Annotating Manuscripts with

A few months ago, AGU introduced a new feature in GEMS – annotating the merged PDF of the manuscript. Senior AGU Pubs staff wrote an Eos Editors’ Vox article about it. AGU has partnered with, an online annotation tool, so that reviewers can highlight text and insert comments. Editors can then add additional comments before making a decision about the paper. The comments are labeled “reviewer 1,” “Editor,” etc., so that the author can identify which of the assessors made the remark. During the revision process, authors can respond to these comments directly in the annotated PDF.


            I have used it a couple of times and I have seen ~10 reviewers use it over the last few months. I think it works really well, so it is it time to publicize this feature and make the community aware of this powerful resource.

When you agree to review a manuscript, you will see this new section on the review page:


It’s just below the link to retrieve the paper and the link for submitting your review. When you click on it, you get a new browser window with the manuscript PDF:


This page already has several sections of text highlighted with example comments written. There are controls across the top bar for navigating around the document. When you highlight some text, a small pop-up window appears below it with the word “annotate” in it:


This opens a text box in the right-hand column in which you can type your comment:


The “You” at the top indicates the originator of the comment, then the highlighted text is repeated, and then a box for writing your comment, including rich text features like inserting hyperlinks, images, and LaTeX-based equations. Along the bottom of the text box is a row of buttons for specifying the type of remark you are making. Is it an overview comment? Pick “Summary.” Do you want to designate it as a “major” or “minor” concern? Go for it. Are you suggesting a small English usage correction? Then pick “Edit.” Are you suggesting a new reference or two, or commenting on a figure? Click that button, then. Finally, there is a “Confidential?” button that you can click if the remark is just to the Editor and not meant for the author. I promise to look through the comments and read these.

Back on the main reviewer page, you can actually see if there are annotations on the “annotated merged PDF.” It should appear as a new link, “Show Summary Table,” like this:


When you click on this, all of the comments in the PDF are shown:


Nice, huh?

Note that you still need to click the link on the main reviewer page to complete the review:


You should answer the pull-down-menu questions and fill in any comments you want in the review text box. It is helpful if you, at the least include a sentence like, “Please see my detailed comments in the online annotated PDF.” This reminds the Editor to go to the annotated PDF and see your comments there. It is also helpful to include a short paragraph summary of your review there. In fact, you can make your review a hybrid of the two, with major comments in the review text box and specific comments embedded in the annotated PDF.

In addition to the Eos article and this blog, there are also more detailed author instructions, reviewer instructions, and even editor instructions at the AGU website. The website also has a really good tutorial. Also, one caveat: it is an interactive web-based tool, so you have to be online to use it.

Also, this whole thing is optional. You don’t have to use it. So far, I’d say that most reviewers do not use it. But most reviewers could be using it, so please consider it. Many reviews include line-identified comments, and this new feature should be easier than typing the location coordinates into your review.


DEI Pledge

As most readers of this blog probably know, JGR Space Physics is a journal of the American Geophysical Union. AGU strives to be a society for Earth and space scientists across the world, but one country is right there in the name…America. In light of recent comments by the President of the United States, I feel compelled to respond with a post. On Martin Luther King Jr. Day here in America, it is a perfect time to push back against racism and other forms of bigotry. I think that silence makes us complicit and I, for one, detest our president’s position.


            When tackling a problem, a diverse workforce brings together many perspectives and makes for a better solution. The USA prides itself on being the world’s melting pot, accepting immigrants from everywhere. A diverse population has helped to make America “Great.” This is exact what the inscription on the Statue of Liberty promotes. Yet, there has always been an undercurrent of racist, bigoted, prejudiced, and/or sexist attitudes in America, with some of the “already privileged” being skeptical and scared of the rise of the “under-privileged.” These feelings are based on ignorance, though. Each time, the rise of an under-privileged group works out well for America. Scientific research, in particular, loves diversity in the workforce.

As a white male of Norwegian descent, I know that I have led a privileged life. I am sure that, who knows how many times, I have benefited from the racism and sexism of others. While I cannot change my past life trajectory, I can steer the future.

So, I pledge to mindfully apply myself towards being a strong supporter of implementing practices at my work and in my daily life that increase diversity, equity, and inclusion. That last phrase is often shortened as DEI. Perhaps you’ve heard that acronym. It’s a good one to know, and I strongly encourage you to adopt a DEI mindset.

For JGR Space Physics authors and reviewers, one way to do this is to practice the Platinum Rule in your interactions with each other and suggest a diverse set of potential reviewers. In the workplace, it can include identifying and confronting Bro Culture and sexist microaggressions. Little by little, we can do a lot.

AGU is working on this too. It has been a strong position of AGU Presidents, and AGU has a Diversity and Inclusion Task Force working right now to review current policy and recommend changes.

            Keep the gates open. Challenge racism, sexism, and bigotry. Promote diversity.

More On Plain Language Summaries

For over a year now, AGU has been including the option of a Plain Language Summary with manuscript submissions to any of its journals. This can be about as long as a regular Abstract to your paper, but should be written so that those outside of space physics can understand it. From the AGU text requirements page, the definition goes like this:

“The plain language summary should be written for a broad audience. It should be free of jargon, acronyms, equations and any technical information that would be unknown to the general public. The purpose is to explain the study to the public. A good summary should state the general problem, what was done, and the result.”

This description should be ingrained in all of us, not just those submitting papers in the near future but also anyone reviewing a manuscript for JGR Space Physics or another AGU journal. Yes, if you are asked to review a paper and it has a Plain Language Summary, then please read it and comment on its quality. This should be considered as an essential part of the review process, just like assessing the Key Points and keywords that the authors have provided for the paper.

AGU now has more information about these Plain Language Summaries to help you write a good one. For me, this advice about creating a Plain Language Summary comes down to the final bullet point: take the time to do it right. This is not something that you should crank out during the GEMS submission process. That not only will just be an initial draft of what it could be but also won’t be vetted by your coauthors. Their name is on the paper too, and the Plain Language Summary is published with the paper, right below the official Abstract, so you should definitely include your coauthors in its creation. Please do not just change a few words from your regular Abstract, but instead write it from scratch and edit it to make it appealing to a nonspecialist audience.

Here is the nice graphic from that webpage, by @JoannaScience:


She did a cartoon for one of my Editors’ Vox articles. This graphic above pretty much sums up how space physics Abstracts are understood by non-space-physicists. Our niche of AGU has to work especially hard at communicating our work to the public; learning how to write a good Plain Language Summary is an excellent start.

AGU has put together a page with some really good Plain Language Summaries. Have a look to see the kind of summary that resonates.

For now, this paragraph is optional, and I have been told that roughly 20% of manuscript submissions include a Plain Language Summary. Writing a good Plain Language Summary, however, greatly increases the chances of your paper being highlighted by AGU in some way. AGU HQ staff read every Plain Language Summary for all accepted papers across all AGU journals. If they come across a good one. At 20%, this is about 5 summaries per day. When they come across a really good one, the paper will, at the very least, receive a social media highlight. They might work with the journal Editor that handled the paper to create an Editors’ Highlight for the paper. Or, it might even be the initial nugget of a Research Spotlight or Editors’ Vox article about the paper. The point is that the paper could be elevated to receive a highlight regardless of what the reviewers and editor thought about its highlight worthiness. If you write a good highlight, then your paper will have an increased chance of receiving special highlight attention from AGU.

While I have not seen stats on whether the various highlighting that AGU does for papers results in more citations, I have seen the stats on page views and full-text downloads, and the link is clear and extremely favorable. Traffic towards the paper is typically greatly enhanced with a highlight. So, it is in your best interest to spend some time on the Plain Language Summary.



Toolkit for Promoting Your Paper

In the lower-left corner of the Author Resources page is a link called “How to Promote Your Paper.” This page has lots of good advice for authors on this topic. While I have written about the Plain Language Summary before and I probably will again in the near future, there is one thing on this page that I would like to bring to your attention today. It is the Toolkit for Authors on how to improve the impact of your paper. There is even a version in Japanese and perhaps other versions, as well.


            This 4-page PDF is packed full of advice on how to structure your paper for maximal discoverability. Specifically, it uses the acronym SEO, Search Engine Optimization, and gives you clear advice on things you can do to improve your paper’s chances of rising to the top of an internet search.

Specifically, here is a synopsis of “the 4 easy steps to SEO” as defined in the document:

(1) Keywords: pick 15-20 keywords, avoiding repeats and test them out to see if similar papers are found

(2)Title: keep it to 15 words or fewer and use 2-4 keywords in the first 65 characters

(3) Abstract: place essential things first and focus on a few of the critical keywords

(4) Links: add a link to your paper from your institution’s website and a Wikipedia page

Those are things to do during manuscript preparation or just after acceptance. Once published, then the document suggests that you share a link to your article with friends in the field and even on social media. Not to the point of annoying people, but a quick email to colleagues will improve the changes that some of them will remember it when they write a paper on a similar topic.

Wiley, the publisher of AGU’s journals, wants you to have a successful and highly cited paper, so they offer tools to help with this. For instance, the JGR Space Physics website helps you monitor the impact and reach of your paper. On a paper’s main page, there is a listing of citations to it (as counted by CrossRef) and the article’s Altmetric score. Wiley offers a service called Kudos that will help you write simple language about your paper, share your short blurb, and track its impact in terms of downloads and citations.

Manuscript Submission Webinar, In Chinese

This is for Chinese-speaking researchers who wish to learn more about publishing in AGU journals. Our very own Yuming Wang, Editor of JGR Space Physics, and Minghua Zhang, the Editor in Chief of JGR Atmospheres, were the featured speakers on a webinar now available from AGU. It can be found on the Author Resources page in the section “For International Authors.” It’s the third entry in the section, “Webinar: Tips for a Successful Manuscript Submission [Chinese].” Yes, the webinar is entirely in Mandarin Chinese, not only the speaking but also the text on the screen. The video is an hour and ten minutes long.


            Note that the link above will eventually take you to a separate page at, where the webinar is archived. You will have to fill out the form for a free registration in order to watch the video. There are actually two screens of questions, the first is your name and contact information and the second is about you as a researcher. It is very easy and quick to register. You will be asked to make up a password for your registration; this is so that you can go back in to the BrightTALK system and see other webinars available from Wiley and AGU.

I like and respect both of these webinar speakers very much.  Minghua was one of the editors traveling with the AGU Pubs crew on our trip through China in October. He lives in the USA now but he grew up in China and, during that trip, I heard him pass on lots of good advice for authors whose first language is not English. I have now worked with Yuming for four years as an editor of JGR Space Physics. He is very thoughtful and I am sure has plenty of useful tips about manuscript preparation, submission, and publication.

For international authors, writing a manuscript for submission to an AGU journal perhaps can be intimidating and even frustrating. I am glad that AGU sponsors these webinars and I hope that you find it useful.

Free e-Book on Scientific Writing

I have a free e-book for you: Writing Scientific Research Articles by Margaret Cargill and Patrick O’Connor.


I am not the source, just the conduit. This is compliments of AGU and Wiley. They have little credit-card-sized “coupons” for downloading and accessing a copy of this book. There is a special code on the back of each card coupon, so each person needs their own card. I think; I haven’t actually tested this, because I only needed one copy.

They actually offered this e-book a couple of years ago. I read it, liked it, and took a bunch of notes. I should pass some of the key points on to you here in this blog. Well, I have, but not specifically as a recap of this book. If you would like the full version from the original authors, then please find me here in New Orleans at the Fall AGU Meeting. I have a small stack of these cards in my pocket. I can probably get more if I run out.

As a teaser, the section headings:

Section 1: A framework for success – typical research article structures

Section 2: When and how to write each article section – a method for writing the first draft

Section 3: Getting your manuscript published – submitting and resubmitting

Section 4: Developing your writing and publication skills further – specialized writing topics, strategies, and advice

Section 5: Provided example articles – for reference, called out throughout the book

I liked the book a lot and found myself agreeing with nearly everything they suggest. I highly recommend it. Find me and I’ll give you a coupon card.

Start Authorship Discussions Early

While on our AGU Pubs trip through China last month, a good piece of advice that AGU Senior VP Brooks Hanson made in his “author advice” presentation was to start conversations about authorship early in the research process. As a researcher goes through the scientific process, the person will most likely discuss the research with colleagues or even get help and resources from colleagues. The interaction could be at the initial stage, when they see something strange in the observational or numerical data and have those initial conversations about what it could be. The interaction could occur at the literature search stage of seeing of the weird thing is already explained by some previously published study. That is, the term “literature search” could be asking a colleague down the hall about a topic and following whatever leads they suggest. The interaction could be at the time of developing the initial hypothesis of what is happening in this strange thing. It could also be in the formulation of the experiments to test that hypothesis, or in the act of conducting those experiments (whether they be data analysis tasks, numerical model runs, new lab or field data collection, or a new theoretical derivation). Or, the interaction could happen very late in the process, at the stage of writing up the study for presentation or publication.

There is a very broad spectrum for this level of interaction of the researcher with all of these different people. It could be participation in a group meeting, where the person chimed in with a few comments or suggestions. It could be a 5-minute talk in the hallway. It could be an hour of flipping through plots on a screen together. It could be writing a new chunk of analysis software or a new subroutine in a model. It could be making plots. Not only should the time involvement be considered, but the significance of the involvement should also be considered. A five-minute conversation that completely changed your thinking on the subject might be worth coauthorship, while many hours of regular participation in a group meeting at which you mentioned the work might not rise to the level of coauthorship. As a research community, we’ve been making this judgment for a long time but, even still, there are no hard and fast rules on what contribution warrants coauthorship.

Dr. Hanson’s advice: broach the question of authorship early. With the CRediT list of author contributions handy, as well as the AGU ethical guidelines of who should be an author, including AGU Council’s thoughts on this topic, researchers should have frank and honest conversations with colleagues making contributions to their work. When you think that someone’s involvement is rising to the level of coauthorship on the eventual presentation and publication of the work, then talk with them about it. Most of us wait until the paper is written before we start to have these conversations with those outside the immediate “primary author” core group (which could just be one or two people). Author role #10 on the AGU page above is worth repeating here:


All coauthors are responsible for the “quality and integrity of the submitted and published manuscript.” Which means that, to be a coauthor, you pretty much have to participate in the “writing – reviewing and editing” CRediT role. That could be your only involvement, but those that participated in the “conceptualization” of the study should also review and edit the manuscript before submission. If someone isn’t prepared to take on the reviewing and editing task, then their contribution has to be very strong in one of the other contributor roles to warrant coauthorship.

So, researchers honing in on results worthy of a manuscript:

  • Make an agreement with potential coauthors, saying something like this: “I think that what you’ve contributed so far warrants coauthorship on my future paper, but there is still more for you to do to get your name on the paper – please read the paper.” You should extract from them a promise to read and comment on the manuscript; without it they probably should decline to be a coauthor.
  • Offer coauthorship to all colleagues that significantly contributed to the work. Think about who impacted the research at each stage of the scientific process and offer them the chance to be a coauthor, with, or course, the additional work of “reviewing and editing” the manuscript.

The question still remains, what amount of interaction rises to the level of a “significant scientific contribution to the work?” I’ve addressed it here but it’s a subjective judgment call.

CRediT Is Here

Contributor Roles Taxonomy, CRediT, is now implemented for new submissions to AGU journals. I had a post on this a few months ago and it’s been in place with Water Resources Research for a year or so, but now it is implemented for all AGU journals, including JGR Space Physics. They have a page listing the various CRediT author roles but a much better description of them is in this Google doc. Here is the main chart from that document:


Corresponding authors, when submitting their manuscript through GEMS, now have the option to fill out these contributor roles for all coauthors on the paper. You don’t have to do it, at least not yet. Also, the current plan is to start displaying these contributor roles as part of the paper’s online information in January 2018, or whenever Wiley completes its software upgrade enabling display of these contributor role designations.

You don’t have to worry about the film credit model of authorship; that is not being implemented anytime soon. We will still have an ordered listing of authors, we will still be citing multi-authored papers by the first author’s last name, and all authors will still be getting full credit in their CVs and h-index calculations. This is just an extra layer of information about the study that will not only increase transparency about the contribution of each author to the study but also make corresponding authors aware of the different roles within a study and think about who should be an author of the eventual paper.

Trip to China

In mid-October I went to China on a publications-awareness-building trip with AGU CEO Chris McEntee, AGU Senior VP for Pubs Brooks Hanson, JGR-Atmospheres Editor in Chief Minghua Zhang, and GRL Editor Andrew Yau. It was a full week of visiting universities and research institutes; 4 in Shanghai and then 3 more in Wuhan. We met many people conducting research in the broad swath of “geoscience” fields from students just beginning their projects to well-known senior members of the community.

I’d like to say thanks to all of our host institutions. The people we met were fantastic and it was a pleasurable week talking with so many researchers at all of these locations. I had a wonderful time visiting your country and your workplaces, I was well fed at every stop, and the hospitality was excellent. Shanghai and Wuhan are delightful cities and I highly encourage others to visit when given the opportunity. It was a really nice week.


Me and my new Shanghai Jiao Tong University mug


I’d also like to thank my travel buddies. Minghua, Andrew, Brooks, and Chris, you are an excellent human beings. I am really glad that I got to spend that week with the four of you.

At each institute, Dr. Hanson would give a talk about publishing in AGU journals. This would start with a few slides about the scope of AGU and its 20 journals, author demographic info, and some updates about AGU’s latest endeavors in scientific publishing. Then we transitioned into more of an author workshop mode, discussing the desired elements in a manuscript submission to an AGU journal. This is where the presentation gave way to conversation, with questions from the audience and with the editors chiming in with stories and advice. We spoke with full rooms at every institute, with the crowd varying depending on the size of the room, from ~30 to ~200.

Here are a few of the key highlights that kept recurring in our “advice to authors” tips:

  • Talk to an editor. If you are unsure of whether your paper is suitable for a particular journal, feel free to contact an editor of that journal and ask. Some studies fall on the borderline between journals, or you might be questioning whether your result is significant enough for a particular journal. Either meeting an editor in person at a conference or sending them an email is a way to help you sort out which journal is the most appropriate for your work.
  • Write a cover letter. For AGU journals, this is just a text box entry during the GEMS submission process, so it is straightforward and easy. This is a great opportunity to explain why your study should be in this particular journal. Less than half of submissions include a cover letter, which is a missed moment to positively influence the editor’s assessment of your manuscript.
  • Write a clear Abstract and Key Points. Editors send the Abstract to potential reviewers, so this is a paragraph used to entice these people to accept the reviewing assignment. I strongly recommend making the finalization of the Abstract as one of the last things you do before submission, ensuring that it clearly yet concisely conveys the motivation for the study, the highlights of the methodology, the key findings, and mention of the significance of the results for the field. Similarly, the Key Points are displayed on the journal website table of contents, so these are one of the first things that potential readers will see, using their clarity and significance to assess whether to read the full article. Please make the drafting of the Key Points an element of paper writing, not something done at the last moment as you upload the paper into GEMS.
  • Have a friend critically read the manuscript. Coauthors should be stepping up to this role, but even beyond that, it is highly encouraged to form a small group of “writing buddies” who will read each other’s papers. Getting feedback from someone not intimately involved in the research is usually highly beneficial to the paper’s chances of eventual publication.
  • Spend time on the Discussion section. This is where the results of the new study should be placed in the context of what is already known, making the case that the new findings are a significant original contribution to the field. Far too many papers cut this section short, instead jumping straight to the summary and conclusions. A weak Discussion section can sink an otherwise compelling study.
  • Scholarly writing is hard, so practice it. Academic writing for journals is a learned skill; no one has a natural-born talent for this task. Just about everyone struggles with scientific writing, has had to completely rewrite whole paragraphs or even sections in the editing process, and has had papers rejected. Even experienced writers get forgetful of the proper technique for good science communication. Do not be discouraged; you are not alone in your pain. What helps? Practice. Making scientific writing a regular habit will improve your ability to write well.

That’s a good start. I’ll write more on this in the coming weeks.

The Film Credit Model of Authors

AGU is moving towards the adoption of a new step in paper publication, assigning contribution roles to the names in the author list. At some point in the “near future,” you as an author will be asked to go through your author list designate who did what for the study. I don’t know when this will happen, but Brooks Hanson, a Senior VP of AGU, is a coauthor on this paper and AGU is gearing up to implement contribution designations. I also don’t know if this will be requested as optional metadata, perhaps as a mandatory submission step. I expect that the research community will have plenty of lead time before it becomes required.

As of now, AGU will still have author lists associated with each paper. There will simply be an extra set of information that provides details of the roles for each author in the list. For a single author paper, this is, of course, overkill, but most papers have more than one author and this extra information could be very useful.

But, what if we didn’t have the list anymore?

I was recently told about a rather radical yet intriguing extrapolation of this process. The original article is here describing the problem of paper authorship and the potential for frustration and annoyance at the placement of names in the list. The author notes that the issue is the fact that the authors names appear in a list and that we as a research community ascribe certain meaning to people’s placement within that list. The suggested solution is summed up in this graphic:


No more first author. No more last author.

They call this is the film credit model of authors. Names are listed next to the roles, jobs, or functions they performed to contribute to the final product. Who is first author of a film? As an example, for The Martian, is it Damon et al. (highlighting the lead actor), or maybe Scott et al. (highlighting the director), or perhaps Goddard et al. (highlighting the executive producer)? We never say any of these. Could that be the case with scholarly articles someday?

This would change the in-line citations of references, because there would no longer be a first author to name in the text. Reference list formatting in papers would also need to be revised because there would not longer be a clear order for the authors. CVs would change, as we list our contributions rather than just our placement in the author list of our publications. Like I said, this is a radical suggestion. It is also, though, a natural progression along the path that AGU is now undertaking.

I’d like to say thanks to Dr. Shane Hanlon at AGU HQ for pointing out this Medium article to me, via a response to my post at AGU Connect. This website, especially the “AGU Community” discussion page for everyone in AGU, is a place for geoscientists (including space physicists) to engage in conversation about scholarly topics. You can sign in with your AGU username and password. There are some topics, like paper authorship, that span well beyond the scope of JGR – Space Physics. Sometimes, I will be posting on such topics over there instead of here, especially if I pose my thoughts as a question rather than a comment. So, look for those discussions and, if interested, then please start responding and posting on that site.