make edits/rewrites. Which means, less blogging but plenty more writing. I shall return.

Before I go though, can I say that I thoroughly love the GenBank sequence submission process? NOT.

It's good to be the king ...

... my latest manuscript is out for peer review.