Introduction
To the editor:
The Brief Communication published by Mazor et al. in the May issue of your journal (Nat. Biotechnol. 25, 563–565, 2007) contained what is becoming an increasingly alarming trend not only in your journal but many other so-called 'top-tier' journals—a lack of documented methodology and information that is essential to faithfully reproduce the science claimed in the manuscript. Surely, the aim of scientific publication is to disseminate scientific information to further advance our knowledge and to allow others to use such information for expansion and possible improvements to the work. Mazor et al. are clearly not the only authors being forced into abbreviated paper formats that follow this trend, which suggests the problem goes significantly deeper.
The communication of scientific information largely requires the evaluation of data and concepts generated by scientific experimentation through the rigorous peer review process and the subsequent publication of approved information by scientific periodicals. Basic scientific research has more or less followed this process since its inception. Nowadays, the sheer volume of research and its fast pace is coupled with the increasingly common practice of scientific publications to overlook, reduce or omit scientific methodology from the pages of published manuscripts. For example, in certain journal manuscripts, critical methodology sections do not physically appear in the final published version—an event contributing to a lack of appropriately reviewed and documented scientific methodology hindering the faithful reproduction of the science claimed in the manuscript. This is a worrying issue that needs addressing for the continued good standing of scientific publication. If the aim of scientific publication is to disseminate scientific information that further advances our knowledge and to allow other researchers to use such information for expansion and possible improvements to the work, then every attempt should be made to include the most critical details in the published manuscript. Although one could argue that the evolution of scientific publication is necessary because of the intense competition for space in the pages of scientific journals, we feel that the current inclination toward the covert display of the scientific method in scientific publications will risk compromising the reproducibility of the science and diminish its significance. In addition, the trend toward the online version of manuscripts becoming the article of record, rather than the longstanding but seemingly outdated printed version, potentially adds to this problem by often relegating methods to supplementary online files that are referred to, but do not physically appear, in the final manuscript.
To illustrate this lessening of scientific methodology from published scientific manuscripts one simply needs to look at the recent publications within scientific journals. Many journals publish brief communications or short reports which, most likely owing to their small size and format, contain an extremely short methodology section or in many cases, no methodology at all to help explain exactly how the results were obtained by the investigators (in the case of Science, published manuscripts are called articles or reports and neither contains a methods section). Here, scientific methods are mainly made available as separate supplementary online bulky text documents that also contain supporting results and other information somehow deemed superfluous to the printed manuscript. Although the additional publication of supporting material as supplementary online information is often necessary and even commendable, how can a reviewer possibly wade through all this information in a timely manner to provide a rational recommendation to the editors on the merits of the manuscript for publication? We suggest that the lack of rigid criteria applied to such supplemental information promotes mistakes and omissions in methodology explanations that can lead to frustrating attempts by colleagues to reproduce the experiments and results claimed in the original publication. In contrast, many journals also publish full-length research articles that adopt the traditional publication format containing the introduction, methods, results and discussion sections. However, too often these methods are minimal and still necessitate augmentation by supplementary online documents that suffer from the same inadequacies as outlined above. The underlying theme is that the poorly described methodology is no longer the exception; it occurs far too frequently.
Several theories may explain this trend of peer-reviewed scientific journals to lack rigorous methodology sections in too many of the published manuscripts: first, due to publishing constraints on space, journal editors are required to keep manuscripts shorter, so authors opt to truncate the methodology or relegate this necessary section to the supplementary online files to avoid restricting the results on display; second, reviewers are overwhelmed with information and simply do not have the time to properly evaluate manuscripts or do not recognize the importance of appropriate methodology sections of manuscripts; third, authors may be somewhat superficial with methods and/or knowingly withhold vital aspects to protect their status as the exponents in the field or to pursue personal financial rewards through patenting and licensing agreements. Although these last two points are extreme views, it is conceivable that reviewers and authors, in addition to the space limitations already determined by journal guidelines, do contribute to the overall insufficiency of methodology currently commonplace in scientific manuscripts. How many of us as authors, when faced with editorial reviews recommending manuscript shortening decide to trim the methods section because it is less important? Additionally, as reviewers how often do we carefully inspect scientific methodology and its consistency?
It is evident that the evolution of scientific publication is warranted due to the extreme competition for journal space brought about by more papers being written. This increased volume is good for scientific communication and its subsequent globalization; however, the process of publication of, and debate over, data and theories needs to remain well regulated. The continued neglect of scientific methodology in publications will, in our opinion, only lead to a reduction of overall scientific quality. Attempts to address this problem by scientific journals have largely centered on the practice of 'attaching' supplementary online files to manuscripts. Although on one hand this approach allows a larger amount of information to be communicated, on the other it produces an almost unlimited quantity of data that are not always sufficiently screened, probably because of the large volume and its assumed secondary importance. Admirably, Nature has recently implemented new guidelines for the addition of methods to their published research articles and letters. Authors are given multiple options (http://www.nature.com/nature/authors/gta/index.html#a5.3) for the appropriate presentation of methods within their manuscripts, avoiding the demotion of Methods to the supplementary section. This approach should be commended and we hope adopted universally by additional scientific periodicals. Aside from these rules, we should all make an extra effort as authors and reviewers to ensure that scientific methodology resumes its rightful position as the foundation of basic scientific research.
