My first scientific publication!

Although this post will probably be quite boring to many, I thought it might be good to show the process by which a scientific paper gets published. While I cannot speak for all atmospheric and climate scientists, I can speak for me, and my story (hence "Climate Through Anecdote"). In my case, it took about two years to learn the model, run the experiments, and submit (2009 - 2011) and less than four months to go through the submittal, peer review, revision, and acceptance process (February 23rd - June 4th, 2011), and finally got published on September 15th. Overall, the submittal/revision/publication process went pretty quickly. So here we go:

0. Read grant or proposal, decide what you're going to do (2009)

1. Run experiments / run models / do science (2010)

These can be described briefly, as parts of them have been written up previously. After my first year of classes and some work on a biofuels project, I began to learn how to run the CCSM (Community Climate Systems Model), work through test runs, make modifications, check the chemistry, and do a lot of the science part of this project. There was no experimenting here. No data gathering. No lab equipment. Climate modeling, for the most part, uses existing models, plus new, creative modifications, or newer data from observations to simulate the global climate. I had both.

I (with tremendous guidance from my advicor) added some artificial tracers (basically, fake chemicals that had particular properties that would elucidate aspects of the model, and through that aspects of the real world) to track the chemistry, transport, and seasonality of Asian emissions as they moved from Asia, over the Pacific, and into the US. Once all of that was finished, and the data was produced, the next step was to...

2. Determine what is worth focusing on, writing, publishing, and exploring (2010)

3. Write it up (Intro/Methods/Results/Discussion/Conclusions) (2010-2011)

I spent about two semesters in this data analysis and write up stage. The two kind of blurred together, where I would average the emissions for the spring, summer, winter, and autumn at various layers in the modeled atmosphere, talk to my adviser, double check my work, document what I did, go back and change the code, or change the area, etc. All the while trying to both figure out and show what Asian emissions were doing over the Pacific. The modeled results showed a large and looming Asian Pollution Plume extending over the Pacific, and over North America during certain seasons.

After many months, I had a set of figures that I thought showed the most interesting aspects of the Asian Plume, and I started to craft them into a story. At the same time, I reviewed all of the relevant literature again, and produced a draft of my paper. Abstract - Intro - Methods - Results - Discussion/Conclusions - References. I gave these to my adviser, and thus we began to...

4. Edit, edit, edit, edit, edit, edit, edit, edit, edit until you and your adviser are satisfied (2011)

This was a frustrating process. I had to juggle all the possible figures, the possible ways of explaining what was happening, the available and relevant literature, the revisions my adviser handed down to me, the changes I wanted and did not want to make, as well as classes and my non-academic life. I usually felt good about a draft I handed in, and when it came back all splotched with red ink, I would feel a little hurt and deflated. I would then read the revisions, reformat, reorder, redo figures, look up new papers and studies, and get another draft. Each time, the paper got better. The story and message solidified. Three or four major figures became the centerpiece of my research. By the time February 2011 came around, I was ready to...

5. Submit (2/23/2011)

We chose the Journal of Geophysical Research - Atmospheres (http://www.agu.org/journals/jd/) to submit to, as this is where a majority of the papers I had read came from, and is more or less the predominant atmospheric and earth science journal out there. The submittal process was tedious. Everything had to be formatted and pieced together just right. The figures had to follow certain rules. I had to merge everything into one big pdf file, as well as individual figures and sections. This took a week or so, and I managed to submit the day before my 25th birthday. Next, I had to...

6. Wait, and do other work

At this point, I had a lot of class assignments to work on, so I more or less forgot about the paper. It often takes several months before you hear back, and so I thought it best just to forget it ever happened. I figured I'd hear back in June or July, and until then I would focus on my classes and future projects. Instead, I got an email within five weeks of my submittal, with the words...

7. Accepted with Substantial Revisions (4/4/2011)

Dear Dr. Brown-Steiner:

Thank you for submitting "Asian influence on surface ozone in the United States: a comparison of regional chemistry, seasonality, and transport mechanisms" to Journal of Geophysical Research - Atmospheres. I have now received 3 reviews of your manuscript, which are attached for your reference, as well as a brief evaluation by an Associate Editor. Based on the review comments, I find that your manuscript may be suitable for publication after substantial revisions.

Wow! Accepted! So soon? And why do they think I'm a doctor? The editor was brief in his comments:

Please address the comments made by the reviewers. Especially address the comments made by Reviewer #2 as to model validation and verification. Please submit your revised manuscript by May 18, 2011.

So my new task was to address every comment made by the three reviewers, in just over a month. So I began to...

8. Address Comments and Substantially Revise (April-May 2011)

Some of the comments were harsh. Others were uplifting. I'll include some of them here, for flavor.

The first reviewer:

This manuscript takes a new and effective approach for quantifying the impact of Asian emissions on US surface ozone. I especially like the breakdown of Asian ozone into baseline, seasonal and chemistry components, as well as the analysis of transport to the surface via the dry airstreams of mid-latitude cyclones. I think the paper will make an important contribution to the scientific literature and I expect that it will eventually be published in JGR. But first the authors need to conduct a borderline major revision to add further discussion on mechanisms that bring ozone to the surface, correct many citation errors and to improve the overall style of the paper.

The third reviewer:

The authors use a 5-year simulation from a chemical transport model (CAM-Chem) to study the influence of Asian emissions on surface ozone over the United States, with a focus on the western and central United States. The study design creatively allows for a clean separation of the role of seasonal changes in transport pathways, seasonal changes in the Asian pollution source, and seasonal changes in chemical evolution of Asian plumes transported into the atmosphere over the United States. The study is suitable for publication inJGR, following the suggested revisions below, which are mainly points of clarification.

And the second reviewer (the "Reviewer #2 mentioned by the editor, so I saved this one for last):

This paper presents a new analysis using the CCSM-CAM global model. As a conceptual analysis, this paper succeeds to present a useful framework for the processes involved in long range transport of ozone. However as a quantitative analysis, it fails due to its lack of any serious evaluation of the model results against observations...While no one expects any model to be perfect, we do expect a serious evaluation of the results against observations and a discussion of how these biases impact the results. The authors have failed to do this. For this reason, the paper should be rejected. The authors need to go beyond the HTAP evaluation and do a better job at evaluating their model results. Insight into the cause of any bias can be examining how the model behaves seasonally, at altitude etc. Assuming the authors wish to redo this analysis then I offer the following additional comments for them to consider...

The first and third reviewer had plenty of minor and moderate comments, specified by the lines in the manuscript, which looked like this:

L35-39. Quantify the increases over some time period. The Cooper et al. 2010 study focused on the free troposphere (not surface) . The HTAP studies, referenced later, also address this point; see Reidmiller et al., ACP, 2009.

L77-78 State that this refers to Asian component only (also L225, L272)

L 111-115 The specific definition of anthropogenic xNOx should be included - biomass burning? Fertilizer? Soil NO? Is there seasonality in the xNOx emissions or does the "seasonality" tracer introduced later solely reflect seasonality in venting of the Asian boundary layer + transport pathways?

L129-133. It's clear later in the text, but best to explain here why the scaling is necessary and also what is meant by "seasonality and chemistry signals".

I was a little sloppy with my citations, and checking my numbers precisely. I am thankful, and startled, at the level of detail that these reviews analyzed and critiqued my paper. The first and third reviewers' comments were fairly straightforward, and very detailed. The second reviewer’s comments were more vague, more substantial, and required a lot more work. Essentially, I created a whole section of supplementary material, that would be available online and not in the actual paper, that compared the model results to known and measured observations all over the US. This included seasonal averages and variations, day/night cycles, and others. It was tedious, and often felt a little pointless. I was rushing through this analysis to get the paper back by the deadline, and others have, and would in the future, do a much better job of this validation and verification of the model I was using. However, it was an actual check of my model output with the real world, so I added the supplemental material, finished the revisions, added the new figures, and proceeded to...

9. Resubmit and Wait (5/18/2011)

Once again, now I tried to forget about the paper. I was thrilled, because it was accepted. But I was worried that they wouldn't approve of my revisions, or want more verification. In less than a month, however, they got back to me, and...

10. Acceptance! (June 13, 2011)

I am pleased to accept "Asian influence on surface ozone in the United States: a comparison of chemistry, seasonality, and transport mechanisms" for publication in Journal of Geophysical Research - Atmospheres.

I was in! It would be published! All that was left was copy editing, some final revisions, color changes, and brief communications with the copy editor, and I would be published. I began to interact with the journal throughout the...

11. Copy Edit

I got various emails with revisions, citation questions, and author queries throughout the summer, and on August 24, 2011 I received my final proof to read through in two days, where I would be...

12. Published (September 15, 2011)!

The wait for final publication took longer than I expected. But finally, after three years, I had my name as the primary author on a scientific publication! You can see the abstract and front material here. And here is a screenshot of it appearing on the "Just Published" tab of the JGR homepage. I could talk a lot more about the peer review process and the research, but I’ve gone on for too long already. Thanks for reading!