On writing a scientific paper

(Part 1 of 4)

For several years now, we have been teaching a Special Topics (one-unit) course at the Marine Science Institute of UP Diliman on what we think is a good way to write a scientific paper. The course is based on what we have learned from our experience with publishing our papers, from reading and reviewing papers written by others, and from our experience with editing a scientific journal ourselves. The topics we cover include why we publish, where we should publish, what to include in our paper, and what to expect about our submission. We talk about the nature and peculiarities of the review process and the specific requirements of some of the journals we are familiar with. We talk about our personal views on how scientific papers should be written. We also talk about the policies that we follow in Philippine Science Letters (http://www.philsciletters.org/), the freely available online journal that we have established to showcase Philippine science and Filipino scientists. The purpose of the course is to familiarize our beginning scientists with the nature (and travails) of writing scientific papers and, hopefully, to ease them into the culture of publishing. The following is a summary of what we cover in the course. 

Why we publish

There are a number of reasons for publishing our scientific results. These include (1) to share the knowledge that we have gained with the rest of the world; (2) to get our work reviewed, validated and accepted by our peers; (3) it is a requirement to get a degree, or to get tenure, to earn a promotion, or even to keep one’s job; (4) to establish a research track record in order to get more research funding; and (5) for prestige and standing, or to win awards. There are also reasons for not wanting to publish our results (more on this later).

Wanting to share our knowledge with the rest of the world is rooted in the most basic reason for doing science: we do science to help improve our world. We don’t work in a vacuum; we avail ourselves of the knowledge gained by others before us and we try to add to that knowledge. This is the most noble reason for publishing — and the most altruistic.

These days, it is usually required to have published a paper to get a Ph.D. In the College of Science of UP Diliman, for example, a requirement for the Ph.D. is that the thesis must have been published, or have been accepted for publication, in a “reputable, refereed scientific journal” (http://www.science.upd.edu.ph/images/PDF/Graduate_Resources/forms/cs_revised_guide_gradprog.pdf). 

More and more universities require a doctoral degree to hire someone in a tenure-track position. Further, publications are usually required to get tenure. And there is a heavy emphasis on publications in promotions.

And then there are the awards reaped from having lots of publications. UP and some other universities give cash awards for international publications. The NAST gives awards for the best publications in local journals. UP has a Scientist Productivity System and DOST has a Scientific Career System, both principally based on publications.

But in our course, we emphasize that the quality of one’s publications, not the number, is a better gauge of the worth of a scientist’s contribution to science, i.e., in terms of his/her publications. The quality and significance of a scientific paper can be gauged by the number of times the paper is cited by other scientists. (To a scientist, nothing is more depressing than to be ignored by one’s peers.) 

There are a number of metrics that are currently being used to assess a scientist’s worth in terms of his/her publications. One that is widely used is the “h-index” (JE Hirsch (2005) Proc Natl Acad Sci USA. 102:16569-16572). Very simply, a scientist’s h-index is N if he has published N papers that had been cited in at least N other papers. The higher the h-index, the higher is the regard that one’s scientific work is held by others. Of course, a scientist may have published only a few, but all very significant, papers and thus has a low h-index. A better gauge of a scientist’s worth in this case would be the number of citations each of his/her papers has received. (For this, you can check Google Scholar.)

(A computer program that one could use to compute h-indices and a few other metrics is “Publish or Perish,” which is freely available at http://www.harzing.com/pop.htm. “Publish or Perish” gives the total number of citations that one’s papers had gotten, as well as the number of citations for each paper.) 

In some universities in developed or more advanced countries, however, researchers’ worth is not measured by their h-index, or the number of citations of their papers, but by the quality of their top few, e.g., five, publications which are carefully evaluated by external experts in their field. This evaluation is made the basis for promotion, or the granting of tenure.

Sadly, these days, there are reasons for not wanting to publish. It boils down to two words: “competition” and “money.”

There is a story of a group that was working on a molecule that plays a major role in a very important disease. Because of its importance, there were several other groups working on the same molecule and the race was on to determine the structure of the molecule (so that inhibitors could be rationally designed). The first group had a sizeable lead over the competition in that it had managed (by accident) to crystallize the molecule, while the others couldn’t, and had determined its structure. The group started publishing its results and made a terrible mistake: it published how they got their crystals! Very quickly, they had lots of competition.

There may be other incentives to postpone publication, not only of methods, but also of results. In some countries, for example, once a result, product, method, etc. had been published, or revealed, it can no longer be patented. Patents could be a source of great monetary rewards and more and more scientists are patenting their methods and results. Understandably, industrial companies wait until after patent applications had been filed before they talk about their results, products, methods, etc. — if they talk about them at all.

(The authors rue the passing of the old culture of sharing results with everyone. Sadly, the “good old days” of cooperation — not competition — are long gone. These days, the credo of many scientists is no longer “publish or perish,” but “patent and prosper.”)

(To be continued)

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Gisela P. Padilla-Concepcion is a professor at the Marine Science Institute, UP Diliman, and is currently UP vice president for academic affairs. She is a member of the NAST. She can be reached at [email protected]. 

Eduardo A. Padlan is a retired research scientist, formerly with the US National Institutes of Health, and is currently serving as an adjunct professor at the Marine Science Institute. He is a corresponding member of the NAST. He can be reached at [email protected].