Tag: scientific publishing

Digging to uncover the roots of scientific writing and publication: how much (if anything) has changed?

By Lisa Hildebrand, MSc student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

In our most recent lab meeting, the GEMM lab discussed a recent paper about how blue whale migrations may be driven by memory and resource tracking (Abrahms et al. 2019). Most of our discussion was about the choices made by the authors in terms of their analyses used and the figures produced, as Leigh always pushes us graduate students to think critically about the scientific papers we read. However, a portion of our discussion focused less on the actual science behind the paper, but more on the language used. This change in direction was initiated by myself as I mentioned how much I liked the phrase “goldilocks zone”, which the authors used to describe an area between 15-17ºC that blue whales tended to occupy for the majority of the annual migration cycle.

The classic goldilocks tale vs. the blue whale version of goldilocks. Source: Slideshare.

What I liked so much about using this phrase was that the authors were using a childhood fairy tale that probably every 5-year old kid knows of to explain some pretty complex science and analysis. Our team then proceeded to go down a rabbit-hole for
a few minutes where we discussed uses of creative words in scientific writing. Although during our meeting we got back on track quite quickly, my mind has still continued down this rabbit-hole for quite some time. I started to wonder about the origins of scientific publication, when and why the structure and style of writing became so rigid, and when and why authors have decided to become a little more creative or colloquial in their writing since then. So, sit back and delve into the history of scientific writing with me…

Humankind has made scientific observations for thousands of years. Perhaps the earliest known culture to have done this are the Mesopotamian peoples who recorded observations of their surroundings around 3,500 BC in Sumer, which is now known as Iraq (Rochberg 2004). Most of the observations relate to astronomy, however there is some evidence to suggest that the Mesopotamians had recognized the existence of Pythagorean triplets (3, 4, 5; 5, 12, 13), long before Pythagoras himself was alive (Hoffman 1999).

However, formal publication of scientific observations is still a relatively new occurrence compared to when the Mesopotamians first started to note down their observations since such documentation of science first occurred in 1665. Interestingly, the birth of scientific publication was achieved by not one journal, but two; Journal des Sçavans in France and Philosophical Transactions of the Royal Society in London. Even though Journal des Sçavans beat out Philosophical Transactions of the Royal Society by publishing its first journal two months before the other, it ultimately lost the fight since it ceased publication in 1792, whereas Philosophical Transactions of the Royal Society is still in print, making it the world’s longest running scientific journal.

 

Journal covers for the first editions of Journal des Sçavans and Philosophical Transactions of the Royal Society from 1665. Source: Wikipedia.

Early publications were descriptive by nature. Instead of planning experiments, carrying them out, detailing results and interpreting them, authors described observations they made about their surroundings. An example is by a certain Mr. R.W. S.R.S from 1693. The opening lines of his publication entitled ‘Some Observations in the Dissection of a Ratt’ are as follows:

“The fore-feet of a Rat resemble those of the Castor. The Hair is also some fine, some course; as in that Animal. The Tail scaly, with Hairs between every Scale, like the Castors, which shews these two Animals to be something akin; and indeed the Water-Rat comes very near to the Beaver, and makes it’s Holes in the bank-sides of Ponds after the same manner.”

While not all publications were as purely descriptive as this example, those that did undertake experiments discussed them in a very chronological and almost basic manner. An example is by Allen Moulen in his publication ‘Some experiments on a black shining sand brought from Virginia, suppos’d to contain iron, made in March 1689’. An excerpt of the paper is as follows:

“6. I flux’d another parcel of it with Salt-Peter and Flowers of Brimstone, without being able to procure any Regulus. 7. I pour’d good Spirit of Salt on a parcel of this Sand, but could observe no Luctation thereby produc’d. 8. I pour’d Spirit of Nitre both strong and weakned with Water on parcels of the same Sand, without being able to discover any Conflict.”

Publications continued to be written in this nature for quite some time, however by the second half of the 19th century, science and the publication thereof distinctly changed and a lot of this can be credited to Louis Pasteur.

Louis Pasteur. Source: Wikipedia.

When Pasteur first had breakthroughs that provided evidence for the germ theory of disease, he was met by a lot of criticism by fellow scientists that were firm believers in the theory of spontaneous generation. As a way to prove that he was right, Pasteur started to document his experiments in extreme detail. This situation and Pasteur’s recognition of the importance of methodology resulted in the idea of reproducibility and essentially in the IMRaD structure we still follow today.

IMRaD stands for Introduction, Methods, Results and Discussion, which for scientists nowadays is probably as comforting as a cuddly blanket or a hot chocolate on a cold day. We find comfort in this structure because in a way it makes writing scientific papers less daunting because it tells us exactly what we need to do. It’s like a checklist with boxes that we can neatly tick off as we fill in the details of each section.

While IMRaD was first initiated during Pasteur’s era, it became widely adopted in the late 1950s when there was a strong boost in scientific output as more money was being funneled to the sciences. The result of this boost was strong pressure on scientific journals and their editors as authors were submitting papers at a never before seen rate. In an effort to keep up with the influx of submissions, editors felt the need to become more stringent and so enforced strict rules on article length, organization and structure, in order to weed out papers that didn’t make the cut right off the bat. This included IMRaD becoming more widely used in journals as a way to bring conformity to the sciences. This resulted in strong pressure on authors to be concise in their writing, which means that there isn’t much room for creativity.

The topic of creativity in scientific writing has long been debated and many suggest that the writing style in publications should be as objective and frank as possible in order to avoid masking the science (Massoudi 2003). However, it has also been suggested by many that by limiting the creativity in scientific writing, you might actually be limiting the creativity going into the scientific process (Bohm & Peat 1987). While I do believe that objectivity and clarity in scientific writing is important, I do not see the harm in authors trying to be a little creative in the communication of their work. Sir Peter Medawar, a Nobel Prize winning biologist summed up this sentiment very nicely in his book ‘Advice to a Young Scientist’ published in 1979:

“Scientists are people of very dissimilar temperaments doing different things in very different ways. Among scientists are collectors, classifiers and compulsive tidier-up; many are detectives by temperament and many are explorers; some are artists and others artisans. There are poet-scientists and philosopher-scientists and even a few mystics. What sort of mind or temperament can all these people be supposed to have in common? Obligative scientist must be very rare, and most people who are in fact scientists could easily have been something else instead.”

I don’t know whether there is a right or a wrong answer on this matter. What I do know though is that I always give an emphatic nod of approval when I see a word not typically seen in scientific writing used creatively in a scientific publication and it often conjures a smile on my face and makes the paper more memorable to me.

It’s interesting to muse about the direction in which scientific writing is heading now. We are still seeing a proliferation in papers that are being submitted and published, and journals being established. However, I think we are starting to see a shift in how strict scientists are in the language that they use for their publications. That is not to say that manuscripts are now submitted filled with colloquialisms, poor grammar and punctuation, but I think there is a certain flexibility in how much creativity can be incorporated into publications. The extent of this flexibility is, I believe, still largely dependent on the journal. Journals that provide very limited word count and space on the page for a publication, like Nature for example, may limit the creative capabilities of authors. However, some of the more “liberal” journals (liberal in terms of length and space), like PLoS ONE, may allow authors to explore their creative writing abilities to a greater extent. In my personal opinion, I would quite like to see more authors take creative risks in their writing.

 

References

Abrahms, B., et al., Memory and resource tracking drive blue whale migrations. PNAS, 2019. 116(12): 5582-5587.

Bohm, D., & Peat F.D. Science, Order, and Creativity.1987. Bantam Books, New York City.

Hoffman, P. The Man Who Loved Numbers: The Story of Paul Erdos and the Search for Mathematical Truth. 1999. Hyperion Books, New York City.

Massoudi, M. Can scientific writing be creative? Journal of Science Education and Technology, 2003. 12(2): 115-128.

Medawar, P. Advice to a Young Scientist. 1979. Basic Books, New York City.

Moulen, A. Some experiments on a black shining sand brought from Virginia, suppos’d to contain iron, made in March 1689. By Allen Moulen, M.D. and Fellow of the Royal Society, since dead. Philosophical Transactions of the Royal Society, 1693. 17: doi.org/10.1098/rstl.1693.0009.

Rochberg, F. The Heavenly Writing: Divination, Horoscopy, and Astronomy in Mesopotamian Culture. 2004. Cambridge University Press, Cambridge.

S.R.S., R.W. Some observations in the dissection of a ratt, communicated by Mr. R.W. S.R.S.Philosophical Transactions of the Royal Society, 1693. 17: doi.org/10.1098/rstl.1693.0006.

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.