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!

Communication . . . I need to do more of it

Randy Olson is coming to Cornell to give a quick workshop on Science Communication. He has a recent book out called "Don't Be Such a Scientist," which I grabbed at the library last week, not knowing he was coming. He also has a movie called "Sizzle: A Global Warming Comedy" which is playing at Cornell Cinema during his time here.

So all of this has resparked my desire to simply write about my work. Make it exiting, if it is (which it's often not), but mostly to be honest, transparent, truthful, and clear. I'm shooting for weekly updates, starting now. So if you're reading this, and I slack off, hold me to it! Scold me!

This week, I'm returning to campus after a hectic summer. I have stacks of daunting, not terribly exiting work ahead of me. More modifications of emissions files. More nitty-gritty fighting with the climate model. A TA-ship, where I'll grade homeworks, and teach a class or two. On top of all that, I'm taking a two-semester sequence of classes called "Mathematical Physics" to give me the tools I need to know what I'm doing.

On top of all that, I have a new house, four new housemates, many beers, ciders, and meads to brew, and a new park in my backyard to explore. Here we go!

When does it get personal?

The impacts of climate change are very often described and thought about in the abstract, especially if you live in a place where there are little or no actual impacts. Statements like "Expect sea levels to rise by 0.5 to 1.0 meters by 2100" or "Expect 5 more extreme heat and smog events every summer by 2050" don't necessarily carry a whole lot of weight. Could a 2 degree Celsius change really impact my life all that much? These projections and estimations, ripe with uncertainty and ranges and controversy, are hard to discern, and hard to feel. They don't touch us. We don't feel it, and therefore tend to ignore it to wait and see.

That urge to wait and see, that abstraction, starts to fade when you can feel it personally. This spring, Lake Champlain (located between New York and Vermont, near Canada), where my family owns a small cottage with about 100 feet of lake front, has had the highest water level since the records started. Below is the 2010 lake level, with the bold red being the maximum level ever observed. You can see during April and May, the lake level has never exceeded 102 feet.

The next graph is the lake level so far for this year, and you can see that the late-April and May period has been record-breaking, by about one foot. In Early May, the lake level exceeded 103 feet for the first time ever.

What does a foot of extra water look like? How much does it impact a shoreline? First, a picture of our shoreline from 2004. Note the tree behind Sam (in the orange hoodie).

Here's a picture taken during a particularly windy day early this May. Note the tree, the same tree that was behind Sam earlier. Also note the water making contact with our little boat house.

Here's a picture from 2002 looking out at the lake. Note the tree (a different tree than before) and a stump just beyond the rock-wall of our shore.

Here's a picture from last weekend. You can see the tree next to my Dad and a friend, and the stump out in the water.

The rock wall has been demolished, and you can see significant erosion, with exposed roots and dirt.

The records of lake level started in the 1800s, so let's say that they've been kept for 200 years. A lake level like this, then, could be considered a 200-year event, and we would expect it to come once every five-generations or so. That "200-year event" phrase is slippery, since we only have one data point. But as my family plans and figures out how to deal with our shoreline, we are trying to determine if we should plan for another 200-year event.

And since there is so much data, and publicity, and controversy regarding global warming, the topic has been brought up. Should we build a wall? How big do we need it to be? What lake level should we plan for? Is this related to global warming, or is it just an extremely unusual year? We're wondering if this 200-year event might become a 100-year event.

And since we don't really know what to expect in the next 100 years, because the planet is changing in observable and predictable ways, because Mother Nature is no longer regular and our historical records no longer hold the same weight that they once did, every new strong storm, extreme weather event, and record lake level has shifted in meaning slightly.

(The same can be said for families struck by the record-setting tornadoes this April, families impacted by Katrina, families impacted by the extreme drought in Australia, families worried about freshwater coming from the Colorado River, or heat-waves in Chicago, and the people living on the drowning island of Tuvalu.)

All of these events, which would be devastating during any era, are no longer necessarily Acts of God, or the regular cycle of Mother Nature. They all now all have a slight tinge of: "Is this something we're doing? Is this partly our fault?" We are having a harder time making decisions, because we can no longer confidently look into the past to get an idea of what the future might bring. And that makes it much more personal.

Wow, how did I get so busy?

I really mean to update this more often than once every three months. But this semester has proven to be very busy, so this has fallen down my priority list.

While I'm here, and before I recap this semester so far, I want to point anyone whose interested to my new Twitter account (www.twitter.com/benjamonian), where I will be linking to interesting atmospheric/climate/science articles, as well as posting what beers I drink, and other twittery things.

I'm taking three classes which are time consuming and challenging. The first is a graduate Advanced Atmospheric Dynamics, which is more a math (calculus) class than anything else. It's all about fronts, waves, cyclones, momentum, vorticity, circulation, and atmospheric processes, but it heavily (very) focused on the math and derivations, rather than contemplation of the processes in a conceptual framework. Therefore, it's rather dull. Math is all well and good, but pages and pages of symbols doesn't satisfy me.

The second is a graduate Multivariate Statistics class, which is great. It's all about how to look at datasets that are too large to easily visualize (e.g. 50 years worth of daily maximum and minimum temperatures over the entire globe) and figure out what patterns exist, how to find them, and how to decide what's an important signal or not. It's also math (linear algebra) intensive, but has more information that I'll actually use.

The third is a one-credit class called The Scientific Method in Practice, and is basically a walk through of Hugh Gaugh, Jr.'s book of the same name, taught by him. It's a wonderful break from all the math, and explores some of the philosophy, methods, thinking, and reasoning behind all the science that I've been using. It's like a breath of fresh air.

In other news, I submitted my first paper to the Journal of Geophysical Research. It took me nearly two years (but there were HUGE learning curves in that time). Hopefully, my other two papers will take only a year (or so). The manuscript is about 6,000 words, with 6 figures, and 2 tables. I'll hear back from the three reviewers in several weeks, and I'll post more on that process to show a slice of the scientist's life. :)

And my current work is starting new simulations with the global climate model, starting a long-term project looking at the emission possibilities for the northeastern US out to 2050. The current task is to compare a model run where we provide observed winds (that's called an offline run) to a run where the model calculates its own winds (called online). Then we'll compare both of those to available observations, to see how well the model does. This should take a long time, but I'd like to tackle it all sooner, rather than later.

There's a quick update. I'll have more soon, like another post regarding the Japanese nuclear power plant, and why we shouldn't worry about the effects here in the US.

Trying to decide what I like, what I want to do, where I want to go

This last month, I've read a lot. Fiction, non-fiction, scientific review papers, magazines, and articles. I managed to complete the three most recent Orion magazines, which I had been saving. I read the Cartoon Guide to Statistics in preparation for my advanced statistics class this semester. I'm reading daily articles from Google News when I'm on my computer on the headlines and news related to climate, weather, poverty, hunger, justice, and the planet in general. I've just completed a review paper on climate-chemistry interactions. I'm in the middle of The Boat of a Million Years, by Poul Anderson.

All of this reading makes me realize how much I've missed writing. During my senior year as an undergrad, I wrote weekly for the school paper. That was fun. I want to write again, but not for a school paper. I'd like to write to a general audience, maybe letters to the editor for newspapers, magazines, and to no one in particular (i.e. this blog). I want to keep writing to keep up the sense of wonder that I feel everyday, in my work, in my interactions with people, and in the world around me.

And I have conflicting goals, not only in who I want to write to, but what I want to write about. I love writing about the Earth as a whole (e.g. the Pale Blue Dot). But I also want to write about the myriad of human struggles, dramas, triumphs, and the infinite complexity and unobserved beauty of water, air, land, and life that is constantly and amazingly chugging along, day by day and second by second on this planet. What I really want to be able to do is write about my daily experience, here in Ithaca, or Cleveland, or wherever I may be, and weave in my personal interpretations of my activities and what I see with the global perspective that refreshes and grounds me.

An article in the most recent Orion magazine (Hope and Feathers, by J. Drew Lanham, Jan/Feb 2011) concludes with a wonderful reflection on an ornithologist's trip to Africa, and the birds, land, people, and struggles that he observed:

The dramatic landscapes awed me at times to tears. I absorbed a modest 126 life birds, watching each new entry to understand it not as just a tick mark but as an organism within the context of the place. But my eyes were also opened to the poverty, the nasty racism still writhing beneath the new democracy, the long trek ahead for the new nation. And although I saw only a fraction of what the nation has to offer, it was enough to help me better understand my connections to nature and humanity, and to realize that the two are not as separate as I'd once though.

That last line especially is something that I want to experience everywhere I go, with every person I meet, every community I get to be a part of, every landscape I see, every meal I get to eat, and every cloud, bird, star, body of water, and plant I encounter.

I want to combine scientific conclusions:

Prediction of future changes due to emission changes and climate initiated atmospheric changes (temperatures, dynamics, humidity biospheric response), can only be made if we have a reasonable understanding of past and present conditions. We need to know the non-linear responses in composition from emission changes caused by human activities, and the behaviour of the chemical active greenhouse gases (CH4, O3, particles). Such knowledge helps us distinguish natural variability from human-induced changes. (Isaksen et al. (2009), Atmospheric Environment, 43)

with editorials:

Fortunately, it has never been easier to find examples of people and organizations that are working fort the kind of changes our culture so badly needs...The burgeoning fields of local economics and local currency, community transition, permaculture, corporate responsibility, alternative health, alternative energy and clean technology, local energy, social and economic justice, sustainable cities, alternative housing, efficient building practices and ecological design, alternative public transportation, climate action, regional agriculture and food systems, and holistic education provide concrete entryways for anyone who is looking to get involved (Orion, January/February, 2011).

and inspiring videos:

Look again at that dot. That's here. That's home. That's us. On it everyone you love, everyone you know, everyone you ever heard of, every human being who ever was, lived out their lives. The aggregate of our joy and suffering, thousands of confident religions, ideologies, and economic doctrines, every hunter and forager, every hero and coward, every creator and destroyer of civilization, every king and peasant, every young couple in love, every mother and father, hopeful child, inventor and explorer, every teacher of morals, every corrupt politician, every "superstar," every "supreme leader," every saint and sinner in the history of our species lived there-on a mote of dust suspended in a sunbeam.  (Carl Sagan, The Pale Blue Dot)

and religious writing:

Go, eat your food with gladness, and drink your wine with a joyful heart, for God has already approved what you do...Enjoy life with your wife, whom you love, all the days of this meaningless life that God has given you under the sun—all your meaningless days. For this is your lot in life and in your toilsome labor under the sun. Whatever your hand finds to do, do it with all your might, for in the realm of the dead, where you are going, there is neither working nor planning nor knowledge nor wisdom. (Ecclesiastes 9, 7-10)

and philosophy:

We are up against mystery. To call this mystery "randomness" or "change" or "fluke" is to take charge of it on behalf of those who do not respect pattern. To call the unknown "random" is to plant the flag by which to colonize and exploit the unknown...To call the unknown by its right name, "mystery," is to suggest that we had better respect the possibility of a larger, unseen pattern that can be damaged or destroyed, and with it, the smaller patterns...If we are up against mystery, then we dare act only on the most modest assumptions (Vitek and Jackson, Virtues of Ignorance, Ch. 1, Toward an Ignorance-Based World View, 2005).

 and fiction:

Nothing is more important than that you see and love the beauty that is right in front of you, or else you will have no defense against the ugliness that will hem you in and come at you in so many ways. 

... when I saw any of those kinds of beauty I knew I was alive, and not just in the sense that when I hit my thumb with a hammer I knew I was alive, but rather in the sense that I was partaking of something--something was passing through me that it was in my nature to be a part of. (both from Anathem, Neal Stephenson) 

And I want to do this every day.