1. health and fitness
2. disease

How to Write a Scientific Paper
(en anglais)
Luke Masson, Ph.D.
National Research Council of Canada
6100 Royalmount Ave.,
Montreal, PQ.
About me
B.Sc. and Ph.D. in Microbial physiology
Post-Doc in Molecular Biology
Current # of Peer-reviewed papers: ~120
(In a broad spectrum of journals from Biochemistry,
Bacteriology, Virology, Mycology, Molecular Biology, Ecology,
Crystallography, and Entomology)
Current # of Book chapters/proceedings papers: 15
Current # of Industrial technical reports: 46
Current experience in teaching scientific writing: 0
Foundation of Scientific writing
Hypothesis model
• Typically students are introduced to scientific experimenting by
way of the hypothesis model.
• An hypothesis is formulated that a researcher would like to test.
Experiments are designed to either prove or disprove this
hypothesis.
• A scientific paper is a means of presenting the results of a
particular experiment – what hypothesis was tested, how it was
tested, what the results of the testing were, and what the results
prove or disprove.
3
Outlining a paper
A good paper has similarities with a good novel.
– Need to set up the plot (Introduction)
– Need to expose the technical details of the plot (Materials & Methods)
– Need to expose the heart of the story (Results section)
– Reader must have a sense of closure by the end
(Discussion/Conclusions).
– The denouement is incomplete leaving the door open to the sequel
(Future directions).
4
Outlining a paper
Although novelists develop their story while writing, they
have a clear outline of the book BEFORE they start.
TIP: It is NEVER too early in your research project to start thinking
in terms of writing a paper.
As you set up your experiments, think about the research elements
that will come together to form a unified story.
Assemble these elements EARLY. Initiating the writing process helps
you see the ‘holes’ in your work. Early detection’ will help to fill in these
holes with additional experiments or controls that would have been
easier to incorporate from the start.
5
Outlining a paper
BUT- it is NOT an novel. It must be precise.
Editing a waterfront store sign: ‘FRESH FISH SOLD HERE’
Of course it's fresh, (we're on the ocean)
Of course it's for sale, (we're not giving it away)
Of course it's here, (duh…otherwise the sign would be someplace else)
The final sign: FISH.
6
General Style
The purpose of scientific writing is not to entertain;
the purpose is to inform.
Scientific writing is written in an objective manner, with
little drama or style.
- The pronouns “I,” “We,” and “They” are typically not used. Instead of
writing “I used MacConkey agar to isolate E. coli,” you should write,
“MacConkey agar was used to isolate E. coli.”
“Only kings, presidents, editors, and people infected with
tapeworms have the right to use the editorial "we."
The writing should be simple and easy to understand
- The style of writing is relatively formal - the use of jargon, clichés,
slang (e.g. gonna) and the overuse of contractions (e.g. can’t) should
be avoided.
7
5 key fixes in writing to make it
more professional and persuasive
1. Sentences can only do one thing at a time.
Sentences are building blocks, not bungee cords; they’re not meant
to be stretched to the limit. Most writers benefit from dividing their
longest sentences into shorter, more muscular ones.
2. Paragraphs can only do one thing at a time.
A paragraph supports a single idea. Every time you address a new
idea, add a line break. Short paragraphs are the most readable.
3. Look closely at -ing
Nouns ending in -ing are fine. (Strong writing, IT consulting, great
fishing.) But constructions like “a forum for building consensus,” or
“The new team will be managing” are inherently weak. Rewrite
them as…… “a forum to build consensus,” and “the team will
manage.”
The rewrite should have fewer words
8
5 key fixes in writing to make it
more professional and persuasive
4. Omit unnecessary and redundant words.
Extra words drain life from your work. The fewer words used to express an
idea, the more punch it has.
Therefore:
Summer months
Regional level
The entire country
On a daily basis (usually
best rewritten to “every day”)
She knew that it was good.
Very
Larger in size… or… shorter in duration… or… a period of one week
“You can nearly always improve sentences
by rewriting them in a lot fewer words. “
9
5 key fixes in writing to make it
more professional and persuasive
5. Reframe 90% of the passive voice.
In some languages like French, the passive voice is considered to be the
height of refinement but it works poorly in scientific writing.
The active voice is less wordy and more precise.
In an active sentence, the person or thing responsible for the action in the
sentence comes first. In a passive sentence, the person or thing acted on
comes first, and the actor is added at the end or not at all.
TIP: To spot passive sentences, look for a form of the verb to be in
your sentence, with the actor either missing or introduced after the
verb using the word "by":
Acetic acid was produced by S. aureus
vs
S. aureus produced acetic acid
10
5 key fixes in writing to make it
more professional and persuasive
It is ok to use the passive voice in M&M.
The reader can safely assumes it was YOU who dissolved the NaCl in
water. The material or experiment is more important that you.
Try turning each passive sentence into an active one.
1) Genetic information is encoded by DNA.
2) The possibility of cold fusion has been examined for many years.
11
5 key fixes in writing to make it
more professional and persuasive
It is ok to use the passive voice in M&M.
The reader can safely assumes it was YOU who dissolved the NaCl in
water. The material or experiment is more important that you.
Try turning each passive sentence into an active one.
1) Genetic information is encoded by DNA.
DNA encodes genetic information.
2) The possibility of cold fusion has been examined for many years.
12
5 key fixes in writing to make it
more professional and persuasive
It is ok to use the passive voice in M&M.
The reader can safely assumes it was YOU who dissolved the NaCl in
water. The material or experiment is more important that you.
Try turning each passive sentence into an active one.
1) Genetic information is encoded by DNA.
DNA encodes genetic information.
2) The possibility of cold fusion has been examined for many years.
Physicists have examined the possibility of cold fusion for many years.
13
General Style
“..preparation of a scientific paper has less to do with
literary skills than with organization”
• Early on in the process, identify the journal (or a few journals) of interest
where you want to publish. Read over the journal’s “Instructions to
Authors” or “Table of Contents” from one issue carefully.
• While the majority of papers follow the standard abstract, introduction,
materials and methods, results, discussion, acknowledgements and
references, there are variations.
• Some journals allow the integration of results and discussion, especially
where there needs to be discussion of early results to justify subsequent
experiments.
14
Title
Why are titles so important?
– Because when one does a literature search, you mainly read the title and if
good (informative) you go to the abstract…the first ‘hook’.
– Thousands of researchers scan PubMed and read your title, only a few will read
further.
– A title is a label. It does not have to be a complete sentence.
The best titles are:
– Those that use the fewest words to describe the paper
– Relatively short (avoid waste words e.g. “Studies on”. Don’t start the title with A,
An, The)
– Specific (“Assessing the action of certain antibiotics on some bacterial
species”)
– Have proper syntax (Isolation of antigens from monkeys using complementfixation techniques.)
– Not too assertive (TGF-beta is a factor required for cellular differentiation.)
– Avoid abbreviations and jargon
Title
Original title:
Microbial source tracking in a small southern California urban
watershed indicates wild animals and growth as the source of fecal
bacteria
Growth or Wild animals as the source of fecal bacteria????
Fecal matter is the source of fecal bacteria.
Microbial source tracking of fecal bacterial contamination in a small
urban watershed indicates both a wild animal origin and subsequent
bacterial growth.
or
Fecal bacterial contamination studies in a small urban watershed
indicate both a wild animal origin and subsequent bacterial growth.
(don’t forget the use of keywords in article searching)
16
Authorship
This is a COMMON problem causing
arguments between collaborators
TIP 1: As a project starts, which involves external collaborators, establish
early who is first and who is last author.
TIP 2: Never, EVER submit a manuscript without having ALL the authors
having seen and read it (apart from courtesy, there are liability issues). This
also extends to conference abstracts.
Authorship
No universal set order but trends in BioSciences usually
follow this order:
•First author. Most important. Usually given to the person that did most of
the work. In my lab, the above or the person who wrote the paper.
There can be ‘two first authors” (it is indicated on title page that the 1st
and 2nd authors contributed equally to the paper).
•Last author. About of equal importance but in a different perspective.
Tells everyone YOU are the senior researcher or Project leader.
•Everyone else gets stuck in between. Some find the order here
important but not really…who remembers ‘second or third place’ hockey
teams? In practice, the second author is thought to have done the
second most work, the third, the third most etc.
Authorship
Who deserves to be an author?
In theory:
Similar to patents and can be anyone who made an important,
substantial contribution to either the design or the execution of the
work.
In practice:
1) Politics can play a role (beneficial to a lab to recruit a Rock Star)
2) ‘Padding’ occurs. Caused by ‘publish or perish’ pressures in today’s
science funding world.
funding
-Get the affiliation of the authors correct: important from an institutional
point of view (many have double affiliations)
- Be generous with authorship: including all who contribute show you are a
good collaborator (don’t mix this up with padding)
Abstract
Arguably, the Title and Abstract are the most important
parts of the paper.
- Few readers get beyond the title. If they do, then fewer get
beyond the abstract.
- Critical to write both well (to get them to read your paper)
It is written as a single paragraph (~ 200-250 words)
- Abstracts tell a story (minipaper). Gives readers enough
information so they can assess whether it is relevant enough to
read further.
- Quality is important. Badly written abstracts can influence a
reviewer’s opinion of the paper.
- The abstract is the 1st thing a reviewer reads. Reviewers often
reach a preliminary judgment after reading the abstract (“A good
paper generally follows a good abstract”).
Abstract
Structural setup
A) Should contain a complete story with four summaries:
1) An introduction summary (principal objectives and scope of the study)
2) A M&M summary (principal methods used)
3) A results summary
4) A conclusions summary.
TIP: Conclusions are extremely important for clarity and are mentioned in the
Abstract, repeated in the Introduction of the paper and finally expanded upon in
the Discussion (this also applies to a good seminar talk)
B) Abstracts are written in the past tense (refers to work already done)
C) Should ONLY contain points written in the text of the paper (no ‘new additions’)
D) Three words. Simple…Simple…Simple. Do not use 200 words when 100 work.
People (reviewers) have short attention spans. Use clear, simple words rather than
‘big’ but less clear words.
Abstract
Many plant-associated bacteria synthesize the phytohormone indoleacetic acid
(IAA). While IAA produced by phytopathogenic bacteria, mainly by the
indoleacetamide pathway, has been implicated in the induction of plant tumors,
it is not clear whether IAA synthesized by beneficial bacteria, usually via the
indolepyruvic acid pathway, is involved in plant growth promotion. To determine
whether bacterial IAA enhances root develop- ment in host plants, the ipdc
gene that encodes indolepyruvate decarboxylase, a key enzyme in the
indolepyruvic acid pathway, was isolated from the plant growth-promoting
bacterium Pseudomonas putida GR12-2 and an IAA-deficient mutant
constructed by insertional mutagenesis. The canola seedling primary roots from
seeds treated with wild-type P. putida GR12-2 were on average 35 to 50%
longer than the roots from seeds treated with the IAA-deficient mutant and the
roots from uninoculated seeds. In addition, exposing mung bean cuttings to
high levels of IAA by soaking them in a suspension of the wild-type strain
stimulated the formation of many, very small, adventitious roots. Formation of
fewer roots was stimulated by treatment with the IAA-deficient mutant. These
results suggest that bacterial IAA plays a major role in the development of the
host plant root system.
22
Abstract
Many plant-associated bacteria synthesize the phytohormone indoleacetic acid
(IAA). While IAA produced by phytopathogenic bacteria, mainly by the
indoleacetamide pathway, has been implicated in the induction of plant tumors,
it is not clear whether IAA synthesized by beneficial bacteria, usually via the
indolepyruvic acid pathway, is involved in plant growth promotion. To determine
whether bacterial IAA enhances root develop- ment in host plants, the ipdc
gene that encodes indolepyruvate decarboxylase, a key enzyme in the
indolepyruvic acid pathway, was isolated from the plant growth-promoting
bacterium Pseudomonas putida GR12-2 and an IAA-deficient mutant
constructed by insertional mutagenesis. The canola seedling primary roots from
seeds treated with wild-type P. putida GR12-2 were on average 35 to 50%
longer than the roots from seeds treated with the IAA-deficient mutant and the
roots from uninoculated seeds. In addition, exposing mung bean cuttings to
high levels of IAA by soaking them in a suspension of the wild-type strain
stimulated the formation of many, very small, adventitious roots. Formation of
fewer roots was stimulated by treatment with the IAA-deficient mutant. These
results suggest that bacterial IAA plays a major role in the development of the
host plant root system.
Introduction summary
M&M
Results
Conclusions
23
Abstract
Many plant-associated bacteria synthesize the phytohormone indoleacetic acid
(IAA). While IAA produced by phytopathogenic bacteria, mainly by the
indoleacetamide pathway, has been implicated in the induction of plant tumors,
it is not clear whether IAA synthesized by beneficial bacteria, usually via the
indolepyruvic acid pathway, is involved in plant growth promotion. To determine
whether bacterial IAA enhances root develop- ment in host plants, the ipdc
gene that encodes indolepyruvate decarboxylase, a key enzyme in the
indolepyruvic acid pathway, was isolated from the plant growth-promoting
bacterium Pseudomonas putida GR12-2 and an IAA-deficient mutant
constructed by insertional mutagenesis. The canola seedling primary roots from
seeds treated with wild-type P. putida GR12-2 were on average 35 to 50%
longer than the roots from seeds treated with the IAA-deficient mutant and the
roots from uninoculated seeds. In addition, exposing mung bean cuttings to
high levels of IAA by soaking them in a suspension of the wild-type strain
stimulated the formation of many, very small, adventitious roots. Formation of
fewer roots was stimulated by treatment with the IAA-deficient mutant. These
results suggest that bacterial IAA plays a major role in the development of the
host plant root system.
Introduction summary
M&M
Results
Conclusions
24
Abstract
Many plant-associated bacteria synthesize the phytohormone indoleacetic acid
(IAA). While IAA produced by phytopathogenic bacteria, mainly by the
indoleacetamide pathway, has been implicated in the induction of plant tumors,
it is not clear whether IAA synthesized by beneficial bacteria, usually via the
indolepyruvic acid pathway, is involved in plant growth promotion. To determine
whether bacterial IAA enhances root develop- ment in host plants, the ipdc
gene that encodes indolepyruvate decarboxylase, a key enzyme in the
indolepyruvic acid pathway, was isolated from the plant growth-promoting
bacterium Pseudomonas putida GR12-2 and an IAA-deficient mutant
constructed by insertional mutagenesis. The canola seedling primary roots from
seeds treated with wild-type P. putida GR12-2 were on average 35 to 50%
longer than the roots from seeds treated with the IAA-deficient mutant and the
roots from uninoculated seeds. In addition, exposing mung bean cuttings to
high levels of IAA by soaking them in a suspension of the wild-type strain
stimulated the formation of many, very small, adventitious roots. Formation of
fewer roots was stimulated by treatment with the IAA-deficient mutant. These
results suggest that bacterial IAA plays a major role in the development of the
host plant root system.
Introduction summary
M&M
Results
Conclusions
25
Abstract
Many plant-associated bacteria synthesize the phytohormone indoleacetic acid
(IAA). While IAA produced by phytopathogenic bacteria, mainly by the
indoleacetamide pathway, has been implicated in the induction of plant tumors,
it is not clear whether IAA synthesized by beneficial bacteria, usually via the
indolepyruvic acid pathway, is involved in plant growth promotion. To determine
whether bacterial IAA enhances root develop- ment in host plants, the ipdc
gene that encodes indolepyruvate decarboxylase, a key enzyme in the
indolepyruvic acid pathway, was isolated from the plant growth-promoting
bacterium Pseudomonas putida GR12-2 and an IAA-deficient mutant
constructed by insertional mutagenesis. The canola seedling primary roots from
seeds treated with wild-type P. putida GR12-2 were on average 35 to 50%
longer than the roots from seeds treated with the IAA-deficient mutant and the
roots from uninoculated seeds. In addition, exposing mung bean cuttings to
high levels of IAA by soaking them in a suspension of the wild-type strain
stimulated the formation of many, very small, adventitious roots. Formation of
fewer roots was stimulated by treatment with the IAA-deficient mutant. These
results suggest that bacterial IAA plays a major role in the development of the
host plant root system.
Introduction summary
M&M
Results
Conclusions
26
Abstract
Despite rapid development and application of a wide range of manufactured metal
oxide nanoparticles (NPs), the understanding of potential risks of using NPs is
less completed, especially at the molecular level. The nematode Caenorhabditis
elegans (C.elegans) has been emerging as an environmental model to study the
molecular mechanism of environmental contaminations, using standard genetic
tools such as the real-time quantitative PCR (RT-qPCR). The most important
factor that may affect the accuracy of RT-qPCR is to choose appropriate genes for
normalization. In this study, we selected 13 reference gene candidates (act-1,
cdc-42, pmp-3, eif-3.C, actin, act-2, csq-1, Y45F10D.4, tba-1, mdh-1, ama-1,
F35G12.2, and rbd-1) to test their expression stability under different doses of
nano-copper oxide (CuO 0, 1, 10, and 50 mg/ mL) using RT-qPCR. Four
algorithms, geNorm, NormFinder, BestKeeper, and the comparative DCt method,
were employed to evaluate these 13 candidates expressions. As a result, tba-1,
Y45F10D.4 and pmp-3 were the most reliable, which may be used as reference
genes in future study of nanoparticle-induced genetic response using C. elegans.
(From PLoS One)
27
Abstract
Despite rapid development and application of a wide range of manufactured metal
oxide nanoparticles (NPs), the understanding of potential risks of using NPs is
, especially at the molecular level. The nematode Caenorhabditis
elegans (C.elegans) has been emerging as an environmental model to study the
molecular
of environmental
, using standard genetic
tools such as the real-time quantitative PCR (RT-qPCR). The most important
factor that may affect the accuracy of RT-qPCR is to choose appropriate genes for
normalization. In this study, we selected 13 reference gene candidates (act-1,
cdc-42, pmp-3, eif-3.C, actin, act-2, csq-1, Y45F10D.4, tba-1, mdh-1, ama-1,
F35G12.2, and rbd-1) to test their expression stability under different doses of
nano-copper oxide (
0, 1, 10, and 50 mg/ mL) using RT-qPCR. Four
algorithms, geNorm, NormFinder, BestKeeper, and the comparative DCt method,
were employed to evaluate these 13 candidates expressions. As a result, tba-1,
Y45F10D.4 and pmp-3 were the most reliable, which may be used as reference
genes in future
of nanoparticle-induced genetic
using C. elegans.
(From PLoS One)
Grammar
28
Abstract
Despite rapid development and application a wide range manufactured metal
oxide nanoparticles (NPs), the understanding of potential risks of using NPs is
less completed, especially at the molecular level. The nematode Caenorhabditis
elegans (C.elegans) has been emerging as an environmental model to study the
molecular mechanism of environmental contaminations, using standard genetic
tools such as the real-time quantitative PCR (RT-qPCR). The most important
factor that may affect the accuracy RT-qPCR is to choose appropriate genes
normalization. In this study, we selected 13 reference gene candidates (act-1,
cdc-42, pmp-3, eif-3.C, actin, act-2, csq-1, Y45F10D.4, tba-1, mdh-1, ama-1,
F35G12.2, and rbd-1) to test their expression stability
different doses
nano-copper oxide (CuO 0, 1, 10, and 50 mg/ mL) using RT-qPCR. Four
algorithms, geNorm, NormFinder, BestKeeper, and the comparative DCt method,
were employed to evaluate these 13 candidates expressions. As a result, tba-1,
Y45F10D.4 and pmp-3 were the most reliable, which may be used as reference
genes in future study of nanoparticle-induced genetic response using C. elegans.
(From PLoS One)
Prepositional
29
Abstract
Despite rapid development and application of a wide range of manufactured metal
oxide nanoparticles (NPs), the understanding of potential risks of using NPs is
less completed, especially at the molecular level. The nematode Caenorhabditis
elegans (C.elegans) has been emerging as an environmental model to study the
molecular mechanism of environmental contaminations, using standard genetic
tools such as the real-time quantitative PCR (RT-qPCR). The most important
factor that may affect the accuracy of RT-qPCR is to choose appropriate genes for
normalization. In this study, we selected 13 reference gene candidates (act-1,
cdc-42, pmp-3, eif-3.C, actin, act-2, csq-1, Y45F10D.4, tba-1, mdh-1, ama-1,
F35G12.2, and rbd-1) to test their expression stability under different doses of
nano-copper oxide (CuO 0, 1, 10, and 50 mg/ mL) using RT-qPCR. Four
algorithms, geNorm, NormFinder, BestKeeper, and the comparative DCt method,
were employed to evaluate these 13 candidates expressions. As a result, tba-1,
Y45F10D.4 and pmp-3
,
as reference
genes in future study of nanoparticle-induced genetic response using C. elegans.
(From PLoS One)
Awkward concluding sentence
Suggests that the others were reliable ….uh…maybe.
30
Introduction
Purpose:
To provide background information
- So the reader can understand the raison d’etre and the
results of the paper without doing a literature search
Written in present tense
- Since one refers to the problem being studied and the current
knowledge about it.
Introduction
General rules
1) Present nature and scope of the problem being studied (most important
as it is another ‘hook’). If the problem is not clear, no one will read further.
Why was this problem chosen? Why is it important?
2) Present appropriate background literature (literature review) to make the
reader understand the problem.
3) Present the methodology used.
Rules 2+3 relate to the first rule.
i.e. Lit. rev. and method choice allows the reader to understand
the problem and how you tried to resolve it
4) Present the principal results of the study.
5) Present the principal conclusions of the study (I call it the Whiz-bang
sentence that reaches out and grabs your readers interest). This is not a
novel. Let the reader read the ‘last chapter’ first.
Material and Methods
“Good science” must be repeatable
• Section where you describe (and defend in some cases) the full details
of the methods mentioned in the Introduction
• Written in past tense (because you describe the way you did the work)
• Written in enough detail so that your work can be reproduced (many
papers get negative comments from reviewer’s here)
• If you cite previous work, it is still good to describe it briefly.
- Readers get irritated if they have to go back to 10 of your previous papers to figure
out what you did!
Material and Methods
Materials:
– Use exact technical specifications.
– Describe the exact source or method of preparation.
– Be precise about where you got your cells, bacteria, viruses etc.
– If you got samples from others and if you describe their results
that were determined from them, be ACCURATE.
Results
Results are written in the past tense (you are describing what you
did and what you found)
Three major themes to the Results section
1) Initiate the different experimental sections with a ‘BRIEF’ overview of
the procedure or experiment without repeating the M&M
2) Present the data (tables and figures).
- Will discuss later about how to present data
35
Results
3) Brief, Brief, BRIEF!!!!!!!
– In great papers, this section is the smallest (if you have properly
written M&M and Discussion).
– Do not present EVERYTHING you have done (thesis is for that).
– Supplementary Materials: This is the section where you put in
the extras that greatly help the paper but are not essential.
– RESULTS is the ‘new knowledge’ and should be extremely precise and
clear.
e.g. It is clearly shown in Table 2 that the protein toxin inhibited larval
growth.…vs….The protein toxin inhibited larval growth (Table 2).
– Normally try to present those results that are meaningful
(negative results can be presented if it is important that you
didn’t find something under your conditions)
36
Discussion
The section feared by MOST!!!
Common discussion errors are:
– Starting the discussion by repeating the results
– Too long and wordy (makes you seem like you are not convinced of your
interpretation of the results - Bullshit Baffles Brains)
– Not clearly stating the significance of the results (test= at the end of the
discussion, are you saying…so what?). Talk about the forest not the trees.
– Not properly showing factual relationships. Results generate the ‘facts’. The
discussion tries to show the relationships between these facts.
What is the relation ship among these ‘facts’?
1)
2)
3)
Two glasses. One with water and one with vodka.
One worm placed in the water, one worm placed in the vodka.
Worm in the water survived, the worm in the vodka died.
- Researcher trains a flea to jump on command and wants to determine the mechanism
- Removed one leg and after saying jump, the flea jumped but not has high as before.
- After he removed each leg, when he said jump, the flea still jumps but each time less
high than the previous jump.
- Removed the last leg, after saying jump, the flea did not move.
37
Discussion
The section feared by MOST!!!
Common discussion errors are:
– Starting the discussion by repeating the results
– Too long and wordy (makes you seem like you are not convinced of your
interpretation of the results - Bullshit Baffles Brains)
– Not clearly stating the significance of the results (test= at the end of the
discussion, are you saying…so what?. Talk about the forest not the trees.
– Not properly showing factual relationships. Results generate the ‘facts’. The
discussion tries to show the relationships between these facts.
What is the relation ship among these ‘facts?
1)
2)
3)
Two glasses. One with water and one with vodka.
One worm placed in the water, one worm placed in the vodka.
Worm in the water survived, the worm in the vodka died.
If you drink vodka, you will not get worms
- Researcher trains a flea to jump on command and wants to determine the mechanism
- Removed one leg and after saying jump, the flea jumped but not has high as before.
- After he removed each leg, when he said jump, the flea still jumps but each time less
high than the previous jump.
- Removed the last leg, after saying jump, the flea did not move.
38
Discussion
The section feared by MOST!!!
Common discussion errors are:
– Starting the discussion by repeating the results
– Too long and wordy (makes you seem like you are not convinced of your
interpretation of the results - Bullshit Baffles Brains)
– Not clearly stating the significance of the results (test= at the end of the
discussion, are you saying…so what?. Talk about the forest not the trees.
– Not properly showing factual relationships. Results generate the ‘facts’. The
discussion tries to show the relationships between these facts.
What is the relation ship among these ‘facts?
1)
2)
3)
Two glasses. One with water and one with vodka.
One worm placed in the water, one worm placed in the vodka.
Worm in the water survived, the worm in the vodka died.
- Researcher trains a flea to jump on command and wants to determine the mechanism
- Removed one leg and after saying jump, the flea jumped but not has high as before.
- After he removed each leg, when he said jump, the flea still jumps but each time less
high than the previous jump.
- Removed the last leg, after saying jump, the flea did not move.
When all legs are removed, the flea becomes deaf
39
Discussion
Essential instructions to write a good discussion
1) Discuss your results by presenting the principles, the relationships and generalizations
shown by the results.
2) Do not be shy to point out the ‘warts and pimples’ in your data. Data is rarely perfect
and a ‘lack of correlation’ may be important.
3) How does your data fit with those of others. Do they agree, disagree? Is there an
obvious explanation for disagreements?
4) Indicate the theoretical and/or practical implications of your work.
– Example. Successful microarray detection of animal fecal contamination in water
– Theoretically we can look at ANY animal contamination
– Can replace PCR with respect to cost (if the number of animals assayed is high
enough)
5) Clearly state your conclusions. For each conclusion summarize the evidence behind
each conclusion.
6) State the significance of the work.
– Best done by a concluding summary or statement at the end of the discussion
about the significance of the work. Normally a paper is NOT a novel BUT in this
particular case, go out with a BANG!!!! It should never just end suddenly.
40
Acknowledgments
Not a scientific section
General etiquette:
1) Acknowledge SIGNIFICANT technical help from others
2) Acknowledge important materials or equipment or analyses contributed
by others
3) Acknowledge the source of financial help
- Grants, fellowships, etc. etc.
4) Do NOT include an author in the acknowledgements
Tip: The Acknowledgments section is to thank people (and
institutions). Therefore put in what you are thanking them for:
- a specific type of help (technical assistance, analyses, paper
proofreading)
- it can also be a contributed idea or interpretation
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References
Straightforward. There are many different styles so follow the journal’s
Instructions to Authors and do NOT deviate from it.
General issues:
1)Using bibliographic software slike EndNote.
- Warning!!! Importing references into your ‘databank’ from different sources
(including manually) is not perfect.
-Print up the ones you plan to use correct them directly in the database.
-Why (since you can fix them up manually in the text)? Helpful when you
format the paper multiple times for submission to journals. Once data is
entered properly, you never have to do it again.
2)Make sure all listed references are accounted for in the text and and vice
versa
3)use published references (avoid websites, theses, conference abstracts
etc.). You can add a website in the text of the paper if essential.
42
Tables and figures
How many figures and tables are enough?
•Variable
•Can be journal dependent
- Personal preference is ~5-7 total in ASM-like journals
•Better question is “Does it REALLY need to be there?”
- Reviewers will tell you to remove them if not
Tables
Generally for tables, either little or repetitive data make lousy
tables. If you can easily put a table into words…do it!
!
Table 1. Effect of aeration on growth of Streptomyces coelicolor
Temp
(oC)
# of
experiments
Aeration of
growth medium
Growtha
24
24
5
5
+b
-
1.9
0
Table 2. Effect of temperature on oak seedling growtha
Temperature oC
-50
-40
-30
-20
-10
0
10
20
30
40
50
60
70
80
90
100
a As
b
determined by OD600nm
+, 500 ml erlynmeyer flasks were shaken at 200 rpm; -, no shaking
Table 3. Adverse effects of nicklecillin in 24 adult patients
No. of patients
14
5
2
1
1
1
aInfecting
Side effect
Diarrhea
Eosinophilia (>5 eos/mm2)
Metallic taste
Yeast vaginitisa
Increased urea nitrogen
Hematuria (8-10 rbc/hpf)
organism was a rare strain of Candida albicans that causes
vaginitis in yeasts but not in humans
Growth at 48h (mm)
0
0
0
0
0
0
0
7
8
9
0
0
0
0
0
0
aEach
seedling was maintained in a 10 x 10x 100cm pot
In a rich growth medium composed of 50% ground Big Macs
and 50% poutine
44
Table errors
When making a table, the data can be presented
either horizontally or vertically.
The best is when the ‘like elements’ read downwards
Table 6. Characteristics of an antibiotic-producing Streptomyces
Determination S. fluoricolor
S. griseus
S. coelicolor S. nocolor
Optimal growth
temp oC
-10
24
28
Color of
mycelium
tan
gray
red
Antibiotic
produced
Yield of
antibiotic
(mg/ml)
fluoricillinmycin
4,108
streptomycin
78
kanamycin
2
Table 6. Characteristics of an antibiotic-producing Streptomyces
Organism
92
purple
S. fluoricolor
S. griseus
S. coelicolor
S. Nocolor
Optimal
growth temp
(oC)
- 10
24
28
92
Color of
mycelium
tan
gray
red
purple
Antibiotic
produced
fluoricillinmycin
streptomycin
kanamycin
neomycin
Yield of
antibiotic
(mg/ml)
4,108
78
2
0
neomycin
0
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Figures
A figure is essentially a table in pictoral form.
Like tables, a graph showing only a few facts is useless
60
54
50
40
# of patients
# of infections
30
Avg # days in hospital
20
10
14
6
0
‘In the test group of 56 patients who were hospitalized for an
average of two weeks, six acquired infections’
TIP: Color figures cost a lot. So determine whether it is really worth it.
(less of an issue in Online journals)
46
Tables
Often one can present data as either a table or a graph
TIP: Tables: mostly used to provide exact numbers
Graphs: mostly used to show trends.
100
90
% of negative cultures
Treatment
2 wks
4 wks
6 wks
8 wks
Streptomycin
5
10
15
20
Isoniazid
8
12
15
15
Streptomycin +
Isoniazid
30
60
80
100
80
Negative cultures (%)
Table 1. Effect of streptomycin, isoniazid, and streptomycin/isoniazid
on Mycobacterium tuberculosis
70
60
50
40
30
20
10
0
0
Both of the above are good, one is superior
2
4
6
Duration of Treatment (weeks)
8
Figure 1. Effect of Streptomycin ( ), isoniazid (∆), and
streptomycin/isoniazid (X) on Mycobacterium tuberculosis
47
Before submission
Do not:
1) Forget to add line and page numbers (instant reject)
2) Ignore spell check in the final proof-reading. Reviewer’s like me HATE
typos.
- If you do not care enough about presenting a relatively errorfree
manuscript, perhaps you were just as careless about getting
the data.
3) Forget to have your peers read the paper and critique it (and to
acknowledge this input). When you get corrections from other authors or
outside experts you don’t have to accept them all – use your judgment.
4) Use the word ‘wish’. E.g. The authors wish to thank Joe Blow for
proofreading the manuscript. The authors THANK JB for…
48
Where to send?
• Balance between appropriateness and impact factor (read
instructions to authors for a description).
– Match your paper to the journal: aim high but be realistic so you don’t
spend a year sending it to lower and lower impact journal
– look at table of contents from past issues, and see if they match the
scope and type of study you are doing
• Increasing trend towards Open Access journals (anyone can freely
download the paper resulting in improved access for the general
public and higher citation rates for the author)
• With time the impact factor of the journal might be less important
than the H-factor: it is important that your peers know your work and
cite it.
49
Reviewers, Editors and other
unattractive people
“Many editors see themselves as gifted sculptors, attempting to turn a
block of marble into a lovely statue, and writers as crude chisels. In actual
fact, the writers are the statues and the editors are pigeons.”
Doug Robarchek
Role of the editor:
1)Receives the paper and decides whether the content is suitable for the journal
2)Makes sure everything is complete (has the figs, tables, etc)
3)Selects the reviewers (initially request sent to members of the editorial board). Normally
two are asked but can be as high as five (my personal record).
Role of the reviewer:
Reads the manuscript and send two things to the editor, their comments on the paper
and a confidential statement giving their acceptance/rejection decision and why.
***Reviewers only RECOMMEND, it is the editor’s decision to accept (or reject).
In ~ 8 weeks, editors send you the comments along with the:
Accept, Reject or Modify decision.
50
Reviewers, Editors and other
unattractive people
Direct acceptance as submitted is VERY RARE (<5%)
A
c
c
e
p
t
e
d
Accepted
51
Reviewers, Editors and other
unattractive people
Modify
• Authors commonly get Modify. This is great!
• Minor revisions= fantastic
– TIP: Unless the revision criticism is >95% wrong, make them without
complaint. In your rebuttal, be POLITE (reviewers and editors are not
paid $$$). Editors will listen more carefully this time to a reviewers yes
or no.
• Major revisions= less so
– Some ask for more work (very bad).
– If two reviewers comment on the same problem, then it IS a problem.
– If one reviewer is completely bad, you can say so (politely) in your
rebuttal.
– Never say an editor is wrong (death sentence).
– Can always submit to another journal.
52
Reviewers, Editors and other
unattractive people
Rejected
3-4 Impact factor journals >50% rejection
Generally editors say either:
1) Unacceptable (bad)
and
- Use the comments to fix the paper and submit elsewhere
- Editors are not perfect. If you get both a bad & good review
the editor went with the bad, you can contact the editor and
explain why you are right and the reviewer was wrong. It CAN
work.
2) Unacceptable in its present form (good)
- Use the comments to fix the paper and resubmit
53
Common Problems not found
by spell check
1) Dangling participles
A participle is a verb that acts like an adjective.
These ‘adjectives’ ending in -ing (and sometimes -ed) must be
used with care (the participle modifies with the noun closest to it).
The participle dangles (hangs) there in your sentence when there is no
proper subject around it.
After dying in the cage, we removed the mice.
After being whipped fiercely, the cook boiled the egg
2) Dangling prepositions
A preposition is something you should never end a sentence with 
–…what we did the work with vs …with which we did the work
Common Problems
3) Run on prepositions
- Identification of the source of pollution in watersheds or in
lakes as well as in rivers.
- In the identification of sources of fecal pollution, we have
included in the design, one pair of universal primers that is able to
amplify a 2kb region in the mitochondrial genome of most animals
prior to the hybridization on the microarray in order to increase the
limit of detection of the method.
Common Problems
3) Run on prepositions
- Identification of the source of pollution in watersheds or in
lakes as well as in rivers.
Pollution source identification in watersheds, lakes and rivers
- In the identification of sources of fecal pollution, we have
included in the design, one pair of universal primers that is able to
amplify a 2kb region in the mitochondrial genome of most animals
prior to the hybridization on the microarray in order to increase the
limit of detection of the method.
Common Problems
3) Run on prepositions
- Identification of the source of pollution in watersheds or in
lakes as well as in rivers.
Pollution source identification in watersheds, lakes and rivers
- In the identification of sources of fecal pollution, we have
included in the design, one pair of universal primers that is able to
amplify a 2kb region in the mitochondrial genome of most animals
prior to the hybridization on the microarray in order to increase the
limit of detection of the method.
To identify fecal pollution sources, we created a step preceding microarray
hybridization in which newly designed universal primers were used to
amplify a 2kb mitochondrial DNA fragment. Inclusion of this step increased
the method’s detection limit.
Common Problems
1) Syntax errors (The arrangement of words in a sentence)
Example: Secreted toxins from enteropathogenic E. coli were found
to kill C. elegans as well as toxins from Pseudomonas aeruginosa
and Bukholderia cepecia.
Example: Thymic humoral factor (THF) is a single, heat-stable
polypeptide isolated from calf thymus composed of 31 amino acids
with a molecular weight of 3200.
58
Common Problems
1) Syntax errors (The arrangement of words in a sentence)
Example: Secreted toxins from enteropathogenic E. coli were found
to kill C. elegans as well as toxins from Pseudomonas aeruginosa
and Bukholderia cepecia. Toxins killing toxins?
Example: Thymic humoral factor (THF) is a single, heat-stable
polypeptide isolated from calf thymus composed of 31 amino acids
with a molecular weight of 3200.
59
Common Problems
1) Syntax errors (The arrangement of words in a sentence)
Example: Secreted toxins from enteropathogenic E. coli were found
to kill C. elegans as well as toxins from Pseudomonas aeruginosa
and Bukholderia cepecia. Toxins killing toxins?
Example: Thymic humoral factor (THF) is a single, heat-stable
polypeptide isolated from calf thymus composed of 31 amino acids
with a molecular weight of 3200. Thymus (not THF) is composed
of 31 aa’s? or has a Mol. Wt. of 3200?
60
Common Problems
2) Numbers
- Spell 1 digit numbers (eight experiments)
- Use numerals for 2 or more digit number (12 experiments)
- Use numerals for units of measure (3ml, 132 ml)
- Try NOT to start a sentence with a number (if you must then
write it out)
- In a series of numbers, in a sentence, use numerals (Water
was given to 3 mice, milk to 6 monkeys, and beer to 14
scientists)
61
Common Problems
3) Homonyms (words that sound the same)
- your (possessive) vs. you’re (contraction),
- hear vs. here
- It’s (a contraction) vs. its (possessive),
- led (verb past tense) vs. lead (verb present tense or a metal)
- their (possessive) vs. there (place/pronoun) vs. they’re (contraction)
4) Non-homonyms
- Then (time related) than (comparative),
- Different from vs. different than (If a noun follows different, use from;
if a phrase follows different, then use that)
- Lose (verb-to no longer possess) and loose (noun, verb or adverb)
- Affect (verb- to influence) and effect (noun-result; verb- to bring
about)
62
Common Problems
5) Hyphens vs Dashes
Hyphens are joiners (use them to create a single idea)
- a man-eating shark
- a fact-based article
Dashes are breakers (indicates a break or an interruption in the
thought- replaces commas)
Don’t use in scientific writing unless:
- indicating a range of values (replaces both "from" and "to”)
(…3 to 7 experiments were performed (3-7 experiments were
performed)
- you want to join two place names (Ottawa-Montreal)
63
Common Problems
6) Using nouns as adjective
- The
mice suffered from liver disease (ok)
- The data was presented to a group of child psychologists
(Were they too young to understand it?)
- The survey was prepared with a team of prenatal experts
(You can be an expert BEFORE you are born?)
7) Problem words
- quite (if you see it, delete it)
- like as a conjunction (it is a preposition. Use “as” instead)
Like I said, you should have used “As”.
- it (when the referring noun is unclear)
(e.g. Free information about venereal disease. To get it call, 555-1212)
64
Random thoughts
Final TIPS
•Make sure you have a proper backup of the paper and figures – bad
things happen,
•When writing updated versions of the paper, make sure you save
previous versions, and renumber new versions (either numerically
Thebestpaperintheworld1.1 or incorporate the date of last revision
Thebestpaperintheword11/9/2012)
65
Thank you
(may you publish often)
66