Thursday, May 30, 2013

The story behind "Exploring the costs of horizontal transfer"

My new review in Trends in Ecology and Evolution went live last week. This paper, while not really experimental, took a little bit of a circuitous route and a bit of luck. For all of you out there sitting on ideas for reviews/opinions but not knowing how to get these published, here's how it happened (with a bit of philosophy of how to be a researcher thrown in).

One of the important skills I first learned in grad school was how to delve headfirst into a completely new topic and figure out the salient and relevant points. Sure, you might get sent a paper of interest by a colleague or have one picked for journal club, and these are great for getting a cliff's notes version of an area of research, but to understand a topic you need to know the background. One of the best ways for me to figure out the background (i.e why is the question interesting, what has been done in the past, what are directions for future research) was to find a review article and use that to point towards new references. These references can be found in the articles themselves, but its also quite helpful to search for other articles that cite the review. It doesn't even have to be a new article, because the rabbit hole of references eventually leads to the present day.

Somewhere along the way I developed a soft spot for the Trends family of journals (I know...Elsevier is evil...fully acknowledged, Frontiers is turning into a great place for reviews in the future). Trends articles were clear, concise, opinionated, and a great foothold for jumping into new areas. While there are other equally great resources for reviews like the Annual Reviews family, Bioessays, MMBR, etc...I set it as a goal early on in grad school to publish a first author article in Trends.

There are two different paths to write a Trends article: 1) you can receive an invitation from one of the editors or 2) you can submit a short pre-proposal and see if an Editor likes the idea. I was part of an invited review once, but this new article was the product of submitting and resubmitting pre-proposals.

When I started my lab I wanted to break away from what my postdoctoral advisor (Jeff Dangl) is known for and get back to my roots in microbial evolution. Sure, I still do a lot of phytopathology work in my lab, but I try to do this in the context of understanding how microbial pathogens evolve and adapt to new environments. This strategy has its positives and negatives, but long story short I found myself writing grant applications where the first page was devoted to explaining why the questions I was asking were interesting and important. This was too much space devoted to justifying my questions. Part of this is my lack of grant writing experiences, but part of this was that I felt I had to explain why I was asking the questions I was asking because, while there were many other articles preceding my ideas, there was no article (*as far as I can tell, point me towards these if they exist and I missed them please!) that laid these questions out in the context I was thinking about. I was simply using too many words to say something that could be easier said in a long review article and then cited.

My first stab at getting this review published was a pre-proposal to Trends in Microbiology. Obviously, this didn't work. I took a little bit of time, re-jiggered the ideas and foci, and submitted another pre-proposal to Trends in Ecology and Evolution (TREE). This time a very kind editor thought enough of what I wrote to give me a chance at a full article. I hadn't actually written the article yet, but the ideas were circulating in my head and most of the references I ended up using were gleaned from iterations of grants I was writing. I had about 3 months to write the full article, which is both plenty of time and not close to enough time, but I was able to pull together a draft and circulate it amongst my colleagues before submitting for formal peer review. This piece actually started out as an opinion, simply because I wasn't really sure if people were thinking about things the way I was. There is a feeling in science where you are both terrified and excited in the same moment. Either you are an idiot who is seeing things that other people have seen before and simply don't recognize this, or you are actually seeing things in a new way. The same feeling occurs when dealing with great new experimental results, except there is an extra option...either your experiment is 1) awesome sauce! 2) a trivial result that other people have seen before but which you haven't realized for one reason or another, or 3) a lab mistake.

 I got the first reviews back and realized that I was onto something that other people were thinking about already ( controversial opinion needed), but that there was definitely a place for what I was writing. It's always difficult to read critique, but the reviewers actually did a great job pointing me towards other papers and helping me discover/emphasize other interesting research findings and directions. Specifically, the first iteration was too heavy on history and specifics and too light on the evolutionary implications of horizontal gene transfer. I made these changes, added a figure (in retrospect, should have changed the font and cut down on whitespace but I'm very happy with the information that it conveys), and sent it back in for a second review. This time it went through without a  hitch, and I celebrated accordingly. Side note: I'm a slightly large person and have a tendency to break things in the house and the lab (My wife calls me Shrek). The sequence of the disruptive protein in figure 1 is an homage to my tendencies. A slightly less than subtle Easter egg, but I like trying to put those in my papers (there are plenty more subtle ones in other papers...). I'm also not alone in doing this.

The take home message is not to worry about whether something is good or not, just submit and see what happens. For a long time I was scared/worried about writing pre-proposals to the Trends editors, but it was a fairly seamless process once I went through it. You don't have to wait for the magical email invitation, just take the initiative and see if your idea flies. I'm writing my first grant after the review is out, and it's definitely much easier to write the background now. The last couple of paragraphs of the review also nicely set up some other manuscripts I'll be submitting this summer.

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