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 theNational
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 theiranalysis 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
assecondary.

The articles in scientific journals are different from news articles in

another way – they must undergo aprocess 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.

Scientific journals: Degrees of specialization

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). Cellfocuses on all areas of biology, NEJM on medicine, and
both Science and Naturepublish 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 theresearch 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.

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:
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 (seeThe 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.

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 Lightand 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
wordingNewton 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, theabstract 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.

Building knowledge and facilitating 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.