Tag: publication

Looking Back: Three Years After Grad School

By Courtney Hann (NOAA Fisheries, West Coast Sustainable Fisheries Division)

Thinking back, as Leigh’s first M.Sc. student for the GEMM Lab, I wonder what poignant insight could have prepared me for my future endeavors. And having faced years of perseverance and dedication in the face of professional unknowns, perhaps the answer is none at all; fore maybe it was the many unknown challenges met that led me to where I am today.

I graduated in December of 2015, with my Masters in Marine Resource Management, and stamped completion of my research with the GEMM Lab. While my research focused on marine mammals, my broader love for the Earth’s oceans and lands guided my determination to help keep our planet’s precious ecosystem resources wild and free. So when I landed a position in terrestrial ecology after graduating, I chose to embrace the challenging decision of jumping away from theoretical research and moving back towards applied research. Consequently, I fell in love with botany, moth identification, birding, and explored the unknowns of a whole new world of conservation biology in Scotland with the Royal Society for the Protection of Birds. Not only was this work incredibly fun, interesting, and spontaneous, it offered me an opportunity to take my knowledge of developing research projects and apply it to nature reserve management. Every survey I completed and dataset I analyzed provided information required to determine the next land management steps for maximizing the conservation of rare and diverse species. From the GEMM Lab, I brought skills on: how to work through what, at times, seemed like an impassible barrier, complete tasks efficiently under a tight deadline, juggle multiple activities and obligations, and still make time to ponder the importance of seeing the bigger picture, while having fun learning new things.

Above: Botanizing and birding in Scotland with the best botanist I have ever known and my boss, Jeff Waddell, with the Royal Society for the Protection of Birds.

For me, the long game of seeing the bigger picture has always been key. And at the end of the day, I remained steadfast in answering the questioned I posed myself: Why do all of this work if not to make a truly positive impact? With that in mind, and with an expiring visa, I moved back to the West Coast of the U.S. and landed a contracting position with NOAA Fisheries. Where I met my second female mentor, Heidi Taylor, who inspired me beyond words and introduced me to the amazing world of fisheries management. All the while, I kept working my second part-time job with the West Coast Regional Planning Body (now called the West Coast Ocean Alliance, WCOA). Working two jobs allowed me to not only accelerate my learning capacity through more opportunities, but also allowed me to extend the reach of growing a positive impact.  For example, I learned about coordinating region-wide ocean management, facilitation of diverse groups, and working with tribes, states, and federal agencies while working for the WCOA. While there were moments that I struggled with overworking and fatigue, my training in graduate school to persevere really kicked in. Driven by the desire to attain a permanent position that complimented my talents and determination to provide sustained help for our Earth’s ecosystems, I worked for what sometimes felt endlessly to reach my goal. Getting there was tough, but well worth it!

One of the most challenging aspects for me was finishing my last publication for the GEMM Lab. I was no longer motivated by the research, since my career path had taken a different turn, and I was already burnt out form working overtime every week. Therefore, if it was not for Leigh’s encouraging words, the promise I made to her to complete the publication, and my other co-author’s invitation to submit a paper for a particular journal, then I likely would have thrown in the towel. I had to re-do the analysis several times, had the paper rejected once, and then ended up re-writing and re-structuring the entire paper for the final publication. In total, it took me two and half years and 100s of hours to complete this paper after graduating. Of course, there was no funding, so I felt a bit like an ongoing graduate student until the paper was finally accepted and the work complete. But the final acceptance of the paper was so sweet, and after years of uncertain challenges, a heavy weight had finally been lifted. So perhaps, if there is one piece of advice I would say to young graduate students, it is to get your work published before you graduate! I had one paper and one book chapter published before I graduated, and that made my life much easier. While I am proud for finishing the final third publication, I would have much preferred to have just taken one extra semester and finished that publication while in school. But regardless, it was completed. And in a catharsis moment, maybe the challenge of completing it taught me the determination I needed to persevere through difficult situations.

Above: Elephant seal expressing my joy of finishing that last publication! Wooohoooooo!

With that publication out of the way, I was able to focus more time on my career. While I no longer use R on a daily basis and do not miss the hours of searching for that one pesky bug, I do analyze, critique, and use scientific literature everyday. Moreover, the critical thinking, creative, and collaborative skills I honed in the GEMM Lab, have been and will be useful for the rest of my life. Those hours of working through complicated statistical analyses and results in Leigh’s office pay off everyday. Reading outside of work, volunteering and working second jobs, all of this I learned from graduate school. Carrying this motivation, hard work, determination, and perseverance on past graduate school was undeniably what led me to where I am today. I have landed my dream job, working for NOAA Fisheries Sustainable Fisheries Division on salmon management and policy, in my dream location, the Pacific Northwest.  My work now ties directly into ongoing management and policy that shapes our oceans, conservation efforts, and fisheries management. I am grateful for all the people who have supported me along the way, with this blog post focusing on the GEMM Lab and Leigh Torres as my advisor. I hope to be a mentor and guide for others along their path, as so many have helped me along mine. Good luck to any grad student reading this now! But more than luck, carry passion and determination forward because that is what will propel you onward on your own path. Thank you GEMM Lab, it is now time for me to enjoy my new job.

Above: Enjoying in my new home in the Pacific Northwest.

 

 

 

Scientific publishing: Impact factor, open access and citations

By Leila Lemos1 and Rachel Ann Hauser-Davis2

1PhD candidate, Fisheries and Wildlife Department, OSU

2PhD, CESTEH/ENSP/Fiocruz, Rio de Janeiro, Brazil

Scientific publishing not only communicates new knowledge, but also is a measure of each scientist’s success: the impact each scientist has on his/her field is often measured by his/her number of publications and the reputation of the journals he/she published in. Therefore, publishing in reputable journals, with a high impact factor, is often essential to get a job, promotion and tenure. So, what is an impact factor?

The impact factor (IF) was first created in the 1960’s and is a measure of a journal’s impact on science, as reflected by the yearly average number of citations to recent articles published in that journal. The IF is used to compare the impact of journals within disciplines. Journals with higher impact factors are deemed as more prestigious and of better quality than those with lower ones.

The IF of a journal for any given year is calculated as the number of citations, received in that year, of articles published in that journal during the two preceding years, divided by the total number of articles published in that journal during the two preceding years, as follows:

In recent years, open access (OA) journals have emerged, changing how we perceive publications. However, the role and significance of IF is still present, valuable and used worldwide.

Conventional (non-open access) journals cover publishing costs through access fees, such as subscriptions, site licenses or download charges, which can be paid by universities, research institutions and, sometimes, by individuals. Papers published in OA journals, on the other hand, are distributed online and free of cost. However, there are still publication costs, which are usually paid by the authors. And, open access article processing charges are not cheap, ranging from a few hundred to several thousand dollars, depending on the field (more thoughts on this theme here).

It seems imbalanced that researchers have to pay for their work to be published. They have carried out a study and have obtained results that should be shared with the community. These results should not be treated as a commercial item to be sold. Also, it ends strengthening those who have resources and weakening those who do not have, increasing the division between Northern and Southern hemispheres, and narrowing the knowledge-production system (Burgman 2018).

Thus, a free-of-charge research paper would be interesting for everyone. PeerJ is a good example of a recent OA, free of publishing costs, peer-reviewed, and scholarly journal, that was released in 2013. It’s a totally new model and pushes the boundaries. In addition, there are hybrid journals (i.e., Conservation Biology) that offer both conventional and OA modes, leaving it to the authors to decide what they prefer (Burgman 2018). In many cases, disadvantaged authors might also be able to appeal for waivers. Thus, authors who cannot pay publishing fees might still see their work getting published.

However, this is not how the publishing system typically works. Therefore, researchers need to determine where to publish based on the journal IF and focus/audience, on the different price structures and fees, and whether it is OA or not.

Researchers in general want their articles to be openly accessible for everyone, not just those who can afford to pay the journal for access, so they can increase visibility of their work. Open access can increase the impact/reach of a research paper by facilitating paper downloads, access, and use in other scientific research, which may, in turn, lead to higher citation rate (Eyesenbach 2006).

Higher citation rates would also improve researchers’ H-index: an author-level metric that measures both productivity and citation impact of a scientist or scholar, based on the scientist’s most cited papers and the number of citations that they have received in publications.

The graph below exemplifies the h-index that is based on the maximum value of h such that the given author/journal has published h papers that have each been cited at least h times. In other words, the index is designed to improve with number of publications or citations. The index can only be compared between researchers from same field, as citation conventions might differ widely among different fields.

H-index from a plot of decreasing citations for numbered papers
Source: Wikipedia

 

However, publishing in an OA journal might easily increase researchers’ H-index and journals’ IF. Many researchers have also considered OA as an “artificial citation enhancer”.

As with any new system, some are opposed to the establishment of the OA system, including researchers, academics, librarians, university administrators, funding agencies, government officials, publishers and editorial staff, among many others (Markin 2017). This opposition claims that OA publishing leads to financial damages to the large publishers worldwide, and, mainly, that this system may damage the peer review system in place today, leading to reduced scientific quality (such as “you pay, you publish” predatory journals that take advantage of the paid system by publishing as fast as possible, without any scientific rigor whatsoever).

However, many reputable journals, such as Elsevier, Springer, Wiley and Blackwell, now offer OA as an option for their established journals. This approach is simply another option for authors, where they may pay if they want for their paper to be available for everyone. Even if this option is available, manuscripts still go through a rigorous peer-review that occurs with both conventional and OA journals. Thus, publishing in OA should be just as rigorous.

Open access papers would be the most “scientifically ethical”, as science is aimed at society, for society, and this type of publishing furthers research reach. However, paying thousands of dollars is sometimes very complicated, as this means less money for fieldwork costs, gears, laboratory analyses, among others.

All in all, OA is a recent development that is changing scientist approach to publication. The future of scientific publication seems uncertain and likely to hold new developments in the near future.

 

References:

Burgman M. 2018. Open access and academic imperialism. Conservation Biology 0 (0): 1–2. DOI: 10.1111/cobi.13248.

Eysenbach G. 2006. Citation Advantage of Open Access Articles. PLoS Biology 4 (5): e157. doi:10.1371/journal.pbio.0040157. PMC 1459247. PMID 16683865.

Markin P. 2017. The Sustainability of Open Access Publishing Models Past a Tipping Point. Open Science. Retrieved 26 April 2017.

Some advice on how to navigate the scientific publication maze

Dr. Leigh Torres, Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute, Oregon State University

Publication of our science in peer-reviewed journals is an extremely important part of our lives as scientists. It’s how we communicate our work, check each other’s work, and improve, develop and grow our scientific fields. So when our manuscript is finally written with great content, we could use some instructions for how to get it through the publication process.  Who gets authorship? How do I respond to reviewers? Who pays for publication costs?

There is some good advice online about manuscript preparation and selecting the right journal. But there is no blueprint for manuscript preparation. That’s because it’s a complicated and variable process to navigate, even when you’ve done it many times. Every paper is different. Every journal has different content and format requirements. And every authorship list is different, with different expectations. As an academic supervisor of many graduate students, and as author on many peer-reviewed papers, I have seen or been a part of more than a few publication blunders, hiccups, road-blocks, and challenges.

Recently I’ve had students puzzle over the nuances of the publication process: “I had no idea that was my role as lead author!”, “How do I tell a reviewer he’s wrong?”, “Who should I recommend as reviewers?” So, I have put together some advice about how to navigate through a few of the more common pitfalls and questions of the scientific publication process. I’m not going to focus on manuscript content, structure, or journal choice – that advice is elsewhere and for authors to evaluate. My intent here is to discuss some of the ‘unwritten’ topics and expectations of the publication process. This guidance and musings are based my 20 years of experience as a scientist trying to navigate the peer-review publication maze myself. I encourage others to add their advice and comments below based on their experiences so that we can engage as a community in an open dialog about these topics, and add transparency to an already difficult and grueling, albeit necessary, process.

Image Credit: Nick at http://www.lab-initio.com/

 

Authorship: Deciding who should – and shouldn’t be – be a co-author on a paper is often a challenging, sensitive, and angst-filled experience. Broad collaboration is so common and often necessary today that we often see very long author lists on papers. It’s best to be inclusive and recognize contribution where it is deserved, but we also don’t want to be handing out co-authorship as a token of appreciation or just to pad someone’s CV or boost their H-index. Indeed, journals don’t want that, and we don’t want to promote that trend. Sometimes it is more appropriate to recognize someone’s contribution in the acknowledgements section.

The best advice I can give about how to determine authorship is advice that was given to me by my graduate advisor, Dr. Andy Read at Duke University: To deserve authorship the person must have contributed to at least three of these five areas: concept development, acquisition of funding, data collection, data analysis, manuscript writing. Of course, this rule is not hard and fast, and thoughtful judgement and discussions are needed. Often someone has contributed to only one or two of these areas, but in such a significant manner that authorship is warranted.

I have also seen situations where someone has contributed only a small, but important, piece of data. What happens then? My gut feeling is this should be an acknowledgment, especially if it’s been published previously, but sometimes the person is recognized as a co-author to ensure inclusion of the data. Is this right? That’s up to you and your supervisor(s), and is often case-specific. But I do think we need to limit authorship-inflation. Some scientists in this situation will gracefully turn down co-authorship and ask only for acknowledgement, while others will demand co-authorship when it’s not fully deserved. This is the authorship jungle we all must navigate, which does not get easier with time or experience. So, it’s best to just accept the complexity and make the best decisions we can based on the science, not necessarily the scientists.

Next, there is the decision of author order, which can be another challenging decision. A student with the largest role in data collection/analysis and writing, will often be the lead author, especially if the paper is also forming a chapter of his/her thesis. But, if lead authorship is not clear (maybe the student’s work focuses on a small part of a much larger project) then its best to discuss authorship order with co-authors sooner rather than later. The lead author should be the person with the largest role in making the study happen, but often a senior scientist, like an academic supervisor, will have established the project and gained the funding support independent of a student’s involvement. This ‘senior scientist’ role is frequently recognized by being listed last in the authorship list – a trend that has developed in the last ~15 years. Or the senior scientists will be the corresponding author. The order of authors in between the first and last author is often grey, muddled and confusing. To sort this order out, I often think about who else had a major role in the project, and list them near the front end, after the lead author. And then after that, it is usually just based on alphabetical order; you can often see this trend when you look at long author lists.

Responsibility as lead author:  The role of a lead author is to ‘herd the cats’. Unless otherwise specified by co-authors/supervisor, this process includes formatting the manuscript as per journal specifications, correspondence with journal editors (letters to editors and response to reviewer comments), correspondence with co-authors, consideration and integration of all co-author comments and edits into the manuscript, manuscript revisions, staying on time with re-submissions to the journal, finding funding for publication costs, and review of final proofs before publication. Phew! Lots to do. To help you through this process, here are some tips:

How to get edits back from co-authors: When you send out the manuscript for edits/comments, give your co-authors a deadline. This deadline should be at least 2 weeks out, but best to give more time if you can. Schedules are so packed these days. And, say in the email something like, ‘If I don’t hear back from you by such and such a date I’ll assume you are happy with the manuscript as is.” This statement often spurs authors to respond.

How to respond to reviewer comments: Always be polite and grateful, even when you completely disagree with the comment or feel the reviewer has not understood your work. Phrases like “we appreciate the feedback”, “we have considered the comment”, and “the reviewers provided thoughtful criticism” are good ways to show appreciation for reviewer comments, even when it’s followed by a ‘but’ statement. When revising a manuscript, you do not need to incorporate all reviewer comments, but you do need to go through each comment one-by-one and say “yes, thanks for this point. We have now done that,” or thoughtfully explain why you have not accepted the reviewer advice.

While receiving negative criticism about your work is hard, I have found that the advice is often right and helpful in the long run. When I first receive reviewer comments back on a manuscript, especially if it is a rejection – yes, this happens, and it sucks – I usually read through it all. Fume a bit. And then put it aside for a week or so. This gives me time to process and think about the feedback. By the time I come back to it, my emotional response has subsided and I can appreciate the critical comments with objectivity.

Journal formatting can be a nightmare: Some editor may read this post and hate me, but my advice is don’t worry too much about formatting a manuscript perfectly to journal specs. During the initial manuscript submission, reviewers will be assessing content, not how well you match the journal’s formatting. So don’t kill yourself at this stage to get everything perfect, although you should be close. Once your paper gets through the first round of reviews, then you should worry about formatting perfectly in the revision.

Who should I recommend as a reviewer? Editors like it when you make their lives easier by recommending appropriate reviewers for your manuscript. Obviously you should not recommend close friends or colleagues. Giving useful, appropriate reviewer suggestions can be challenging. My best advice for this step is to look at the authors you have referenced in the manuscript. Those authors referenced multiple times may have interest in your work, and be related to the subject matter.

Who pays or how to pay for publication? Discuss this issue with your co-authors/supervisor and plan ahead. Most journals have publication fees that often range between $1000 and $2000. Sometimes color figures cost more. And, if you want your paper to be open access, plan on paying > $3000. So, when deciding on a journal, keep these costs in mind if you are on a limited budget. These days I add at least $2000 to almost every project budget to pay for publication costs. Publication is expensive, which is ridiculous considering we as scientists provide the content, review the content for free, and then often have to pay for the papers once published. But that’s the frustrating, unbalanced racket of scientific publication today – a topic for another time, but this article is definitely worth a read, if interested.

So that’s it from me. Please add your advice, feedback, and thoughts below in the comments section.