中科院上海有机化学研究所研究生讲座,
中科院上海有机化学研究所研究生讲座
, 2010年
2010年6月
HOW TO
WRITE AND PUBLISH A
SCIENTIFIC PAPER
PART II
授课教师：王任小研究员
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
Important Ingredients in a Scientific Paper
1 Effective organization
1.
• Follow the standard format
• Organize ideas logically within that format
2. Appropriate
pp p
language
g g
3 Nice
3.
Ni illustrations!
ill t ti
!
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
2
Writing is Easy
“Writing is easy. All you do is to stare at a blank
paper
p until drops
p of blood form on y
your
sheet of p
forehead.”
Gene Fowler
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
3
Three Steps to Finish a Paper
1. Make
M k preparations.
2. Start to write each section, and finish the draft.
3 Revise,
3.
Revise revise and revise.
revise
中国科学院上海有机化学研究所
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4
1. Make Preparations
 Thi
Think
k about
b t th
the aims
i and
d highlights
hi hli ht off your
work. Decide them as early as possible.
 Gather scientific contents: results, data,
references
f
and
d even id
ideas.
 Write a formal outline first
first.
Tip: Start all these preparations while the work is
still
ill on-going.
i
中国科学院上海有机化学研究所
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5
Prepare a Good Outline
Title
I
Introduction
d i
• Point A
• Point B
• Point C
Methods
• Step I
• Step II
• Step III
Tab.1
Tab.2
Tab 3
Tab.3
R l & Di
Results
Discussion
i
• Point A
• Point B
• Point C
Conclusion
References
Fig.1
Fi 2
Fig.2
Fig.3
1. Set the title.
2. List the main points in
section
each section.
3. Make all tables and
figures in publication
quality.
4. List the references.
5. Then, discuss with your
director.
中国科学院上海有机化学研究所
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6
Why to Write an Outline First?
 The outline presents your material in a logical
manner.
 The outline helps to organize your ideas.
 The outline reveals what
results are still missing, and
you know what still
thus y
needs to be done!
中国科学院上海有机化学研究所
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7
2. Start to Write
Tip 1.
1 Schedule your time for writing
writing.
Tip 2. Write section by section.
Tip
p 3. Use references!
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8
Tip 1. Schedule Your Time for Writing
 Writing
g needs blocks of time. Thus,, schedule your
y
time carefully, and find a quiet place to write.
 How much time does one need to finish writing a
typical
yp
paper?
p p About two weeks if one makes good
g
preparations.





Methods
M
th d and
d Material:
M t i l 1-2
1 2 days
d
Results: 1-2 days
I t d ti and
Introduction
d Discussion:
Di
i
3-5
35d
days
Figures, tables, and references: 1-3 days
Ab
Abstract
& Title:
Ti l 1/2 day
d
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
9
Keep Writing Once Started
The leap frog method: Do not interrupt your
writing to search for small details (data, reference
and etc).
etc) For
Fo instead,
instead make notes and move
mo e on,
on
and fill up the missing information later.
中国科学院上海有机化学研究所
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10
Tip 2. Write Section by Section
1. Methods and Material
• Experiments 1, 2, 3 …
2 Results
2.
R l and
d Supporting
S
i Information
I f
i
• Experiments
p
1, 2, 3 …
3. Introduction
• Points A,
A B,
B C…
C
4. Discussion & Conclusion
• Points A, B, C…
5 Abstract & Title
5.
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11
What to Discuss?
 Highlight the brilliance of your work: you really
need to know about others’ work; otherwise
it cannot be done.
done
 Cite
Ci relevant
l
references
f
and
d comment on other
h
researchers’work.
 If y
you do not know what to discuss,, be concise
then.
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
12
The Brain Storm Method
While y
you are gathering
g
g scientific contents, ideas
for your paper may occur to you …… Write down
these ideas!
中国科学院上海有机化学研究所
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13
A True Example of Brain Storm
李贺（790～816），字长吉，
李贺（
），字长吉，
世称“诗鬼”，与李白、李商隐三
人并称唐代“三李”。李贺因仕途
并称唐代
李
李贺因途
失意，就把全部精力用在写诗上。
外出时背锦囊得句即写囊中
外出时背一锦囊，得句即写投囊中，
暮归足成诗篇。
中国科学院上海有机化学研究所
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14
Organize Your Points
List the points you wish to make in each section,
sort and resort them until you are pleased with
the order
order.
A
B
C
D
E
F
Methods:
( ？) 石头有多重，大象就有多重。
石头有多重大象就有多重
( ？) 然后称称石头有多重。
( ？)) 先
先把大象赶上船。
象
( ？) 看看船沉到哪里，在齐水面高的地方画一道线。
( ？) 开始往船上装大石头，直到船沉到画线的地方。
( ？)) 再把大象赶上岸。
再把大象赶岸
中国科学院上海有机化学研究所
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15
Tip 3. Use References!
 Get very familiar with the recent review articles
your problem
p
under study.
y
on y
 Collect the references to be cited in your paper.
 Select out the key references (3‾10)
(3‾10), and learn
how to write your paper from them!
中国科学院上海有机化学研究所
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16
Effective imitation
Like doing research itself, good writing is largely a matter
of effective imitation.
“依葫芦画瓢”
葫芦
Thus, collect highly regarded scientific papers relevant to
your work, and learn how these papers are written:
 How are they structured? What types of data,
data tables and
figures are typical?
 What are the standard phrases that you could use to present
your own work?
y do discussion?
 How do they
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Citing Others’ Statements
Correction citation:
e.g. In this sense, we agree with the statement made
by somebody:“Good writing is largely a matter of
effective imitation.”[refs]
Wrong conduction: This is plagiarism(剽窃)!
ee.g.
g Thus,
Thus we believe that good writing is largely a
matter of effective imitation.
中国科学院上海有机化学研究所
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18
The Elements of A Scientific Paper
The paper
Sections
Paragraphs
g p
Sentences
Organize sentences logically into paragraphs; organize
the paragraphs in each section logically , and then you
have the whole paper.
中国科学院上海有机化学研究所
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19
Write Good Sentences
 What makes bad sentences?
 Not clear enough
 Not accurate enough
 Not concise enough
 Try to use short sentences.
 One sentence
sentence, one topic.
topic
中国科学院上海有机化学研究所
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20
Example of Long, Bad Sentence
“Taken altogether,
g
our results suggest
gg that the workflow
can be a valuable tool for ligand identification and
optimization,
p
being
g able to automatically
y and efficiently
y
refine docking poses, which sometimes may not be
accurate, and rank the compounds
p
based on more
accurate scoring functions.”
中国科学院上海有机化学研究所
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21
Example of Long, Bad Sentence
“However, adding a polarization term to the potential
energy function needs extra parameterization of atomic
polarizability and consumes more computational time
and resource, which may limit its application to MD
simulation for binding mode study between protein and
designed compound in drug discovery project, because
designed molecules are very diverse and parameterization
of atomic polarizability is a tedious work. ”
中国科学院上海有机化学研究所
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22
Organize Your Sentences
“The amino acid sequence of hSMS1 used in our study was retrieved
from
f om PubMed
P bMed (access ID = NP_671512).
NP 671512) It has 413 amino acids long
with six transmembrane (TM) region [1]. However, truncation of Nterminal and C
C-terminal of hSMS1 will not influence its activity [2]. So
we only built the core sequence regions (M130-Q353).”
“The amino acid sequence of hSMS1 used in our study was retrieved
from PubMed (access ID = NP_671512). It has a total of 413 amino
acid residues
residues. The structure of hSMS1 has an N-terminal
N terminal domain,
domain a
transmembrane domain, and a C-terminal domain [1]. Recently,
Jiang
g et al demonstrated that truncation of the N- and C-terminal
domains of hSMS1 did not abort its biological activity [2]. Thus, only
the core of hSMS1 (M130-Q353) was considered in our study.”
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23
Tense in Scientific Writing
 Whenever y
you state previously
p
y published
p
findings,
g,
you should use the present tense since they are
established knowledge.
g
• e.g. “C-H bond activation is not a new reaction.”
 Your own present work must be referred to in the past
tense since it is not p
presumed to be established
knowledge yet.
• e.g. “We
“W observed
b
d that
h C-H
C H bond
b d was activated
i
d through
h
ha
new reaction.”
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
24
Tense in Scientific Writing
In a typical paper, you will normally go back and forth
between the past and present tenses.
 M
Most off the
h Abstract
Ab
should
h ld b
be iin the
h past tense, as you are
referring to your own present results.
 The Methods and Results sections should be in the past tense,
as you describe what you did and what you found.
 Much of the Introduction and Discussion should be in the
present tense, because these sections often emphasize
p
p
previously established knowledge.
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25
Exceptions
• References to tables, figures and so on.
–e.g.
e g “Table
Table 1 shows that ……”
• Description on the results of calculations and
statistical analysis
analysis.
–e.g.
g “The standard deviation of three p
parallel
measurements is 1.0 kcal/mol.”
中国科学院上海有机化学研究所
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26
Active Voice versus Passive Voice
• As a general rule, the active voice should be used more
in scientific writing.
e.g.
–The
The authors found that ……
–It was found that ……
• The passive voice may work well for the Methods
section.
e.g. The mouse was injected with ……
中国科学院上海有机化学研究所
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The Elusive Grammar
Please do not expect that
the English language is fully
scientific
scientific.
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Grammar by Google!
To determine which one is more appropriate:
pp p
 “One
One still could argue …”
–Google returns 38.9M hits.
 “One could still argue …”
–Google returns 44.1M hits.
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29
A Couple of “Minor” Issues






Correct use of some common words
Euphemistic words and jargon
Correct use of numbers
Proper use of abbreviations
Units of measurement
Punctuations
中国科学院上海有机化学研究所
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30
Correct Use of Common Words
Certain words are wrongly used by thousands of times in
i tifi writing.
iti
scientific
• Amount or Number?
–e.g. “An amount of cash” is correct; whereas“An amount of
coins” is wrong.
• Like or As?
–e.g. Like
Lik I said,
id this
hi sentence should
h ld rather
h start with
i h “As”.
“A ”
• While or Whereas?
–When a time relationship exists, “while”is correct; otherwise,
“whereas” would be a better choice.
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31
Misuse of Common Words
• Each / every
–e.g. “If I had a dollar for every mistake I have made, I
would have one dollar. If I had a dollar for each mistake I
h
have
made,
d I would
ld be
b a millionaire.”
illi
i ”
• Where to put the word
word“only”?
only ?
e.g.
–Only
Only I hit him in the face yesterday
yesterday.
–I only hit him in the face yesterday.
yesterday.
–II hit only him in the face yesterday
–I hit him only in the face yesterday.
–II hit him in the face only yesterday.
yesterday
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Euphemistic Words
Euphemistic (委婉的) words and phrases normally
should be avoided.
Do not write:
D
i
“Some in the population suffered mortal
consequence from the lead in the flour.”
But write:
“Some people died as a result of eating bread made
f
from
lead-containing
l d
i i fl
flour.”
”
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33
Jargon
Jargon: (1) Confused unintelligible language; (2)
Obscure and often pretentious language. (3)
Technical terminology of a special activity or group.
Do not write:
“The resultant experimental data indicate that there
is no utility in belaboring a deceased equine.”
equine.
But write:
“It is of no use to beat a dead horse.”
Check out Appendix 2 in our text book!
中国科学院上海有机化学研究所
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34
Correct Use of Numbers
If style for numbers is not specified, here are the general
guidelines to follow:
 One-digit number should be spelled out; numbers of two or
more digits should be expressed as numerals.
e.g. Three experiments, 13 experiments.
 If a number comes with the standard unit, it should always
be expressed as numeral.
e.g. 3 ml, 13 ml
 Do not start a sentence with a numeral. Reword your
sentence or spell out the number.
e.g. Thirteen experiments were conducted … ; A total amount of 3 ml
alcohol was added to …
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Proper Use of Abbreviations
Spell out the word or term first,
first followed by the
abbreviation within parentheses.
e.g. deoxyribonucleic
d
ib
l i acid
id (DNA)
 D
Do not use an abbreviation
bb i i in
i the
h Title.
Ti l
 Do not use any abbreviation in the Abstract unless
it is a must.
y, abbreviations may
y be used if a
 In the text body,
long word or phrase will appear repeatedly.
中国科学院上海有机化学研究所
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36
Examples of Standard Abbreviations
 Some standard abbreviations
“etc.” means “so on”;; “et al.” means “other
people”; “i.e.” means “that is”, and “e.g.”
means “for example”.
p
 Widely accepted abbreviations for some
technical terms
Nuclear
N
l
magnetic
i resonance (NMR),
(NMR) high-pressure
hi h
liquid chromatography (HPLC)
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No Abbreviations of Your Own Please
“Although
g bonded Zn-ligand
g
interactions p
preserve the observed
geometry of the metal-binding site, they would not be suitable in
cases where the coordination number (CN) of Zn2+ changes as in the
f ldi / f ldi off Z
folding/unfolding
Zn-finger
fi
proteins
i …”
”
J. Am. Chem. Soc. 2005,, 127,, 4921-4929.
“Both protein design (PD) and virtual drug screening (VDS)
depend on algorithms that can rapidly and accurately predict the
energy of a given protein or protein-ligand complex.”
J. Med. Chem. 2009, 52, 5673–5684.
Do not use abbreviations for common terms!!!
中国科学院上海有机化学研究所
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38
Units of Measurements
Number
Prefix
Abbreviation
Examples
10‐15
femto
femto‐
f
fs
10‐12
pico‐
p
ps
10‐9
nano‐
n
ns, nM, nm, ng
,
,
, g
10‐6
micro‐

s, M, m, g
10‐3
milli‐
m
ms, mM, mm, mg
10‐2
centi‐
c
cm
10‐1
deci‐
d
dm
102
hecto‐
h
hm, hg
103
kilo‐
k
km, kg
106
mega‐
M
MB MHz
MB, MHz
109
giga‐
G
GB, GHz
1012
tera‐
T
TB
1015
peta‐
P
Pm (1 light year = 9.461Pm)
中国科学院上海有机化学研究所
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39
Punctuations
Do not use any ’ in written language.
language
Do not write
Do write
you’re
’
you are
I’ll
I will
can’t
can not or cannot
shouldn’t
should not
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
40
Good Habits in Scientific Writing




Structure sentences simply.
simply
Use proper syntax.
Use mainly active voice.
Use words accurately; delete needless words;
use short and familiar words.
 Avoid strings of nouns; use verbs rather than
nouns made from them.
 Minimize use of abbreviations.
中国科学院上海有机化学研究所
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41
3. Revise, Revise and Revise
Good writing is largely a matter of good revising.
revising
First, cool down for a while.
First
while Then,
Then revise your
paper by yourself. Then, show it to others, and
revise more with their feedbacks.
–Follow
Follow the useful suggestions
suggestions.
–Even if a suggestion misses your point, you may
want to state your point more clearly.
l l
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42
What to Revise?
 Does the manuscript include all the necessary
information? Does it contain anything it should not?
 Is all of the information accurate?
 Is everything logically organized?
 Have you stated your points briefly and directly?
 Is what you say consistent throughout?
 Are
A grammar, spelling,
ll
punctuation, and
d word
d use
correct throughout?
 Are all figures and tables well designed?
p comply
p y with the instructions?
 Does the manuscript
中国科学院上海有机化学研究所
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43
On Automatic Formatting and Template
When you finalize your manuscript:
 Use plain text as much as possible!
 Remove automatic formatting (such as dynamic
links) provided by the word processing software
unless it is absolutely necessary.
necessary
 Do not use a template unless it is required.
required
中国科学院上海有机化学研究所
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44
Summary
The basic format of a scientific paper
Individual Sections
Paragraphs
g p
Sentences & Words
The overall structure of my lectures on scientific
writing.
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45
An Additional Reference
Edited by Anne M. Coghill and
Lorrin R. Garson
ISBN: 9780841239999
The electronic
Th
l
i version
i off
this book is available in our
lib
library!
!
中国科学院上海有机化学研究所
Shanghai Institute of Organic Chemistry, CAS
46
The ACS Style Guide
Part 1: Scientific Communication
•
•
•
•
•
•
•
•
Chapter 1: Ethics in Scientific Publication Chapter 2: Scientific Papers Chapter 3: The Editorial Process Chapter 4: Writing Style and Word Usage Chapter 5: Electronic Submission of Manuscripts Using Web‐Based
Chapter 5: Electronic Submission of Manuscripts Using Web
Based Systems Systems
Chapter 6: Peer Review Chapter 7: Copyright Basics Chapter 8: Markup Languages and the Datument Part 2: Style Guidelines
•
•
•
•
•
•
•
•
•
•
Chapter 9: Grammar, Punctuation, and Spelling Chapter 10: Editorial Style
Chapter 10: Editorial Style Chapter 11: Numbers, Mathematics, and Units of Measure Chapter 12: Names and Numbers for Chemical Compounds Chapter 13: Conventions in Chemistry Chapter 14: References Chapter 15: Figures Chapter 16: Tables Chapter 17: Chemical Structures
Chapter 17: Chemical Structures Chapter 18: Selected Bibliography 中国科学院上海有机化学研究所
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47
Suggested Homework
Select one recently published paper that interests
you, read it through, summarize it into a 200word abstract,
abstract and then compare your writing
with the one published.
中国科学院上海有机化学研究所
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48
Learn the Tools for Writing
 Software for word processing: Microsoft Word
 Software for making chemical sketches:
ChemDraw/Chem3D
 Software for data analysis and making scientific
graphs: Origin (No Excel please!)
 Software for reference managing: EndNote
中国科学院上海有机化学研究所
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49