Basic reading, writing and
informatics skills for biomedical
research
Segment 7. The structure of a
scientific article
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2012
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Types of scientific writing
– Grant application
– Mestrado or Doutorado proposal
– Research article
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Abstract
Brief communication
Research article
Review
Methods/Techniques
Supplementary content
Book chapter
Monograph
Patent
Conference proceedings
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You are writing for the readers
– “In order to understand how best to improve writing,
we would do well to understand better how readers
go about reading. It does not matter how pleased an
author might be to have converted all the right data
into sentences and paragraphs; it matters only
whether a large majority of the reading audience
accurately perceives what the author had in mind.”
• George D. Gopen and Judith A. Swan in “The Science of
Scientific Writing” – available on the web site.
– Clarity, relevance, believability, repeatability
– Back to Bishop Spratt “…bringing all things as near
the Mathematical plainness…”
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Language styles and communication
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Conversation
Meeting minutes
Chemical patent
Legal document
Car owner manual
Yellow pages
Computer software
Newspaper article
– Which styles are similar to a scientific journal article ?
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“…Mathematical plainness…”
• Structure
– Article sections, paragraphs
– Individual sentences, number of clauses
– Word order in sentences
• Order
– General to specific
– Lists
• Links
– “Tokens” provide landmarks within body text
• Translation
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Some simple rules - word order
• Por 37 votos a favor e 11 abstenções (deputados
ausentes), foi aprovado, ontem, na Assembléia Legislativa,
a 2a versão do Projeto de Lei Antinepotismo que prevê a
proibição de contratação de parentes até terceiro grau no
Poder Executivo.
• A 2a versão do Projeto de Lei Antinepotismo, que prevê a
proibição de contratação de parentes até terceiro grau no
Poder Executivo, foi aprovado ontem por 37 votos a favor e
11 abstenções (deputados ausentes) na Assembléia
Legislativa
• Diario de Pernambuco 20 Set 2007
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Example – sentence order
• The smallest of the URF's (URFA6L), a 207-nucleotide (nt) reading
frame overlapping out of phase the NH2-terminal portion of the
adenosinetriphosphatase (ATPase) subunit 6 gene has been
identified as the animal equivalent of the recently discovered yeast
H+-ATPase subunit 8 gene.
• The functional significance of the other URF's has been, on the
contrary, elusive.
• Recently, however, immunoprecipitation experiments with
antibodies to purified, rotenone-sensitive NADH-ubiquinone oxidoreductase [hereafter referred to as respiratory chain NADH
dehydrogenase or complex I] from bovine heart, as well as enzyme
fractionation studies, have indicated that six human URF's (that is,
URF1, URF2, URF3, URF4, URF4L, and URF5, hereafter referred
to as ND1, ND2, ND3, ND4, ND4L, and ND5) encode subunits of
complex I.
• This is a large complex that also contains many subunits
synthesized in the cytoplasm.
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Example – sentence order
• The smallest of the URF's, URFA6L, has been identified as the
animal equivalent of the recently discovered yeast H+-ATPase
subunit 8 gene.
• However, the functional significance of other URF's has been
more elusive.
• Recently, several human URF's have been shown to encode
subunits of rotenone-sensitive NADH-ubiquinone oxido-reductase.
• This is a large complex that also contains many subunits
synthesized in the cytoplasm - it will be referred to hereafter as
respiratory chain NADH dehydrogenase or complex I.
• Six subunits of Complex I were shown by enzyme fractionation
studies and immunoprecipitation experiments to be encoded by six
human URF's (URF1, URF2, URF3, URF4, URF4L, and URF5);
these URF's will be referred to subsequently as ND1, ND2, ND3,
ND4, ND4L and ND5.
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The structure of a scientific paper
• A scientific paper is a written report describing original
research results whose format has been defined by
centuries of developing tradition, editorial practice,
scientific ethics and the interplay with printing and
publishing services.
• The result of this process is that virtually every scientific
paper has a title, abstract, introduction, materials and
methods, results and discussion – the so-called IMRD
structure.
• Most publications have rules about a paper's format: So
read the Journal’s Instructions for Authors first!
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More on simple rules
Each section has a specific purpose
Research proposals (and research articles) tell a story
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Susan Ruff Spring 2007
Summary of main components
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Title
Author
Keywords
Abstract/Summary
Introduction
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• Materials and Methods
• Results
• Tables
• Figures
• Discussion
• References
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Summary of main components comments
– Each section has a specific purpose – try not
to mix them !
– Some journals publish supplementary data
sets
– Some journals/fields require deposition of
certain data in a public database prior to
reviewing the manuscript
– ALWAYS read the journal’s Instructions to
Authors before starting to write
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Instructions to authors
Brazilian Journal of Medical and Biological Research
Scope and policy
Page charges
Manuscript criteria and information
Manuscript Submission
Paper format
Cell Biology
Biological activity of natural products
Authorship information
Editorial review and processing
Manuscript preparation
Writing a good abstract
Tables
Figures
References
Manuscript check list
Related Links
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Naming authors
André Luiz Cabral Monteiro de Azevedo Santiago
Clarissa Daisy Costa Albuquerque
Eliane Maria Soares-Ventura
Neide Santos
Bethânia de Araújo Silva Amaral
Maria Tereza Cartaxo Muniz
Flávio José da Costa Ramos
Cecília S.C. Melo
Raquel dos Santos Vera Cruz
Vera Lúcia Lins de Morais
Terezinha de Jesus Marques–Salles
Maria Auxiliadora de Queiroz Cavalcanti
Galba Maria de Campos Takaki
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Title
• A title should be the fewest possible words that
accurately describe the content of the paper.
• Omit all waste words such as "A study of ...",
"Investigations of ...", "Observations on ...", etc.
• Remember, the title appears in the search
results
• And, indexing and abstracting services depend
on the accuracy of the title, extracting from it
keywords used for cross-referencing and
computer searching.
• So, an improperly titled paper may never reach
the audience for which it was intended, so be
specific.
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Titles – some good examples
• The Transcriptional Coactivator CAMTA2 Stimulates Cardiac
Growth by Opposing Class II Histone Deacetylases
• Reversal of Histone Lysine Trimethylation by the JMJD2 Family of
Histone Demethylases
• Similar Frontal and Distinct Posterior Cortical Regions Mediate
Visual and Auditory Perceptual Awareness.
• Circadian Regulator CLOCK Is a Histone Acetyltransferase
• Wntless is a Conserved Membrane Protein Dedicated to the
Secretion of Wnt Proteins from Signaling Cells
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Titles – some not so good examples
• Cloning and nucleotide sequencing of three heat shock
protein genes (hsp90, hsc70, and hsp19.5) from the
diamondback moth, Plutella xylostella (L.) and their
expression in relation to developmental stage and
temperature. (Result ?, length)
• Effect of docosahexaenoic acid-rich fish oil
supplementation on human leukocyte function. (Result ?)
• Effects of repetitive TMS on visually evoked potentials
and EEG in the anesthetized cat: dependence on
stimulus frequency and train duration. (Acronyms, order
and length)
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Keywords
• The keyword list provides the opportunity
to add alternative indexing terms, in
addition to those already present in the
title.
• Judicious use of keywords may increase
the ease with which interested readers can
locate your article in a database such as
SciELO or ScienceDirect.
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Abstract
• A well-prepared abstract enables the reader to
identify the basic content of a document quickly
and accurately, and thus to decide whether to read
the document in its entirety.
• The abstract should summarize the results and
principal conclusions.
• Do not include details of the methods used unless
the study is methodological, i.e. primarily
concerned with methods.
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Abstract
• Do not repeat information contained in the title. The
abstract, together with the title, must be selfcontained as it is published separately from the
paper in abstracting/indexing services
• Omit all references to the literature and to tables or
figures
• Omit obscure abbreviations and acronyms even
though they may be defined in main body of the
paper.
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The abstract has a well-defined
structure
White adipose tissue (WAT) serves as the primary energy depot in the
body by storing fat. During development, fat cell precursors (i.e.,
preadipocytes) undergo a hypertrophic response as they mature into lipidladen adipocytes. However, the mechanisms that regulate adipocyte size
and mass remain undefined. Herein, we demonstrate that the membrane
anchored metalloproteinase, MT1-MMP, coordinates adipocyte
differentiation in vivo. In the absence of the protease, WAT development is
aborted, leaving tissues populated by mini-adipocytes which render null
mice lipodystrophic. Hence, MT1-MMP acts as a 3-D-specific adipogenic
factor that directs the dynamic adipocyte-ECM interactions critical to WAT
development.
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Possible autosomal origin of macro B
chromosomes in two grasshopper species
The acrocentric macro B chromosomes of Rhammatocerus brasiliensis
(Acrididae, Gomphocerinae) and Xyleus discoideus angulatus
(Romaleidae, Romaleinae) are highly similar to the X chromosome in
each species in terms of morphology, size and pycnosis. However, the
results of FISH experiments using 45S and 5S rDNA probes suggest that
in both species the B chromosomes are most likely of autosomal origin. In
R. brasiliensis, B chromosome 5S rDNA is similar to that of L2, L3, M5
and S11 autosomes, whereas the X chromosome lacks both rDNA
families. In X. d. angulatus 45S rDNA is absent in B chromosomes,
whereas the X chromosome contains one of the two 45S rDNA clusters in
the genome. B chromosomes were found in all nine R. brasiliensis
populations analyzed, indicating that they are widely distributed in
Northeastern Brazil. This absence of any significant variation suggests
high inter-population gene flow presumably due to the abundance of the
species on several types of vegetation and its relatively high flight
capability.
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A different Abstract style
– Background: Markers of inflammation such as high sensitivity C-reactive protein (CRP)
were shown to be elevated in patients with hypertension. Small trials using statin therapy
showed blood-pressure (BP) reductions, but it is unknown whether this association extends
to larger populations. The objective of this study was to determine whether statin use was
associated with better blood-pressure control in adults with hypertension and whether
inflammation levels mediated this relationship.
– Methods: This was a cross-sectional study of 2584 hypertensive adults aged _40 years
with no known cardiovascular disease from the National Health and Nutrition Examination
Survey 1999–2002. Logistic regression models were calculated to determine whether there
was an association between statin use and blood-pressure control. C-reactive protein was
added to the full model to determine its impact on the association.
– Results: Compared with people not using statin medication, significantly more statin users
had their blood pressure under control (52.2% v 38.0%). After adjustment for demographic
factors, statin users were two times (95% confidence interval [CI], 1.46 to 2.72) more likely
to have their blood pressure under control (_140/90 mm Hg) than nonusers. After further
adjustment for body mass index, diabetes, smoking, exercise, low-salt diet, and
antihypertensive medications, the likelihood of having blood pressure under control
remained more likely among statin users (odds ratio, 1.46; 95% CI, 1.05 to 2.05). The
association between statin use and lower BP was most evident among participants who
used antihypertensive medication as well as statins and was unchanged with the addition
of CRP to the model.
– Conclusions: Statin use was associated with a BP level _140/90 mm Hg in a
representative sample of US adults with hypertension. Levels of CRP did not attenuate the
association. Further studies are needed to explore the effects of statin use on blood
pressure and to determine how best to apply this knowledge in clinical care.
– From the American Journal of Hypertension
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Resource value affects territorial defense by
Broad-tailed and Rufous hummingbirds
Territorial behavior of Broad-tailed (Selasphorous platycercus) and Rufous
(Selasphorous rufus) hummingbirds in Colorado was measured at sites with
feeders containing10%, 20%, and 30% sucrose solutions, respectively. The
presence or absence of territory holders, number of intruders, and intensity of
defense were measured at the three levels of energy availability. Migrating
Rufous Hummingbirds displaced Broad-tailed Hummingbirds from territories they
had defended during the breeding season; Broad-tailed Hummingbirds then
defended only lower quality sites. Both Broad-tailed and Rufous hummingbirds
employed more energetically expensive behaviors when defending high quality
sites, with longer chases more often supplemented with chip calls and hovering.
Other investigators have suggested that chip calls and hovering are precursors to
a chase. However, I found that chasing was the default response to the presence
of an intruder. Chip calls and hovering were added to intensify a chase. In the few
cases where chip calls were uttered or hovering occurred without a chase,
Rufous Hummingbirds were more likely to exhibit this behavior than Broad-tailed
Hummingbirds.
©2006 Journal of Field Ornithology.
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Introduction
• The most important function of the introduction is to
establish the significance of your current work: Why was
there a need to conduct the study?
• The introduction begins by introducing the reader to the
pertinent literature, leading from the general to the
particular
• The most important function of the introduction is to
establish the significance of your current work: Why was
there a need to conduct the study?
• Having introduced the pertinent literature and
demonstrated the need for the current study, you should
state clearly the scope and objectives.
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Introduction
• Introduce references so they do not interfere with the
flow of your argument: first write the text without
references so that it reads smoothly, then add in the
references at the end of sentences or phrases so they
do not interrupt your flow.
• Avoid a list of points or bullets; use prose
• The introduction can finish with the statement of
objectives or, with a brief statement of the principal
findings. Either way, the reader must have an idea of
where the paper is heading to follow the development of
the evidence.
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Introduction – common problems
Far too much time spent on lofty and noble intentions
Little or no time spent linking proposed study to current state of the field
General-to-particular structure lacking
Purpose of study not clear
No or few references
‘Because so little is known…’ – references incomplete and out-of-date
Note: these problems apply just as well to manuscripts in Portuguese
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An example
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Ectomycorrhizal fungi (EMF) have a fundamental role in nutrient absorption of many
plant species.
Tree species of ecological and economic relevance in reforestation programs depend
on ectomycorrhizal symbiosis, especially in soils contaminated by mining activities.
The ability of EMF to reduce the toxicity of heavy metal ions (e.g. copper) in their host
plants is accompanied by the decrease of metal concentrations in the aerial part of
the plant.
Due to increased absorption of these metals by the EM roots and the accumulation in
the extra radical mycelium, greater tolerance to such elements is achieved by the
host.
Research has been conducted to determine the sensitivity of EMF to a variety of
potentially toxic metals to understand the diverse mechanisms through which the
fungi may tolerate heavy metals.
Enzymatic activity is important for the mobilization and transference of soil nutrients
through EM fungi towards the host plant.
In this study we investigate the effects of copper and phosphorus concentrations on
mycelial growth and enzymatic activities of the EM fungi Pisolithus microcarpus,
Chondrogaster angustisporus and Suillus sp. in two growth experiments.
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Materials and Methods
• The main purpose of the 'Materials and Methods' section is to
provide enough detail for a competent worker to repeat your study
and reproduce the results.
• Equipment and materials available off the shelf should be described
briefly (e.g. Licor underwater quantum sensor, Model LI 192SB) and
sources of materials should be given if there is variation in quality
among supplies.
• Modifications to equipment or equipment constructed specifically for
the study should be carefully described in detail. The method used
to prepare unusual reagents, fixatives, and stains should be stated
exactly, though reference to standard recipes in other works will
suffice.
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Materials and Methods
• The usual order of presentation of methods is chronological.
However, related methods may need to be described together and
strict chronological order cannot always be followed.
• If your methods are new (i.e. unpublished), you must provide all the
detail required to repeat them. However, if a method has been
previously published, only the name of the method and a literature
reference need be given.
• Be precise in describing measurements and include errors of
measurement. Ordinary statistical methods should be used without
comment; advanced or unusual methods may require a literature
citation.
• Show your materials and methods section to a colleague. Ask if they
would have difficulty in repeating your study
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Results
• In the results section you present your findings: display
items (figures and tables) are central in this section.
• Present the data, digested and condensed, with
important trends extracted and described.
• Present your results in the order that makes the overall
significance of your work clearest. Note that this may
not necessarily match the order in which the experiments
were performed.
• Because the results comprise the new knowledge that
you are contributing to the world, it is important that your
findings be clearly and simply stated.
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Results
• Do not say "It is clearly evident from Fig. 1 that bird
species richness increased with habitat complexity". Say
instead "Bird species richness increased with habitat
complexity (Fig. 1)".
• However, don't be too concise. Readers cannot be
expected to extract important trends from the data
unaided. Few will bother.
• Combine the use of text, tables and figures to condense
data and highlight trends. In doing so be sure to refer to
the guidelines for preparing tables and figures.
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Tables and Figures
– All tables and figures should be put into a contextual
framework in the corresponding text, e.g. a table of
strains used should be mentioned in the Materials
and Methods
– A good rule of thumb is that it should be possible to
figure out the meaning of a Table or Figure without
referring to the text. Tables and figures should
typically summarize results, not present large
amounts of raw data.
– When possible, the results should provide some way
of evaluating the reproducibility or statistical
significance of any numbers presented
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Constructing tables
• DO include a caption and column headings that
contain enough information for the reader to
understand the table without reference to the
text. The caption should be at the head of the
table.
• DO organize the table so that like elements read
down, not across.
• DO present the data in a table or in the text, but
never present the same data in both forms.
• DO choose units of measurement so as to avoid
the use of an excessive number of digits.
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Constructing tables
• DON'T include tables that are not referred to in the text.
• DON'T be tempted to 'dress up' your report by
presenting data in the form of tables or figures that could
easily be replaced by a sentence or two of text.
Whenever a table or columns within a table can be
readily put into words, do it.
• DON'T include columns of data that contain the same
value throughout. If the value is important to the table
include it in the caption or as a footnote to the table.
• DON'T use vertical lines to separate columns unless
absolutely necessary.
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Constructing Figures
• DO include a legend describing the figure.
It should be succinct yet provide sufficient
information for the reader to interpret the
figure without reference to the text. The
legend should be below the figure.
• DO provide each axis with a brief but
informative title (including units of
measurement).
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Constructing Figures
• DON'T include figures that are not referred to in the text, usually in
the text of the results section.
• DON'T be tempted to 'dress up' your report by presenting data in the
form of figures that could easily be replaced by a sentence or two of
text.
• DON'T fill the entire A4 page with the graph leaving little room for
axis numeration, axis titles and the caption. The entire figure should
lie within reasonable margins (say 3 cm margin on the left side, 2 cm
margins on the top, bottom and right side of the page).
• DON'T extend the axes very far beyond the range of the data. For
example, if the data range between 0 and 78, the axis should extend
no further than a value of 80.
• DON'T use colour, unless absolutely necessary. It is very expensive,
and the costs are usually passed on to the author. Colour in figures
may look good in an assignment or thesis, but it means redrawing in
preparation for publication.
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Table design
0%
2%
4%
6%
8%
8.38 (±1.15)
8.49 (±0,90)
9.67 (±1.29)
10,72 (±2,88)
-
Subglobose
9.38 (±1.44) x
8.44 (±1.18)
9.93 (±1.40) x
8.94(±2.8)
10.2 (±2.42)
x 9.19 (±0.97)
10.95 (±0.9) x
9.93 (±1.41)
12.52 (±1.13) x
10.3 (±0.93)
Subglobose
to ellipsoidal
11.4 (±1.5) x
9.60 (±1,.2)
10.87 (±0.64) x
9.30 (±1.15)
11.24 (±1.0) x
8.916 (±0.10)
11.94 (±1.28) x
10.27 (±0.82)
13.32 (±1.92) x
11.25 (±1.12)
10.89 (±0.43) x
9.9 (±2.66)
13.28 (±3.60) x
10.5 (±1.54)
12.45 (±1.51) x
9.12 (±1.14)
12.55 (±1.72) x
9.75 (±1.22)
15.37 (±1.66) x
11.62 (±1.23)
Form/%
NaCl
Globose
Ellipsoidal
Table 1 - Average size (μm) of C. elegans sporangioles in Hesseltine &
Anderson culture media with 0, 2, 4, 6 and 8% NaCl at 20ºC.
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Figure design
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Figure design
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Discussion
• In the discussion you should discuss what
principles have been established or reinforced;
what generalizations can be drawn; how your
findings compare to the findings of others or to
expectations based on previous work; and
whether there any theoretical/practical
implications of your work.
• When you address these questions, it is crucial
that your discussion rests firmly on the evidence
presented in the results section.
• Refer briefly to your results to support your
discussion statements.
• Do not extend your conclusions beyond those
that are directlyCopyright:
supported
by your results.
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2012
Discussion
• A brief paragraph of speculation about what your
results may mean in a general sense is usually
acceptable, but should not form the bulk of the
discussion.
• Be sure to address the objectives of the study in
the discussion and to discuss the significance of
the results.
• Don't leave the reader thinking "So what?".
• End the discussion with a short summary or
conclusion regarding the significance of the
work.
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Discussion
• What are the main conclusions of your
study ?
• How do these results advance our
understanding of the field ?
• What new questions do they raise ?
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References
The HH morphogen controls many key development processes, with different thresholds specifying distinct
outcomes1, 2, 3, 4. In Drosophila wing discs, HH proteins secreted by posterior (P) compartment cells move
into the anterior (A) compartment to form a local concentration gradient5, 6. Low levels of HH suffice to
induce the expression of decapentaplegic (dpp), whereas high levels are required to induce patched (ptc)
and engrailed (en) (Supplementary Fig. 1)7, 8, 9.
Nature 450, 252-258 (8 November 2007)
The HH morphogen controls many key development processes, with
different thresholds specifying distinct outcomes1, 2, 3, 4.
In Drosophila wing discs, HH proteins secreted by posterior (P)
compartment cells move into the anterior (A) compartment to form a local
concentration gradient5, 6.
Low levels of HH suffice to induce the expression of decapentaplegic
(dpp), whereas high levels are required to induce patched (ptc) and
engrailed (en) (Supplementary Fig. 1)7, 8, 9.
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References - purpose
• By placing references at strategic points in the
text, the reader is able to retrieve the evidence
being used to support a particular argument or
statement
• In this way the reader is able to recreate the
logical train of thought that led the author to a
particular conclusion
• Any mistakes in reference use could result in
rejection of your article
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References - format
• A list of references ordered alphabetically by author's
surname, or by number, depending on the publication,
must be provided at the end of your paper.
• The reference list should contain all references cited in
the text but no more.
• Include with each reference details of the author, year of
publication, title of article, name of journal or book and
place of publication of books, volume and page
numbers.
• Different journals may have a different referencing
styles, so read the Instructions to Authors first
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There are several possible causes of mis-citation.
•
•
•
•
•
First, some younger researchers simply do not know the rules.
Second, they may know the rules but are unable to locate the literature,
because it does not exist online and/or because the idea of visiting the
library and taking a journal off the shelf is anathema.
Third, the original source may somehow appear "old- fashioned" and
therefore inappropriate. It is probably true that researchers have always
been biased towards citing research done during their own career, but
ignoring research done in previous generations misrepresents history.
Fourth, young researchers often say that there is too much literature and
they cannot be expected to know it all. This is no excuse. It is hard keeping
up with the literature, but knowing the literature is what being a researcher
is all about. For well-known discoveries such as natural selection or the
structure of DNA, the relevant references are also well known. But for many
other areas, the most appropriate references are less obvious and may
require effort to locate. Indolence is no excuse for mis- citation.
Fifth, and perhaps most insidiously of all, some researchers deliberately fail
to cite competitors' work to enhance the (apparent) novelty of their own
work. All five of these causes seem to be part of a general erosion of
scholarship in schools and universities.
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Where are the rules of citation set out?
•
•
•
I looked at three books I had to hand: an undergraduate study guide to
science, a book on what science is and another on communicating science,
all published in the past six years. Not one of them stated the rules for
citation.
So what are they? The rule is that you cite the first reference to report a
particular fact or concept, giving credit where credit is due. Sometimes, of
course, it is not absolutely clear when a particular discovery was made, and
the ludicrous extreme in biology (and much else) would be to trace
everything back to Aristotle. The best strategy is to cite the original source,
probably followed by a reference to a more recent review of the topic. What
is neither appropriate nor acceptable is to cite a recent paper (not a review)
that simply mentions the topic.
How are today's researchers supposed to know the rules? The obvious
answer to this is through their undergraduate training, and if not, then
through their postgraduate years. The fact that mis-citation is so widespread
suggests that as university teachers we are failing to do this properly. This
may be true, but what is perhaps worse is the widespread rewarding of
mediocrity in education that allows undergraduates to get away without
absorbing many of the attributes of being a good researcher.
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Does it matter that researchers mis-cite the literature?
• Yes, it does.
• First, appropriate citation is the foundation of science. As the Nobel
laureate Peter Medawar said, being first is what matters; there are
no prizes for being the second person to discover something.
Priority rules in science are written in stone; they form the bedrock of
the entire enterprise.
• Verification by second and later "discoverers" is important, but being
first is what matters. Researchers who make important discoveries
should get due credit for their work, and it is those citations that
determine a scientist's standing in the field.
• Mis-citation undermines the very process of scientific endeavour.
Not citing the literature appropriately is poor scholarship and
perverts history.
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References – common problems
• Few or no references given !
• References not up-to-date
• Multiple references used in place of reasoning
to support complex key assumptions, e.g. A?>B
and B?>C, therefore A>C.
• Reference incorrect
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Deposition of data in public repositories
– Nucleotide sequences can be deposited with the DNA
Data Bank of Japan (DDBJ), European Molecular
Biology Laboratory (EMBL/EBI) Nucleotide Sequence
Database, or GenBank (National Center for
Biotechnology Information).
– Protein sequences can be deposited with SwissProt
or the Protein Information Resource (PIR).
– Protein structures can be deposited with one of the
members of the Worldwide Protein Data Bank.
Nucleic Acids structures can be deposited with the
Nucleic Acid Database at Rutgers. Crystal structures
of organic compounds can be deposited with the
Cambridge Crystallographic Data Centre.
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Plagiary and ‘language re-use’
The act of plagiarizing or appropriating the
ideas, writings, or inventions of another
without due acknowledgment; specifically the
stealing of passages either for word or in
substance, from the writings of another and
publishing them as one's own
If you use somebody else’s words, make this
clear by using quotation marks and a
reference
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Summary
• Each section of the manuscript has a specific
function
• Each paragraph has a specific function and
should be presented in a logical order
• Ditto each sentence within the paragraph.
• Within each sentence, try to move from the
general to the particular
• Punctuation alters meaning, so use it sparingly
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Common manuscript problems
• Failure to state the purpose of the study
• Failure to keep function of sections clear
and distinct
• Including non-essential data
• Treating the Introduction and/or
Discussion as an opportunity to review the
entire field
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Practical activity 7a - The Structure of a
Scientific Article
•
The Case of the Ivory-billed Woodpecker
•
At approximately 1:30 in the afternoon on February 11, 2004, Gene Sparling spotted a large black and white woodpecker while
kayaking on a rural bayou in Monroe County, Arkansas. The notes he posted to his website about the sighting caught the
attention of Tim Gallagher and Bobby Harrison, two university researchers, and triggered a year-long research effort that
resulted in the publication of a peer-reviewed paper in the journal Science. The link below gives free access to this research
article. To learn more about scientific writing, including how research papers are organized, how they are reviewed, and how
they contribute to our understanding of the scientific world, read the article and then try the exercise below.
•
See original paper by Fitzpatrick et al. (2005) "Ivory-billed Woodpecker (Campephilus principalis) Persists in Continental North
America" Science 308:1460-1462. See also this site for further discussion about the issues raised by this paper.
•
Questions about the article's format:
•
Indicate where in the article the Introduction section ends and the Materials and Methods section begins and explain why you
choose this point in the article.
Indicate where in the article the Materials and Methods section ends and the Results section begins and explain why you
choose this point in the article.
Indicate where in the article the Results section ends and the Discussion section begins and explain why you choose this point
in the article.
Questions about the article's content:
•
•
•
•
•
•
•
•
When testing a research hypothesis, which the researcher has good reason to believe is true, it is customary to use a first test a
null hypothesis. This is typically a hypothesis that there is no difference or no association between variables being tested. What
is the null hypothesis in this article with respect to the data discussed?
What evidence do the researchers present disprove their null hypothesis ?
Why is the data presented graphically and how do these visual representations help the interpretation of the article?
Based on the evidence presented, is the hypothesis that the ivory-billed woodpecker still exists now a proven fact ?
What happened subsequently ?
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Practical 7 – cont’d
• Practical activity 7b - Reconstructing abstracts
• Download the Word document which contains four article abstracts
deconstructed as a random series of sentences. Now put the
sentences back in their original order.
• Practical activity 7c - Identifying key reference points
• Download the Word document which contains introductions to
scientific articles which have been stripped of references. Indicate
which sentences contain statements that should be supported by
references.
• Practical activity 7d - Identifying problems with a document's
logical structure.
• This document is an edited version of an introduction to a research
article about copper toxicity in plants. Identify places where there are
rapid jumps or breaks in the logical structure of the document and
discuss
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