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Wednesday Micro Hits
Wednesday, August 17, 2011
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Is it worth getting an education?
Thursday, July 7, 2011
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Miscellany
Tuesday, June 28, 2011

It Gets Better
Thursday, June 2, 2011
May (4)

Wednesday Micro Hits
Wednesday, May 11, 2011

My first experience with science writing (Part 1 of 2)
Tuesday, May 10, 2011

This is why we get vaccinated
Thursday, May 5, 2011

Monday Morning Jam
Monday, May 2, 2011
April (2)

Saturday Morning Serenade
Saturday, April 23, 2011

So long, farewell ...
Friday, April 1, 2011
March (10)

Stay Tuned ...
Thursday, March 31, 2011

From the Union of Concerned Scientists
Tuesday, March 15, 2011

Week 23 - Hockey Pool
Monday, March 14, 2011

March Madness
Monday, March 14, 2011

Saturday Morning Serenade
Saturday, March 12, 2011

What a bargain!
Wednesday, March 9, 2011

Wednesday Micro Hits
Wednesday, March 9, 2011

Technique Overload
Monday, March 7, 2011

Saturday Morning Serenade
Saturday, March 5, 2011

Et tu FDA?
Wednesday, March 2, 2011
February (10)

Saturday Morning Serenade - A Hip Edition
Saturday, February 26, 2011

Saturday Morning Serenade
Saturday, February 19, 2011

Wednesday Micro Hits (on Thursday!)
Thursday, February 17, 2011

HR1
Wednesday, February 16, 2011

Happy Valentine's Day
Monday, February 14, 2011

Saturday Morning Serenade
Saturday, February 12, 2011

The GOP War on Science
Wednesday, February 9, 2011

Wednesday Micro Hits
Wednesday, February 9, 2011

People, how about some ...
Tuesday, February 8, 2011

Saturday Morning Serenade
Saturday, February 5, 2011
January (21)

Saturday Morning Serenade
Saturday, January 29, 2011

Sacrifice
Friday, January 28, 2011

Are you married to your reagents?
Thursday, January 27, 2011

Wednesday Micro Hits
Wednesday, January 26, 2011

Common Sense Tip #1
Tuesday, January 25, 2011

Saturday Morning Serenade
Saturday, January 22, 2011

From the Baby Boomers, a Big "Screw You"
Friday, January 21, 2011

Student Worker - More Student or More Worker?
Friday, January 21, 2011

Wednesday Micro Hits
Wednesday, January 19, 2011

Saturday Morning Serenade
Saturday, January 15, 2011

Holy moly!
Friday, January 14, 2011

Thursday Pondering
Thursday, January 13, 2011

The Electronic Office
Thursday, January 13, 2011

Wednesday Micro Hits
Wednesday, January 12, 2011

Saturday Morning Serenade
Saturday, January 8, 2011

The Plug - January Edition
Friday, January 7, 2011

Bits 'N Pieces
Thursday, January 6, 2011

Latest Manuscript Review
Wednesday, January 5, 2011

The $4 gallon of gas
Wednesday, January 5, 2011

Our slowly shrinking (and dying) planet
Tuesday, January 4, 2011

It's 2011 already? For reals?
Monday, January 3, 2011
2010 (46)
December (9)

Saturday Morning Serenade
Saturday, December 11, 2010

The State of Microbiology
Thursday, December 9, 2010

Wednesday Micro Hits
Wednesday, December 8, 2010

2010 blogging meme
Tuesday, December 7, 2010

The Environmental Impact of the Christmas Season
Tuesday, December 7, 2010

Music Snobbery
Thursday, December 2, 2010

Phantom Power
Thursday, December 2, 2010

What's Your Name?
Wednesday, December 1, 2010

Wednesday Micro Hits
Wednesday, December 1, 2010
November (8)

Saturday Morning Serenade
Saturday, November 27, 2010

Awakening from the food coma ...
Friday, November 26, 2010

Wednesday Micro Hits
Wednesday, November 24, 2010

Donor's Choose Final Followup (Recipes #3 and #4)
Tuesday, November 23, 2010

A Monday Mess
Monday, November 22, 2010

Saturday Morning Serenade
Saturday, November 6, 2010

Wednesday Micro Hits (Peer-Review Edition)
Wednesday, November 3, 2010

Day 2 of the ASA-CSSA-SSSA Meeting (#ACSMtg)
Wednesday, November 3, 2010
October (29)

ASA-CSSA-SSSA Meeting - Day 1
Sunday, October 31, 2010

Stayin' Alive
Sunday, October 31, 2010

Saturday Morning Serenade
Saturday, October 30, 2010

Wednesday Micro Hits (Vol. 4)
Wednesday, October 27, 2010

ASA-CSSA-SSSA Early Career Program
Monday, October 25, 2010

Saturday Morning Serenade
Saturday, October 23, 2010

Wednesday Micro Hits (Vol. 3)
Wednesday, October 20, 2010

Donor's Choose - Family Recipe Number 1
Sunday, October 17, 2010

Making Good on Donor's Choose Bribe - Comfort Food Recipe 1
Saturday, October 16, 2010

Saturday Morning Serenade
Saturday, October 16, 2010

Friday Wrap-Up and Random Thoughts (Vol. 2)
Friday, October 15, 2010

First I Begged, Now I Bribe
Thursday, October 14, 2010

Finding Out Things The Hard Way(TM)
Wednesday, October 13, 2010

Wednesday Micro Hits (Vol 2)
Wednesday, October 13, 2010

Here's where I start begging ...
Tuesday, October 12, 2010

#UnK3rn3d: Life Outside the Lab?
Tuesday, October 12, 2010

First fleas, now frogs?
Tuesday, October 12, 2010

No Fleas Please
Monday, October 11, 2010

My next Research Blogging article has been chosen ...
Sunday, October 10, 2010

Saturday Morning Serenade
Saturday, October 9, 2010

Donor's Choose
Friday, October 8, 2010

Friday Wrap-up and Random Thoughts
Friday, October 8, 2010

RB: Waste Not, Want Not.
Thursday, October 7, 2010

Research Blogging
Wednesday, October 6, 2010

Wednesday Micro Hits
Wednesday, October 6, 2010

What if I were not a microbiologist ...
Tuesday, October 5, 2010

TJ's Tips on Manuscript Review
Monday, October 4, 2010

Chinese plagiarism and the death of English-language journals
Friday, October 1, 2010

Allow Me a Formal Introduction
Friday, October 1, 2010
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Thomas Joseph

It's a Micro World after all is a blog dedicated to discussing pretty much whatever I feel like. When I delve into scientific matters it will primarily be discussing microbiology (agricultural, bioenergy, and environmental focus). Otherwise, I'll probably ramble on about sports and life.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Recent Comments
Comment by Brian Krueger, PhD in The rumors of my death ...

Sweet, looking forward to those posts.  I feel like I should be doing the same thing, but I keep finding myself hitting the "print" button. . . .Read More
Feb 03, 2012, 3:18pm
Comment by JaySeeDub in Wednesday Micro Hits

I'd be hopeful to see a bigger, general push towards organic farming. But, the realities of scale and market urinate incessantly upon that hope. For a large supplier that ships out millions of eggs. . .Read More
Aug 17, 2011, 3:56pm
Comment by old timer in Is it worth getting an education?

I understand your point about critical thinking and I also believe that it is not stressed enough in higher education.  However, I have had students (first year graduate) who lacked the building . . .Read More
Aug 08, 2011, 11:15am
Comment by Alchemystress in Is it worth getting an education?

Great post lots to think over. I agree critical thinking is not encouraged. I have had straight A college students in my lab/class that when asked to apply the knowledge they learned in lecture to . . .Read More
Jul 10, 2011, 11:04am

I didn't have the numbers, so I looked some up. I was thinking in terms of *number of institutions* not *number of students*. I think the principle would hold for number of students, but quite poss. . .Read More
Jul 08, 2011, 4:27pm
Awesome Stuff
Monday, October 4, 2010

I remember the first time I was asked, in an official capacity*, to review a manuscript. I was excited because I had finally been asked by my peers to partake in one of the essential elements of publishable science ... the peer review. I was also extremely nervous. Would I review the manuscript with the same attention to detail as the other reviewers? Would I miss critical elements? Would I make a fool out of myself and recommend acceptance of a paper which was clearly junk (or vice versa)?

Fears aside, I proceeded with the review, which given all my anxiety took far longer than it needed to. In the end, I think I handed in a good review**, and I've been following a similar pattern of reviewing ever since then. Since I'm fresh off my latest review (a rejection, unfortunately) I figured now is a pretty good time to put my thoughts down on paper (the intertubez).

1. The first issues to consider will come when you get the email asking you whether or not you'd be able to do the review. First, do you have the time? IIRC, the typical reviewer reviews about seven papers and change a year (I'll have to find the data on that, but it was blogged about recently), which comes out to less than one a month. When I accept a review, I figure that it'll take me about an afternoon (3 hours) to get the whole process completed. That includes downloading the manuscript, reading it, doing any lit searches necessary, writing up my review, and sending it back to the journal. I don't think three hours is all that much time to donate to peer-review (considering ~160 working hours a minimum a month), so I try to shoot for at least one review each month. Sometimes they come in spurts, where you'll get several review requests, so you'll definitely have to learn how to say no. I've tried doing three reviews at a time ... it's a pain in the rear, so I refuse to do more than one at a time now***. Second, do you have the expertise? In the journals I work with, I get to figure this out by reading the title and abstract. This should be enough to go on, provided the authors put together a good title and abstract. Make sure you read them both before accepting (often the accept link will come before the abstract ... why they do this, I haven't the foggiest).

2. So you've decided you have the time and the expertise. Now go and download the manuscript. At this point, if its not a double-blind review (a couple of journals I review for do it in this manner), I go to SCOPUS and do a lit search for the first and last authors. I'll sort through their recently (last 3-5 years) published work on the same subject and skim through the Introduction, M&M, figures/tables, and Conclusions of those manuscripts. Since I'm skimming, this takes me usually all of 30 minutes (that's the beauty of PDFs). Sometimes there isn't much there, sometimes there is a lot ... if there is a ton of work (and I'm not already familiar with their work), I'll look to see what they've cited (listed in their MS) and what they haven't (what's left in SCOPUS) and I'll randomly pick from both. I then read the submitted paper. At this point I'll notice if the writing style is "too similar" (i.e., they were too liberal in applying the copy/paste) and I'll make note of it for the editor (in the "Editor Only" section of my review). I won't reject a manuscript based solely on this issue, as I think it's an issue for the Assoc. Editor and Editor. I'd like to say finding issues like this is fairly uncommon, but it's more common than even I'd like to admit.

3. I always print out a copy of the manuscript I'm reviewing and I mark it liberally. I also have a Word document opened at the same time in which I put my reviewer comments (which saves me from having to do it afterwards). When making comments I always am sure to state what section I'm in, what page I'm on, and what line number I am referring to: (e.g. Introduction, Page 2, Line 55: The authors state that such and such ...). Which brings me to another general comment for those submitting a manuscript ... if you're going to renumber your lines on every page, number your pages! Though being able to say "Line 303 has a problem ..." is really a nice thing to be able to say if there is only one Line 303 in the entire manuscript. While the editors are supposed to keep track of issues like spelling and grammar, the reviewer really should keep track of these things as well. If there are a couple of typos in the manuscript, I'll make note of them and correct them in my review (e.g., Results, Page 20, Line 15: "teh" should be changed to "the".) This is fine if there are only a few instances of this. If there are almost too many to list, I'll write something akin to the following: This manuscript suffers from multiple typographical and/or grammatical errors. These errors make the manuscript unfit for publication and should be addressed prior to any consideration for acceptance. At this point, there really is no point in listing every single one. Also, if there is an issue which crops up all the time in the manuscript (e.g., the authors fail to italicize genus and species names) I'll make mention of it the first couple of times and then write a general note (e.g., The reviewer has pointed out several instances of the authors failure to italicize genus and species. This error crops up throughout the manuscript and needs to be addressed fully). On my printed copy I'll write down "Huh?" or "What about X, Y, and Z?" and return to those comments later once my review is done. Sometimes these are due to poor wording, in which case I'll say "Line 25 is hard to comprehend, consider revising." and sometimes this is because the researchers overreach in their analysis (see #4).

4. The first three steps are a lot of clerical/busy work, and we've gone over the paper in a very broad manner. Sometimes papers can be rejected before even getting to critiquing the science, though unless the paper is so thoroughly incomprehensible as to be worthless, you really should critique the science before firing off a "This paper reads like crud, makes no sense, stinks, and should be rejected" recommendation. It's always nice to give the authors some glimmer of hope and actually attend to the hard work they've put into their experiments. So now you're in the Results (or Results and Discussion) section. You'll be analyzing the figures, looking at how they interpret the data, and what their conclusions are. Are they overreaching and/or overstating (i.e., if a reaction works with 25% efficiency, saying there is minimal substrate left is overreaching) their case? Is there data not shown? Why is that data left unshown but other data is shown? If the data really needs to be shown, say so. Do their results fly in the face of the rest of the field? If so do they acknowledge/address this discrepancy? Do they give a reasonable explanation? Or do they just ignore it? If they ignore it, point it out and provide references. Force them to explain it in their response to the reviewers. Also, do the experiments address the hypothesis or objectives which were stated in the Introduction? Is there a clear flow of ideas throughout the manuscript, or is it all herky-jerky and appears to be put together by a toddler with ADHD? If there is no objective for the manuscript, is there a point in accepting it? Perhaps, depending upon the journal, but more often than not, the manuscript probably needs to find a more suitable home than the journal you're reviewing for.

5. At this point I then transfer (or have already done so) my notes to my word document. I begin my review by summarizing the authors work, and then listing the issues I have with the writing (grammar/spelling) and the science. If I disagree with an interpretation, I'll state so and explain what I think the data is saying. Also, I may or may not recommend an additional experiment to see who may be right. I try to make a point of not asking for an experiment which cannot be done readily. I also will not ask for a protocol which I know to be extremely expensive and/or outside the area of the lab (e.g., if their whole paper was based on RFLP analysis, I will not ask them to perform a secondary MLST protocol involving six additional genes)  At this point it becomes the editors task to decide if my request is a reasonable one or not. If I have a problem with an experiment (lack of controls, etc), I'll ask for them in a revised figure/table. The point here is to, I think, keep the requests reasonable. I wouldn't ask for an additional $10K metagenomic array after the authors have done five or six. I wouldn't expect them to go out and buy a qPCR machine either. At the same time, if you think the issue is critical enough that the manuscript hinges on having this question answered ... say so!

6. When you've logged back into the review site, there is often a section where you can send comments specifically to the editor. My main review seen by the authors shows my overall summary of their work, as well as point by point critiques. I will also list any problems I have with their work, offer my own viewpoint, and make suggestions on how to clarify the issue. In my comments to the editor, I'll then make my recommendation, make note of any potential copy/paste and/or figure/table lifting from earlier publications, and offer a view on the acceptance-worthiness of the manuscript.

Overall, I figure this process takes me about 3 hours from start to finish. Over the course of a year, this winds up taking about 30 hours or so of my time. Not all of it is done during work (sometimes I'll take them home with me), but I figure a job well done by me will hopefully result in a job well done for me on my next manuscript submission. I'm also sure there are points I've missed in this entry, but that's what the comments section is for, right?

 

*Sure my grad and postdoc advisers had asked me to review manuscripts before, but those were to be handed in to them, for them to then use them in their own review. When I was asked specifically to submit a review, I was the one taking all the credit and all the blame.

**I say this because they keep asking me to do more reviews, but it could just as well mean that they can't find anybody better or anybody at all. Not sure if it's good to be the "best of the worst".

***If I'm doing a review, and then get a request to review the manuscript from someone I know (likely I was listed as a recommendation to review) I'll take it on. You never know when I'll need my own back scratched in the future!

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Blog Comments

Prabodh Kandala
Texas Tech University Health Science Center
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Dear TJ, does review time vary with paper to paper? Usually, I see too much data in double digit impact fact journals. Don't they take more time? Just curious.


Prabodh Kandala
Texas Tech University Health Science Center
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"but I figure a job well done by me will hopefully result in a job well done for me on my next manuscript submission". Liked this sentence.

I have one more question. Does attitude towards reviewing a paper change based on the journal and its impact factor? I see few journals staying in the same impact for years together and doesn't improve at all.

Thanks much for this post. I just took a print out of it and filed in my "Careers" file.


Thomas Joseph
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Prabodh, yeah the three hours is an approximation. There are a number of factors which can shorten or lengthen the time to review a manuscript. Ironically enough, I think the papers I've seriously considered sending back for "major revisions" and/or rejection are some of the ones which I spend more time on, trying to make absolutely sure that I'm rejecting or requiring massive revisions for the proper reasons.

In regards to "too much data", I have on more than one occasion said that certain figures/tables were not necessary for the manuscript and should be excluded due to being superfluous. I suppose that this takes additional time to read and digest and then put it in context of the bigger picture, but not by much. Case in point, this latest manuscript I read, there were five figures which could have easily been merged into one 5 panel figure. Even more, it really needed 3 ADDITIONAL panels incorporated into it. I haven't really come across a manuscript that was "too ambitious". The journals I typically review for have IF's ranging from around 2 to 6, so maybe the authors are already breaking their manuscripts down to get more than one pub out of the data.


Thomas Joseph
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Prabodh Kandala said:

I have one more question. Does attitude towards reviewing a paper change based on the journal and its impact factor? I see few journals staying in the same impact for years together and doesn't improve at all.

Thomas Joseph replies:

For me, no, it doesn't matter. I try to put as much pride and effort into every review I do regardless of what journal I'm reviewing for. Now granted, I have tried to pick up my reviewing game for a certain journal which I've been continually impressed with in regards to the reviews they perform (their average turnaround time is under three weeks, every review I've ever gotten back has been meticulously reviewed and discussed with great recommendations for furthering the manuscript, etc). Yes, their IF factor is higher than some of the others I review for ... but I picked up my game because I knew how they did reviews, not because I was impressed with their IF.

I apologize for the formatting issues, I can't seem to figure out how to get this to unquote my response. Argh!


Prabodh Kandala
Texas Tech University Health Science Center
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Thanks for explaining TJ.


Dr. Zeek
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Ok, so I just have to comment that (a) thank you for the great post and (b) your first paragraph is EXACTLY how I feel right now about the whole review process.  I am scared out of my gourd for the very reasons you lsited.  Sure, I ahve looked over/reviewed some things for post-doc boss, but, like you said, it goes through someone else who can tell me if I am being incredibly dumb before I *look* incredibly dumb.  At least, now, I realize that I am not alone in feeling this.


Genomic Repairman
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Any paper that is within my scope of interest that passes across my PI's desk, I generally get to take a crack at it.  I usually take all evening to do like TJ says and go through previous papers to get a feel for the PI and first author's work.  Then I start dissecting the paper apart, usually I gloss over the abstract then go straight for the M&M and then look their figures over to make my own conclusions before I read theirs.  Its nice that folks like TJ try to review a fair number of manuscripts as a decent amount of PI's I'm seeing are playing the I'm too busy card and declining.


Thomas Joseph
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Hi Dr. Zeek, you are definitely NOT alone in those feelings. The first couple of times I felt completely out of my element. Fortunately, a couple of the journals I reviewed for allowed me to view my fellow reviewers comments, and I found that by and large, I was inline with their own thoughts. After that, I just worked on my routine and kept trying to do the best job I could. Sooner or later, the tentativeness will pass. :)

 

Welcome to LabSpaces!


John F
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Well done article.  I especially like reviewing the authors previous publications first.  That is a great first step in the review process.


Thomas Joseph
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Welcome to LabSpaces John F. and thanks for the compliment. I literally stumbled across that first step in one of my early reviews, and have seen it crop up a handful of times in the past couple of years. I understand the argument of "you can't plagiarize your own work" (and am sympathetic to it), but there still are a vast array of copyright infringement laws (and rights authors sign away when publishing) and they need to be taken into account. Fortunately, I just leave it up to the associate editor ... it's their headache, not mine. Wink


Cricket42
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Thank you for this post!  I just finishished stubbling through my one of my first reviews of a paper and I think it would have been much easier if I had seen this first.  I'm definitely going to save this for next time.

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