Did you know?

Did you know that scientific literature goes all the way back to 600BCE? Although scientific articles have changed some - for example, Issac Newton wrote about the fun he had with prisms in a 1672 scientific article - the basics remain the same. This ensured that published research becomes part of the archive of scientific knowledge upon which other scientists can build.

We've all read the headlines at the supermarket checkout line: "Aliens Abduct New Jersey School Teacher" or "Quadruplets Born to 99-Year-Old Woman: Exclusive Photos Inside." Journals like the National Enquirer sell copies by publishing sensational headlines, and most readers believe only a fraction of what is printed. A person more interested in news than gossip could buy a publication like Time, Newsweek or Discover. These magazines publish information on current news and events, including recent scientific advances. These are not original reports of scientific research, however. In fact, most of these stories include phrases like, "A group of scientists recently published their findings on..." So where do scientists publish their findings?

Scientists publish their original research in scientific journals, which are fundamentally different from news magazines. The articles in scientific journals are not written by journalists – they are written by scientists. Scientific articles are not sensational stories intended to entertain the reader with an amazing discovery, nor are they news stories intended to summarize recent scientific events, nor even records of every successful and unsuccessful research venture. Instead, scientists write articles to describe their findings to the community in a transparent manner.

Scientific journals vs. popular media

Within a scientific article, scientists present their research questions, the methods by which the question was approached, and the results they achieved using those methods. In addition, they present their analysis of the data and describe some of the interpretations and implications of their work. Because these articles report new work for the first time, they are called primary literature. In contrast, articles or news stories that review or report on scientific research already published elsewhere are referred to as secondary.

The articles in scientific journals are different from news articles in another way – they must undergo a process called peer review, in which other scientists (the professional peers of the authors) evaluate the quality and merit of research before recommending whether or not it should be published (see our Peer Review module). This is a much lengthier and more rigorous process than the editing and fact-checking that goes on at news organizations. The reason for this thorough evaluation by peers is that a scientific article is more than a snapshot of what is going on at a certain time in a scientist's research. Instead, it is a part of what is collectively called the scientific literature, a global archive of scientific knowledge. When published, each article expands the library of scientific literature available to all scientists and contributes to the overall knowledge base of the discipline of science.

Comprehension Checkpoint

Articles published in scientific literature are considered primary literature when

(A)__they are more important than articles in newspapers.

(B)__they report new research for the first time.

Scientific journals: Degrees of specialization

Figure 1: Nature: An example of a scientific journal.

There are thousands of scientific journals that publish research articles. These journals are diverse and can be distinguished according to their field of specialization. Among the most broadly targeted and competitive are journals like Cell, the New England Journal of Medicine (NEJM), Nature, and Science that all publish a wide variety of research articles (see Figure 1 for an example). Cell focuses on all areas of biology, NEJM on medicine, and both Science and Nature publish articles in all areas of science. Scientists submit manuscripts for publication in these journals when they feel their work deserves the broadest possible audience.

Just below these journals in terms of their reach are the top-tier disciplinary journals like Analytical Chemistry, Applied Geochemistry, Neuron, Journal of Geophysical Research, and many others. These journals tend to publish broad-based research focused on specific disciplines, such as chemistry, geology, neurology, nuclear physics, etc.

Next in line are highly specialized journals, such as the American Journal of Potato Research, Grass and Forage Science, the Journal of Shellfish Research, Neuropeptides, Paleolimnology, and many more. While the research published in various journals does not differ in terms of the quality or the rigor of the science described, it does differ in its degree of specialization: These journals tend to be more specialized, and thus appeal to a more limited audience.

All of these journals play a critical role in the advancement of science and dissemination of information (see our Utilizing the Scientific Literature module for more information). However, to understand how science is disseminated through these journals, you must first understand how the articles themselves are formatted and what information they contain. While some details about format vary between journals and even between articles in the same journal, there are broad characteristics that all scientific journal articles share.

Comprehension Checkpoint

Representing data graphically

(A)__means to take a photograph

(B)__make it easier to interpret complex datasets.

The standard format of journal articles

In June of 2005, the journal Science published a research report on a sighting of the ivory-billed woodpecker, a bird long considered extinct in North America (Fitzpatrick et al., 2005). The work was of such significance and broad interest that it was displayed prominently on the cover (Figure 2) and highlighted by an editorial at the front of the journal (Kennedy, 2005). The authors were aware that their findings were likely to be controversial, and they worked especially hard to make their writing clear. Although the article has no headings within the text, it can easily be divided into sections:

Figure 2: A picture of the cover of Science from June 3, 2005. image © American Association for the Advancement of Science/Cornell Lab of Ornithology

Title and authors: The title of a scientific article should concisely and accurately summarize the research. Here, the title used is "Ivory-billed Woodpecker (Campephilus principalis) Persists in North America." While it is meant to capture attention, journals avoid using misleading or overly sensational titles (you can imagine that a tabloid might use the headline "Long-dead Giant Bird Attacks Canoeists!"). The names of all scientific contributors are listed as authors immediately after the title. You may be used to seeing one or maybe two authors for a book or newspaper article, but this article has seventeen authors! It's unlikely that all seventeen of those authors sat down in a room and wrote the manuscript together. Instead, the authorship reflects the distribution of the workload and responsibility for the research, in addition to the writing. By convention, the scientist who performed most of the work described in the article is listed first, and it is likely that the first author did most of the writing. Other authors had different contributions; for example, Gene Sparling is the person who originally spotted the bird in Arkansas and was subsequently contacted by the scientists at the Cornell Laboratory of Ornithology. In some cases, but not in the woodpecker article, the last author listed is the senior researcher on the project, or the scientist from whose lab the project originated. Increasingly, journals are requesting that authors detail their exact contributions to the research and writing associated with a particular study.

Abstract: The abstract is the first part of the article that appears right after the listing of authors in an article. In it, the authors briefly describe the research question, the general methods, and the major findings and implications of the work. Providing a summary like this at the beginning of an article serves two purposes: First, it gives readers a way to decide whether the article in question discusses research that interests them, and second, it is entered into literature databases as a means of providing more information to people doing scientific literature searches. For both purposes, it is important to have a short version of the full story. In this case, all of the critical information about the timing of the study, the type of data collected, and the potential interpretations of the findings is captured in four straightforward sentences as seen below:

The ivory-billed woodpecker (Campephilus principalis), long suspected to be extinct, has been rediscovered in the Big Woods region of eastern Arkansas. Visual encounters during 2004 and 2005, and analysis of a video clip from April 2004, confirm the existence of at least one male. Acoustic signatures consistent with Campephilus display drums also have been heard from the region. Extensive efforts to find birds away from the primary encounter site remain unsuccessful, but potential habitat for a thinly distributed source population is vast (over 220,000 hectares).

Introduction: The central research question and important background information are presented in the introduction. Because science is a process that builds on previous findings, relevant and established scientific knowledge is cited in this section and then listed in the References section at the end of the article. In many articles, a heading is used to set this and subsequent sections apart, but in the woodpecker article the introduction consists of the first three paragraphs, in which the history of the decline of the woodpecker and previous studies are cited. The introduction is intended to lead the reader to understand the authors' hypothesis and means of testing it. In addition, the introduction provides an opportunity for the authors to show that they are aware of the work that scientists have done before them and how their results fit in, explicitly building on existing knowledge.

Materials and methods: In this section, the authors describe the research methods they used (see The Practice of Science module for more information on these methods). All procedures, equipment, measurement parameters, etc. are described in detail sufficient for another researcher to evaluate and/or reproduce the research. In addition, authors explain the sources of error and procedures employed to reduce and measure the uncertainty in their data (see our Uncertainty, Error, and Confidence module). The detail given here allows other scientists to evaluate the quality of the data collected. This section varies dramatically depending on the type of research done. In an experimental study, the experimental set-up and procedure would be described in detail, including the variables, controls, and treatment. The woodpecker study used a descriptive research approach, and the materials and methods section is quite short, including the means by which the bird was initially spotted (on a kayaking trip) and later photographed and videotaped.

Results: The data collected during the research are presented in this section, both in written form and using tables, graphs, and figures (see our Using Graphs and Visual Data module). In addition, all statistical and data analysis techniques used are presented (see our Statistics in Science module). Importantly, the data should be presented separately from any interpretation by the authors. This separation of data from interpretation serves two purposes: First, it gives other scientists the opportunity to evaluate the quality of the actual data, and second, it allows others to develop their own interpretations of the findings based on their background knowledge and experience. In the woodpecker article, the data consist largely of photographs and videos (see Figure 3 for an example). The authors include both the raw data (the photograph) and their analysis (the measurement of the tree trunk and inferred length of the bird perched on the trunk). The sketch of the bird on the right-hand side of the photograph is also a form of analysis, in which the authors have simplified the photograph to highlight the features of interest. Keeping the raw data (in the form of a photograph) facilitated reanalysis by other scientists: In early 2006, a team of researchers led by the American ornithologist David Sibley reanalyzed the photograph in Figure 3 and came to the conclusion that the bird was not an ivory-billed woodpecker after all (Sibley et al, 2006).

Figure 3: An example of the data presented in the Ivory-billed woodpecker article (Fitzpatrick et al., 2005, Figure 1). image © Science

Discussion and conclusions: In this section, authors present their interpretation of the data, often including a model or idea they feel best explains their results. They also present the strengths and significance of their work. Naturally, this is the most subjective section of a scientific research article as it presents interpretation as opposed to strictly methods and data, but it is not speculation by the authors. Instead, this is where the authors combine their experience, background knowledge, and creativity to explain the data and use the data as evidence in their interpretation (see our Data Analysis and Interpretation module). Often, the discussion section includes several possible explanations or interpretations of the data; the authors may then describe why they support one particular interpretation over the others. This is not just a process of hedging their bets – this how scientists say to their peers that they have done their homework and that there is more than one possible explanation. In the woodpecker article, for example, the authors go to great lengths to describe why they believe the bird they saw is an ivory-billed woodpecker rather than a variant of the more common pileated woodpecker, knowing that this is a likely potential rebuttal to their initial findings. A final component of the conclusions involves placing the current work back into a larger context by discussing the implications of the work. The authors of the woodpecker article do so by discussing the nature of the woodpecker habitat and how it might be better preserved.

In many articles, the results and discussion sections are combined, but regardless, the data are initially presented without interpretation.

References: Scientific progress requires building on existing knowledge, and previous findings are recognized by directly citing them in any new work. The citations are collected in one list, commonly called "References," although the precise format for each journal varies considerably. The reference list may seem like something you don't actually read, but in fact it can provide a wealth of information about whether the authors are citing the most recent work in their field or whether they are biased in their citations towards certain institutions or authors. In addition, the reference section provides readers of the article with more information about the particular research topic discussed. The reference list for the woodpecker article includes a wide variety of sources that includes books, other journal articles, and personal accounts of bird sightings.

Supporting material: Increasingly, journals make supporting material that does not fit into the article itself – like extensive data tables, detailed descriptions of methods, figures, and animations – available online. In this case, the video footage shot by the authors is available online, along with several other resources.

Comprehension Checkpoint

Scientists who wish to replicate the research described in a journal article map pay particular attention to the __ section.

(A)__materials and methods

(B)__discussion

Reading the primary literature

The format of a scientific article may seem overly structured compared to many other things you read, but it serves a purpose by providing an archive of scientific research in the primary literature that we can build on. Though isolated examples of that archive go as far back as 600 BCE (see the Babylonian tablets in our Description in Scientific Research module), the first consistently published scientific journal was the Philosophical Transactions of the Royal Society of London, edited by Henry Oldenburg for the Royal Society beginning in 1666 (see our Scientific Institutions and Societies module). These early scientific writings include all of the components listed above, but the writing style is surprisingly different than a modern journal article. For example, Isaac Newton opened his 1672 article "New Theory About Light and Colours" with the following:

I shall without further ceremony acquaint you, that in the beginning of the Year 1666...I procured me a Triangular glass-Prisme, to try therewith the celebrated Phenomena of Colours. And in order thereto having darkened my chamber, and made a small hole in my window-shuts, to let in a convenient quantity of the Suns light, I placed my Prisme at his entrance, that it might be thereby refracted to the opposite wall. It was at first a very pleasing divertissement, to view the vivid and intense colours produced thereby; but after a while applying my self to consider them more circumspectly, I became surprised to see them in an oblong form; which, according to the received laws of Refraction, I expected should have been circular. (Newton, 1672)

Figure 4: Isaac Newton described the rainbow produced by a prism as a "pleasing divertissement." image © NASA

Newton describes his materials and methods in the first few sentences ("... a small hole in my window-shuts"), describes his results ("an oblong form"), refers to the work that has come before him ("the received laws of Refraction"), and highlights how his results differ from his expectations. Today, however, Newton's statement that the "colours" produced were a "very pleasing divertissement" would be out of place in a scientific article (Figure 4). Much more typically, modern scientific articles are written in an objective tone, typically without statements of personal opinion to avoid any appearance of bias in the interpretation of their results. Unfortunately, this tone often results in overuse of the passive voice, with statements like "a Triangular glass-Prisme was procured" instead of the wording Newton chose: "I procured me a Triangular glass-Prisme." The removal of the first person entirely from the articles reinforces the misconception that science is impersonal, boring, and void of creativity, lacking the enjoyment and surprise described by Newton. The tone can sometimes be misleading if the study involves many authors, making it unclear who did what work. The best scientific writers are able to both present their work in an objective tone and make their own contributions clear.

The scholarly vocabulary in scientific articles can be another obstacle to reading the primary literature. Materials and Methods sections often are highly technical in nature and can be confusing if you are not intimately familiar with the type of research being conducted. There is a reason for all of this vocabulary, however: An explicit, technical description of materials and methods provides a means for other scientists to evaluate the quality of the data presented and can often provide insight to scientists on how to replicate or extend the research described.

The tone and specialized vocabulary of the modern scientific article can make it hard to read, but understanding the purpose and requirements for each section can help you decipher the primary literature. Learning to read scientific articles is a skill, and like any other skill, it requires practice and experience to master. It is not, however, an impossible task.

Strange as it seems, the most efficient way to tackle a new article may be through a piecemeal approach, reading some but not all the sections and not necessarily in their order of appearance. For example, the abstract of an article will summarize its key points, but this section can often be dense and difficult to understand. Sometimes the end of the article may be a better place to start reading. In many cases, authors present a model that fits their data in this last section of the article. The discussion section may emphasize some themes or ideas that tie the story together, giving the reader some foundation for reading the article from the beginning. Even experienced scientists read articles this way – skimming the figures first, perhaps, or reading the discussion and then going back to the results. Often, it takes a scientist multiple readings to truly understand the authors' work and incorporate it into their personal knowledge base in order to build on that knowledge.

Comprehension Checkpoint

In 1672, Issac Newton published his research on light and colors. He included a statement about how entertaining prisms were. Newton's work

(A)__can be dismissed as unscientific.

(B)__contained the basic components of scientific writing.

Building knowledge and faciliating discussion

The process of science does not stop with the publication of the results of research in a scientific article. In fact, in some ways, publication is just the beginning. Scientific journals also provide a means for other scientists to respond to the work they publish; like many newspapers and magazines, most scientific journals publish letters from their readers.

Unlike the common "Letters to the Editor" of a newspaper, however, the letters in scientific journals are usually critical responses to the authors of a research study in which alternative interpretations are outlined. When such a letter is received by a journal editor, it is typically given to the original authors so that they can respond, and both the letter and response are published together. Nine months after the original publication of the woodpecker article, Science published a letter (called a "Comment") from David Sibley and three of his colleagues, who reinterpreted the Fitzpatrick team's data and concluded that the bird in question was a more common pileated woodpecker, not an ivory-billed woodpecker (Sibley et al., 2006). The team from the Cornell lab wrote a response supporting their initial conclusions, and Sibley's team followed that up with a response of their own in 2007 (Fitzpatrick et al., 2006; Sibley at al., 2007). As expected, the research has generated significant scientific controversy and, in addition, has captured the attention of the public, spreading the story of the controversy into the popular media.

Summary

Using a brief history of scientific writing, this module provides an introduction to the structure and contents of scientific journal articles. Key difference between scientific journals and popular media are explained. The module offer advice on how to approach the reading of a scientific article.

Key Concepts

Scientists make their research available to the scientific community by publishing it in scientific journals.
In scientific papers, scientists explain the research they are building on, the research methods, data and data analysis techniques, and their interpretation of the data.
Understanding how to read scientific papers is a critical skill for scientists and students of science.