Soliciting Input on arXiv

My post last month generated some interesting discussion, both comments on the post but also emails and in-person conversations directly with me. It seems that arXiv is only marginally used by the Earth and planetary space physics communities but is extensively used by the solar physics community.

We have started a conversation among the JGR Space Physics editorial board, AGU staff, and the AGU Publications Committee about the issue of non-profit preprint repositories and their relationship to AGU’s dual publication policy. We are trying to identify and discuss the pros and cons of such repositories, their current usage by various communities, and if/how AGU should revise its stance on this topic. The short answer is that the evidence is mixed, the opinions varied, and decision is difficult. Steadily and surely, though, we’re making progress and moving our discussion forward.

I would like to solicit community input on this topic. Please share with us your thoughts, joys, concerns, and suggestions about your experiences with arXiv or other preprint/reprint sharing sites. You can do this several ways: post a comment below; send me an email; or contact any of the other editors of JGR Space Physics. We want to hear from you and we want to include the community perspective in this discussion.

Live from the SWMF Users Meeting

As I sit here at the inaugural “SWMF Users Meeting” here at the University of Michigan, I realize that I am listening to many talks in space physics subdisciplines that are far from my regular stomping grounds. It’s an interesting day, though, and reminds me that we all too often limit our scientific interactions to others working in our immediate niche of space physics. This is natural; we have limited time to listen to others and so we focus on attending presentations within our specialty. There is a lot to learn from interdisciplinary interactions, though, and I highly encourage everyone to take the time to listen to presentations beyond their normal scientific comfort zone.

We have several opportunities to do this in the coming years. For one, there is the LWS Workshop on “Evolving Solar Activity and Its Influence on Space and Earth” in early November. The organizers intentionally invited a broad range of solar, heliospheric, magnetospheric, and ionosphere-thermosphere researchers to come together and spend a few days talking with each other. I am a huge fan of these cross-fertilizing meetings and I am looking forward to the week in Portland. Soon after this, of course, there is the Fall AGU Meeting in mid-December. With over 20,000 attendees, this meeting can feel overwhelming. It’s a fairly easy thing to stay in the particular room of your discipline and spend the entire week among familiar concepts. This meeting, though, also makes it easy to wander into the adjacent room or poster aisle and experience a very different set of presentations. It’s worth your while to do this every now and then. This spring, we have back-to-back-to-back opportunities for interdisciplinary interaction, with the European Geosciences Union General Assembly in Vienna in mid-March, the inaugural Triennial Earth-Sun Summit, the joint SPA-SPD meeting to be held in Indianapolis in late April, and the AGU Joint Assembly in Montreal the following week. Finally, more opportunities for such interaction exist at the summer meetings of IUGG General Assembly (in Prague in late June) and the AOGS Annual Meeting (in Singapore in early August). I am sure I am forgetting other meetings of this nature, but you get the idea…we have lots of opportunities for extending our scientific experience beyond our regular boundaries.

To tie this post to JGR Space Physics: on the publication front, I encourage you to read papers that are not only in your specialty but also across the scope of the journal. Yes, this takes time, and it is easy to sign up for an alert that tailors the notification to your exact interest. However, it is useful to occasionally read a paper outside of your normal area of expertise.

Submitting to Earth and Space Sciences

As I look through my stack of work for the weekend ahead, I see that I have waiting for me the Nth round version of my grad student’s paper that we are preparing for Earth and Space Sciences. It’s nearly there and I hope we submit it in the next week. With this, I get to check off a goal to myself to submit a manuscript to ESS within the year. Woohoo! I think that I will still try fo r a first-author submission to it as well, but for now, this counts.

For those that haven’t discovered its existence yet, Earth and Space Sciences is the newest AGU journal, just launched this summer.

ESS_olbannerright

The paper we’re submitting is a model verification and validation paper. While the paper does not include much in the way of new scientific results, it is a thorough numerical description and grid resolution test suite, along with some parameter studies of physical quantity inputs to show the code is producing expected values. In addition to original scientific contributions to any field spanning the gamut across the AGU disciplines, model development and testing is one of the kinds of papers that ESS would like to publish for the community. It’s also a great place to go with newly available data sets or data processing techniques. I think this new journal will have an excellent partnership with JGR as the two journals complement each other’s breadth, content, and scope.

Like AGU’s other recent journals, it’s fully Open Access, which means higher publication fees but then the published papers are instantly available for anyone to read, no subscription needed. A beautiful thing about the launch of ESS is that all publication fees are waived for manuscripts submitted through December 19, 2014. That is, now is the time to finalize that paper and get it into the review system with ESS.

Please join me in supporting AGU’s latest journal and submit a paper to it in the coming months. Oh yeah, and one to JGR Space Physics as well!

Posting Papers on ArXiv

Some have asked about posting preprints or reprints of articles submitted to JGR Space Physics on the arXiv.org website. The official AGU position on this issue is clear but not explicitly spelled out for the particular case of arXiv. The pertinent link is AGU’s dual publication policy that includes these lines:

“Posting of a preprint of an article via electronic media does not constitute prior publication unless with a service which provides archiving with citation protocols and public retrieval capabilities. In the latter case removal of the preprint from the archive will be sufficient for AGU to consider it as unpublished.”

While the arXiv site does not assign a digital object identifier resolvable at http://dx.doi.org, the website follows a standardized “citation protocol” and is fully citable in the reference list of another paper. The short answer to the question of, “Can I post my JGR Space Physics preprint on arXiv?” is “no.”

You can, however, post it to your own personal website. If you do this, then please follow AGU’s policy on such postings and clearly state that it has been submitted to JGR Space Physics. After acceptance, then please change the statement to say, “accepted for publication with JGR Space Physics.” In fact, at this point, it is best to give proper reference and include the DOI so that others can go the AGU/Wiley page where it is located. After publication, the formatted “published” version can only be made available elsewhere is the author pays for Open Access. If you have paid this extra fee, then please feel free to post the Wiley-formatted version of the article wherever you choose. Otherwise, only the “unformatted manuscript” (i.e., the final submitted/accepted version without the Wiley publication-ready formatting) can be posted on your website, again clearly stating that it is “published in JGR Space Physics.”

Six months after publication, the formatted version can now be placed into an “institutional archive,” which includes the arXiv.org site, as long as the copyright information and official DOI of the paper is clearly posted.

Finally, twenty-four months after publication, the formatted version becomes Open Access at the Wiley site (for those that didn’t pay the Open Access fee earlier).

In short, AGU does not want you to post preprints to arXiv of your work that will be or has been submitted to an AGU journal. Because arXiv has a citation protocol, it counts as a publication and therefore such posting counts as dual publication. Yes, it counts even though it is not peer reviewed when posted at that site. Only after it has been accepted and published in the AGU journal can it be made available at arXiv, with a reference listing that directs the reader to the AGU version of the paper.

More On AGU’s Data Policy

There’s a new Eos article that was just published this week about AGU’s Data Policy. It can be found here:

http://onlinelibrary.wiley.com/doi/10.1002/eost.v95.37/issuetoc?campaign=woletoc

Written by Brooks Hanson, the Director of Publications at AGU HQ, and Rob van der Hilst, the chair of the AGU Publications Committee, it gives historical context and broader perspective on why AGU is now enforcing this policy with every manuscript that is submitted to any of its journals. I highly encourage everyone to read it.

To very quickly summarize, the reason behind the policy is reproducibility of the results and veracity of the scientific findings. I agree with the Data Policy and think that it is a worthwhile goal for which all of us should strive.

In addition, the article serves as an open call for research community members to participate in an upcoming conference on data availability and archiving. This meeting is in early October, just a few weeks away, so if you have interest in being part of this discussion, then please contact Brooks or Rob immediately.

Observational data in the field of space physics is usually available at the Coordinated Data Analysis Website, Planetary Data System, one of the World Data Centers, or a mission-specific or an instrument-specific website. These are all legitimate locations to which you can direct readers to find the data used in your study. If it is from a smaller experiment, such as a rocket or balloon flight, a short-lived field campaign, or laboratory data, then the observations used in the manuscript should be made available by the authors at a personal website, an institutional server, or even as an electronic supplement to the paper.

Numerical data is very similar to the latter case above: unless it is a CCMC simulation and the results are available through their run output repository, then the authors need to make available any code results that were used for any plot or value in the paper. Again, this can be made available at a personal website, an institutional server, or as electronic supplements to the manuscript.

The Eos article includes a couple of paragraphs about the Data Policy requirement of the availability of computer codes. If commercial software was used, then simply stating the names of those packages is sufficient. If code was written to process data or solve equations, though, the ideal would be to have all of this be open source code so others can error check the code and ensure the correctness of the calculation. Making code available is the goal, but AGU is also giving each journal editorial board discretion to implement this policy specifically for their field. The editors of JGR Space Physics would like to have all codes be open source and available, but we realize the code is your intellectual property and so we are not requiring this availability as a stipulation of publication. The output from the model, however, is “numerical data” and needs to be available for others to download (from somewhere) and examine. When you submit a paper to JGR Space Physics, you will be asked to provide a statement about the availability of modeled data as well as instrumental data.

For more on this topic, the Data Policy can be found here and I have written a couple of other posts about the policy, when it first became enforced and later to help clarify the model availability issue.

Why Reject At All?

One of the biggest categories for complaints to me regarding manuscripts is when I decide to reject a manuscript. Some authors accept the decision and move on with one of the options discussed in my previous post. Others, however, feel the need to argue their case with me and try to get the decision reversed.

First of all, please feel free to email me. I like to hear from you, even when it is a complaint about my decision. I think that, in nearly all cases, more communication is better than less, and an occasional email exchange about a paper is part of the job.

That said, the question is still out there: why reject at all? Why not always send it back as a major revision, and if it can’t be revised in the 2-month turnaround time, then it should be withdrawn and resubmitted when ready. Authors know how much time it will take to make the revision, so why should I prejudge this for them?

To continue the theme with another reason to opt for “rejection” rather than “major revision”: I reject papers because multiple major revisions could lead to very misleading “initial submission date” for the paper. That is, people could submit half-baked and incomplete papers just to get that date locked in, and then follow up with revision upon revision until it is finally acceptable. I really do not want that to be the case at JGR Space Physics.

There is an implicit understanding between author and editor at the time of submission. Authors are expected to be submitting a manuscript worthy of consideration for publication in the journal, and editors are then expected to give that manuscript full consideration for publication. If a paper is deemed to need serious work to be worthy of publication, then it wasn’t really ready for submission. The initial submission date, therefore, is not a true measure of when it was submitted as a manuscript worthy of full consideration for publication.

Thus, I reject some papers, as do the other editors. Note that as an author, I try and sometimes fail at meeting this implicit understanding. I was recently second author on a paper that was rejected (yes, this calendar year, with a member of “my” editorial board making this decision). After rereading the manuscript, though, I realized that it did not reflect the elements of a great paper, and contained too much extraneous information and was not focused on the original contribution to the field. I include this story to come to this: please don’t take it personally when your paper is rejected. Anyone can have his or her paper rejected. The editors are being as careful, thoughtful, objective, and unbiased as possible in their decision-making process.

Revision Versus Rejection

            When deciding about a manuscript (accept, revise, or reject), I have two levels of revision: minor and major. The language and tone of the two letters is slightly different, but functionally for the author and for the GEMS system, there is really only one difference: the turnaround time. For a minor revision, the authors are given one month, and for a major revision, the window is two months. There are some papers that I reject because I think the paper is clearly not ready for the journal, but there are other times when I have to make a judgment call. Do I think the authors can do this work in two months? If my answer is no, then I will often reject the paper instead of giving them a major revision decision.

            That said, authors know best how much time they need to revise a paper. If it takes more than 2 months, then they will withdraw the manuscript and resubmit it when it is ready. If it takes them less time, then it was appropriate to give them the major revision decision and keep the original manuscript number and initial submission date. So, why even reject papers at all? Why not just let authors decide?

            It’s a fair question and one with which I struggle regularly. So far, I am often deciding in favor of a major revision rather than reject, therefore letting the author “self-reject” if the changes cannot be made in the turnaround window provided.

            There is a big and fundamental difference, however, in the decision for major revision and rejection. If it is only a major revision, then there is still a connection of this manuscript with JGR Space Physics and there is an implicit obligation for the author to resubmit it to JGR Space Physics when it is ready. That is, even when the decision has been made and the email sent, the decision of major revision means that it is still in the review process with JGR Space Physics, just with the author rather than with the referees or the editor.

            Rejecting the paper frees the author to go elsewhere with the manuscript. The authors could then resubmit immediately to another journal, revise it to whatever level they see fit and submit it to another journal, or make the revisions in the decision letter and compile replies to the reviewers and resubmit it to JGR Space Physics. We hope that authors choose the third of these options, but with a rejection, they can choose either of the other two options.

            Therefore, sometimes I reject papers based on the reviews. It’s a necessary and useful tool for both editors and authors.

Elements of a Great Paper

            To continue the thread of why I took this job, another reason for me is to help shepherd the community to write great papers. This is mainly done by guiding referees to do a more thorough job at reviewing manuscripts, scrutinizing every aspect of it to make sure the study is conducted and presented as optimally as possible. This direction to the referees, however, can be treated as advice to authors.

            The introduction should weave a story of previous studies on the chosen topic to build to the climax of the thesis statement: the unresolved question that still needs to be addressed. It should include citations and discussion of all relevant papers, including those very recently published to show the continued need for another investigation in this area. However, it should not drift beyond the those absolutely necessary to make the point, and should not include an exhaustive listing of papers in tangential or indirectly related fields. The introduction should be focused and make the case that the question is worthy of attention.

            The methodology section needs to describe the experimental set up at a level so that others can repeat the analysis. By experiment, I mean the describing the observations and the sensors used to make those observations and/or the numerical model and the run configurations used for the simulations. It is perfectly acceptable to make this section very short, as long sufficient citations are included of previous papers that give the full details of the technique. Quotations of previous papers are also legitimate, especially in this section. If the set up is new or the analysis method has changed, then the section needs to be longer to fully describe what is new in this methodology. For observations, it should be demonstrated that the sensor is properly calibrated and the measurements are reliable. For simulations, it should be shown that the model has been verified against analytical solutions with grid convergence tests and conservation checks.

            The results section should objectively present the data and describe the main features of interest in the plots or tables. For this section in particular, it is vital to judge the manuscript against the criterion of “only what’s needed to make the point.” It is easy for authors to include far more information than is necessary to address the problem. On the other hand, enough content should be given to convincingly support the eventual findings of the study.

            Next comes the discussion section. Sometimes this is intermixed with the presentation of the results and other times it is intermixed with the conclusions and summary of the study; that’s the author’s choice in how they structure it. This section should bridge the gap from the objective presentation of the results to the conclusion addressing the question posed at the end of the introduction. It should make the case that the findings are an original and significant contribution to the field. It should mention and address any substantial caveats to the study and note any limitations to the applicability of the conclusions.

            Some papers will have a final conclusions or summary section. I personally like this as a stand-alone section to the manuscript so that readers can quickly skip to the main findings of the study. It should repeat what has already been stated earlier in the paper and not include any new analysis points.

            There are a few other considerations to ensure a great paper. One is that the title should be an appropriate distillation of the main focus of the study. It shouldn’t contain many, if any, acronyms, and should focus on the scientific discovery rather than the methodology used to make the advancement. The abstract should be a concise yet complete summary of the study that explains not only the finding but also the reasoning behind its significance. Tables and figures should be readable, understandable, and adequately and objectively described in the captions. The prose should be publication quality and not need extensive corrective proof-reading.

            In short, a great paper contains, in an easily readable and understandable presentation, all that is necessary to convey the significance of the findings…and nothing else.  I hope that referees heed this direction and write reviews with this in mind.

 

Why Do This Job?

            Most people are supportive of the position of journal editor, but occasionally I get asked the question, “Why did you take on this job?” It’s a very good question, because the job takes a lot of time away from doing other things in my life. In addition, I am “the obstacle,” the roadblock to the smooth and timely publication of your paper. Who wants that job?! It’s a universal assumption that authors think their manuscript is worthy of acceptance without revision, and I, with the help of the solicited referees, am the gatekeeper deciding that it needs more modifications. Or worse, deciding that the modifications are too great and therefore I reject that version of the manuscript.

            So, why did I agree? One big reason is that I know people who are/were getting frustrated with JGR-Space Physics and I thought up some ways to alleviate that angst. That is, I was (and still am) concerned about the prestige of the journal and wanted to do what I can to keep it a premiere publication. This concern is not really about the standing of JGR relative to other space physics journals; it is about the journal’s stature beyond our field and a perception about space physics as a discipline. I did not want to see its reputation slip and be a reflection on our entire field.

            To address this looming “stature gap” relative to other fields, I first had to understand the irritation with JGR. Some of it had to do with the immediate issue of production snafus with the transition to Wiley. For others, it was dissatisfaction with the editorial system and process. For some, it was a very specific affront and they refused to publish in JGR anymore. Many of these personal disappointments had taken place years ago, yet they still held it against the journal.

            For a portion of these issues and concerns, the answer was already in place but the community didn’t know about it yet. I wanted to increase communication from the editorial board to the space physicists we serve, removing the opaque barrier of secrecy to our work and helping the community understand what we do. I think that people are reasonable and if they become familiar with the editorial process, then they will better comprehend our decisions.

            For other problems that people have with the journal, I wanted to open up a conversation with the community so that these issues can be identified and addressed. Again, this blog is helping with that, but I would also like people to feel comfortable directly emailing me with a question or comment about how JGR works. The more information you have about the process, the better. Ignorance is a huge driver of fear and frustration, and so the more that I can communicate with you to let you know what we do as editors, what AGU staff do to process manuscripts, and what Wiley staff do to convert the accepted manuscript into a published paper, the better.

            Note that being open about the process does not mean being easy on the manuscripts. I and the other editors will still demand revisions and occasionally reject papers. The bar for publication is still high and papers must make a significant original contribution to our knowledge of space physics in order to be published in the journal. That said, if you have any questions about why, then please just ask.

New Space Weather EiC

            As it was just announced in the SPA newsletter, please join me in congratulating Delores Knipp to the editorial helm at Space Weather! It’s been a six-month process, but the decision has been made that she will be the new Editor-in-Chief of this journal and its print version counterpart, Space Weather Quarterly.

            Dr. Knipp, a Research Professor in Aerospace Engineering at the University of Colorado in Boulder, is in the midst of transitioning into this new role and will officially take over from the outgoing EiC, Lou Lanzerotti, in October. I look forward to working with Delores as part of the AGU journal EiC crew as well as through our inter-journal communication between JGR Space Physics and Space Weather.

            I would also like to take this opportunity to thank Lou for his decade-plus history of service to the space physics community as the inaugural editor of this journal. I agree with Jim Klimchuk in his newsletter post, “It is largely because of Lou’s incredible dedication, energy, and wisdom that Space Weather and the Quarterly are the premier publications that they are today.” Congratulations, Lou, on a successful and prosperous tenure as EiC!

            Finally, I’d like to add a manuscript submission comment to this post. JGR Space Physics and Space Weather are closely-related journals and authors sometimes have a difficult time determining to which of these journals a particular manuscript should be submitted. Overlap between these journals can be minimized by clarifying the scope of the two journals: JGR Space Physics is the place for advancements in our knowledge of space science, i.e., of the processes controlling how rarefied neutral and charged particles move and their relationship with electric and magnetic fields throughout the solar system. Space Weather focuses on the application of this understanding toward an advancement of knowledge on the issue of space environment effects on technological or biological systems. It connects the space research community with engineering and operations groups working in fields that are affected by those rarified neutral and charged particle populations and/or electric and magnetic fields in outer space. We occasionally reject manuscripts based on this delineation of scope, encouraging the authors to resubmit the paper to the other journal. On this note, an upgrade in the works for the GEMS system will allow us to shift such submissions directly to another AGU journal (with the permission of the author), rather than requiring the author to resubmit from the beginning at the GEMS site for that other journal.