How to write a scientific paper in English

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Lecture 2
How to write a scientific paper in English
20 August 2007
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Lecture schedule
Lecture Date Time 1. Introduction to
scientific writing 8/20 900-1020 2. How to
write a scientific paper in English 8/20 1500-16
20 3. Earth structure and plate
tectonics 8/21 900-1100 4. Circulation of the
atmosphere 8/21 1300-1500 5. Water and ocean
structure 8/22 1000-1100 6. Continental
margins and ocean basins 8/22 1300-1500 7.
Sediment 8/23 1000-1100 8. Marine
resources 8/23 1300-1400 9. Circulation of
the ocean 8/24 1100-1230
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How to write a scientific paper in English 1) The
three steps of science 2) What to do before
writing a paper 3) How to write a paper 4) How to
get your paper published 5) Tips for giving a
talk 6) Tips for preparing a poster
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The 3 Steps of Science
3. Communicate results

• Idea

2. Experiment
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The 3 Steps of Science
Research is not complete until it is
communicated. Scientists must write!
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How to write a scientific paper in English 1) The
three steps of science 2) What to do before
writing a paper 3) How to write a paper 4) How to
get your paper published 5) Tips for giving a
talk 6) Tips for preparing a poster 7) Tips for
writing e-mail
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What to do before writing literature search -
textbooks - review articles indexes
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• Indexes
• gt350,000 biological research papers are
  published every year
• For thorough and efficient searches on
  particular topics, use one or more indexing
  services.
• Using these services, you can examine up to 40
  years of source material in a few seconds.

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• Widely used indexing services
• Science Citation Index
• unique tool for locating references on a
  specific topic
• provides access to bibliographic information,
  author abstracts, and cited references found in
  3,700 of the world's leading scholarly science
  and technical journals
• http//scientific.thomson.com/products/sci/

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• Widely used indexing services
• Science Citation Index
• Current Contents
• puts the best library in the world at your
  fingertips
• gt8000 journals are covered
• http//scientific.thomson.com/products/sci/
• http//www.thomsonscientific.jp/products/ccc/

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• You can also search for information using the
  World Wide Web.
• Many print journals now offer full-text on-line
  access through the Web.
• Also, Google has a search engine (Google
  Scholar http//scholar.google.com/)
• It is in English, but is very easy to use.

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Here is a list of useful engines for searching
the Web Google http//www.google.com Google
Scholar http//scholar.google.com/ Scirus http/
/www.scirus.com Surfwax http//www.surfwax.com

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How to write a scientific paper in English 1) The
three steps of science 2) What to do before
writing a paper 3) How to write a paper 4) How to
get your paper published 5) Tips for giving a
talk 6) Tips for preparing a poster
20
Scientific writing is different from other types
of writing   1) Scientific writing should be
simple and clear. Its purpose is to inform. 2)
Scientific writing is very organized. Each
scientific paper is organized in the same way
(IMRAD Introduction, Methods, Results and
Discussion).
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Basic format of a research paper
Title Abstract Introduction Materials and
Methods Results Discussion Acknowledgments Referen
ces (Literature Cited)
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Write your paper in the following order 1)
Results 2) Materials and Methods 3)
Discussion 4) Introduction 5) References (or
Literature Cited) 6) Abstract
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How to write the Results This is the most
important part of your paper. The Results should
be short and clear, without wordiness.   Give
only the results. - no discussion or references.
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• Use different verb tenses to present different
  information
• Something done during the study
• past tense  
• Something in the paper itself (figure, table)
• present tense
• Something which is generally accepted as true
• present tense

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• Figures and Tables
• Use tables and figures to organize large amounts
  of data. Then describe the important results in
  the text.
• Tables for exact values
• Figures for trends relationships
  effects
• Figures and tables should be easy to understand
  without the reader having to refer to the text.

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In your figures, 1) label each axis 2) tick
marks 3) show meaning of symbols 4) use large
symbols 5) figure legend
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• Some things to avoid in the Results section
• Do not reiterate each value from a Figure or
  Table in the text - only the key result or trends
  that each conveys.
• Do not present the same data in both a Table and
  Figure - this is redundant and a waste of space
  and energy. Choose which format best shows the
  result.

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How to write the Materials and Methods

• Clearly explain how you carried out your study in
  the following general structure and organization
• the subjects used (plant, animal, etc.) and
  their pre-experiment handling and care, and when
  and where the study was carried out
• if a field study, a description of the study
  site, including the physical and biological
  features, and precise location
• experimental or sampling design (i.e., how the
  experiment or study was structured. For example,
  controls, treatments, the variable(s) measured,
  how many samples were collected, replication,
  etc.)
• the protocol for collecting data (i.e., how the
  experimental procedures were carried out), and,
• how the data were analyzed (statistical
  procedures used).

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How to write the Materials and Methods This
section must be written so that the reader can
repeat the same experiments or follow the same
model to confirm your results.
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Materials and Methods This section should be
brief but informative. Write most of this section
in the past tense. No results!
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Discussion - Key points  1) Explain the
importance of your findings, but do not repeat
the Results section. 2) Relate your work to the
findings of other studies 3) State your
conclusions clearly with the reasons for them. 4)
Do not introduce new results in the Discussion.
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In the Discussion, use both present and past
tense. other people's work - present your
own results - past Do not repeat descriptions of
other people's findings if they are in the
Introduction.
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Introduction 1) give a background of work in
your field 2) tell the reader why your research
is important
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• Rules for a good Introduction
• Why is the subject important?
• 2) Review the pertinent literature to orient the
  reader
• 3) Much of the Introduction should be in the
  present tense
• 4) Do not write too much usually 3-6 paragraphs
  are enough.
• 5) Clearly state the study objective in the last
  paragraph.

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• Literature Cited
• Cite by author and year of publication.
• (Nakamura, 2001).
• Nakamura (2001) showed that ..
• 2) Cite authors only by their last names.
• 3) Cite works by two authors using the last names
  of both
• (e.g., Ikeda and Nakamura, 2003)

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• Literature Cited
• 4) Cite works by three or more authors using the
  last name of the first author, followed by et al.
  (meaning and others)
• (Areechon et al. 2006)
• 5) Cite information directly by your instructor
  (orally or through e-mail) in the text as
  follows
• (N. Areechon, personal communication, Oct. 2006)
• Do not list a personal communication in your
  Literature Cited section.

• Formats differ from journal to journal.
• Check the one you have chosen

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• Title key points
• The Title should succinctly describe the content
  of the paper.
• Include key words.
• Keep it short and specific, but not too general.
  
• Write your title after you have written the rest
  of your paper.

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• How to list the authors
• Decide who will be authors before you start
  writing the first draft.
• Agree on the order of the authors names
• The list only authors who actively contributed
  to the study.

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Abstract The abstract should give the most
important information about your study. Think of
it as a short version of your paper.
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• Abstract
• state the principle objectives and scope of the
  investigation
• describe the methods used
• summarize the results
• state the main conclusions

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State the study objective in the first
sentence. The influences of suspended mussel
and infaunal clam cultivation on benthic
metabolism and nutrient cycling were compared in
Goro lagoon, Italy. (Nizzoli et al.). We
examined the diel vertical migration of squid in
warm core ring and cold water mass areas in the
transition region of the western North Pacific.
(Watanabe et al.)
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• Write most or all the Abstract in the past tense,
  because it refers to work done in your study
• 2) Do not give any information or conclusion in
  the Abstract that is not stated in the paper.
•  3) Do not include references or refer to tables
  or figures.
•  4) The length of your Abstract should be kept to
  about 200-300 words maximum

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• Acknowledgments
• Acknowledge any significant help that you
  received from any individual, whether in your
  laboratory or elsewhere.
• We thank Taro Yamada for assistance with the
  experiments and Yoji Suzuki for valuable
  discussion.
•  2) Acknowledge any outside financial assistance,
  such as grants, contracts or fellowships.
• This study was supported by a grant from the
  Japan Society for the Promotion of Science.
• 3) Place the Acknowledgments between the
  Discussion and the Literature Cited.

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How to write a scientific paper in English 1)
Helpful books 2) What to do before writing a
paper 3) How to write a paper 4) How to get your
paper published 5) Tips for giving a talk 6) Tips
for preparing a poster
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• Choosing a journal
• Refer to the abstracting services and indexes to
  help identify possible journals for publication.
• 2) After you identify possible journals, look at
  some recent issues on line.
• Nearly all will have two items of special
  interest
• 1) a statement of the journals scope

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From Marine Biology
Field of research
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From Marine Biology
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Impact Factor Scientists generally view journals
as having different degrees of prestige. Every
year, the Journal Citation Reports publishes an
"impact factor" for each scientific journal. This
number is often used to rank journals.
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Impact Factor The impact factor of a given
journal is calculated as the number of citations
in a given year to papers published in that
journal in the preceding two years, divided by
the number of papers the journal published in the
same 2-year period.
http//en.wikipedia.org/wiki/Impact_factor
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Choosing a journal 2) After you identify possible
journals, look at some recent issues on line.
Nearly all will have two items of special
interest 1) a statement of the journals
scope 2) Instructions to Authors (ITA)
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Checklist 1. Make sure the manuscript is
double-spaced.
2. There are two basic type font styles 1)
serif 2) sans serif In text of manuscript, use
a serif font - New York - Times  
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3. On 1st page title author name(s),
affiliation(s), corresponding
address, telephone fax
numbers e-mail address 2nd page
Abstract 4. Number all pages  
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5. Always send a cover letter with your
manuscript when you send the manuscript to a
journal for review. This letter is very
important, and should be given careful
thought. (see Appendix I (p. 22) for an example
of a cover letter).
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Review Process
You
Editor
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Reviewers (Referees)
Review Process
You
Editor
Anonymous
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Reviewers (Referees)
Review Process
You
Editor
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Proofs Check every sentence for mistakes. Read
through your proofs 3-4 times.  
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How to write a scientific paper in English 1)
Helpful books 2) What to do before writing a
paper 3) How to write a paper 4) How to get your
paper published 5) Tips for giving a talk 6) Tips
for preparing a poster
60
How to give a talk 1. Relax 2. Speak slowly. 3.
Look at the audience as much as possible Do not
talk to the screen! 4. Do not read your talk. 5.
Use short sentences. 6. Make sure your figures
are large and easy to read.
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Table 2. Prey items identified from stomach
contents of Berryteuthis anonychus collected in
the northeast Pacific during May 1999. IRI
standardized index of relative importance. IRI
values in parentheses are those for lt60 mm ML
and gt60 mm ML squid. Frequency of occurrence was
calculated based on the number of stomachs
containing food. - prey taxon not present in
stomachs. number wet mass frequency
of IRI (lt60 mm ML, gt60 mmML) Taxon () () occ
urrence ()   Copepoda 70.2 85.3 74.2 86.5
(80.9, 84.8) Candacia columbiae 0.2 0.1 1.9 Can
dacia sp. lt0.1 lt0.1 0.4 Metridia
pacifica 0.2 lt0.1 2.2 Neocalanus
cristatus 35.0 50.4 23.2 Neocalanus
plumchrus/flemingeri 3.1 1.8 12.4 Neocalanus
spp. 30.0 32.3 33.3 Pleuromamma
spp. 0.1 lt0.1 1.9 Calanoida (generalized
form) 0.5 0.3 4.9 Calanoida (specialized
form) 0.1 0.1 0.4 Unidentified
Calanoida 0.9 0.3 14.2 Unidentified
Copepoda 0.1 0.1 2.6   Chaetognatha 23.9 10.8 4
7.6 12.4 (18.1, 13.9) Parasagitta
elegens 23.8 10.7 47.2 Unidentified
Chaetognatha 0.1 0.1 1.1   Amphipoda 4.6 2.5 19
.1 1.0 (1.0, 1.3) Hyperia medusarum 0.8 0.9 2.2
Themisto pacifica 2.5 0.9 7.5 Unidentified
Hyperiidae 0.4 0.5 0.7 Unidentified
Physocephalata lt0.1 lt0.1 0.4 Unidentified
Hyperiidea 0.7 0.2 7.5 Unidentified
Amphipoda 0.1 lt0.1 1.9   Euphausiacea 0.5 0.9
4.5 lt0.1 (lt0.1, 0.1) Euphausia
pacifica lt0.1 0.4 0.5 Thysanoessa
sp. lt0.1 lt0.1 0.4 Unidentified
Euphausiacea 0.5 0.5 3.7   Ostracoda lt0.1 lt0.1
1.1 lt0.1 (lt0.1, -)   Unidentified
fish lt0.1 0.8 0.4 lt0.1 (-, lt0.1) Unidentified
gelatinous prey lt0.1 lt0.1 0.4 lt0.1 (lt0.1,
-)   Unidentified crustacea 0.1 lt0.1 1.1   Unide
ntified material 0.6 0.1 18.7  

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• How to give a talk
• 7. Beware of laser pointers.
• Do not make people dizzy!
• 8. Do not put the text of your talk on your
  slides.
• You want the audience to listen to you, not read
  your notes.
• 9. Do not exceed your time limit.
• 10. Paraphrase each question before answering it.

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How to write a scientific paper in English 1)
Helpful books 2) What to do before writing a
paper 3) How to write a paper 4) How to get your
paper published 5) Tips for giving a talk 6) Tips
for preparing a poster
64

• How to prepare a poster
• An effective poster must include less detail than
  you would include in a formal publication or even
  in a talk.
• It should highlight
• the major questions asked
• the major results achieved, and
• the major conclusions drawn
• It should contain the least possible amount of
  text (lt1000 words)

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• Title
• Should convey the "issue," the approach, and the
  system (organism)
• Use "sentence case" not title case or all
  caps
• Font abuse in inbred versus outbred populations
  of Homo sapiens
• Font Abuse in Inbred Versus Outbred Populations
  of Homo Sapiens
• FONT ABUSE IN INBRED VERSUS OUTBRED POPULATIONS
  OF HOMO SAPIENS
• Maximum length 1-2 lines.

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• Abstract
• Do not include an abstract on a poster!
• If you are presenting your poster at a meeting,
  you will probably be asked to submit an abstract
  this abstract is for inclusion in the "meeting
  catalog," not for on your poster.

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• Introduction
• Get your viewer interested about the issue or
  question while using the absolute minimum of
  background information and definitions
• It is good to use a photograph in this section
  if it can get your viewers oriented on your
  organism or study question quickly
• Maximum length approximately 200 words.

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• Materials and methods
• Briefly describe experimental equipment and
  methods, but not with the detail used for a
  manuscript
• Use figures and tables to illustrate
  experimental design if possible
• Use flow charts (the type with text and drawings
  within boxes) to summarize reaction steps or
  timing of experimental procedures
• Maximum length approximately 200 words

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• Results
• Present only the most important results
• This is always the largest section.
• Maximum length approximately 200 words, not
  counting figure legends

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• Common mistakes in posters
• 1) The number one mistake is to make your poster
  too long.
• use no more than 1000 words.

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http//www.flickr.com/photos/northendgirl/65530659
/in/pool-368476_at_N21/
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• Common mistakes in posters
• 1) The number one mistake is to make your poster
  too long.
• use no more than 1000 words
• 2) Use a non-serif font (e.g., Helvetica) for
  title and headings and a serif font (e.g.,
  Palatino) for body text

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How to prepare a poster This paragraph is set in
Times New Roman, which is a serif typeface. The
word serif refers to the little feet that are
present at the tops and bottoms of the
characters. Serifs help to make characters more
unique and thus make it easier to read blocks of
text. Another example of serif typefaces is
Palatino. This paragraph is set in Arial, which
is a sans serif typeface. Sans serif typestyles
are good for titles and headings. Other examples
of sans serif typefaces include Helvetica and
Verdana.
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How to prepare a poster Titles and headings
should appear larger than other text, but not too
large. The text should also be legible from about
2-m away. Section Font class Font
size Title sans serif gt90 pt. Headings sans
serif 36-48 pt. Text serif 30-36 pt.
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• Common mistakes in posters
• 3) Avoid blocks of text longer than 10 sentences.
• 4) Use italics instead of underlining.
• 5) Complete the entire poster on a single
  platform.
• switching from PC to Mac or from Mac to PC can
  cause problems

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Molecular species identification and morphology
of gonatid squid paralarvae from the North
Pacific
Saya Shimura1,, Syuiti Abe1, John R. Bower2,
Tsunemi Kubodera3 Yasunori Sakurai1
1 - Graduate School of Fisheries, Hokkaido
University, Japan 2 - Northern Biosphere Field
Science Center, Hokkaido University, Japan 3 -
National Science Museum, Japan
- shimura_at_fish.hokudai.ac.jp
Results
Objective
Gonatid squids play a key role in the North
Pacific ecosystem, yet the life histories of most
gonatids are poorly understood. Studies of their
paralarvae are hampered by identification
uncertainties, particularly for the earliest
stages. In this poster, we describe the method we
are now using to identify these paralarvae.
Chromatophores
none
none
full
Method

• Paralarvae were collected
• during 3 cruises in 2003-2004.

full
full
partial
or
Oshoro Maru
Bongo net
2) Specimens were divided into morphotypes
based on physical characteristics.
Molecular identification of Morphotypes

• Conclusions
• Using the method described here, we positively
  identified the paralarvae of two important
  gonatid species in the North Pacific
  Berryteuthis anonychus, and Gonatopsis borealis.
• DNA sequence data from 3 of our 5 morphotypes
  differ from previously published sequence data,
  and they remain unidentified.
• Chromatophore patterns are particularly useful in
  distinguishing morphotypes.
• When we complete this study, we will construct
  an identification key to the newly hatched stages
  of the gonatids for further field studies!

? Berryteuthis anonychus


3) The PCR was used to amplify and sequence the
COI gene.
? Gonatopsis borealis

1. Extraction 2. PCR amplification 3. Sequencing
? Gonatopsis sp. A

region
? Gonatopsis sp. B
Cytochrome c oxidase submit?gene
mtDNA
4) Sequence data were compared with data from
adults to identify the morphotypes.
? Gonatopsis sp. C
undetermined





adults
paralarvae






Molecular Identification of morphotypes

data from T. Kubodera data from DDBJ
(OUT GROUP)
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A website with some good information are
preparing posters http//www.swarthmore.edu/NatSc
i/cpurrin1/posteradvice.htm
Tips for using E-mail (pp. 17-21) Appendix I.
Example of a cover letter (p. 22)
John Bower akaika_at_fish.hokudai.ac.jp